Starting phenix.real_space_refine on Thu Nov 20 12:45:03 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/5ftm_3298/11_2025/5ftm_3298.cif Found real_map, /net/cci-nas-00/data/ceres_data/5ftm_3298/11_2025/5ftm_3298.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/5ftm_3298/11_2025/5ftm_3298.map" default_real_map = "/net/cci-nas-00/data/ceres_data/5ftm_3298/11_2025/5ftm_3298.map" model { file = "/net/cci-nas-00/data/ceres_data/5ftm_3298/11_2025/5ftm_3298.cif" } default_model = "/net/cci-nas-00/data/ceres_data/5ftm_3298/11_2025/5ftm_3298.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.005 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 30 5.49 5 Mg 6 5.21 5 S 186 5.16 5 C 21636 2.51 5 N 6090 2.21 5 O 6606 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 34554 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 5700 Number of conformers: 1 Conformer: "" Number of residues, atoms: 728, 5700 Classifications: {'peptide': 728} Link IDs: {'PCIS': 3, 'PTRANS': 36, 'TRANS': 688} Chain breaks: 1 Chain: "B" Number of atoms: 5700 Number of conformers: 1 Conformer: "" Number of residues, atoms: 728, 5700 Classifications: {'peptide': 728} Link IDs: {'PCIS': 3, 'PTRANS': 36, 'TRANS': 688} Chain breaks: 1 Chain: "C" Number of atoms: 5700 Number of conformers: 1 Conformer: "" Number of residues, atoms: 728, 5700 Classifications: {'peptide': 728} Link IDs: {'PCIS': 3, 'PTRANS': 36, 'TRANS': 688} Chain breaks: 1 Chain: "D" Number of atoms: 5700 Number of conformers: 1 Conformer: "" Number of residues, atoms: 728, 5700 Classifications: {'peptide': 728} Link IDs: {'PCIS': 3, 'PTRANS': 36, 'TRANS': 688} Chain breaks: 1 Chain: "E" Number of atoms: 5700 Number of conformers: 1 Conformer: "" Number of residues, atoms: 728, 5700 Classifications: {'peptide': 728} Link IDs: {'PCIS': 3, 'PTRANS': 36, 'TRANS': 688} Chain breaks: 1 Chain: "F" Number of atoms: 5700 Number of conformers: 1 Conformer: "" Number of residues, atoms: 728, 5700 Classifications: {'peptide': 728} Link IDs: {'PCIS': 3, 'PTRANS': 36, 'TRANS': 688} Chain breaks: 1 Chain: "A" Number of atoms: 59 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 59 Unusual residues: {' MG': 1, 'ADP': 1, 'AGS': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 59 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 59 Unusual residues: {' MG': 1, 'ADP': 1, 'AGS': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 59 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 59 Unusual residues: {' MG': 1, 'ADP': 1, 'AGS': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 59 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 59 Unusual residues: {' MG': 1, 'ADP': 1, 'AGS': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "E" Number of atoms: 59 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 59 Unusual residues: {' MG': 1, 'ADP': 1, 'AGS': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "F" Number of atoms: 59 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 59 Unusual residues: {' MG': 1, 'ADP': 1, 'AGS': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 7.15, per 1000 atoms: 0.21 Number of scatterers: 34554 At special positions: 0 Unit cell: (164.268, 175.084, 102.752, 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 186 16.00 P 30 15.00 Mg 6 11.99 O 6606 8.00 N 6090 7.00 C 21636 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: 2.89 Conformation dependent library (CDL) restraints added in 1.2 seconds 8688 Ramachandran restraints generated. 4344 Oldfield, 0 Emsley, 4344 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8148 Finding SS restraints... Secondary structure from input PDB file: 198 helices and 54 sheets defined 46.0% alpha, 9.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.49 Creating SS restraints... Processing helix chain 'A' and resid 42 through 50 Processing helix chain 'A' and resid 85 through 92 removed outlier: 4.210A pdb=" N ASN A 91 " --> pdb=" O VAL A 87 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LEU A 92 " --> pdb=" O VAL A 88 " (cutoff:3.500A) Processing helix chain 'A' and resid 135 through 140 removed outlier: 3.749A pdb=" N PHE A 139 " --> pdb=" O LEU A 135 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N LEU A 140 " --> pdb=" O LYS A 136 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 135 through 140' Processing helix chain 'A' and resid 202 through 206 removed outlier: 3.883A pdb=" N ILE A 206 " --> pdb=" O TYR A 203 " (cutoff:3.500A) Processing helix chain 'A' and resid 209 through 226 removed outlier: 3.520A pdb=" N GLN A 215 " --> pdb=" O LYS A 211 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N LEU A 222 " --> pdb=" O GLU A 218 " (cutoff:3.500A) Proline residue: A 223 - end of helix Processing helix chain 'A' and resid 226 through 233 removed outlier: 4.036A pdb=" N PHE A 230 " --> pdb=" O HIS A 226 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LYS A 231 " --> pdb=" O PRO A 227 " (cutoff:3.500A) Processing helix chain 'A' and resid 250 through 263 Processing helix chain 'A' and resid 271 through 277 Processing helix chain 'A' and resid 280 through 296 removed outlier: 4.008A pdb=" N SER A 284 " --> pdb=" O GLY A 280 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ALA A 289 " --> pdb=" O ASN A 285 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N PHE A 290 " --> pdb=" O LEU A 286 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LYS A 295 " --> pdb=" O GLU A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 305 through 310 removed outlier: 4.152A pdb=" N ILE A 309 " --> pdb=" O GLU A 305 " (cutoff:3.500A) Processing helix chain 'A' and resid 318 through 333 removed outlier: 3.732A pdb=" N VAL A 325 " --> pdb=" O GLU A 321 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N SER A 326 " --> pdb=" O ARG A 322 " (cutoff:3.500A) Processing helix chain 'A' and resid 354 through 358 Processing helix chain 'A' and resid 373 through 386 removed outlier: 3.516A pdb=" N GLU A 379 " --> pdb=" O THR A 375 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ILE A 383 " --> pdb=" O GLU A 379 " (cutoff:3.500A) Processing helix chain 'A' and resid 398 through 403 Processing helix chain 'A' and resid 407 through 426 removed outlier: 3.736A pdb=" N CYS A 415 " --> pdb=" O LEU A 411 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N LYS A 425 " --> pdb=" O GLN A 421 " (cutoff:3.500A) Processing helix chain 'A' and resid 426 through 431 removed outlier: 4.002A pdb=" N ILE A 430 " --> pdb=" O LYS A 426 " (cutoff:3.500A) Processing helix chain 'A' and resid 439 through 445 Processing helix chain 'A' and resid 448 through 456 removed outlier: 3.776A pdb=" N PHE A 452 " --> pdb=" O THR A 448 " (cutoff:3.500A) Processing helix chain 'A' and resid 482 through 493 Processing helix chain 'A' and resid 493 through 499 removed outlier: 3.816A pdb=" N VAL A 497 " --> pdb=" O VAL A 493 " (cutoff:3.500A) Processing helix chain 'A' and resid 523 through 536 removed outlier: 4.030A pdb=" N ILE A 531 " --> pdb=" O LEU A 527 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ALA A 532 " --> pdb=" O ALA A 528 " (cutoff:3.500A) Processing helix chain 'A' and resid 544 through 551 removed outlier: 3.557A pdb=" N MET A 550 " --> pdb=" O GLU A 546 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N TRP A 551 " --> pdb=" O LEU A 547 " (cutoff:3.500A) Processing helix chain 'A' and resid 559 through 568 Processing helix chain 'A' and resid 579 through 588 removed outlier: 4.105A pdb=" N ALA A 583 " --> pdb=" O LEU A 579 " (cutoff:3.500A) Processing helix chain 'A' and resid 598 through 609 removed outlier: 3.857A pdb=" N ASN A 602 " --> pdb=" O ASP A 598 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N GLN A 603 " --> pdb=" O ARG A 599 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ILE A 604 " --> pdb=" O VAL A 600 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N GLU A 607 " --> pdb=" O GLN A 603 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N ASP A 609 " --> pdb=" O LEU A 605 " (cutoff:3.500A) Processing helix chain 'A' and resid 625 through 629 removed outlier: 3.562A pdb=" N ILE A 629 " --> pdb=" O PRO A 626 " (cutoff:3.500A) Processing helix chain 'A' and resid 630 through 635 removed outlier: 3.683A pdb=" N ARG A 635 " --> pdb=" O ALA A 632 " (cutoff:3.500A) Processing helix chain 'A' and resid 649 through 661 removed outlier: 3.742A pdb=" N ALA A 655 " --> pdb=" O LYS A 651 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LEU A 657 " --> pdb=" O ARG A 653 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N LEU A 661 " --> pdb=" O LEU A 657 " (cutoff:3.500A) Processing helix chain 'A' and resid 671 through 679 removed outlier: 3.508A pdb=" N LYS A 677 " --> pdb=" O GLU A 673 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N MET A 678 " --> pdb=" O PHE A 674 " (cutoff:3.500A) Processing helix chain 'A' and resid 683 through 705 removed outlier: 3.595A pdb=" N CYS A 695 " --> pdb=" O CYS A 691 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ILE A 699 " --> pdb=" O CYS A 695 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ARG A 700 " --> pdb=" O LYS A 696 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N GLU A 701 " --> pdb=" O LEU A 697 " (cutoff:3.500A) Processing helix chain 'A' and resid 732 through 740 Processing helix chain 'A' and resid 751 through 761 Processing helix chain 'A' and resid 762 through 766 removed outlier: 3.797A pdb=" N ARG A 766 " --> pdb=" O GLN A 763 " (cutoff:3.500A) Processing helix chain 'B' and resid 42 through 50 Processing helix chain 'B' and resid 85 through 92 removed outlier: 4.211A pdb=" N ASN B 91 " --> pdb=" O VAL B 87 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LEU B 92 " --> pdb=" O VAL B 88 " (cutoff:3.500A) Processing helix chain 'B' and resid 135 through 140 removed outlier: 3.749A pdb=" N PHE B 139 " --> pdb=" O LEU B 135 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N LEU B 140 " --> pdb=" O LYS B 136 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 135 through 140' Processing helix chain 'B' and resid 202 through 206 removed outlier: 3.883A pdb=" N ILE B 206 " --> pdb=" O TYR B 203 " (cutoff:3.500A) Processing helix chain 'B' and resid 209 through 226 removed outlier: 3.521A pdb=" N GLN B 215 " --> pdb=" O LYS B 211 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N LEU B 222 " --> pdb=" O GLU B 218 " (cutoff:3.500A) Proline residue: B 223 - end of helix Processing helix chain 'B' and resid 226 through 233 removed outlier: 4.036A pdb=" N PHE B 230 " --> pdb=" O HIS B 226 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LYS B 231 " --> pdb=" O PRO B 227 " (cutoff:3.500A) Processing helix chain 'B' and resid 250 through 263 Processing helix chain 'B' and resid 271 through 277 Processing helix chain 'B' and resid 280 through 296 removed outlier: 4.008A pdb=" N SER B 284 " --> pdb=" O GLY B 280 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ALA B 289 " --> pdb=" O ASN B 285 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N PHE B 290 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LYS B 295 " --> pdb=" O GLU B 291 " (cutoff:3.500A) Processing helix chain 'B' and resid 305 through 310 removed outlier: 4.152A pdb=" N ILE B 309 " --> pdb=" O GLU B 305 " (cutoff:3.500A) Processing helix chain 'B' and resid 318 through 333 removed outlier: 3.733A pdb=" N VAL B 325 " --> pdb=" O GLU B 321 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N SER B 326 " --> pdb=" O ARG B 322 " (cutoff:3.500A) Processing helix chain 'B' and resid 354 through 358 Processing helix chain 'B' and resid 373 through 386 removed outlier: 3.517A pdb=" N GLU B 379 " --> pdb=" O THR B 375 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ILE B 383 " --> pdb=" O GLU B 379 " (cutoff:3.500A) Processing helix chain 'B' and resid 398 through 403 Processing helix chain 'B' and resid 407 through 426 removed outlier: 3.736A pdb=" N CYS B 415 " --> pdb=" O LEU B 411 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N LYS B 425 " --> pdb=" O GLN B 421 " (cutoff:3.500A) Processing helix chain 'B' and resid 426 through 431 removed outlier: 4.002A pdb=" N ILE B 430 " --> pdb=" O LYS B 426 " (cutoff:3.500A) Processing helix chain 'B' and resid 439 through 445 Processing helix chain 'B' and resid 448 through 456 removed outlier: 3.777A pdb=" N PHE B 452 " --> pdb=" O THR B 448 " (cutoff:3.500A) Processing helix chain 'B' and resid 482 through 493 Processing helix chain 'B' and resid 493 through 499 removed outlier: 3.816A pdb=" N VAL B 497 " --> pdb=" O VAL B 493 " (cutoff:3.500A) Processing helix chain 'B' and resid 523 through 536 removed outlier: 4.030A pdb=" N ILE B 531 " --> pdb=" O LEU B 527 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ALA B 532 " --> pdb=" O ALA B 528 " (cutoff:3.500A) Processing helix chain 'B' and resid 544 through 551 removed outlier: 3.557A pdb=" N MET B 550 " --> pdb=" O GLU B 546 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N TRP B 551 " --> pdb=" O LEU B 547 " (cutoff:3.500A) Processing helix chain 'B' and resid 559 through 568 Processing helix chain 'B' and resid 579 through 588 removed outlier: 4.105A pdb=" N ALA B 583 " --> pdb=" O LEU B 579 " (cutoff:3.500A) Processing helix chain 'B' and resid 598 through 609 removed outlier: 3.857A pdb=" N ASN B 602 " --> pdb=" O ASP B 598 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N GLN B 603 " --> pdb=" O ARG B 599 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ILE B 604 " --> pdb=" O VAL B 600 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N GLU B 607 " --> pdb=" O GLN B 603 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N ASP B 609 " --> pdb=" O LEU B 605 " (cutoff:3.500A) Processing helix chain 'B' and resid 625 through 629 removed outlier: 3.563A pdb=" N ILE B 629 " --> pdb=" O PRO B 626 " (cutoff:3.500A) Processing helix chain 'B' and resid 630 through 635 removed outlier: 3.683A pdb=" N ARG B 635 " --> pdb=" O ALA B 632 " (cutoff:3.500A) Processing helix chain 'B' and resid 649 through 661 removed outlier: 3.742A pdb=" N ALA B 655 " --> pdb=" O LYS B 651 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LEU B 657 " --> pdb=" O ARG B 653 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N LEU B 661 " --> pdb=" O LEU B 657 " (cutoff:3.500A) Processing helix chain 'B' and resid 671 through 679 removed outlier: 3.508A pdb=" N LYS B 677 " --> pdb=" O GLU B 673 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N MET B 678 " --> pdb=" O PHE B 674 " (cutoff:3.500A) Processing helix chain 'B' and resid 683 through 705 removed outlier: 3.594A pdb=" N CYS B 695 " --> pdb=" O CYS B 691 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ILE B 699 " --> pdb=" O CYS B 695 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ARG B 700 " --> pdb=" O LYS B 696 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N GLU B 701 " --> pdb=" O LEU B 697 " (cutoff:3.500A) Processing helix chain 'B' and resid 732 through 740 Processing helix chain 'B' and resid 751 through 761 Processing helix chain 'B' and resid 762 through 766 removed outlier: 3.797A pdb=" N ARG B 766 " --> pdb=" O GLN B 763 " (cutoff:3.500A) Processing helix chain 'C' and resid 42 through 50 Processing helix chain 'C' and resid 85 through 92 removed outlier: 4.211A pdb=" N ASN C 91 " --> pdb=" O VAL C 87 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LEU C 92 " --> pdb=" O VAL C 88 " (cutoff:3.500A) Processing helix chain 'C' and resid 135 through 140 removed outlier: 3.748A pdb=" N PHE C 139 " --> pdb=" O LEU C 135 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N LEU C 140 " --> pdb=" O LYS C 136 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 135 through 140' Processing helix chain 'C' and resid 202 through 206 removed outlier: 3.883A pdb=" N ILE C 206 " --> pdb=" O TYR C 203 " (cutoff:3.500A) Processing helix chain 'C' and resid 209 through 226 removed outlier: 3.521A pdb=" N GLN C 215 " --> pdb=" O LYS C 211 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N LEU C 222 " --> pdb=" O GLU C 218 " (cutoff:3.500A) Proline residue: C 223 - end of helix Processing helix chain 'C' and resid 226 through 233 removed outlier: 4.037A pdb=" N PHE C 230 " --> pdb=" O HIS C 226 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N LYS C 231 " --> pdb=" O PRO C 227 " (cutoff:3.500A) Processing helix chain 'C' and resid 250 through 263 Processing helix chain 'C' and resid 271 through 277 Processing helix chain 'C' and resid 280 through 296 removed outlier: 4.009A pdb=" N SER C 284 " --> pdb=" O GLY C 280 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ALA C 289 " --> pdb=" O ASN C 285 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N PHE C 290 " --> pdb=" O LEU C 286 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LYS C 295 " --> pdb=" O GLU C 291 " (cutoff:3.500A) Processing helix chain 'C' and resid 305 through 310 removed outlier: 4.152A pdb=" N ILE C 309 " --> pdb=" O GLU C 305 " (cutoff:3.500A) Processing helix chain 'C' and resid 318 through 333 removed outlier: 3.500A pdb=" N ILE C 324 " --> pdb=" O VAL C 320 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N VAL C 325 " --> pdb=" O GLU C 321 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N SER C 326 " --> pdb=" O ARG C 322 " (cutoff:3.500A) Processing helix chain 'C' and resid 354 through 358 Processing helix chain 'C' and resid 373 through 386 removed outlier: 3.516A pdb=" N GLU C 379 " --> pdb=" O THR C 375 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ILE C 383 " --> pdb=" O GLU C 379 " (cutoff:3.500A) Processing helix chain 'C' and resid 398 through 403 Processing helix chain 'C' and resid 407 through 426 removed outlier: 3.736A pdb=" N CYS C 415 " --> pdb=" O LEU C 411 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N LYS C 425 " --> pdb=" O GLN C 421 " (cutoff:3.500A) Processing helix chain 'C' and resid 426 through 431 removed outlier: 4.001A pdb=" N ILE C 430 " --> pdb=" O LYS C 426 " (cutoff:3.500A) Processing helix chain 'C' and resid 439 through 445 Processing helix chain 'C' and resid 448 through 456 removed outlier: 3.776A pdb=" N PHE C 452 " --> pdb=" O THR C 448 " (cutoff:3.500A) Processing helix chain 'C' and resid 482 through 493 Processing helix chain 'C' and resid 493 through 499 removed outlier: 3.815A pdb=" N VAL C 497 " --> pdb=" O VAL C 493 " (cutoff:3.500A) Processing helix chain 'C' and resid 523 through 536 removed outlier: 4.030A pdb=" N ILE C 531 " --> pdb=" O LEU C 527 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ALA C 532 " --> pdb=" O ALA C 528 " (cutoff:3.500A) Processing helix chain 'C' and resid 544 through 551 removed outlier: 3.557A pdb=" N MET C 550 " --> pdb=" O GLU C 546 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N TRP C 551 " --> pdb=" O LEU C 547 " (cutoff:3.500A) Processing helix chain 'C' and resid 559 through 568 Processing helix chain 'C' and resid 579 through 588 removed outlier: 4.104A pdb=" N ALA C 583 " --> pdb=" O LEU C 579 " (cutoff:3.500A) Processing helix chain 'C' and resid 598 through 609 removed outlier: 3.857A pdb=" N ASN C 602 " --> pdb=" O ASP C 598 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N GLN C 603 " --> pdb=" O ARG C 599 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ILE C 604 " --> pdb=" O VAL C 600 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N GLU C 607 " --> pdb=" O GLN C 603 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N ASP C 609 " --> pdb=" O LEU C 605 " (cutoff:3.500A) Processing helix chain 'C' and resid 625 through 629 removed outlier: 3.563A pdb=" N ILE C 629 " --> pdb=" O PRO C 626 " (cutoff:3.500A) Processing helix chain 'C' and resid 630 through 635 removed outlier: 3.683A pdb=" N ARG C 635 " --> pdb=" O ALA C 632 " (cutoff:3.500A) Processing helix chain 'C' and resid 649 through 661 removed outlier: 3.742A pdb=" N ALA C 655 " --> pdb=" O LYS C 651 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N LEU C 657 " --> pdb=" O ARG C 653 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N LEU C 661 " --> pdb=" O LEU C 657 " (cutoff:3.500A) Processing helix chain 'C' and resid 671 through 679 removed outlier: 3.509A pdb=" N LYS C 677 " --> pdb=" O GLU C 673 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N MET C 678 " --> pdb=" O PHE C 674 " (cutoff:3.500A) Processing helix chain 'C' and resid 683 through 705 removed outlier: 3.595A pdb=" N CYS C 695 " --> pdb=" O CYS C 691 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ILE C 699 " --> pdb=" O CYS C 695 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ARG C 700 " --> pdb=" O LYS C 696 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N GLU C 701 " --> pdb=" O LEU C 697 " (cutoff:3.500A) Processing helix chain 'C' and resid 732 through 740 Processing helix chain 'C' and resid 751 through 761 Processing helix chain 'C' and resid 762 through 766 removed outlier: 3.797A pdb=" N ARG C 766 " --> pdb=" O GLN C 763 " (cutoff:3.500A) Processing helix chain 'D' and resid 42 through 50 Processing helix chain 'D' and resid 85 through 92 removed outlier: 4.210A pdb=" N ASN D 91 " --> pdb=" O VAL D 87 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LEU D 92 " --> pdb=" O VAL D 88 " (cutoff:3.500A) Processing helix chain 'D' and resid 135 through 140 removed outlier: 3.749A pdb=" N PHE D 139 " --> pdb=" O LEU D 135 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N LEU D 140 " --> pdb=" O LYS D 136 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 135 through 140' Processing helix chain 'D' and resid 202 through 206 removed outlier: 3.883A pdb=" N ILE D 206 " --> pdb=" O TYR D 203 " (cutoff:3.500A) Processing helix chain 'D' and resid 209 through 226 removed outlier: 3.520A pdb=" N GLN D 215 " --> pdb=" O LYS D 211 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N LEU D 222 " --> pdb=" O GLU D 218 " (cutoff:3.500A) Proline residue: D 223 - end of helix Processing helix chain 'D' and resid 226 through 233 removed outlier: 4.036A pdb=" N PHE D 230 " --> pdb=" O HIS D 226 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LYS D 231 " --> pdb=" O PRO D 227 " (cutoff:3.500A) Processing helix chain 'D' and resid 250 through 263 Processing helix chain 'D' and resid 271 through 277 Processing helix chain 'D' and resid 280 through 296 removed outlier: 4.008A pdb=" N SER D 284 " --> pdb=" O GLY D 280 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ALA D 289 " --> pdb=" O ASN D 285 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N PHE D 290 " --> pdb=" O LEU D 286 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LYS D 295 " --> pdb=" O GLU D 291 " (cutoff:3.500A) Processing helix chain 'D' and resid 305 through 310 removed outlier: 4.152A pdb=" N ILE D 309 " --> pdb=" O GLU D 305 " (cutoff:3.500A) Processing helix chain 'D' and resid 318 through 333 removed outlier: 3.732A pdb=" N VAL D 325 " --> pdb=" O GLU D 321 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N SER D 326 " --> pdb=" O ARG D 322 " (cutoff:3.500A) Processing helix chain 'D' and resid 354 through 358 Processing helix chain 'D' and resid 373 through 386 removed outlier: 3.516A pdb=" N GLU D 379 " --> pdb=" O THR D 375 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ILE D 383 " --> pdb=" O GLU D 379 " (cutoff:3.500A) Processing helix chain 'D' and resid 398 through 403 Processing helix chain 'D' and resid 407 through 426 removed outlier: 3.736A pdb=" N CYS D 415 " --> pdb=" O LEU D 411 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N LYS D 425 " --> pdb=" O GLN D 421 " (cutoff:3.500A) Processing helix chain 'D' and resid 426 through 431 removed outlier: 4.001A pdb=" N ILE D 430 " --> pdb=" O LYS D 426 " (cutoff:3.500A) Processing helix chain 'D' and resid 439 through 445 Processing helix chain 'D' and resid 448 through 456 removed outlier: 3.776A pdb=" N PHE D 452 " --> pdb=" O THR D 448 " (cutoff:3.500A) Processing helix chain 'D' and resid 482 through 493 Processing helix chain 'D' and resid 493 through 499 removed outlier: 3.816A pdb=" N VAL D 497 " --> pdb=" O VAL D 493 " (cutoff:3.500A) Processing helix chain 'D' and resid 523 through 536 removed outlier: 4.029A pdb=" N ILE D 531 " --> pdb=" O LEU D 527 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ALA D 532 " --> pdb=" O ALA D 528 " (cutoff:3.500A) Processing helix chain 'D' and resid 544 through 551 removed outlier: 3.557A pdb=" N MET D 550 " --> pdb=" O GLU D 546 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N TRP D 551 " --> pdb=" O LEU D 547 " (cutoff:3.500A) Processing helix chain 'D' and resid 559 through 568 Processing helix chain 'D' and resid 579 through 588 removed outlier: 4.105A pdb=" N ALA D 583 " --> pdb=" O LEU D 579 " (cutoff:3.500A) Processing helix chain 'D' and resid 598 through 609 removed outlier: 3.857A pdb=" N ASN D 602 " --> pdb=" O ASP D 598 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N GLN D 603 " --> pdb=" O ARG D 599 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ILE D 604 " --> pdb=" O VAL D 600 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N GLU D 607 " --> pdb=" O GLN D 603 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N ASP D 609 " --> pdb=" O LEU D 605 " (cutoff:3.500A) Processing helix chain 'D' and resid 625 through 629 removed outlier: 3.561A pdb=" N ILE D 629 " --> pdb=" O PRO D 626 " (cutoff:3.500A) Processing helix chain 'D' and resid 630 through 635 removed outlier: 3.683A pdb=" N ARG D 635 " --> pdb=" O ALA D 632 " (cutoff:3.500A) Processing helix chain 'D' and resid 649 through 661 removed outlier: 3.742A pdb=" N ALA D 655 " --> pdb=" O LYS D 651 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LEU D 657 " --> pdb=" O ARG D 653 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N LEU D 661 " --> pdb=" O LEU D 657 " (cutoff:3.500A) Processing helix chain 'D' and resid 671 through 679 removed outlier: 3.508A pdb=" N LYS D 677 " --> pdb=" O GLU D 673 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N MET D 678 " --> pdb=" O PHE D 674 " (cutoff:3.500A) Processing helix chain 'D' and resid 683 through 705 removed outlier: 3.596A pdb=" N CYS D 695 " --> pdb=" O CYS D 691 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ILE D 699 " --> pdb=" O CYS D 695 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ARG D 700 " --> pdb=" O LYS D 696 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N GLU D 701 " --> pdb=" O LEU D 697 " (cutoff:3.500A) Processing helix chain 'D' and resid 732 through 740 Processing helix chain 'D' and resid 751 through 761 Processing helix chain 'D' and resid 762 through 766 removed outlier: 3.797A pdb=" N ARG D 766 " --> pdb=" O GLN D 763 " (cutoff:3.500A) Processing helix chain 'E' and resid 42 through 50 Processing helix chain 'E' and resid 85 through 92 removed outlier: 4.210A pdb=" N ASN E 91 " --> pdb=" O VAL E 87 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LEU E 92 " --> pdb=" O VAL E 88 " (cutoff:3.500A) Processing helix chain 'E' and resid 135 through 140 removed outlier: 3.750A pdb=" N PHE E 139 " --> pdb=" O LEU E 135 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N LEU E 140 " --> pdb=" O LYS E 136 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 135 through 140' Processing helix chain 'E' and resid 202 through 206 removed outlier: 3.883A pdb=" N ILE E 206 " --> pdb=" O TYR E 203 " (cutoff:3.500A) Processing helix chain 'E' and resid 209 through 226 removed outlier: 3.520A pdb=" N GLN E 215 " --> pdb=" O LYS E 211 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N LEU E 222 " --> pdb=" O GLU E 218 " (cutoff:3.500A) Proline residue: E 223 - end of helix Processing helix chain 'E' and resid 226 through 233 removed outlier: 4.036A pdb=" N PHE E 230 " --> pdb=" O HIS E 226 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LYS E 231 " --> pdb=" O PRO E 227 " (cutoff:3.500A) Processing helix chain 'E' and resid 250 through 263 Processing helix chain 'E' and resid 271 through 277 Processing helix chain 'E' and resid 280 through 296 removed outlier: 4.008A pdb=" N SER E 284 " --> pdb=" O GLY E 280 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ALA E 289 " --> pdb=" O ASN E 285 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N PHE E 290 " --> pdb=" O LEU E 286 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LYS E 295 " --> pdb=" O GLU E 291 " (cutoff:3.500A) Processing helix chain 'E' and resid 305 through 310 removed outlier: 4.151A pdb=" N ILE E 309 " --> pdb=" O GLU E 305 " (cutoff:3.500A) Processing helix chain 'E' and resid 318 through 333 removed outlier: 3.733A pdb=" N VAL E 325 " --> pdb=" O GLU E 321 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N SER E 326 " --> pdb=" O ARG E 322 " (cutoff:3.500A) Processing helix chain 'E' and resid 354 through 358 Processing helix chain 'E' and resid 373 through 386 removed outlier: 3.516A pdb=" N GLU E 379 " --> pdb=" O THR E 375 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ILE E 383 " --> pdb=" O GLU E 379 " (cutoff:3.500A) Processing helix chain 'E' and resid 398 through 403 Processing helix chain 'E' and resid 407 through 426 removed outlier: 3.736A pdb=" N CYS E 415 " --> pdb=" O LEU E 411 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N LYS E 425 " --> pdb=" O GLN E 421 " (cutoff:3.500A) Processing helix chain 'E' and resid 426 through 431 removed outlier: 4.002A pdb=" N ILE E 430 " --> pdb=" O LYS E 426 " (cutoff:3.500A) Processing helix chain 'E' and resid 439 through 445 Processing helix chain 'E' and resid 448 through 456 removed outlier: 3.776A pdb=" N PHE E 452 " --> pdb=" O THR E 448 " (cutoff:3.500A) Processing helix chain 'E' and resid 482 through 493 Processing helix chain 'E' and resid 493 through 499 removed outlier: 3.816A pdb=" N VAL E 497 " --> pdb=" O VAL E 493 " (cutoff:3.500A) Processing helix chain 'E' and resid 523 through 536 removed outlier: 4.030A pdb=" N ILE E 531 " --> pdb=" O LEU E 527 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ALA E 532 " --> pdb=" O ALA E 528 " (cutoff:3.500A) Processing helix chain 'E' and resid 544 through 551 removed outlier: 3.557A pdb=" N MET E 550 " --> pdb=" O GLU E 546 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N TRP E 551 " --> pdb=" O LEU E 547 " (cutoff:3.500A) Processing helix chain 'E' and resid 559 through 568 Processing helix chain 'E' and resid 579 through 588 removed outlier: 4.104A pdb=" N ALA E 583 " --> pdb=" O LEU E 579 " (cutoff:3.500A) Processing helix chain 'E' and resid 598 through 609 removed outlier: 3.857A pdb=" N ASN E 602 " --> pdb=" O ASP E 598 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N GLN E 603 " --> pdb=" O ARG E 599 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ILE E 604 " --> pdb=" O VAL E 600 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N GLU E 607 " --> pdb=" O GLN E 603 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N ASP E 609 " --> pdb=" O LEU E 605 " (cutoff:3.500A) Processing helix chain 'E' and resid 625 through 629 removed outlier: 3.562A pdb=" N ILE E 629 " --> pdb=" O PRO E 626 " (cutoff:3.500A) Processing helix chain 'E' and resid 630 through 635 removed outlier: 3.683A pdb=" N ARG E 635 " --> pdb=" O ALA E 632 " (cutoff:3.500A) Processing helix chain 'E' and resid 649 through 661 removed outlier: 3.742A pdb=" N ALA E 655 " --> pdb=" O LYS E 651 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LEU E 657 " --> pdb=" O ARG E 653 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N LEU E 661 " --> pdb=" O LEU E 657 " (cutoff:3.500A) Processing helix chain 'E' and resid 671 through 679 removed outlier: 3.508A pdb=" N LYS E 677 " --> pdb=" O GLU E 673 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N MET E 678 " --> pdb=" O PHE E 674 " (cutoff:3.500A) Processing helix chain 'E' and resid 683 through 705 removed outlier: 3.595A pdb=" N CYS E 695 " --> pdb=" O CYS E 691 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ILE E 699 " --> pdb=" O CYS E 695 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ARG E 700 " --> pdb=" O LYS E 696 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N GLU E 701 " --> pdb=" O LEU E 697 " (cutoff:3.500A) Processing helix chain 'E' and resid 732 through 740 Processing helix chain 'E' and resid 751 through 761 Processing helix chain 'E' and resid 762 through 766 removed outlier: 3.797A pdb=" N ARG E 766 " --> pdb=" O GLN E 763 " (cutoff:3.500A) Processing helix chain 'F' and resid 42 through 50 Processing helix chain 'F' and resid 85 through 92 removed outlier: 4.211A pdb=" N ASN F 91 " --> pdb=" O VAL F 87 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LEU F 92 " --> pdb=" O VAL F 88 " (cutoff:3.500A) Processing helix chain 'F' and resid 135 through 140 removed outlier: 3.750A pdb=" N PHE F 139 " --> pdb=" O LEU F 135 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N LEU F 140 " --> pdb=" O LYS F 136 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 135 through 140' Processing helix chain 'F' and resid 202 through 206 removed outlier: 3.883A pdb=" N ILE F 206 " --> pdb=" O TYR F 203 " (cutoff:3.500A) Processing helix chain 'F' and resid 209 through 226 removed outlier: 3.521A pdb=" N GLN F 215 " --> pdb=" O LYS F 211 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N LEU F 222 " --> pdb=" O GLU F 218 " (cutoff:3.500A) Proline residue: F 223 - end of helix Processing helix chain 'F' and resid 226 through 233 removed outlier: 4.036A pdb=" N PHE F 230 " --> pdb=" O HIS F 226 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LYS F 231 " --> pdb=" O PRO F 227 " (cutoff:3.500A) Processing helix chain 'F' and resid 250 through 263 Processing helix chain 'F' and resid 271 through 277 Processing helix chain 'F' and resid 280 through 296 removed outlier: 4.008A pdb=" N SER F 284 " --> pdb=" O GLY F 280 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ALA F 289 " --> pdb=" O ASN F 285 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N PHE F 290 " --> pdb=" O LEU F 286 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LYS F 295 " --> pdb=" O GLU F 291 " (cutoff:3.500A) Processing helix chain 'F' and resid 305 through 310 removed outlier: 4.152A pdb=" N ILE F 309 " --> pdb=" O GLU F 305 " (cutoff:3.500A) Processing helix chain 'F' and resid 318 through 333 removed outlier: 3.732A pdb=" N VAL F 325 " --> pdb=" O GLU F 321 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N SER F 326 " --> pdb=" O ARG F 322 " (cutoff:3.500A) Processing helix chain 'F' and resid 354 through 358 Processing helix chain 'F' and resid 373 through 386 removed outlier: 3.517A pdb=" N GLU F 379 " --> pdb=" O THR F 375 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ILE F 383 " --> pdb=" O GLU F 379 " (cutoff:3.500A) Processing helix chain 'F' and resid 398 through 403 Processing helix chain 'F' and resid 407 through 426 removed outlier: 3.736A pdb=" N CYS F 415 " --> pdb=" O LEU F 411 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N LYS F 425 " --> pdb=" O GLN F 421 " (cutoff:3.500A) Processing helix chain 'F' and resid 426 through 431 removed outlier: 4.002A pdb=" N ILE F 430 " --> pdb=" O LYS F 426 " (cutoff:3.500A) Processing helix chain 'F' and resid 439 through 445 Processing helix chain 'F' and resid 448 through 456 removed outlier: 3.776A pdb=" N PHE F 452 " --> pdb=" O THR F 448 " (cutoff:3.500A) Processing helix chain 'F' and resid 482 through 493 Processing helix chain 'F' and resid 493 through 499 removed outlier: 3.816A pdb=" N VAL F 497 " --> pdb=" O VAL F 493 " (cutoff:3.500A) Processing helix chain 'F' and resid 523 through 536 removed outlier: 4.030A pdb=" N ILE F 531 " --> pdb=" O LEU F 527 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ALA F 532 " --> pdb=" O ALA F 528 " (cutoff:3.500A) Processing helix chain 'F' and resid 544 through 551 removed outlier: 3.557A pdb=" N MET F 550 " --> pdb=" O GLU F 546 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N TRP F 551 " --> pdb=" O LEU F 547 " (cutoff:3.500A) Processing helix chain 'F' and resid 559 through 568 Processing helix chain 'F' and resid 579 through 588 removed outlier: 4.105A pdb=" N ALA F 583 " --> pdb=" O LEU F 579 " (cutoff:3.500A) Processing helix chain 'F' and resid 598 through 609 removed outlier: 3.857A pdb=" N ASN F 602 " --> pdb=" O ASP F 598 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N GLN F 603 " --> pdb=" O ARG F 599 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ILE F 604 " --> pdb=" O VAL F 600 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N GLU F 607 " --> pdb=" O GLN F 603 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N ASP F 609 " --> pdb=" O LEU F 605 " (cutoff:3.500A) Processing helix chain 'F' and resid 625 through 629 removed outlier: 3.562A pdb=" N ILE F 629 " --> pdb=" O PRO F 626 " (cutoff:3.500A) Processing helix chain 'F' and resid 630 through 635 removed outlier: 3.682A pdb=" N ARG F 635 " --> pdb=" O ALA F 632 " (cutoff:3.500A) Processing helix chain 'F' and resid 649 through 661 removed outlier: 3.742A pdb=" N ALA F 655 " --> pdb=" O LYS F 651 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LEU F 657 " --> pdb=" O ARG F 653 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N LEU F 661 " --> pdb=" O LEU F 657 " (cutoff:3.500A) Processing helix chain 'F' and resid 671 through 679 removed outlier: 3.508A pdb=" N LYS F 677 " --> pdb=" O GLU F 673 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N MET F 678 " --> pdb=" O PHE F 674 " (cutoff:3.500A) Processing helix chain 'F' and resid 683 through 705 removed outlier: 3.595A pdb=" N CYS F 695 " --> pdb=" O CYS F 691 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ILE F 699 " --> pdb=" O CYS F 695 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ARG F 700 " --> pdb=" O LYS F 696 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N GLU F 701 " --> pdb=" O LEU F 697 " (cutoff:3.500A) Processing helix chain 'F' and resid 732 through 740 Processing helix chain 'F' and resid 751 through 761 Processing helix chain 'F' and resid 762 through 766 removed outlier: 3.797A pdb=" N ARG F 766 " --> pdb=" O GLN F 763 " (cutoff:3.500A) Processing sheet with id=AA, first strand: chain 'A' and resid 26 through 27 Processing sheet with id=AB, first strand: chain 'A' and resid 29 through 30 Processing sheet with id=AC, first strand: chain 'A' and resid 40 through 41 Processing sheet with id=AD, first strand: chain 'A' and resid 56 through 59 Processing sheet with id=AE, first strand: chain 'A' and resid 115 through 118 removed outlier: 8.175A pdb=" N HIS A 115 " --> pdb=" O VAL A 166 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N VAL A 166 " --> pdb=" O HIS A 115 " (cutoff:3.500A) Processing sheet with id=AF, first strand: chain 'A' and resid 126 through 127 removed outlier: 3.526A pdb=" N THR A 127 " --> pdb=" O ILE A 437 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF Processing sheet with id=AG, first strand: chain 'A' and resid 145 through 146 Processing sheet with id=AH, first strand: chain 'A' and resid 241 through 243 Processing sheet with id=AI, first strand: chain 'A' and resid 538 through 543 removed outlier: 3.696A pdb=" N ASP A 640 " --> pdb=" O GLY A 513 " (cutoff:3.500A) removed outlier: 6.110A pdb=" N LEU A 515 " --> pdb=" O ASP A 640 " (cutoff:3.500A) removed outlier: 4.656A pdb=" N LEU A 642 " --> pdb=" O LEU A 515 " (cutoff:3.500A) removed outlier: 7.446A pdb=" N TYR A 517 " --> pdb=" O LEU A 642 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N TYR A 644 " --> pdb=" O TYR A 517 " (cutoff:3.500A) Processing sheet with id=BA, first strand: chain 'B' and resid 26 through 27 Processing sheet with id=BB, first strand: chain 'B' and resid 29 through 30 Processing sheet with id=BC, first strand: chain 'B' and resid 40 through 41 Processing sheet with id=BD, first strand: chain 'B' and resid 56 through 59 Processing sheet with id=BE, first strand: chain 'B' and resid 115 through 118 removed outlier: 8.175A pdb=" N HIS B 115 " --> pdb=" O VAL B 166 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N VAL B 166 " --> pdb=" O HIS B 115 " (cutoff:3.500A) Processing sheet with id=BF, first strand: chain 'B' and resid 126 through 127 removed outlier: 3.526A pdb=" N THR B 127 " --> pdb=" O ILE B 437 " (cutoff:3.500A) No H-bonds generated for sheet with id=BF Processing sheet with id=BG, first strand: chain 'B' and resid 145 through 146 Processing sheet with id=BH, first strand: chain 'B' and resid 241 through 243 Processing sheet with id=BI, first strand: chain 'B' and resid 538 through 543 removed outlier: 3.696A pdb=" N ASP B 640 " --> pdb=" O GLY B 513 " (cutoff:3.500A) removed outlier: 6.111A pdb=" N LEU B 515 " --> pdb=" O ASP B 640 " (cutoff:3.500A) removed outlier: 4.656A pdb=" N LEU B 642 " --> pdb=" O LEU B 515 " (cutoff:3.500A) removed outlier: 7.445A pdb=" N TYR B 517 " --> pdb=" O LEU B 642 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N TYR B 644 " --> pdb=" O TYR B 517 " (cutoff:3.500A) Processing sheet with id=CA, first strand: chain 'C' and resid 26 through 27 Processing sheet with id=CB, first strand: chain 'C' and resid 29 through 30 Processing sheet with id=CC, first strand: chain 'C' and resid 40 through 41 Processing sheet with id=CD, first strand: chain 'C' and resid 56 through 59 Processing sheet with id=CE, first strand: chain 'C' and resid 115 through 118 removed outlier: 8.175A pdb=" N HIS C 115 " --> pdb=" O VAL C 166 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N VAL C 166 " --> pdb=" O HIS C 115 " (cutoff:3.500A) Processing sheet with id=CF, first strand: chain 'C' and resid 126 through 127 removed outlier: 3.527A pdb=" N THR C 127 " --> pdb=" O ILE C 437 " (cutoff:3.500A) No H-bonds generated for sheet with id=CF Processing sheet with id=CG, first strand: chain 'C' and resid 145 through 146 Processing sheet with id=CH, first strand: chain 'C' and resid 241 through 243 Processing sheet with id=CI, first strand: chain 'C' and resid 538 through 543 removed outlier: 3.696A pdb=" N ASP C 640 " --> pdb=" O GLY C 513 " (cutoff:3.500A) removed outlier: 6.110A pdb=" N LEU C 515 " --> pdb=" O ASP C 640 " (cutoff:3.500A) removed outlier: 4.656A pdb=" N LEU C 642 " --> pdb=" O LEU C 515 " (cutoff:3.500A) removed outlier: 7.445A pdb=" N TYR C 517 " --> pdb=" O LEU C 642 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N TYR C 644 " --> pdb=" O TYR C 517 " (cutoff:3.500A) Processing sheet with id=DA, first strand: chain 'D' and resid 26 through 27 Processing sheet with id=DB, first strand: chain 'D' and resid 29 through 30 Processing sheet with id=DC, first strand: chain 'D' and resid 40 through 41 Processing sheet with id=DD, first strand: chain 'D' and resid 56 through 59 Processing sheet with id=DE, first strand: chain 'D' and resid 115 through 118 removed outlier: 8.175A pdb=" N HIS D 115 " --> pdb=" O VAL D 166 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N VAL D 166 " --> pdb=" O HIS D 115 " (cutoff:3.500A) Processing sheet with id=DF, first strand: chain 'D' and resid 126 through 127 removed outlier: 3.525A pdb=" N THR D 127 " --> pdb=" O ILE D 437 " (cutoff:3.500A) No H-bonds generated for sheet with id=DF Processing sheet with id=DG, first strand: chain 'D' and resid 145 through 146 Processing sheet with id=DH, first strand: chain 'D' and resid 241 through 243 Processing sheet with id=DI, first strand: chain 'D' and resid 538 through 543 removed outlier: 3.697A pdb=" N ASP D 640 " --> pdb=" O GLY D 513 " (cutoff:3.500A) removed outlier: 6.110A pdb=" N LEU D 515 " --> pdb=" O ASP D 640 " (cutoff:3.500A) removed outlier: 4.656A pdb=" N LEU D 642 " --> pdb=" O LEU D 515 " (cutoff:3.500A) removed outlier: 7.446A pdb=" N TYR D 517 " --> pdb=" O LEU D 642 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N TYR D 644 " --> pdb=" O TYR D 517 " (cutoff:3.500A) Processing sheet with id=EA, first strand: chain 'E' and resid 26 through 27 Processing sheet with id=EB, first strand: chain 'E' and resid 29 through 30 Processing sheet with id=EC, first strand: chain 'E' and resid 40 through 41 Processing sheet with id=ED, first strand: chain 'E' and resid 56 through 59 Processing sheet with id=EE, first strand: chain 'E' and resid 115 through 118 removed outlier: 8.174A pdb=" N HIS E 115 " --> pdb=" O VAL E 166 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N VAL E 166 " --> pdb=" O HIS E 115 " (cutoff:3.500A) Processing sheet with id=EF, first strand: chain 'E' and resid 126 through 127 removed outlier: 3.526A pdb=" N THR E 127 " --> pdb=" O ILE E 437 " (cutoff:3.500A) No H-bonds generated for sheet with id=EF Processing sheet with id=EG, first strand: chain 'E' and resid 145 through 146 Processing sheet with id=EH, first strand: chain 'E' and resid 241 through 243 Processing sheet with id=EI, first strand: chain 'E' and resid 538 through 543 removed outlier: 3.696A pdb=" N ASP E 640 " --> pdb=" O GLY E 513 " (cutoff:3.500A) removed outlier: 6.111A pdb=" N LEU E 515 " --> pdb=" O ASP E 640 " (cutoff:3.500A) removed outlier: 4.657A pdb=" N LEU E 642 " --> pdb=" O LEU E 515 " (cutoff:3.500A) removed outlier: 7.446A pdb=" N TYR E 517 " --> pdb=" O LEU E 642 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N TYR E 644 " --> pdb=" O TYR E 517 " (cutoff:3.500A) Processing sheet with id=FA, first strand: chain 'F' and resid 26 through 27 Processing sheet with id=FB, first strand: chain 'F' and resid 29 through 30 Processing sheet with id=FC, first strand: chain 'F' and resid 40 through 41 Processing sheet with id=FD, first strand: chain 'F' and resid 56 through 59 Processing sheet with id=FE, first strand: chain 'F' and resid 115 through 118 removed outlier: 8.175A pdb=" N HIS F 115 " --> pdb=" O VAL F 166 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N VAL F 166 " --> pdb=" O HIS F 115 " (cutoff:3.500A) Processing sheet with id=FF, first strand: chain 'F' and resid 126 through 127 removed outlier: 3.526A pdb=" N THR F 127 " --> pdb=" O ILE F 437 " (cutoff:3.500A) No H-bonds generated for sheet with id=FF Processing sheet with id=FG, first strand: chain 'F' and resid 145 through 146 Processing sheet with id=FH, first strand: chain 'F' and resid 241 through 243 Processing sheet with id=FI, first strand: chain 'F' and resid 538 through 543 removed outlier: 3.696A pdb=" N ASP F 640 " --> pdb=" O GLY F 513 " (cutoff:3.500A) removed outlier: 6.110A pdb=" N LEU F 515 " --> pdb=" O ASP F 640 " (cutoff:3.500A) removed outlier: 4.656A pdb=" N LEU F 642 " --> pdb=" O LEU F 515 " (cutoff:3.500A) removed outlier: 7.446A pdb=" N TYR F 517 " --> pdb=" O LEU F 642 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N TYR F 644 " --> pdb=" O TYR F 517 " (cutoff:3.500A) 1229 hydrogen bonds defined for protein. 3417 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: 7.72 Time building geometry restraints manager: 3.83 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.38: 13464 1.38 - 1.55: 21318 1.55 - 1.73: 54 1.73 - 1.90: 288 1.90 - 2.07: 6 Bond restraints: 35130 Sorted by residual: bond pdb=" C4 AGS D 901 " pdb=" C5 AGS D 901 " ideal model delta sigma weight residual 1.386 1.469 -0.083 1.00e-02 1.00e+04 6.90e+01 bond pdb=" C4 AGS A 901 " pdb=" C5 AGS A 901 " ideal model delta sigma weight residual 1.386 1.469 -0.083 1.00e-02 1.00e+04 6.90e+01 bond pdb=" C4 AGS E 901 " pdb=" C5 AGS E 901 " ideal model delta sigma weight residual 1.386 1.469 -0.083 1.00e-02 1.00e+04 6.88e+01 bond pdb=" C4 AGS B 901 " pdb=" C5 AGS B 901 " ideal model delta sigma weight residual 1.386 1.469 -0.083 1.00e-02 1.00e+04 6.88e+01 bond pdb=" C4 AGS C 901 " pdb=" C5 AGS C 901 " ideal model delta sigma weight residual 1.386 1.468 -0.082 1.00e-02 1.00e+04 6.80e+01 ... (remaining 35125 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.08: 45745 3.08 - 6.16: 1511 6.16 - 9.24: 225 9.24 - 12.32: 13 12.32 - 15.40: 20 Bond angle restraints: 47514 Sorted by residual: angle pdb=" N GLU C 314 " pdb=" CA GLU C 314 " pdb=" C GLU C 314 " ideal model delta sigma weight residual 113.17 98.21 14.96 1.26e+00 6.30e-01 1.41e+02 angle pdb=" N GLU F 314 " pdb=" CA GLU F 314 " pdb=" C GLU F 314 " ideal model delta sigma weight residual 113.17 98.24 14.93 1.26e+00 6.30e-01 1.40e+02 angle pdb=" N GLU D 314 " pdb=" CA GLU D 314 " pdb=" C GLU D 314 " ideal model delta sigma weight residual 113.17 98.24 14.93 1.26e+00 6.30e-01 1.40e+02 angle pdb=" N GLU A 314 " pdb=" CA GLU A 314 " pdb=" C GLU A 314 " ideal model delta sigma weight residual 113.17 98.24 14.93 1.26e+00 6.30e-01 1.40e+02 angle pdb=" N GLU E 314 " pdb=" CA GLU E 314 " pdb=" C GLU E 314 " ideal model delta sigma weight residual 113.17 98.25 14.92 1.26e+00 6.30e-01 1.40e+02 ... (remaining 47509 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.45: 21424 30.45 - 60.90: 296 60.90 - 91.35: 54 91.35 - 121.80: 0 121.80 - 152.24: 6 Dihedral angle restraints: 21780 sinusoidal: 9210 harmonic: 12570 Sorted by residual: dihedral pdb=" CD ARG D 377 " pdb=" NE ARG D 377 " pdb=" CZ ARG D 377 " pdb=" NH1 ARG D 377 " ideal model delta sinusoidal sigma weight residual 0.00 58.03 -58.03 1 1.00e+01 1.00e-02 4.52e+01 dihedral pdb=" CD ARG C 377 " pdb=" NE ARG C 377 " pdb=" CZ ARG C 377 " pdb=" NH1 ARG C 377 " ideal model delta sinusoidal sigma weight residual 0.00 58.00 -58.00 1 1.00e+01 1.00e-02 4.51e+01 dihedral pdb=" CD ARG E 377 " pdb=" NE ARG E 377 " pdb=" CZ ARG E 377 " pdb=" NH1 ARG E 377 " ideal model delta sinusoidal sigma weight residual 0.00 57.97 -57.97 1 1.00e+01 1.00e-02 4.51e+01 ... (remaining 21777 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.067: 3720 0.067 - 0.133: 1383 0.133 - 0.200: 205 0.200 - 0.266: 43 0.266 - 0.333: 1 Chirality restraints: 5352 Sorted by residual: chirality pdb=" CA ILE A 731 " pdb=" N ILE A 731 " pdb=" C ILE A 731 " pdb=" CB ILE A 731 " both_signs ideal model delta sigma weight residual False 2.43 2.77 -0.33 2.00e-01 2.50e+01 2.77e+00 chirality pdb=" CA ARG E 313 " pdb=" N ARG E 313 " pdb=" C ARG E 313 " pdb=" CB ARG E 313 " both_signs ideal model delta sigma weight residual False 2.51 2.76 -0.25 2.00e-01 2.50e+01 1.62e+00 chirality pdb=" CA GLU C 314 " pdb=" N GLU C 314 " pdb=" C GLU C 314 " pdb=" CB GLU C 314 " both_signs ideal model delta sigma weight residual False 2.51 2.76 -0.25 2.00e-01 2.50e+01 1.59e+00 ... (remaining 5349 not shown) Planarity restraints: 6234 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG E 377 " 0.923 9.50e-02 1.11e+02 4.14e-01 1.04e+02 pdb=" NE ARG E 377 " -0.057 2.00e-02 2.50e+03 pdb=" CZ ARG E 377 " -0.004 2.00e-02 2.50e+03 pdb=" NH1 ARG E 377 " -0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG E 377 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG D 377 " 0.923 9.50e-02 1.11e+02 4.14e-01 1.04e+02 pdb=" NE ARG D 377 " -0.057 2.00e-02 2.50e+03 pdb=" CZ ARG D 377 " -0.004 2.00e-02 2.50e+03 pdb=" NH1 ARG D 377 " -0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG D 377 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG C 377 " 0.922 9.50e-02 1.11e+02 4.13e-01 1.03e+02 pdb=" NE ARG C 377 " -0.057 2.00e-02 2.50e+03 pdb=" CZ ARG C 377 " -0.004 2.00e-02 2.50e+03 pdb=" NH1 ARG C 377 " -0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG C 377 " 0.022 2.00e-02 2.50e+03 ... (remaining 6231 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 3152 2.71 - 3.26: 36707 3.26 - 3.81: 53668 3.81 - 4.35: 69107 4.35 - 4.90: 113220 Nonbonded interactions: 275854 Sorted by model distance: nonbonded pdb=" OD1 ASP B 373 " pdb=" N ALA B 374 " model vdw 2.163 3.120 nonbonded pdb=" OD1 ASP A 373 " pdb=" N ALA A 374 " model vdw 2.163 3.120 nonbonded pdb=" OD1 ASP D 373 " pdb=" N ALA D 374 " model vdw 2.163 3.120 nonbonded pdb=" OD1 ASP C 373 " pdb=" N ALA C 374 " model vdw 2.163 3.120 nonbonded pdb=" OD1 ASP E 373 " pdb=" N ALA E 374 " model vdw 2.163 3.120 ... (remaining 275849 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: 0.11 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 1.500 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: 0.610 Check model and map are aligned: 0.100 Set scattering table: 0.090 Process input model: 30.660 Find NCS groups from input model: 0.310 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: 0.000 Load rotamer database and sin/cos tables:1.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.700 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8105 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 : 0.014 0.124 35130 Z= 0.623 Angle : 1.339 15.400 47514 Z= 0.762 Chirality : 0.067 0.333 5352 Planarity : 0.017 0.414 6234 Dihedral : 12.081 152.244 13632 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 23.62 Ramachandran Plot: Outliers : 0.71 % Allowed : 7.57 % Favored : 91.71 % Rotamer: Outliers : 0.51 % Allowed : 2.53 % Favored : 96.96 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.68 (0.10), residues: 4344 helix: -4.15 (0.07), residues: 1584 sheet: -2.40 (0.17), residues: 684 loop : -2.35 (0.11), residues: 2076 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.002 ARG F 766 TYR 0.039 0.004 TYR C 138 PHE 0.052 0.006 PHE C 516 TRP 0.022 0.005 TRP F 551 HIS 0.014 0.005 HIS C 317 Details of bonding type rmsd covalent geometry : bond 0.01373 (35130) covalent geometry : angle 1.33939 (47514) hydrogen bonds : bond 0.29171 ( 1229) hydrogen bonds : angle 10.03316 ( 3417) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8688 Ramachandran restraints generated. 4344 Oldfield, 0 Emsley, 4344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8688 Ramachandran restraints generated. 4344 Oldfield, 0 Emsley, 4344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 870 residues out of total 3714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 851 time to evaluate : 1.350 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 VAL cc_start: 0.5665 (t) cc_final: 0.5244 (m) REVERT: A 148 LYS cc_start: 0.6461 (mttt) cc_final: 0.6179 (mmtt) REVERT: A 173 TYR cc_start: 0.4843 (p90) cc_final: 0.4269 (p90) REVERT: A 546 GLU cc_start: 0.8695 (tm-30) cc_final: 0.8368 (tm-30) REVERT: B 39 VAL cc_start: 0.5699 (t) cc_final: 0.5259 (m) REVERT: B 148 LYS cc_start: 0.6494 (mttt) cc_final: 0.6268 (mmtt) REVERT: B 442 MET cc_start: 0.7469 (mmt) cc_final: 0.7126 (mmt) REVERT: B 546 GLU cc_start: 0.8732 (tm-30) cc_final: 0.8387 (tm-30) REVERT: C 39 VAL cc_start: 0.5605 (t) cc_final: 0.5188 (m) REVERT: C 148 LYS cc_start: 0.6550 (mttt) cc_final: 0.6310 (mmtm) REVERT: C 173 TYR cc_start: 0.5009 (p90) cc_final: 0.4355 (p90) REVERT: C 393 ASP cc_start: 0.6423 (p0) cc_final: 0.6091 (p0) REVERT: C 442 MET cc_start: 0.7517 (mmt) cc_final: 0.7115 (mmt) REVERT: C 449 MET cc_start: 0.7982 (tpp) cc_final: 0.7781 (tpp) REVERT: C 478 ASP cc_start: 0.8550 (t0) cc_final: 0.8347 (m-30) REVERT: C 546 GLU cc_start: 0.8730 (tm-30) cc_final: 0.8378 (tm-30) REVERT: D 39 VAL cc_start: 0.5541 (t) cc_final: 0.5110 (m) REVERT: D 148 LYS cc_start: 0.6439 (mttt) cc_final: 0.6156 (mmtt) REVERT: D 173 TYR cc_start: 0.4799 (p90) cc_final: 0.4247 (p90) REVERT: D 546 GLU cc_start: 0.8686 (tm-30) cc_final: 0.8362 (tm-30) REVERT: E 39 VAL cc_start: 0.5660 (t) cc_final: 0.5065 (m) REVERT: E 148 LYS cc_start: 0.6437 (mttt) cc_final: 0.6218 (mmtt) REVERT: E 442 MET cc_start: 0.7471 (mmt) cc_final: 0.7177 (mmt) REVERT: E 546 GLU cc_start: 0.8738 (tm-30) cc_final: 0.8393 (tm-30) REVERT: F 39 VAL cc_start: 0.5500 (t) cc_final: 0.5060 (m) REVERT: F 148 LYS cc_start: 0.6522 (mttt) cc_final: 0.6313 (mmtm) REVERT: F 173 TYR cc_start: 0.4851 (p90) cc_final: 0.4210 (p90) REVERT: F 393 ASP cc_start: 0.6494 (p0) cc_final: 0.6211 (p0) REVERT: F 442 MET cc_start: 0.7526 (mmt) cc_final: 0.7166 (mmt) REVERT: F 546 GLU cc_start: 0.8758 (tm-30) cc_final: 0.8405 (tm-30) outliers start: 19 outliers final: 0 residues processed: 864 average time/residue: 0.2703 time to fit residues: 343.4486 Evaluate side-chains 428 residues out of total 3714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 428 time to evaluate : 1.150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 197 optimal weight: 5.9990 chunk 388 optimal weight: 10.0000 chunk 215 optimal weight: 5.9990 chunk 20 optimal weight: 8.9990 chunk 132 optimal weight: 20.0000 chunk 261 optimal weight: 8.9990 chunk 248 optimal weight: 10.0000 chunk 207 optimal weight: 5.9990 chunk 401 optimal weight: 0.7980 chunk 424 optimal weight: 0.0270 chunk 155 optimal weight: 10.0000 overall best weight: 3.7644 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 337 GLN A 348 ASN A 533 ASN A 538 ASN A 603 GLN A 692 GLN ** B 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 348 ASN B 533 ASN B 538 ASN B 603 GLN B 692 GLN B 764 GLN C 285 ASN ** C 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 533 ASN C 538 ASN C 603 GLN C 692 GLN ** D 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 337 GLN D 348 ASN D 533 ASN D 538 ASN D 603 GLN D 692 GLN ** E 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 348 ASN E 533 ASN E 538 ASN E 603 GLN E 692 GLN E 764 GLN F 183 HIS ** F 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 533 ASN F 538 ASN F 603 GLN F 692 GLN Total number of N/Q/H flips: 34 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.149082 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.114771 restraints weight = 58694.157| |-----------------------------------------------------------------------------| r_work (start): 0.3523 rms_B_bonded: 2.57 r_work: 0.3311 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.3311 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8051 moved from start: 0.2954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 35130 Z= 0.193 Angle : 0.867 8.598 47514 Z= 0.444 Chirality : 0.051 0.170 5352 Planarity : 0.006 0.048 6234 Dihedral : 9.762 143.170 4926 Min Nonbonded Distance : 2.302 Molprobity Statistics. All-atom Clashscore : 13.48 Ramachandran Plot: Outliers : 0.28 % Allowed : 6.68 % Favored : 93.05 % Rotamer: Outliers : 1.86 % Allowed : 8.70 % Favored : 89.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.04 (0.11), residues: 4344 helix: -2.29 (0.10), residues: 1698 sheet: -1.63 (0.18), residues: 666 loop : -1.74 (0.13), residues: 1980 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 377 TYR 0.022 0.003 TYR D 244 PHE 0.017 0.002 PHE A 516 TRP 0.006 0.002 TRP D 551 HIS 0.008 0.002 HIS D 317 Details of bonding type rmsd covalent geometry : bond 0.00426 (35130) covalent geometry : angle 0.86703 (47514) hydrogen bonds : bond 0.06013 ( 1229) hydrogen bonds : angle 6.15824 ( 3417) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8688 Ramachandran restraints generated. 4344 Oldfield, 0 Emsley, 4344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8688 Ramachandran restraints generated. 4344 Oldfield, 0 Emsley, 4344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 630 residues out of total 3714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 561 time to evaluate : 1.311 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 36 ASN cc_start: 0.6080 (t0) cc_final: 0.5844 (t0) REVERT: A 39 VAL cc_start: 0.5538 (t) cc_final: 0.5204 (m) REVERT: A 83 ARG cc_start: 0.5854 (mmt90) cc_final: 0.5491 (mmt90) REVERT: A 134 TYR cc_start: 0.6102 (m-80) cc_final: 0.5869 (m-10) REVERT: A 440 GLU cc_start: 0.6986 (pm20) cc_final: 0.6677 (tp30) REVERT: A 449 MET cc_start: 0.7672 (tpp) cc_final: 0.6618 (ttm) REVERT: A 546 GLU cc_start: 0.8363 (tm-30) cc_final: 0.8122 (tm-30) REVERT: A 560 ARG cc_start: 0.7658 (mtp180) cc_final: 0.7100 (mtp180) REVERT: A 599 ARG cc_start: 0.7749 (ptp90) cc_final: 0.7184 (ptt90) REVERT: B 39 VAL cc_start: 0.5533 (t) cc_final: 0.5207 (m) REVERT: B 83 ARG cc_start: 0.5876 (mmt90) cc_final: 0.5609 (mmt90) REVERT: B 134 TYR cc_start: 0.6155 (m-80) cc_final: 0.5697 (m-10) REVERT: B 440 GLU cc_start: 0.7115 (pm20) cc_final: 0.6788 (tp30) REVERT: B 449 MET cc_start: 0.7661 (tpp) cc_final: 0.6633 (ttm) REVERT: B 550 MET cc_start: 0.6394 (tpt) cc_final: 0.6180 (ptm) REVERT: B 551 TRP cc_start: 0.5522 (t60) cc_final: 0.5147 (t60) REVERT: B 560 ARG cc_start: 0.7709 (mtp180) cc_final: 0.7202 (mtp180) REVERT: B 599 ARG cc_start: 0.7680 (ptp90) cc_final: 0.7095 (ptt90) REVERT: C 36 ASN cc_start: 0.6084 (t0) cc_final: 0.5827 (t0) REVERT: C 39 VAL cc_start: 0.5743 (t) cc_final: 0.5443 (m) REVERT: C 393 ASP cc_start: 0.6423 (p0) cc_final: 0.6211 (p0) REVERT: C 440 GLU cc_start: 0.6950 (pm20) cc_final: 0.6620 (tp30) REVERT: C 546 GLU cc_start: 0.8292 (tm-30) cc_final: 0.7997 (tm-30) REVERT: C 550 MET cc_start: 0.6465 (tpt) cc_final: 0.6217 (ptm) REVERT: C 560 ARG cc_start: 0.7650 (mtp180) cc_final: 0.6781 (mtp180) REVERT: C 564 ASP cc_start: 0.7485 (m-30) cc_final: 0.7255 (m-30) REVERT: D 39 VAL cc_start: 0.5519 (t) cc_final: 0.5182 (m) REVERT: D 134 TYR cc_start: 0.6110 (m-80) cc_final: 0.5875 (m-10) REVERT: D 440 GLU cc_start: 0.6960 (pm20) cc_final: 0.6666 (tp30) REVERT: D 449 MET cc_start: 0.7661 (tpp) cc_final: 0.6636 (ttm) REVERT: D 546 GLU cc_start: 0.8311 (tm-30) cc_final: 0.8080 (tm-30) REVERT: D 560 ARG cc_start: 0.7629 (mtp180) cc_final: 0.7096 (mtp180) REVERT: D 599 ARG cc_start: 0.7772 (ptp90) cc_final: 0.7213 (ptt90) REVERT: E 36 ASN cc_start: 0.6047 (t0) cc_final: 0.5708 (t0) REVERT: E 39 VAL cc_start: 0.5255 (t) cc_final: 0.4967 (m) REVERT: E 83 ARG cc_start: 0.5848 (mmt90) cc_final: 0.5576 (mmt90) REVERT: E 134 TYR cc_start: 0.6155 (m-80) cc_final: 0.5678 (m-10) REVERT: E 148 LYS cc_start: 0.6213 (mttt) cc_final: 0.5872 (mmtt) REVERT: E 440 GLU cc_start: 0.7106 (pm20) cc_final: 0.6795 (tp30) REVERT: E 449 MET cc_start: 0.7610 (tpp) cc_final: 0.6589 (ttm) REVERT: E 550 MET cc_start: 0.6407 (tpt) cc_final: 0.6198 (ptm) REVERT: E 551 TRP cc_start: 0.5520 (t60) cc_final: 0.5141 (t60) REVERT: E 560 ARG cc_start: 0.7677 (mtp180) cc_final: 0.7145 (mtp180) REVERT: E 599 ARG cc_start: 0.7697 (ptp90) cc_final: 0.7127 (ptt90) REVERT: F 36 ASN cc_start: 0.6103 (t0) cc_final: 0.5824 (t0) REVERT: F 39 VAL cc_start: 0.5553 (t) cc_final: 0.5241 (m) REVERT: F 134 TYR cc_start: 0.6081 (m-80) cc_final: 0.5855 (m-10) REVERT: F 148 LYS cc_start: 0.6182 (mttt) cc_final: 0.5865 (mmtt) REVERT: F 440 GLU cc_start: 0.6910 (pm20) cc_final: 0.6594 (tp30) REVERT: F 442 MET cc_start: 0.7115 (mmt) cc_final: 0.6858 (mmt) REVERT: F 449 MET cc_start: 0.7730 (tpp) cc_final: 0.7258 (tpp) REVERT: F 546 GLU cc_start: 0.8308 (tm-30) cc_final: 0.8012 (tm-30) REVERT: F 550 MET cc_start: 0.6437 (tpt) cc_final: 0.6198 (ptm) REVERT: F 560 ARG cc_start: 0.7620 (mtp180) cc_final: 0.6753 (mtp180) REVERT: F 564 ASP cc_start: 0.7490 (m-30) cc_final: 0.7254 (m-30) outliers start: 69 outliers final: 48 residues processed: 606 average time/residue: 0.2556 time to fit residues: 236.1905 Evaluate side-chains 479 residues out of total 3714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 431 time to evaluate : 1.093 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 ASN Chi-restraints excluded: chain A residue 342 ILE Chi-restraints excluded: chain A residue 371 ILE Chi-restraints excluded: chain A residue 388 MET Chi-restraints excluded: chain A residue 448 THR Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 531 ILE Chi-restraints excluded: chain A residue 701 GLU Chi-restraints excluded: chain A residue 731 ILE Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 342 ILE Chi-restraints excluded: chain B residue 371 ILE Chi-restraints excluded: chain B residue 448 THR Chi-restraints excluded: chain B residue 531 ILE Chi-restraints excluded: chain B residue 697 LEU Chi-restraints excluded: chain B residue 701 GLU Chi-restraints excluded: chain C residue 32 ILE Chi-restraints excluded: chain C residue 85 ASN Chi-restraints excluded: chain C residue 198 LEU Chi-restraints excluded: chain C residue 371 ILE Chi-restraints excluded: chain C residue 448 THR Chi-restraints excluded: chain C residue 492 LEU Chi-restraints excluded: chain C residue 531 ILE Chi-restraints excluded: chain C residue 697 LEU Chi-restraints excluded: chain D residue 85 ASN Chi-restraints excluded: chain D residue 342 ILE Chi-restraints excluded: chain D residue 371 ILE Chi-restraints excluded: chain D residue 388 MET Chi-restraints excluded: chain D residue 448 THR Chi-restraints excluded: chain D residue 492 LEU Chi-restraints excluded: chain D residue 531 ILE Chi-restraints excluded: chain D residue 701 GLU Chi-restraints excluded: chain E residue 85 ASN Chi-restraints excluded: chain E residue 342 ILE Chi-restraints excluded: chain E residue 371 ILE Chi-restraints excluded: chain E residue 448 THR Chi-restraints excluded: chain E residue 531 ILE Chi-restraints excluded: chain E residue 697 LEU Chi-restraints excluded: chain E residue 701 GLU Chi-restraints excluded: chain F residue 32 ILE Chi-restraints excluded: chain F residue 85 ASN Chi-restraints excluded: chain F residue 198 LEU Chi-restraints excluded: chain F residue 371 ILE Chi-restraints excluded: chain F residue 448 THR Chi-restraints excluded: chain F residue 492 LEU Chi-restraints excluded: chain F residue 531 ILE Chi-restraints excluded: chain F residue 697 LEU Chi-restraints excluded: chain F residue 701 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 215 optimal weight: 10.0000 chunk 270 optimal weight: 3.9990 chunk 248 optimal weight: 7.9990 chunk 111 optimal weight: 6.9990 chunk 284 optimal weight: 9.9990 chunk 125 optimal weight: 8.9990 chunk 310 optimal weight: 9.9990 chunk 7 optimal weight: 8.9990 chunk 89 optimal weight: 30.0000 chunk 39 optimal weight: 2.9990 chunk 149 optimal weight: 7.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 348 ASN A 398 GLN ** B 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 348 ASN ** C 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 348 ASN D 398 GLN ** E 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 348 ASN ** F 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 398 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.147620 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.115534 restraints weight = 58881.228| |-----------------------------------------------------------------------------| r_work (start): 0.3536 rms_B_bonded: 2.37 r_work: 0.3310 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3310 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8057 moved from start: 0.3454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 35130 Z= 0.208 Angle : 0.791 8.347 47514 Z= 0.400 Chirality : 0.050 0.161 5352 Planarity : 0.006 0.060 6234 Dihedral : 9.446 141.481 4926 Min Nonbonded Distance : 2.304 Molprobity Statistics. All-atom Clashscore : 11.86 Ramachandran Plot: Outliers : 0.28 % Allowed : 7.53 % Favored : 92.20 % Rotamer: Outliers : 3.12 % Allowed : 10.55 % Favored : 86.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.24 (0.12), residues: 4344 helix: -1.36 (0.12), residues: 1716 sheet: -1.50 (0.18), residues: 666 loop : -1.44 (0.14), residues: 1962 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG F 599 TYR 0.019 0.002 TYR F 138 PHE 0.020 0.002 PHE A 516 TRP 0.013 0.002 TRP F 551 HIS 0.007 0.002 HIS C 340 Details of bonding type rmsd covalent geometry : bond 0.00485 (35130) covalent geometry : angle 0.79141 (47514) hydrogen bonds : bond 0.04990 ( 1229) hydrogen bonds : angle 5.67728 ( 3417) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8688 Ramachandran restraints generated. 4344 Oldfield, 0 Emsley, 4344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8688 Ramachandran restraints generated. 4344 Oldfield, 0 Emsley, 4344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 576 residues out of total 3714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 460 time to evaluate : 1.393 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 VAL cc_start: 0.5516 (t) cc_final: 0.5166 (m) REVERT: A 83 ARG cc_start: 0.5952 (mmt90) cc_final: 0.5732 (mmt90) REVERT: A 134 TYR cc_start: 0.6091 (m-80) cc_final: 0.5864 (m-10) REVERT: A 449 MET cc_start: 0.7633 (tpp) cc_final: 0.6685 (ttm) REVERT: A 599 ARG cc_start: 0.7625 (ptp90) cc_final: 0.7017 (ttp80) REVERT: A 692 GLN cc_start: 0.7880 (mm-40) cc_final: 0.7538 (mm-40) REVERT: B 39 VAL cc_start: 0.5447 (t) cc_final: 0.5118 (m) REVERT: B 134 TYR cc_start: 0.6116 (m-80) cc_final: 0.5604 (m-10) REVERT: B 449 MET cc_start: 0.7635 (tpp) cc_final: 0.6595 (ttm) REVERT: B 551 TRP cc_start: 0.5503 (t60) cc_final: 0.5038 (t60) REVERT: B 560 ARG cc_start: 0.7848 (mtp180) cc_final: 0.7285 (mtp180) REVERT: C 39 VAL cc_start: 0.5676 (t) cc_final: 0.5397 (m) REVERT: C 365 ARG cc_start: 0.8538 (mmt90) cc_final: 0.8167 (mmt90) REVERT: C 442 MET cc_start: 0.7163 (mmp) cc_final: 0.6470 (mmt) REVERT: C 449 MET cc_start: 0.7581 (tpp) cc_final: 0.6633 (ttm) REVERT: C 560 ARG cc_start: 0.7798 (mtp180) cc_final: 0.6928 (mtp180) REVERT: C 599 ARG cc_start: 0.7849 (ptp-170) cc_final: 0.7319 (ttp80) REVERT: D 39 VAL cc_start: 0.5553 (t) cc_final: 0.5207 (m) REVERT: D 134 TYR cc_start: 0.6109 (m-80) cc_final: 0.5847 (m-10) REVERT: D 449 MET cc_start: 0.7635 (tpp) cc_final: 0.6695 (ttm) REVERT: D 599 ARG cc_start: 0.7621 (ptp90) cc_final: 0.7020 (ttp80) REVERT: D 686 ASP cc_start: 0.7601 (m-30) cc_final: 0.7211 (m-30) REVERT: E 39 VAL cc_start: 0.5204 (t) cc_final: 0.4937 (m) REVERT: E 134 TYR cc_start: 0.6115 (m-80) cc_final: 0.5589 (m-10) REVERT: E 148 LYS cc_start: 0.6052 (mttt) cc_final: 0.5819 (mtpp) REVERT: E 449 MET cc_start: 0.7664 (tpp) cc_final: 0.6633 (ttm) REVERT: E 551 TRP cc_start: 0.5485 (t60) cc_final: 0.5060 (t60) REVERT: F 39 VAL cc_start: 0.5522 (t) cc_final: 0.5236 (m) REVERT: F 134 TYR cc_start: 0.6048 (m-80) cc_final: 0.5846 (m-10) REVERT: F 365 ARG cc_start: 0.8547 (mmt90) cc_final: 0.8140 (mmt90) REVERT: F 440 GLU cc_start: 0.6836 (pm20) cc_final: 0.6612 (tp30) REVERT: F 449 MET cc_start: 0.7616 (tpp) cc_final: 0.7309 (tpp) REVERT: F 560 ARG cc_start: 0.7811 (mtp180) cc_final: 0.6911 (mtp180) REVERT: F 599 ARG cc_start: 0.7857 (ptp-170) cc_final: 0.7348 (ttp80) outliers start: 116 outliers final: 82 residues processed: 539 average time/residue: 0.2318 time to fit residues: 194.6021 Evaluate side-chains 484 residues out of total 3714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 402 time to evaluate : 1.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 ASN Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 146 ILE Chi-restraints excluded: chain A residue 198 LEU Chi-restraints excluded: chain A residue 342 ILE Chi-restraints excluded: chain A residue 371 ILE Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 427 MET Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 448 THR Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 531 ILE Chi-restraints excluded: chain A residue 661 LEU Chi-restraints excluded: chain A residue 701 GLU Chi-restraints excluded: chain A residue 731 ILE Chi-restraints excluded: chain B residue 85 ASN Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 342 ILE Chi-restraints excluded: chain B residue 371 ILE Chi-restraints excluded: chain B residue 378 LEU Chi-restraints excluded: chain B residue 447 VAL Chi-restraints excluded: chain B residue 448 THR Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain B residue 531 ILE Chi-restraints excluded: chain B residue 558 ASN Chi-restraints excluded: chain B residue 697 LEU Chi-restraints excluded: chain B residue 701 GLU Chi-restraints excluded: chain C residue 85 ASN Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain C residue 198 LEU Chi-restraints excluded: chain C residue 342 ILE Chi-restraints excluded: chain C residue 371 ILE Chi-restraints excluded: chain C residue 427 MET Chi-restraints excluded: chain C residue 447 VAL Chi-restraints excluded: chain C residue 448 THR Chi-restraints excluded: chain C residue 492 LEU Chi-restraints excluded: chain C residue 531 ILE Chi-restraints excluded: chain C residue 558 ASN Chi-restraints excluded: chain C residue 661 LEU Chi-restraints excluded: chain C residue 697 LEU Chi-restraints excluded: chain D residue 85 ASN Chi-restraints excluded: chain D residue 123 VAL Chi-restraints excluded: chain D residue 198 LEU Chi-restraints excluded: chain D residue 342 ILE Chi-restraints excluded: chain D residue 371 ILE Chi-restraints excluded: chain D residue 378 LEU Chi-restraints excluded: chain D residue 427 MET Chi-restraints excluded: chain D residue 447 VAL Chi-restraints excluded: chain D residue 448 THR Chi-restraints excluded: chain D residue 492 LEU Chi-restraints excluded: chain D residue 501 ASP Chi-restraints excluded: chain D residue 531 ILE Chi-restraints excluded: chain D residue 661 LEU Chi-restraints excluded: chain D residue 701 GLU Chi-restraints excluded: chain E residue 85 ASN Chi-restraints excluded: chain E residue 123 VAL Chi-restraints excluded: chain E residue 198 LEU Chi-restraints excluded: chain E residue 342 ILE Chi-restraints excluded: chain E residue 371 ILE Chi-restraints excluded: chain E residue 378 LEU Chi-restraints excluded: chain E residue 447 VAL Chi-restraints excluded: chain E residue 448 THR Chi-restraints excluded: chain E residue 492 LEU Chi-restraints excluded: chain E residue 531 ILE Chi-restraints excluded: chain E residue 558 ASN Chi-restraints excluded: chain E residue 697 LEU Chi-restraints excluded: chain E residue 701 GLU Chi-restraints excluded: chain F residue 85 ASN Chi-restraints excluded: chain F residue 123 VAL Chi-restraints excluded: chain F residue 198 LEU Chi-restraints excluded: chain F residue 231 LYS Chi-restraints excluded: chain F residue 342 ILE Chi-restraints excluded: chain F residue 371 ILE Chi-restraints excluded: chain F residue 447 VAL Chi-restraints excluded: chain F residue 448 THR Chi-restraints excluded: chain F residue 492 LEU Chi-restraints excluded: chain F residue 531 ILE Chi-restraints excluded: chain F residue 558 ASN Chi-restraints excluded: chain F residue 661 LEU Chi-restraints excluded: chain F residue 697 LEU Chi-restraints excluded: chain F residue 701 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 309 optimal weight: 1.9990 chunk 284 optimal weight: 20.0000 chunk 174 optimal weight: 9.9990 chunk 386 optimal weight: 7.9990 chunk 28 optimal weight: 10.0000 chunk 122 optimal weight: 5.9990 chunk 108 optimal weight: 7.9990 chunk 180 optimal weight: 5.9990 chunk 29 optimal weight: 20.0000 chunk 245 optimal weight: 7.9990 chunk 135 optimal weight: 5.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 317 HIS ** 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 = 0.3978 r_free = 0.3978 target = 0.147630 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.115583 restraints weight = 58556.055| |-----------------------------------------------------------------------------| r_work (start): 0.3537 rms_B_bonded: 2.39 r_work: 0.3313 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3313 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8058 moved from start: 0.3876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 35130 Z= 0.185 Angle : 0.741 7.701 47514 Z= 0.373 Chirality : 0.049 0.155 5352 Planarity : 0.006 0.048 6234 Dihedral : 9.176 138.685 4926 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 10.76 Ramachandran Plot: Outliers : 0.25 % Allowed : 7.64 % Favored : 92.10 % Rotamer: Outliers : 3.93 % Allowed : 12.49 % Favored : 83.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.84 (0.12), residues: 4344 helix: -0.99 (0.12), residues: 1758 sheet: -1.42 (0.19), residues: 618 loop : -1.21 (0.14), residues: 1968 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 83 TYR 0.017 0.002 TYR B 138 PHE 0.018 0.002 PHE A 576 TRP 0.008 0.001 TRP E 551 HIS 0.006 0.002 HIS F 384 Details of bonding type rmsd covalent geometry : bond 0.00430 (35130) covalent geometry : angle 0.74140 (47514) hydrogen bonds : bond 0.04335 ( 1229) hydrogen bonds : angle 5.40369 ( 3417) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8688 Ramachandran restraints generated. 4344 Oldfield, 0 Emsley, 4344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8688 Ramachandran restraints generated. 4344 Oldfield, 0 Emsley, 4344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 588 residues out of total 3714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 146 poor density : 442 time to evaluate : 1.364 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 VAL cc_start: 0.5581 (t) cc_final: 0.5204 (m) REVERT: A 83 ARG cc_start: 0.6036 (mmt90) cc_final: 0.5832 (mmt90) REVERT: A 134 TYR cc_start: 0.6140 (m-80) cc_final: 0.5870 (m-10) REVERT: A 239 ARG cc_start: 0.8048 (OUTLIER) cc_final: 0.7647 (ptt-90) REVERT: A 449 MET cc_start: 0.7699 (OUTLIER) cc_final: 0.7438 (tpp) REVERT: A 599 ARG cc_start: 0.7693 (ptp90) cc_final: 0.7172 (ttp80) REVERT: A 692 GLN cc_start: 0.7816 (mm-40) cc_final: 0.7499 (mm-40) REVERT: B 39 VAL cc_start: 0.5452 (t) cc_final: 0.5168 (m) REVERT: B 294 GLU cc_start: 0.7330 (tp30) cc_final: 0.6978 (tp30) REVERT: B 551 TRP cc_start: 0.5478 (t60) cc_final: 0.5177 (t60) REVERT: B 599 ARG cc_start: 0.7779 (ptp90) cc_final: 0.7259 (ttp80) REVERT: C 39 VAL cc_start: 0.5707 (t) cc_final: 0.5422 (m) REVERT: C 158 MET cc_start: 0.7810 (mmm) cc_final: 0.7452 (mtt) REVERT: C 365 ARG cc_start: 0.8572 (mmt90) cc_final: 0.8148 (mmt90) REVERT: C 449 MET cc_start: 0.7701 (tpp) cc_final: 0.7259 (tpp) REVERT: C 599 ARG cc_start: 0.7888 (ptp-170) cc_final: 0.7329 (ttp80) REVERT: D 39 VAL cc_start: 0.5592 (t) cc_final: 0.5219 (m) REVERT: D 83 ARG cc_start: 0.6079 (mmt90) cc_final: 0.5623 (mmm-85) REVERT: D 239 ARG cc_start: 0.8058 (OUTLIER) cc_final: 0.7600 (ptt-90) REVERT: D 449 MET cc_start: 0.7708 (OUTLIER) cc_final: 0.7449 (tpp) REVERT: D 599 ARG cc_start: 0.7723 (ptp90) cc_final: 0.7199 (ttp80) REVERT: E 39 VAL cc_start: 0.5212 (t) cc_final: 0.4942 (m) REVERT: E 66 GLU cc_start: 0.6480 (mp0) cc_final: 0.5446 (pt0) REVERT: E 83 ARG cc_start: 0.6099 (mmt90) cc_final: 0.5696 (mmm-85) REVERT: E 294 GLU cc_start: 0.7324 (tp30) cc_final: 0.7027 (tp30) REVERT: E 449 MET cc_start: 0.7632 (tpp) cc_final: 0.7357 (tpp) REVERT: E 551 TRP cc_start: 0.5442 (t60) cc_final: 0.5164 (t60) REVERT: E 599 ARG cc_start: 0.7777 (ptp90) cc_final: 0.7245 (ttp80) REVERT: F 39 VAL cc_start: 0.5598 (t) cc_final: 0.5309 (m) REVERT: F 66 GLU cc_start: 0.6199 (mp0) cc_final: 0.4924 (mt-10) REVERT: F 83 ARG cc_start: 0.6176 (mmt90) cc_final: 0.5700 (mmm-85) REVERT: F 148 LYS cc_start: 0.5999 (mttt) cc_final: 0.5447 (mmtm) REVERT: F 158 MET cc_start: 0.7822 (mmm) cc_final: 0.7334 (mtt) REVERT: F 442 MET cc_start: 0.7119 (mmp) cc_final: 0.6461 (mmt) REVERT: F 449 MET cc_start: 0.7659 (tpp) cc_final: 0.7350 (tpp) REVERT: F 494 GLN cc_start: 0.8408 (OUTLIER) cc_final: 0.8181 (mm110) REVERT: F 599 ARG cc_start: 0.7919 (ptp-170) cc_final: 0.7350 (ttp80) outliers start: 146 outliers final: 103 residues processed: 546 average time/residue: 0.2376 time to fit residues: 204.9843 Evaluate side-chains 496 residues out of total 3714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 388 time to evaluate : 1.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 85 ASN Chi-restraints excluded: chain A residue 146 ILE Chi-restraints excluded: chain A residue 198 LEU Chi-restraints excluded: chain A residue 218 GLU Chi-restraints excluded: chain A residue 239 ARG Chi-restraints excluded: chain A residue 342 ILE Chi-restraints excluded: chain A residue 371 ILE Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 427 MET Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 448 THR Chi-restraints excluded: chain A residue 449 MET Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 501 ASP Chi-restraints excluded: chain A residue 531 ILE Chi-restraints excluded: chain A residue 661 LEU Chi-restraints excluded: chain A residue 701 GLU Chi-restraints excluded: chain A residue 731 ILE Chi-restraints excluded: chain A residue 746 SER Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 85 ASN Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 218 GLU Chi-restraints excluded: chain B residue 281 GLU Chi-restraints excluded: chain B residue 342 ILE Chi-restraints excluded: chain B residue 371 ILE Chi-restraints excluded: chain B residue 378 LEU Chi-restraints excluded: chain B residue 427 MET Chi-restraints excluded: chain B residue 448 THR Chi-restraints excluded: chain B residue 469 VAL Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain B residue 501 ASP Chi-restraints excluded: chain B residue 531 ILE Chi-restraints excluded: chain B residue 692 GLN Chi-restraints excluded: chain B residue 697 LEU Chi-restraints excluded: chain B residue 701 GLU Chi-restraints excluded: chain B residue 746 SER Chi-restraints excluded: chain C residue 58 LEU Chi-restraints excluded: chain C residue 85 ASN Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain C residue 146 ILE Chi-restraints excluded: chain C residue 198 LEU Chi-restraints excluded: chain C residue 342 ILE Chi-restraints excluded: chain C residue 371 ILE Chi-restraints excluded: chain C residue 427 MET Chi-restraints excluded: chain C residue 447 VAL Chi-restraints excluded: chain C residue 448 THR Chi-restraints excluded: chain C residue 492 LEU Chi-restraints excluded: chain C residue 531 ILE Chi-restraints excluded: chain C residue 661 LEU Chi-restraints excluded: chain C residue 697 LEU Chi-restraints excluded: chain C residue 746 SER Chi-restraints excluded: chain D residue 58 LEU Chi-restraints excluded: chain D residue 85 ASN Chi-restraints excluded: chain D residue 198 LEU Chi-restraints excluded: chain D residue 218 GLU Chi-restraints excluded: chain D residue 239 ARG Chi-restraints excluded: chain D residue 342 ILE Chi-restraints excluded: chain D residue 371 ILE Chi-restraints excluded: chain D residue 378 LEU Chi-restraints excluded: chain D residue 427 MET Chi-restraints excluded: chain D residue 447 VAL Chi-restraints excluded: chain D residue 448 THR Chi-restraints excluded: chain D residue 449 MET Chi-restraints excluded: chain D residue 471 VAL Chi-restraints excluded: chain D residue 492 LEU Chi-restraints excluded: chain D residue 501 ASP Chi-restraints excluded: chain D residue 531 ILE Chi-restraints excluded: chain D residue 661 LEU Chi-restraints excluded: chain D residue 692 GLN Chi-restraints excluded: chain D residue 701 GLU Chi-restraints excluded: chain E residue 84 MET Chi-restraints excluded: chain E residue 85 ASN Chi-restraints excluded: chain E residue 123 VAL Chi-restraints excluded: chain E residue 198 LEU Chi-restraints excluded: chain E residue 218 GLU Chi-restraints excluded: chain E residue 342 ILE Chi-restraints excluded: chain E residue 371 ILE Chi-restraints excluded: chain E residue 378 LEU Chi-restraints excluded: chain E residue 427 MET Chi-restraints excluded: chain E residue 447 VAL Chi-restraints excluded: chain E residue 448 THR Chi-restraints excluded: chain E residue 469 VAL Chi-restraints excluded: chain E residue 492 LEU Chi-restraints excluded: chain E residue 501 ASP Chi-restraints excluded: chain E residue 531 ILE Chi-restraints excluded: chain E residue 692 GLN Chi-restraints excluded: chain E residue 697 LEU Chi-restraints excluded: chain E residue 701 GLU Chi-restraints excluded: chain E residue 746 SER Chi-restraints excluded: chain F residue 58 LEU Chi-restraints excluded: chain F residue 85 ASN Chi-restraints excluded: chain F residue 123 VAL Chi-restraints excluded: chain F residue 198 LEU Chi-restraints excluded: chain F residue 231 LYS Chi-restraints excluded: chain F residue 371 ILE Chi-restraints excluded: chain F residue 427 MET Chi-restraints excluded: chain F residue 447 VAL Chi-restraints excluded: chain F residue 448 THR Chi-restraints excluded: chain F residue 492 LEU Chi-restraints excluded: chain F residue 494 GLN Chi-restraints excluded: chain F residue 531 ILE Chi-restraints excluded: chain F residue 661 LEU Chi-restraints excluded: chain F residue 697 LEU Chi-restraints excluded: chain F residue 701 GLU Chi-restraints excluded: chain F residue 746 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 278 optimal weight: 9.9990 chunk 29 optimal weight: 0.0270 chunk 215 optimal weight: 6.9990 chunk 375 optimal weight: 30.0000 chunk 323 optimal weight: 9.9990 chunk 70 optimal weight: 0.0970 chunk 221 optimal weight: 6.9990 chunk 392 optimal weight: 6.9990 chunk 39 optimal weight: 7.9990 chunk 148 optimal weight: 0.8980 chunk 45 optimal weight: 8.9990 overall best weight: 3.0040 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 285 ASN A 317 HIS B 317 HIS D 285 ASN ** D 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 285 ASN ** E 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3993 r_free = 0.3993 target = 0.148820 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.116208 restraints weight = 58785.706| |-----------------------------------------------------------------------------| r_work (start): 0.3545 rms_B_bonded: 2.55 r_work: 0.3318 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.3318 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8048 moved from start: 0.4214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 35130 Z= 0.136 Angle : 0.670 7.019 47514 Z= 0.336 Chirality : 0.046 0.184 5352 Planarity : 0.005 0.047 6234 Dihedral : 8.797 130.592 4926 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 9.61 Ramachandran Plot: Outliers : 0.16 % Allowed : 7.62 % Favored : 92.22 % Rotamer: Outliers : 3.58 % Allowed : 13.89 % Favored : 82.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.58 (0.13), residues: 4344 helix: -0.70 (0.12), residues: 1794 sheet: -1.29 (0.19), residues: 618 loop : -1.14 (0.14), residues: 1932 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 65 TYR 0.017 0.002 TYR D 244 PHE 0.012 0.001 PHE A 563 TRP 0.010 0.001 TRP E 551 HIS 0.005 0.001 HIS B 384 Details of bonding type rmsd covalent geometry : bond 0.00305 (35130) covalent geometry : angle 0.67028 (47514) hydrogen bonds : bond 0.03710 ( 1229) hydrogen bonds : angle 5.11706 ( 3417) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8688 Ramachandran restraints generated. 4344 Oldfield, 0 Emsley, 4344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8688 Ramachandran restraints generated. 4344 Oldfield, 0 Emsley, 4344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 582 residues out of total 3714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 133 poor density : 449 time to evaluate : 1.544 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 VAL cc_start: 0.5375 (t) cc_final: 0.5035 (m) REVERT: A 66 GLU cc_start: 0.6462 (mp0) cc_final: 0.5292 (mt-10) REVERT: A 122 THR cc_start: 0.6490 (m) cc_final: 0.6238 (p) REVERT: A 239 ARG cc_start: 0.8081 (OUTLIER) cc_final: 0.7713 (ptt-90) REVERT: A 449 MET cc_start: 0.7730 (OUTLIER) cc_final: 0.7478 (tpp) REVERT: A 599 ARG cc_start: 0.7665 (ptp90) cc_final: 0.7100 (ttp80) REVERT: A 679 THR cc_start: 0.7902 (OUTLIER) cc_final: 0.7548 (p) REVERT: A 692 GLN cc_start: 0.7840 (mm-40) cc_final: 0.7624 (mm110) REVERT: B 39 VAL cc_start: 0.5400 (t) cc_final: 0.5132 (m) REVERT: B 66 GLU cc_start: 0.6448 (mp0) cc_final: 0.5713 (pt0) REVERT: B 83 ARG cc_start: 0.6149 (mmt90) cc_final: 0.5736 (mmm-85) REVERT: B 550 MET cc_start: 0.6596 (tpt) cc_final: 0.6383 (ptm) REVERT: B 599 ARG cc_start: 0.7755 (ptp90) cc_final: 0.7248 (ttp80) REVERT: C 39 VAL cc_start: 0.5566 (t) cc_final: 0.5292 (m) REVERT: C 66 GLU cc_start: 0.6424 (mp0) cc_final: 0.5512 (pt0) REVERT: C 83 ARG cc_start: 0.6137 (mmt90) cc_final: 0.5703 (mmm-85) REVERT: C 122 THR cc_start: 0.6610 (m) cc_final: 0.6355 (p) REVERT: C 158 MET cc_start: 0.7813 (mmm) cc_final: 0.7575 (mtt) REVERT: C 449 MET cc_start: 0.7617 (tpp) cc_final: 0.7192 (tpp) REVERT: C 599 ARG cc_start: 0.7795 (ptp-170) cc_final: 0.7323 (ttp80) REVERT: D 39 VAL cc_start: 0.5360 (t) cc_final: 0.5021 (m) REVERT: D 66 GLU cc_start: 0.6313 (mp0) cc_final: 0.5184 (mt-10) REVERT: D 83 ARG cc_start: 0.6092 (mmt90) cc_final: 0.5606 (mmm-85) REVERT: D 122 THR cc_start: 0.6495 (m) cc_final: 0.6239 (p) REVERT: D 239 ARG cc_start: 0.8129 (OUTLIER) cc_final: 0.7762 (ptt-90) REVERT: D 449 MET cc_start: 0.7690 (OUTLIER) cc_final: 0.7449 (tpp) REVERT: D 599 ARG cc_start: 0.7667 (ptp90) cc_final: 0.7106 (ttp80) REVERT: D 692 GLN cc_start: 0.7589 (OUTLIER) cc_final: 0.7167 (tp40) REVERT: E 39 VAL cc_start: 0.5230 (t) cc_final: 0.4964 (m) REVERT: E 66 GLU cc_start: 0.6297 (mp0) cc_final: 0.5619 (pt0) REVERT: E 83 ARG cc_start: 0.6125 (mmt90) cc_final: 0.5729 (mmm-85) REVERT: E 550 MET cc_start: 0.6625 (tpt) cc_final: 0.6404 (ptm) REVERT: E 599 ARG cc_start: 0.7740 (ptp90) cc_final: 0.7229 (ttp80) REVERT: F 39 VAL cc_start: 0.5523 (t) cc_final: 0.5233 (m) REVERT: F 66 GLU cc_start: 0.6213 (mp0) cc_final: 0.5166 (mt-10) REVERT: F 83 ARG cc_start: 0.6227 (mmt90) cc_final: 0.5748 (mmm-85) REVERT: F 122 THR cc_start: 0.6548 (m) cc_final: 0.6272 (p) REVERT: F 158 MET cc_start: 0.7853 (mmm) cc_final: 0.7496 (mtt) REVERT: F 442 MET cc_start: 0.7205 (mmp) cc_final: 0.6560 (mmt) REVERT: F 449 MET cc_start: 0.7624 (tpp) cc_final: 0.7271 (tpp) REVERT: F 599 ARG cc_start: 0.7790 (ptp-170) cc_final: 0.7314 (ttp80) outliers start: 133 outliers final: 92 residues processed: 541 average time/residue: 0.2467 time to fit residues: 209.5857 Evaluate side-chains 497 residues out of total 3714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 399 time to evaluate : 1.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 198 LEU Chi-restraints excluded: chain A residue 218 GLU Chi-restraints excluded: chain A residue 239 ARG Chi-restraints excluded: chain A residue 285 ASN Chi-restraints excluded: chain A residue 342 ILE Chi-restraints excluded: chain A residue 371 ILE Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain A residue 427 MET Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 448 THR Chi-restraints excluded: chain A residue 449 MET Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 501 ASP Chi-restraints excluded: chain A residue 531 ILE Chi-restraints excluded: chain A residue 661 LEU Chi-restraints excluded: chain A residue 679 THR Chi-restraints excluded: chain A residue 731 ILE Chi-restraints excluded: chain B residue 58 LEU Chi-restraints excluded: chain B residue 85 ASN Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 218 GLU Chi-restraints excluded: chain B residue 281 GLU Chi-restraints excluded: chain B residue 342 ILE Chi-restraints excluded: chain B residue 371 ILE Chi-restraints excluded: chain B residue 378 LEU Chi-restraints excluded: chain B residue 447 VAL Chi-restraints excluded: chain B residue 448 THR Chi-restraints excluded: chain B residue 531 ILE Chi-restraints excluded: chain B residue 582 ILE Chi-restraints excluded: chain B residue 692 GLN Chi-restraints excluded: chain B residue 701 GLU Chi-restraints excluded: chain B residue 746 SER Chi-restraints excluded: chain C residue 58 LEU Chi-restraints excluded: chain C residue 85 ASN Chi-restraints excluded: chain C residue 198 LEU Chi-restraints excluded: chain C residue 218 GLU Chi-restraints excluded: chain C residue 342 ILE Chi-restraints excluded: chain C residue 427 MET Chi-restraints excluded: chain C residue 447 VAL Chi-restraints excluded: chain C residue 448 THR Chi-restraints excluded: chain C residue 479 ILE Chi-restraints excluded: chain C residue 492 LEU Chi-restraints excluded: chain C residue 531 ILE Chi-restraints excluded: chain C residue 582 ILE Chi-restraints excluded: chain C residue 661 LEU Chi-restraints excluded: chain C residue 692 GLN Chi-restraints excluded: chain C residue 697 LEU Chi-restraints excluded: chain C residue 746 SER Chi-restraints excluded: chain D residue 58 LEU Chi-restraints excluded: chain D residue 123 VAL Chi-restraints excluded: chain D residue 198 LEU Chi-restraints excluded: chain D residue 218 GLU Chi-restraints excluded: chain D residue 239 ARG Chi-restraints excluded: chain D residue 285 ASN Chi-restraints excluded: chain D residue 371 ILE Chi-restraints excluded: chain D residue 378 LEU Chi-restraints excluded: chain D residue 420 LEU Chi-restraints excluded: chain D residue 427 MET Chi-restraints excluded: chain D residue 447 VAL Chi-restraints excluded: chain D residue 448 THR Chi-restraints excluded: chain D residue 449 MET Chi-restraints excluded: chain D residue 492 LEU Chi-restraints excluded: chain D residue 531 ILE Chi-restraints excluded: chain D residue 661 LEU Chi-restraints excluded: chain D residue 692 GLN Chi-restraints excluded: chain D residue 701 GLU Chi-restraints excluded: chain D residue 746 SER Chi-restraints excluded: chain E residue 58 LEU Chi-restraints excluded: chain E residue 85 ASN Chi-restraints excluded: chain E residue 198 LEU Chi-restraints excluded: chain E residue 218 GLU Chi-restraints excluded: chain E residue 285 ASN Chi-restraints excluded: chain E residue 342 ILE Chi-restraints excluded: chain E residue 371 ILE Chi-restraints excluded: chain E residue 378 LEU Chi-restraints excluded: chain E residue 447 VAL Chi-restraints excluded: chain E residue 448 THR Chi-restraints excluded: chain E residue 504 LEU Chi-restraints excluded: chain E residue 531 ILE Chi-restraints excluded: chain E residue 582 ILE Chi-restraints excluded: chain E residue 692 GLN Chi-restraints excluded: chain E residue 697 LEU Chi-restraints excluded: chain E residue 701 GLU Chi-restraints excluded: chain F residue 85 ASN Chi-restraints excluded: chain F residue 218 GLU Chi-restraints excluded: chain F residue 231 LYS Chi-restraints excluded: chain F residue 371 ILE Chi-restraints excluded: chain F residue 492 LEU Chi-restraints excluded: chain F residue 531 ILE Chi-restraints excluded: chain F residue 558 ASN Chi-restraints excluded: chain F residue 582 ILE Chi-restraints excluded: chain F residue 661 LEU Chi-restraints excluded: chain F residue 692 GLN Chi-restraints excluded: chain F residue 697 LEU Chi-restraints excluded: chain F residue 701 GLU Chi-restraints excluded: chain F residue 746 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 329 optimal weight: 30.0000 chunk 76 optimal weight: 2.9990 chunk 361 optimal weight: 8.9990 chunk 394 optimal weight: 0.0970 chunk 327 optimal weight: 8.9990 chunk 312 optimal weight: 0.1980 chunk 181 optimal weight: 20.0000 chunk 32 optimal weight: 7.9990 chunk 279 optimal weight: 20.0000 chunk 178 optimal weight: 10.0000 chunk 3 optimal weight: 0.4980 overall best weight: 2.3582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 317 HIS A 660 ASN B 660 ASN C 317 HIS C 660 ASN D 317 HIS D 660 ASN E 660 ASN F 285 ASN F 317 HIS F 660 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.148708 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.116362 restraints weight = 58485.461| |-----------------------------------------------------------------------------| r_work (start): 0.3548 rms_B_bonded: 2.59 r_work: 0.3315 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.3315 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8041 moved from start: 0.4452 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 35130 Z= 0.125 Angle : 0.651 6.551 47514 Z= 0.325 Chirality : 0.046 0.157 5352 Planarity : 0.005 0.048 6234 Dihedral : 8.639 126.438 4926 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 9.68 Ramachandran Plot: Outliers : 0.16 % Allowed : 7.30 % Favored : 92.54 % Rotamer: Outliers : 3.47 % Allowed : 14.73 % Favored : 81.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.36 (0.13), residues: 4344 helix: -0.49 (0.12), residues: 1794 sheet: -1.20 (0.19), residues: 636 loop : -1.05 (0.14), residues: 1914 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 338 TYR 0.015 0.001 TYR D 244 PHE 0.012 0.001 PHE F 152 TRP 0.008 0.001 TRP E 551 HIS 0.005 0.001 HIS A 317 Details of bonding type rmsd covalent geometry : bond 0.00281 (35130) covalent geometry : angle 0.65117 (47514) hydrogen bonds : bond 0.03511 ( 1229) hydrogen bonds : angle 4.98754 ( 3417) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8688 Ramachandran restraints generated. 4344 Oldfield, 0 Emsley, 4344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8688 Ramachandran restraints generated. 4344 Oldfield, 0 Emsley, 4344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 556 residues out of total 3714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 129 poor density : 427 time to evaluate : 1.420 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 VAL cc_start: 0.5361 (t) cc_final: 0.5010 (m) REVERT: A 66 GLU cc_start: 0.6363 (mp0) cc_final: 0.5277 (mt-10) REVERT: A 83 ARG cc_start: 0.5937 (mmt90) cc_final: 0.5462 (mmm-85) REVERT: A 239 ARG cc_start: 0.8097 (OUTLIER) cc_final: 0.7750 (ptt-90) REVERT: A 321 GLU cc_start: 0.7310 (tt0) cc_final: 0.7045 (tt0) REVERT: A 449 MET cc_start: 0.7748 (OUTLIER) cc_final: 0.7506 (tpp) REVERT: A 599 ARG cc_start: 0.7642 (ptp90) cc_final: 0.7094 (ttp80) REVERT: A 679 THR cc_start: 0.7924 (OUTLIER) cc_final: 0.7539 (p) REVERT: A 692 GLN cc_start: 0.7896 (mm-40) cc_final: 0.7676 (mm110) REVERT: B 39 VAL cc_start: 0.5467 (t) cc_final: 0.5214 (m) REVERT: B 66 GLU cc_start: 0.6452 (mp0) cc_final: 0.5323 (mt-10) REVERT: B 83 ARG cc_start: 0.6053 (mmt90) cc_final: 0.5657 (mmm-85) REVERT: B 321 GLU cc_start: 0.7412 (tt0) cc_final: 0.7157 (tt0) REVERT: B 427 MET cc_start: 0.6888 (mmp) cc_final: 0.6580 (mmm) REVERT: B 494 GLN cc_start: 0.8257 (OUTLIER) cc_final: 0.8030 (mm110) REVERT: B 599 ARG cc_start: 0.7778 (ptp90) cc_final: 0.7294 (ttp80) REVERT: B 661 LEU cc_start: 0.8373 (OUTLIER) cc_final: 0.8162 (pp) REVERT: C 39 VAL cc_start: 0.5519 (t) cc_final: 0.5237 (m) REVERT: C 66 GLU cc_start: 0.6445 (mp0) cc_final: 0.5154 (mt-10) REVERT: C 83 ARG cc_start: 0.6130 (mmt90) cc_final: 0.5728 (mmm-85) REVERT: C 122 THR cc_start: 0.6637 (m) cc_final: 0.6393 (p) REVERT: C 449 MET cc_start: 0.7693 (tpp) cc_final: 0.7300 (tpp) REVERT: C 494 GLN cc_start: 0.8316 (OUTLIER) cc_final: 0.7976 (mm110) REVERT: C 599 ARG cc_start: 0.7834 (ptp-170) cc_final: 0.7289 (ttp80) REVERT: C 679 THR cc_start: 0.7899 (OUTLIER) cc_final: 0.7454 (p) REVERT: D 39 VAL cc_start: 0.5347 (t) cc_final: 0.4998 (m) REVERT: D 66 GLU cc_start: 0.6248 (mp0) cc_final: 0.5224 (mt-10) REVERT: D 83 ARG cc_start: 0.6120 (mmt90) cc_final: 0.5621 (mmm-85) REVERT: D 239 ARG cc_start: 0.8127 (OUTLIER) cc_final: 0.7783 (ptt-90) REVERT: D 449 MET cc_start: 0.7714 (OUTLIER) cc_final: 0.7462 (tpp) REVERT: D 550 MET cc_start: 0.6149 (ptt) cc_final: 0.5675 (ptp) REVERT: D 599 ARG cc_start: 0.7662 (ptp90) cc_final: 0.7118 (ttp80) REVERT: D 679 THR cc_start: 0.7883 (OUTLIER) cc_final: 0.7446 (p) REVERT: D 692 GLN cc_start: 0.7637 (OUTLIER) cc_final: 0.7185 (tp40) REVERT: E 39 VAL cc_start: 0.5284 (t) cc_final: 0.5009 (m) REVERT: E 66 GLU cc_start: 0.6338 (mp0) cc_final: 0.5264 (mt-10) REVERT: E 83 ARG cc_start: 0.6106 (mmt90) cc_final: 0.5702 (mmm-85) REVERT: E 321 GLU cc_start: 0.7388 (tt0) cc_final: 0.7077 (tt0) REVERT: E 427 MET cc_start: 0.6891 (mmp) cc_final: 0.6584 (mmm) REVERT: E 494 GLN cc_start: 0.8248 (OUTLIER) cc_final: 0.8015 (mm110) REVERT: E 599 ARG cc_start: 0.7792 (ptp90) cc_final: 0.7267 (ttp80) REVERT: E 661 LEU cc_start: 0.8376 (OUTLIER) cc_final: 0.8167 (pp) REVERT: E 679 THR cc_start: 0.7869 (OUTLIER) cc_final: 0.7446 (p) REVERT: F 39 VAL cc_start: 0.5492 (t) cc_final: 0.5234 (m) REVERT: F 66 GLU cc_start: 0.6155 (mp0) cc_final: 0.5194 (mt-10) REVERT: F 83 ARG cc_start: 0.6174 (mmt90) cc_final: 0.5743 (mmm-85) REVERT: F 122 THR cc_start: 0.6588 (OUTLIER) cc_final: 0.6332 (p) REVERT: F 158 MET cc_start: 0.7849 (mmm) cc_final: 0.7590 (mtm) REVERT: F 427 MET cc_start: 0.6585 (mmp) cc_final: 0.6346 (mmm) REVERT: F 442 MET cc_start: 0.7182 (mmp) cc_final: 0.6515 (mmt) REVERT: F 449 MET cc_start: 0.7721 (tpp) cc_final: 0.7314 (tpp) REVERT: F 494 GLN cc_start: 0.8374 (OUTLIER) cc_final: 0.8114 (mm110) REVERT: F 599 ARG cc_start: 0.7826 (ptp-170) cc_final: 0.7308 (ttp80) REVERT: F 679 THR cc_start: 0.7872 (OUTLIER) cc_final: 0.7431 (p) outliers start: 129 outliers final: 101 residues processed: 511 average time/residue: 0.2500 time to fit residues: 200.4434 Evaluate side-chains 516 residues out of total 3714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 118 poor density : 398 time to evaluate : 1.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 85 ASN Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 198 LEU Chi-restraints excluded: chain A residue 218 GLU Chi-restraints excluded: chain A residue 239 ARG Chi-restraints excluded: chain A residue 342 ILE Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain A residue 427 MET Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 448 THR Chi-restraints excluded: chain A residue 449 MET Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 501 ASP Chi-restraints excluded: chain A residue 531 ILE Chi-restraints excluded: chain A residue 661 LEU Chi-restraints excluded: chain A residue 679 THR Chi-restraints excluded: chain A residue 701 GLU Chi-restraints excluded: chain A residue 731 ILE Chi-restraints excluded: chain A residue 746 SER Chi-restraints excluded: chain A residue 747 VAL Chi-restraints excluded: chain B residue 58 LEU Chi-restraints excluded: chain B residue 85 ASN Chi-restraints excluded: chain B residue 218 GLU Chi-restraints excluded: chain B residue 281 GLU Chi-restraints excluded: chain B residue 342 ILE Chi-restraints excluded: chain B residue 378 LEU Chi-restraints excluded: chain B residue 447 VAL Chi-restraints excluded: chain B residue 448 THR Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain B residue 494 GLN Chi-restraints excluded: chain B residue 531 ILE Chi-restraints excluded: chain B residue 582 ILE Chi-restraints excluded: chain B residue 661 LEU Chi-restraints excluded: chain B residue 692 GLN Chi-restraints excluded: chain B residue 697 LEU Chi-restraints excluded: chain B residue 701 GLU Chi-restraints excluded: chain B residue 746 SER Chi-restraints excluded: chain B residue 747 VAL Chi-restraints excluded: chain C residue 58 LEU Chi-restraints excluded: chain C residue 85 ASN Chi-restraints excluded: chain C residue 198 LEU Chi-restraints excluded: chain C residue 218 GLU Chi-restraints excluded: chain C residue 371 ILE Chi-restraints excluded: chain C residue 427 MET Chi-restraints excluded: chain C residue 447 VAL Chi-restraints excluded: chain C residue 448 THR Chi-restraints excluded: chain C residue 479 ILE Chi-restraints excluded: chain C residue 492 LEU Chi-restraints excluded: chain C residue 494 GLN Chi-restraints excluded: chain C residue 531 ILE Chi-restraints excluded: chain C residue 582 ILE Chi-restraints excluded: chain C residue 661 LEU Chi-restraints excluded: chain C residue 679 THR Chi-restraints excluded: chain C residue 692 GLN Chi-restraints excluded: chain C residue 697 LEU Chi-restraints excluded: chain C residue 746 SER Chi-restraints excluded: chain C residue 747 VAL Chi-restraints excluded: chain D residue 58 LEU Chi-restraints excluded: chain D residue 85 ASN Chi-restraints excluded: chain D residue 123 VAL Chi-restraints excluded: chain D residue 198 LEU Chi-restraints excluded: chain D residue 218 GLU Chi-restraints excluded: chain D residue 239 ARG Chi-restraints excluded: chain D residue 378 LEU Chi-restraints excluded: chain D residue 420 LEU Chi-restraints excluded: chain D residue 427 MET Chi-restraints excluded: chain D residue 447 VAL Chi-restraints excluded: chain D residue 448 THR Chi-restraints excluded: chain D residue 449 MET Chi-restraints excluded: chain D residue 492 LEU Chi-restraints excluded: chain D residue 531 ILE Chi-restraints excluded: chain D residue 582 ILE Chi-restraints excluded: chain D residue 661 LEU Chi-restraints excluded: chain D residue 679 THR Chi-restraints excluded: chain D residue 692 GLN Chi-restraints excluded: chain D residue 701 GLU Chi-restraints excluded: chain D residue 746 SER Chi-restraints excluded: chain E residue 58 LEU Chi-restraints excluded: chain E residue 85 ASN Chi-restraints excluded: chain E residue 198 LEU Chi-restraints excluded: chain E residue 218 GLU Chi-restraints excluded: chain E residue 342 ILE Chi-restraints excluded: chain E residue 371 ILE Chi-restraints excluded: chain E residue 378 LEU Chi-restraints excluded: chain E residue 448 THR Chi-restraints excluded: chain E residue 492 LEU Chi-restraints excluded: chain E residue 494 GLN Chi-restraints excluded: chain E residue 504 LEU Chi-restraints excluded: chain E residue 531 ILE Chi-restraints excluded: chain E residue 582 ILE Chi-restraints excluded: chain E residue 661 LEU Chi-restraints excluded: chain E residue 679 THR Chi-restraints excluded: chain E residue 692 GLN Chi-restraints excluded: chain E residue 697 LEU Chi-restraints excluded: chain E residue 701 GLU Chi-restraints excluded: chain E residue 746 SER Chi-restraints excluded: chain E residue 747 VAL Chi-restraints excluded: chain F residue 58 LEU Chi-restraints excluded: chain F residue 85 ASN Chi-restraints excluded: chain F residue 122 THR Chi-restraints excluded: chain F residue 218 GLU Chi-restraints excluded: chain F residue 231 LYS Chi-restraints excluded: chain F residue 285 ASN Chi-restraints excluded: chain F residue 447 VAL Chi-restraints excluded: chain F residue 448 THR Chi-restraints excluded: chain F residue 492 LEU Chi-restraints excluded: chain F residue 494 GLN Chi-restraints excluded: chain F residue 531 ILE Chi-restraints excluded: chain F residue 582 ILE Chi-restraints excluded: chain F residue 661 LEU Chi-restraints excluded: chain F residue 679 THR Chi-restraints excluded: chain F residue 692 GLN Chi-restraints excluded: chain F residue 697 LEU Chi-restraints excluded: chain F residue 701 GLU Chi-restraints excluded: chain F residue 746 SER Chi-restraints excluded: chain F residue 747 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 318 optimal weight: 9.9990 chunk 421 optimal weight: 9.9990 chunk 80 optimal weight: 20.0000 chunk 260 optimal weight: 3.9990 chunk 212 optimal weight: 10.0000 chunk 150 optimal weight: 9.9990 chunk 217 optimal weight: 6.9990 chunk 120 optimal weight: 9.9990 chunk 171 optimal weight: 5.9990 chunk 149 optimal weight: 20.0000 chunk 73 optimal weight: 20.0000 overall best weight: 7.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 285 ASN D 285 ASN E 285 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.145878 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.113222 restraints weight = 58958.533| |-----------------------------------------------------------------------------| r_work (start): 0.3502 rms_B_bonded: 2.47 r_work: 0.3266 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.3266 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8109 moved from start: 0.4402 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 35130 Z= 0.221 Angle : 0.756 9.060 47514 Z= 0.377 Chirality : 0.050 0.178 5352 Planarity : 0.006 0.052 6234 Dihedral : 9.122 137.303 4926 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 10.26 Ramachandran Plot: Outliers : 0.30 % Allowed : 8.31 % Favored : 91.39 % Rotamer: Outliers : 4.55 % Allowed : 14.49 % Favored : 80.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.50 (0.13), residues: 4344 helix: -0.68 (0.12), residues: 1788 sheet: -1.18 (0.20), residues: 618 loop : -1.08 (0.14), residues: 1938 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG F 465 TYR 0.018 0.002 TYR D 138 PHE 0.020 0.002 PHE A 576 TRP 0.011 0.002 TRP B 551 HIS 0.008 0.002 HIS A 384 Details of bonding type rmsd covalent geometry : bond 0.00522 (35130) covalent geometry : angle 0.75573 (47514) hydrogen bonds : bond 0.04312 ( 1229) hydrogen bonds : angle 5.28538 ( 3417) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8688 Ramachandran restraints generated. 4344 Oldfield, 0 Emsley, 4344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8688 Ramachandran restraints generated. 4344 Oldfield, 0 Emsley, 4344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 574 residues out of total 3714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 169 poor density : 405 time to evaluate : 1.500 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 VAL cc_start: 0.5477 (t) cc_final: 0.5108 (m) REVERT: A 66 GLU cc_start: 0.6397 (mp0) cc_final: 0.5269 (mt-10) REVERT: A 83 ARG cc_start: 0.6073 (mmt90) cc_final: 0.5613 (mmm-85) REVERT: A 239 ARG cc_start: 0.8220 (OUTLIER) cc_final: 0.7878 (ptt-90) REVERT: A 449 MET cc_start: 0.7758 (OUTLIER) cc_final: 0.7415 (tpp) REVERT: A 599 ARG cc_start: 0.7931 (ptp90) cc_final: 0.7449 (ttp80) REVERT: A 679 THR cc_start: 0.7972 (OUTLIER) cc_final: 0.7597 (p) REVERT: A 692 GLN cc_start: 0.7959 (mm-40) cc_final: 0.7710 (mm110) REVERT: B 39 VAL cc_start: 0.5390 (t) cc_final: 0.5100 (m) REVERT: B 66 GLU cc_start: 0.6439 (mp0) cc_final: 0.5661 (pt0) REVERT: B 83 ARG cc_start: 0.6041 (mmt90) cc_final: 0.5526 (mmm-85) REVERT: B 122 THR cc_start: 0.6584 (m) cc_final: 0.6370 (p) REVERT: B 427 MET cc_start: 0.6954 (mmp) cc_final: 0.6591 (mmm) REVERT: B 449 MET cc_start: 0.7628 (tpp) cc_final: 0.7286 (tpp) REVERT: B 494 GLN cc_start: 0.8305 (OUTLIER) cc_final: 0.8098 (mm110) REVERT: B 599 ARG cc_start: 0.7977 (ptp90) cc_final: 0.7483 (ttp80) REVERT: B 661 LEU cc_start: 0.8445 (OUTLIER) cc_final: 0.8216 (pp) REVERT: B 679 THR cc_start: 0.7992 (OUTLIER) cc_final: 0.7578 (p) REVERT: C 39 VAL cc_start: 0.5608 (t) cc_final: 0.5334 (m) REVERT: C 66 GLU cc_start: 0.6489 (mp0) cc_final: 0.5739 (pt0) REVERT: C 122 THR cc_start: 0.6580 (OUTLIER) cc_final: 0.6343 (p) REVERT: C 147 ARG cc_start: 0.6302 (tpt-90) cc_final: 0.6089 (tpt-90) REVERT: C 285 ASN cc_start: 0.7946 (OUTLIER) cc_final: 0.7595 (m-40) REVERT: C 321 GLU cc_start: 0.7605 (tt0) cc_final: 0.7274 (tt0) REVERT: C 449 MET cc_start: 0.7714 (OUTLIER) cc_final: 0.7319 (tpp) REVERT: C 494 GLN cc_start: 0.8351 (OUTLIER) cc_final: 0.7988 (mm110) REVERT: C 599 ARG cc_start: 0.7987 (ptp-170) cc_final: 0.7583 (ttp80) REVERT: C 679 THR cc_start: 0.7952 (OUTLIER) cc_final: 0.7505 (p) REVERT: D 39 VAL cc_start: 0.5469 (t) cc_final: 0.5102 (m) REVERT: D 66 GLU cc_start: 0.6161 (mp0) cc_final: 0.5613 (pt0) REVERT: D 83 ARG cc_start: 0.6116 (mmt90) cc_final: 0.5806 (mmt90) REVERT: D 147 ARG cc_start: 0.6399 (tpt-90) cc_final: 0.6147 (tpt-90) REVERT: D 239 ARG cc_start: 0.8228 (OUTLIER) cc_final: 0.7856 (ptt-90) REVERT: D 321 GLU cc_start: 0.7387 (tt0) cc_final: 0.7035 (tt0) REVERT: D 449 MET cc_start: 0.7707 (tpp) cc_final: 0.6700 (ttm) REVERT: D 550 MET cc_start: 0.6329 (ptt) cc_final: 0.6119 (ptm) REVERT: D 599 ARG cc_start: 0.7933 (ptp90) cc_final: 0.7399 (ttp80) REVERT: D 679 THR cc_start: 0.7989 (OUTLIER) cc_final: 0.7570 (p) REVERT: D 692 GLN cc_start: 0.7682 (OUTLIER) cc_final: 0.7233 (tp40) REVERT: E 39 VAL cc_start: 0.5186 (t) cc_final: 0.4908 (m) REVERT: E 66 GLU cc_start: 0.6349 (mp0) cc_final: 0.5310 (mt-10) REVERT: E 83 ARG cc_start: 0.6110 (mmt90) cc_final: 0.5598 (mmm-85) REVERT: E 122 THR cc_start: 0.6547 (m) cc_final: 0.6313 (p) REVERT: E 427 MET cc_start: 0.6950 (mmp) cc_final: 0.6586 (mmm) REVERT: E 449 MET cc_start: 0.7621 (tpp) cc_final: 0.7291 (tpp) REVERT: E 494 GLN cc_start: 0.8271 (OUTLIER) cc_final: 0.8067 (mm110) REVERT: E 599 ARG cc_start: 0.7942 (ptp90) cc_final: 0.7453 (ttp80) REVERT: E 661 LEU cc_start: 0.8449 (OUTLIER) cc_final: 0.8219 (pp) REVERT: E 679 THR cc_start: 0.7997 (OUTLIER) cc_final: 0.7573 (p) REVERT: F 39 VAL cc_start: 0.5511 (t) cc_final: 0.5215 (m) REVERT: F 66 GLU cc_start: 0.6253 (mp0) cc_final: 0.5708 (pt0) REVERT: F 83 ARG cc_start: 0.6187 (mmt90) cc_final: 0.5975 (mmt90) REVERT: F 122 THR cc_start: 0.6591 (OUTLIER) cc_final: 0.6325 (p) REVERT: F 147 ARG cc_start: 0.6356 (tpt-90) cc_final: 0.6080 (tpt-90) REVERT: F 158 MET cc_start: 0.7998 (mmm) cc_final: 0.7691 (mtt) REVERT: F 427 MET cc_start: 0.6706 (mmp) cc_final: 0.6374 (mmm) REVERT: F 449 MET cc_start: 0.7704 (tpp) cc_final: 0.7150 (tpp) REVERT: F 494 GLN cc_start: 0.8422 (OUTLIER) cc_final: 0.8185 (mm110) REVERT: F 599 ARG cc_start: 0.7981 (ptp-170) cc_final: 0.7584 (ttp80) REVERT: F 679 THR cc_start: 0.7957 (OUTLIER) cc_final: 0.7507 (p) outliers start: 169 outliers final: 119 residues processed: 518 average time/residue: 0.2451 time to fit residues: 200.1211 Evaluate side-chains 533 residues out of total 3714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 139 poor density : 394 time to evaluate : 1.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 70 ILE Chi-restraints excluded: chain A residue 85 ASN Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 198 LEU Chi-restraints excluded: chain A residue 218 GLU Chi-restraints excluded: chain A residue 239 ARG Chi-restraints excluded: chain A residue 371 ILE Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain A residue 427 MET Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 448 THR Chi-restraints excluded: chain A residue 449 MET Chi-restraints excluded: chain A residue 479 ILE Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 531 ILE Chi-restraints excluded: chain A residue 582 ILE Chi-restraints excluded: chain A residue 661 LEU Chi-restraints excluded: chain A residue 679 THR Chi-restraints excluded: chain A residue 731 ILE Chi-restraints excluded: chain A residue 746 SER Chi-restraints excluded: chain A residue 747 VAL Chi-restraints excluded: chain B residue 58 LEU Chi-restraints excluded: chain B residue 85 ASN Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 218 GLU Chi-restraints excluded: chain B residue 281 GLU Chi-restraints excluded: chain B residue 342 ILE Chi-restraints excluded: chain B residue 371 ILE Chi-restraints excluded: chain B residue 447 VAL Chi-restraints excluded: chain B residue 448 THR Chi-restraints excluded: chain B residue 469 VAL Chi-restraints excluded: chain B residue 479 ILE Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain B residue 494 GLN Chi-restraints excluded: chain B residue 504 LEU Chi-restraints excluded: chain B residue 531 ILE Chi-restraints excluded: chain B residue 661 LEU Chi-restraints excluded: chain B residue 679 THR Chi-restraints excluded: chain B residue 692 GLN Chi-restraints excluded: chain B residue 697 LEU Chi-restraints excluded: chain B residue 701 GLU Chi-restraints excluded: chain B residue 746 SER Chi-restraints excluded: chain B residue 747 VAL Chi-restraints excluded: chain C residue 58 LEU Chi-restraints excluded: chain C residue 70 ILE Chi-restraints excluded: chain C residue 85 ASN Chi-restraints excluded: chain C residue 122 THR Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain C residue 198 LEU Chi-restraints excluded: chain C residue 285 ASN Chi-restraints excluded: chain C residue 371 ILE Chi-restraints excluded: chain C residue 427 MET Chi-restraints excluded: chain C residue 447 VAL Chi-restraints excluded: chain C residue 448 THR Chi-restraints excluded: chain C residue 449 MET Chi-restraints excluded: chain C residue 479 ILE Chi-restraints excluded: chain C residue 492 LEU Chi-restraints excluded: chain C residue 494 GLN Chi-restraints excluded: chain C residue 508 MET Chi-restraints excluded: chain C residue 531 ILE Chi-restraints excluded: chain C residue 582 ILE Chi-restraints excluded: chain C residue 661 LEU Chi-restraints excluded: chain C residue 679 THR Chi-restraints excluded: chain C residue 692 GLN Chi-restraints excluded: chain C residue 697 LEU Chi-restraints excluded: chain C residue 746 SER Chi-restraints excluded: chain C residue 747 VAL Chi-restraints excluded: chain D residue 58 LEU Chi-restraints excluded: chain D residue 85 ASN Chi-restraints excluded: chain D residue 123 VAL Chi-restraints excluded: chain D residue 198 LEU Chi-restraints excluded: chain D residue 218 GLU Chi-restraints excluded: chain D residue 239 ARG Chi-restraints excluded: chain D residue 371 ILE Chi-restraints excluded: chain D residue 378 LEU Chi-restraints excluded: chain D residue 420 LEU Chi-restraints excluded: chain D residue 427 MET Chi-restraints excluded: chain D residue 447 VAL Chi-restraints excluded: chain D residue 448 THR Chi-restraints excluded: chain D residue 479 ILE Chi-restraints excluded: chain D residue 492 LEU Chi-restraints excluded: chain D residue 501 ASP Chi-restraints excluded: chain D residue 504 LEU Chi-restraints excluded: chain D residue 531 ILE Chi-restraints excluded: chain D residue 661 LEU Chi-restraints excluded: chain D residue 679 THR Chi-restraints excluded: chain D residue 692 GLN Chi-restraints excluded: chain D residue 697 LEU Chi-restraints excluded: chain D residue 701 GLU Chi-restraints excluded: chain D residue 746 SER Chi-restraints excluded: chain E residue 58 LEU Chi-restraints excluded: chain E residue 85 ASN Chi-restraints excluded: chain E residue 123 VAL Chi-restraints excluded: chain E residue 198 LEU Chi-restraints excluded: chain E residue 218 GLU Chi-restraints excluded: chain E residue 342 ILE Chi-restraints excluded: chain E residue 371 ILE Chi-restraints excluded: chain E residue 447 VAL Chi-restraints excluded: chain E residue 448 THR Chi-restraints excluded: chain E residue 469 VAL Chi-restraints excluded: chain E residue 479 ILE Chi-restraints excluded: chain E residue 492 LEU Chi-restraints excluded: chain E residue 494 GLN Chi-restraints excluded: chain E residue 504 LEU Chi-restraints excluded: chain E residue 531 ILE Chi-restraints excluded: chain E residue 661 LEU Chi-restraints excluded: chain E residue 679 THR Chi-restraints excluded: chain E residue 692 GLN Chi-restraints excluded: chain E residue 697 LEU Chi-restraints excluded: chain E residue 701 GLU Chi-restraints excluded: chain E residue 746 SER Chi-restraints excluded: chain E residue 747 VAL Chi-restraints excluded: chain F residue 58 LEU Chi-restraints excluded: chain F residue 70 ILE Chi-restraints excluded: chain F residue 85 ASN Chi-restraints excluded: chain F residue 122 THR Chi-restraints excluded: chain F residue 123 VAL Chi-restraints excluded: chain F residue 146 ILE Chi-restraints excluded: chain F residue 198 LEU Chi-restraints excluded: chain F residue 231 LYS Chi-restraints excluded: chain F residue 371 ILE Chi-restraints excluded: chain F residue 447 VAL Chi-restraints excluded: chain F residue 448 THR Chi-restraints excluded: chain F residue 479 ILE Chi-restraints excluded: chain F residue 492 LEU Chi-restraints excluded: chain F residue 494 GLN Chi-restraints excluded: chain F residue 531 ILE Chi-restraints excluded: chain F residue 558 ASN Chi-restraints excluded: chain F residue 582 ILE Chi-restraints excluded: chain F residue 661 LEU Chi-restraints excluded: chain F residue 679 THR Chi-restraints excluded: chain F residue 692 GLN Chi-restraints excluded: chain F residue 697 LEU Chi-restraints excluded: chain F residue 701 GLU Chi-restraints excluded: chain F residue 746 SER Chi-restraints excluded: chain F residue 747 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 89 optimal weight: 10.0000 chunk 212 optimal weight: 7.9990 chunk 40 optimal weight: 4.9990 chunk 232 optimal weight: 6.9990 chunk 76 optimal weight: 9.9990 chunk 327 optimal weight: 6.9990 chunk 66 optimal weight: 6.9990 chunk 79 optimal weight: 5.9990 chunk 395 optimal weight: 10.0000 chunk 30 optimal weight: 5.9990 chunk 80 optimal weight: 0.9980 overall best weight: 4.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 285 ASN C 285 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.146694 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.114118 restraints weight = 58667.436| |-----------------------------------------------------------------------------| r_work (start): 0.3517 rms_B_bonded: 2.45 r_work: 0.3290 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.3290 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8080 moved from start: 0.4541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 35130 Z= 0.168 Angle : 0.693 8.060 47514 Z= 0.347 Chirality : 0.048 0.209 5352 Planarity : 0.005 0.050 6234 Dihedral : 8.944 134.058 4926 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 10.00 Ramachandran Plot: Outliers : 0.28 % Allowed : 7.50 % Favored : 92.22 % Rotamer: Outliers : 4.15 % Allowed : 15.54 % Favored : 80.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.41 (0.13), residues: 4344 helix: -0.58 (0.12), residues: 1788 sheet: -1.12 (0.20), residues: 618 loop : -1.07 (0.14), residues: 1938 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG F 465 TYR 0.015 0.002 TYR E 138 PHE 0.013 0.002 PHE A 576 TRP 0.014 0.001 TRP E 551 HIS 0.005 0.001 HIS A 384 Details of bonding type rmsd covalent geometry : bond 0.00392 (35130) covalent geometry : angle 0.69302 (47514) hydrogen bonds : bond 0.03869 ( 1229) hydrogen bonds : angle 5.17187 ( 3417) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8688 Ramachandran restraints generated. 4344 Oldfield, 0 Emsley, 4344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8688 Ramachandran restraints generated. 4344 Oldfield, 0 Emsley, 4344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 570 residues out of total 3714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 154 poor density : 416 time to evaluate : 1.750 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 VAL cc_start: 0.5424 (t) cc_final: 0.5067 (m) REVERT: A 66 GLU cc_start: 0.6421 (mp0) cc_final: 0.5716 (pt0) REVERT: A 83 ARG cc_start: 0.6080 (mmt90) cc_final: 0.5625 (mmm-85) REVERT: A 239 ARG cc_start: 0.8204 (OUTLIER) cc_final: 0.7846 (ptt-90) REVERT: A 449 MET cc_start: 0.7741 (OUTLIER) cc_final: 0.7365 (tpp) REVERT: A 599 ARG cc_start: 0.7691 (ptp90) cc_final: 0.7146 (ttp80) REVERT: A 679 THR cc_start: 0.7925 (OUTLIER) cc_final: 0.7555 (p) REVERT: A 692 GLN cc_start: 0.7915 (mm-40) cc_final: 0.7679 (mm110) REVERT: B 39 VAL cc_start: 0.5400 (t) cc_final: 0.5110 (m) REVERT: B 66 GLU cc_start: 0.6498 (mp0) cc_final: 0.5331 (mt-10) REVERT: B 83 ARG cc_start: 0.6071 (mmt90) cc_final: 0.5585 (mmm-85) REVERT: B 122 THR cc_start: 0.6548 (m) cc_final: 0.6340 (p) REVERT: B 427 MET cc_start: 0.6950 (mmp) cc_final: 0.6545 (mmm) REVERT: B 449 MET cc_start: 0.7556 (tpp) cc_final: 0.7232 (tpp) REVERT: B 494 GLN cc_start: 0.8270 (OUTLIER) cc_final: 0.8070 (mm110) REVERT: B 560 ARG cc_start: 0.7801 (mtp180) cc_final: 0.7162 (mtp180) REVERT: B 599 ARG cc_start: 0.7637 (ptp90) cc_final: 0.7013 (ttp80) REVERT: B 679 THR cc_start: 0.7930 (OUTLIER) cc_final: 0.7494 (p) REVERT: C 39 VAL cc_start: 0.5555 (t) cc_final: 0.5283 (m) REVERT: C 66 GLU cc_start: 0.6431 (mp0) cc_final: 0.5227 (mt-10) REVERT: C 122 THR cc_start: 0.6589 (OUTLIER) cc_final: 0.6350 (p) REVERT: C 321 GLU cc_start: 0.7585 (tt0) cc_final: 0.7275 (tt0) REVERT: C 449 MET cc_start: 0.7692 (OUTLIER) cc_final: 0.7324 (tpp) REVERT: C 494 GLN cc_start: 0.8326 (OUTLIER) cc_final: 0.7985 (mm110) REVERT: C 599 ARG cc_start: 0.7931 (ptp-170) cc_final: 0.7511 (ttp80) REVERT: C 679 THR cc_start: 0.7885 (OUTLIER) cc_final: 0.7415 (p) REVERT: D 39 VAL cc_start: 0.5466 (t) cc_final: 0.5108 (m) REVERT: D 66 GLU cc_start: 0.6243 (mp0) cc_final: 0.5235 (mt-10) REVERT: D 239 ARG cc_start: 0.8229 (OUTLIER) cc_final: 0.7897 (ptt-90) REVERT: D 321 GLU cc_start: 0.7393 (tt0) cc_final: 0.7112 (tt0) REVERT: D 449 MET cc_start: 0.7649 (OUTLIER) cc_final: 0.6670 (ttm) REVERT: D 599 ARG cc_start: 0.7926 (ptp90) cc_final: 0.7391 (ttp80) REVERT: D 679 THR cc_start: 0.7889 (OUTLIER) cc_final: 0.7462 (p) REVERT: D 692 GLN cc_start: 0.7641 (OUTLIER) cc_final: 0.7396 (mm110) REVERT: E 39 VAL cc_start: 0.5202 (t) cc_final: 0.4919 (m) REVERT: E 66 GLU cc_start: 0.6327 (mp0) cc_final: 0.6055 (mm-30) REVERT: E 83 ARG cc_start: 0.6111 (mmt90) cc_final: 0.5623 (mmm-85) REVERT: E 122 THR cc_start: 0.6537 (m) cc_final: 0.6300 (p) REVERT: E 427 MET cc_start: 0.6922 (mmp) cc_final: 0.6526 (mmm) REVERT: E 449 MET cc_start: 0.7567 (tpp) cc_final: 0.7244 (tpp) REVERT: E 494 GLN cc_start: 0.8253 (OUTLIER) cc_final: 0.8049 (mm110) REVERT: E 560 ARG cc_start: 0.7825 (mtp180) cc_final: 0.7169 (mtp180) REVERT: E 599 ARG cc_start: 0.7633 (ptp90) cc_final: 0.7002 (ttp80) REVERT: E 679 THR cc_start: 0.7946 (OUTLIER) cc_final: 0.7511 (p) REVERT: F 39 VAL cc_start: 0.5510 (t) cc_final: 0.5247 (m) REVERT: F 66 GLU cc_start: 0.6244 (mp0) cc_final: 0.5245 (mt-10) REVERT: F 122 THR cc_start: 0.6541 (OUTLIER) cc_final: 0.6266 (p) REVERT: F 158 MET cc_start: 0.7980 (mmm) cc_final: 0.7727 (mtt) REVERT: F 427 MET cc_start: 0.6637 (mmp) cc_final: 0.6289 (mmm) REVERT: F 449 MET cc_start: 0.7671 (tpp) cc_final: 0.7180 (tpp) REVERT: F 494 GLN cc_start: 0.8388 (OUTLIER) cc_final: 0.8149 (mm110) REVERT: F 599 ARG cc_start: 0.7941 (ptp-170) cc_final: 0.7542 (ttp80) REVERT: F 679 THR cc_start: 0.7882 (OUTLIER) cc_final: 0.7418 (p) outliers start: 154 outliers final: 114 residues processed: 511 average time/residue: 0.2442 time to fit residues: 196.3053 Evaluate side-chains 528 residues out of total 3714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 132 poor density : 396 time to evaluate : 1.507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 ASN Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 198 LEU Chi-restraints excluded: chain A residue 218 GLU Chi-restraints excluded: chain A residue 239 ARG Chi-restraints excluded: chain A residue 371 ILE Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain A residue 427 MET Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 448 THR Chi-restraints excluded: chain A residue 449 MET Chi-restraints excluded: chain A residue 479 ILE Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 531 ILE Chi-restraints excluded: chain A residue 582 ILE Chi-restraints excluded: chain A residue 661 LEU Chi-restraints excluded: chain A residue 679 THR Chi-restraints excluded: chain A residue 731 ILE Chi-restraints excluded: chain A residue 746 SER Chi-restraints excluded: chain A residue 747 VAL Chi-restraints excluded: chain B residue 58 LEU Chi-restraints excluded: chain B residue 85 ASN Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 218 GLU Chi-restraints excluded: chain B residue 281 GLU Chi-restraints excluded: chain B residue 291 GLU Chi-restraints excluded: chain B residue 342 ILE Chi-restraints excluded: chain B residue 371 ILE Chi-restraints excluded: chain B residue 447 VAL Chi-restraints excluded: chain B residue 448 THR Chi-restraints excluded: chain B residue 479 ILE Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain B residue 494 GLN Chi-restraints excluded: chain B residue 504 LEU Chi-restraints excluded: chain B residue 531 ILE Chi-restraints excluded: chain B residue 679 THR Chi-restraints excluded: chain B residue 692 GLN Chi-restraints excluded: chain B residue 697 LEU Chi-restraints excluded: chain B residue 701 GLU Chi-restraints excluded: chain B residue 746 SER Chi-restraints excluded: chain B residue 747 VAL Chi-restraints excluded: chain C residue 85 ASN Chi-restraints excluded: chain C residue 122 THR Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain C residue 198 LEU Chi-restraints excluded: chain C residue 285 ASN Chi-restraints excluded: chain C residue 371 ILE Chi-restraints excluded: chain C residue 427 MET Chi-restraints excluded: chain C residue 447 VAL Chi-restraints excluded: chain C residue 448 THR Chi-restraints excluded: chain C residue 449 MET Chi-restraints excluded: chain C residue 479 ILE Chi-restraints excluded: chain C residue 492 LEU Chi-restraints excluded: chain C residue 494 GLN Chi-restraints excluded: chain C residue 508 MET Chi-restraints excluded: chain C residue 531 ILE Chi-restraints excluded: chain C residue 582 ILE Chi-restraints excluded: chain C residue 661 LEU Chi-restraints excluded: chain C residue 679 THR Chi-restraints excluded: chain C residue 692 GLN Chi-restraints excluded: chain C residue 697 LEU Chi-restraints excluded: chain C residue 746 SER Chi-restraints excluded: chain C residue 747 VAL Chi-restraints excluded: chain D residue 58 LEU Chi-restraints excluded: chain D residue 70 ILE Chi-restraints excluded: chain D residue 85 ASN Chi-restraints excluded: chain D residue 123 VAL Chi-restraints excluded: chain D residue 198 LEU Chi-restraints excluded: chain D residue 218 GLU Chi-restraints excluded: chain D residue 239 ARG Chi-restraints excluded: chain D residue 371 ILE Chi-restraints excluded: chain D residue 378 LEU Chi-restraints excluded: chain D residue 420 LEU Chi-restraints excluded: chain D residue 427 MET Chi-restraints excluded: chain D residue 447 VAL Chi-restraints excluded: chain D residue 448 THR Chi-restraints excluded: chain D residue 449 MET Chi-restraints excluded: chain D residue 479 ILE Chi-restraints excluded: chain D residue 492 LEU Chi-restraints excluded: chain D residue 504 LEU Chi-restraints excluded: chain D residue 531 ILE Chi-restraints excluded: chain D residue 582 ILE Chi-restraints excluded: chain D residue 661 LEU Chi-restraints excluded: chain D residue 679 THR Chi-restraints excluded: chain D residue 692 GLN Chi-restraints excluded: chain D residue 697 LEU Chi-restraints excluded: chain D residue 746 SER Chi-restraints excluded: chain E residue 58 LEU Chi-restraints excluded: chain E residue 70 ILE Chi-restraints excluded: chain E residue 85 ASN Chi-restraints excluded: chain E residue 123 VAL Chi-restraints excluded: chain E residue 198 LEU Chi-restraints excluded: chain E residue 218 GLU Chi-restraints excluded: chain E residue 291 GLU Chi-restraints excluded: chain E residue 342 ILE Chi-restraints excluded: chain E residue 371 ILE Chi-restraints excluded: chain E residue 447 VAL Chi-restraints excluded: chain E residue 448 THR Chi-restraints excluded: chain E residue 479 ILE Chi-restraints excluded: chain E residue 492 LEU Chi-restraints excluded: chain E residue 494 GLN Chi-restraints excluded: chain E residue 504 LEU Chi-restraints excluded: chain E residue 531 ILE Chi-restraints excluded: chain E residue 679 THR Chi-restraints excluded: chain E residue 692 GLN Chi-restraints excluded: chain E residue 697 LEU Chi-restraints excluded: chain E residue 701 GLU Chi-restraints excluded: chain E residue 746 SER Chi-restraints excluded: chain E residue 747 VAL Chi-restraints excluded: chain F residue 85 ASN Chi-restraints excluded: chain F residue 122 THR Chi-restraints excluded: chain F residue 123 VAL Chi-restraints excluded: chain F residue 231 LYS Chi-restraints excluded: chain F residue 342 ILE Chi-restraints excluded: chain F residue 371 ILE Chi-restraints excluded: chain F residue 447 VAL Chi-restraints excluded: chain F residue 448 THR Chi-restraints excluded: chain F residue 492 LEU Chi-restraints excluded: chain F residue 494 GLN Chi-restraints excluded: chain F residue 531 ILE Chi-restraints excluded: chain F residue 558 ASN Chi-restraints excluded: chain F residue 582 ILE Chi-restraints excluded: chain F residue 661 LEU Chi-restraints excluded: chain F residue 679 THR Chi-restraints excluded: chain F residue 692 GLN Chi-restraints excluded: chain F residue 697 LEU Chi-restraints excluded: chain F residue 701 GLU Chi-restraints excluded: chain F residue 746 SER Chi-restraints excluded: chain F residue 747 VAL Chi-restraints excluded: chain F residue 757 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 277 optimal weight: 0.9990 chunk 266 optimal weight: 10.0000 chunk 40 optimal weight: 8.9990 chunk 9 optimal weight: 5.9990 chunk 365 optimal weight: 20.0000 chunk 281 optimal weight: 6.9990 chunk 87 optimal weight: 30.0000 chunk 191 optimal weight: 6.9990 chunk 412 optimal weight: 9.9990 chunk 45 optimal weight: 8.9990 chunk 415 optimal weight: 7.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 285 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.146214 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.113773 restraints weight = 58578.615| |-----------------------------------------------------------------------------| r_work (start): 0.3510 rms_B_bonded: 2.54 r_work: 0.3282 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.3282 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8092 moved from start: 0.4610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 35130 Z= 0.186 Angle : 0.712 7.636 47514 Z= 0.357 Chirality : 0.048 0.180 5352 Planarity : 0.005 0.051 6234 Dihedral : 8.970 134.182 4926 Min Nonbonded Distance : 2.301 Molprobity Statistics. All-atom Clashscore : 10.11 Ramachandran Plot: Outliers : 0.28 % Allowed : 8.08 % Favored : 91.64 % Rotamer: Outliers : 4.39 % Allowed : 15.70 % Favored : 79.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.42 (0.13), residues: 4344 helix: -0.57 (0.12), residues: 1788 sheet: -1.11 (0.20), residues: 618 loop : -1.09 (0.14), residues: 1938 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG F 83 TYR 0.016 0.002 TYR E 138 PHE 0.015 0.002 PHE A 576 TRP 0.008 0.001 TRP E 551 HIS 0.006 0.002 HIS A 384 Details of bonding type rmsd covalent geometry : bond 0.00437 (35130) covalent geometry : angle 0.71230 (47514) hydrogen bonds : bond 0.03929 ( 1229) hydrogen bonds : angle 5.18713 ( 3417) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8688 Ramachandran restraints generated. 4344 Oldfield, 0 Emsley, 4344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8688 Ramachandran restraints generated. 4344 Oldfield, 0 Emsley, 4344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 566 residues out of total 3714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 163 poor density : 403 time to evaluate : 1.467 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 VAL cc_start: 0.5405 (t) cc_final: 0.5049 (m) REVERT: A 66 GLU cc_start: 0.6391 (mp0) cc_final: 0.5724 (pt0) REVERT: A 83 ARG cc_start: 0.6075 (mmt90) cc_final: 0.5633 (mmm-85) REVERT: A 239 ARG cc_start: 0.8263 (OUTLIER) cc_final: 0.7930 (ptt-90) REVERT: A 449 MET cc_start: 0.7745 (OUTLIER) cc_final: 0.7465 (tpp) REVERT: A 560 ARG cc_start: 0.7809 (mtp180) cc_final: 0.7177 (mtp180) REVERT: A 599 ARG cc_start: 0.7788 (ptp90) cc_final: 0.7279 (ttp80) REVERT: A 679 THR cc_start: 0.7937 (OUTLIER) cc_final: 0.7556 (p) REVERT: A 692 GLN cc_start: 0.7935 (mm-40) cc_final: 0.7538 (mm110) REVERT: B 39 VAL cc_start: 0.5325 (t) cc_final: 0.5029 (m) REVERT: B 66 GLU cc_start: 0.6514 (mp0) cc_final: 0.5714 (pt0) REVERT: B 83 ARG cc_start: 0.6097 (mmt90) cc_final: 0.5757 (mmm-85) REVERT: B 122 THR cc_start: 0.6565 (m) cc_final: 0.6342 (p) REVERT: B 427 MET cc_start: 0.6852 (mmp) cc_final: 0.6443 (mmm) REVERT: B 449 MET cc_start: 0.7539 (tpp) cc_final: 0.7202 (tpp) REVERT: B 560 ARG cc_start: 0.7865 (mtp180) cc_final: 0.7227 (mtp180) REVERT: B 599 ARG cc_start: 0.7735 (ptp90) cc_final: 0.7170 (ttp80) REVERT: C 39 VAL cc_start: 0.5511 (t) cc_final: 0.5241 (m) REVERT: C 66 GLU cc_start: 0.6444 (mp0) cc_final: 0.5696 (pt0) REVERT: C 122 THR cc_start: 0.6545 (OUTLIER) cc_final: 0.6312 (p) REVERT: C 321 GLU cc_start: 0.7542 (tt0) cc_final: 0.7145 (tt0) REVERT: C 449 MET cc_start: 0.7687 (OUTLIER) cc_final: 0.7331 (tpp) REVERT: C 492 LEU cc_start: 0.9073 (OUTLIER) cc_final: 0.8870 (mp) REVERT: C 494 GLN cc_start: 0.8344 (OUTLIER) cc_final: 0.7994 (mm110) REVERT: C 599 ARG cc_start: 0.7950 (ptp-170) cc_final: 0.7517 (ttp80) REVERT: D 39 VAL cc_start: 0.5413 (t) cc_final: 0.5065 (m) REVERT: D 66 GLU cc_start: 0.6233 (mp0) cc_final: 0.5639 (pt0) REVERT: D 83 ARG cc_start: 0.5911 (mmt90) cc_final: 0.5551 (mmm-85) REVERT: D 239 ARG cc_start: 0.8255 (OUTLIER) cc_final: 0.7950 (ptt-90) REVERT: D 449 MET cc_start: 0.7655 (OUTLIER) cc_final: 0.6693 (ttm) REVERT: D 599 ARG cc_start: 0.7974 (ptp90) cc_final: 0.7508 (ttp80) REVERT: D 679 THR cc_start: 0.7919 (OUTLIER) cc_final: 0.7488 (p) REVERT: D 692 GLN cc_start: 0.7625 (OUTLIER) cc_final: 0.7375 (mm110) REVERT: E 39 VAL cc_start: 0.5197 (t) cc_final: 0.4930 (m) REVERT: E 66 GLU cc_start: 0.6342 (mp0) cc_final: 0.5663 (pt0) REVERT: E 83 ARG cc_start: 0.6071 (mmt90) cc_final: 0.5733 (mmm-85) REVERT: E 122 THR cc_start: 0.6546 (m) cc_final: 0.6320 (p) REVERT: E 427 MET cc_start: 0.6808 (mmp) cc_final: 0.6401 (mmm) REVERT: E 449 MET cc_start: 0.7550 (tpp) cc_final: 0.7195 (tpp) REVERT: E 560 ARG cc_start: 0.7882 (mtp180) cc_final: 0.7212 (mtp180) REVERT: E 599 ARG cc_start: 0.7739 (ptp90) cc_final: 0.7166 (ttp80) REVERT: F 39 VAL cc_start: 0.5357 (t) cc_final: 0.5084 (m) REVERT: F 66 GLU cc_start: 0.6232 (mp0) cc_final: 0.5684 (pt0) REVERT: F 122 THR cc_start: 0.6549 (OUTLIER) cc_final: 0.6268 (p) REVERT: F 158 MET cc_start: 0.8016 (mmm) cc_final: 0.7741 (mtt) REVERT: F 173 TYR cc_start: 0.5581 (p90) cc_final: 0.4440 (p90) REVERT: F 427 MET cc_start: 0.6675 (mmp) cc_final: 0.6298 (mmm) REVERT: F 449 MET cc_start: 0.7676 (tpp) cc_final: 0.7170 (tpp) REVERT: F 494 GLN cc_start: 0.8392 (OUTLIER) cc_final: 0.8152 (mm110) REVERT: F 560 ARG cc_start: 0.7842 (mtp180) cc_final: 0.7173 (mtp180) REVERT: F 599 ARG cc_start: 0.7947 (ptp-170) cc_final: 0.7527 (ttp80) outliers start: 163 outliers final: 126 residues processed: 504 average time/residue: 0.2471 time to fit residues: 196.1545 Evaluate side-chains 539 residues out of total 3714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 139 poor density : 400 time to evaluate : 1.525 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 ILE Chi-restraints excluded: chain A residue 85 ASN Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 146 ILE Chi-restraints excluded: chain A residue 198 LEU Chi-restraints excluded: chain A residue 218 GLU Chi-restraints excluded: chain A residue 239 ARG Chi-restraints excluded: chain A residue 371 ILE Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain A residue 427 MET Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 448 THR Chi-restraints excluded: chain A residue 449 MET Chi-restraints excluded: chain A residue 479 ILE Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 501 ASP Chi-restraints excluded: chain A residue 504 LEU Chi-restraints excluded: chain A residue 531 ILE Chi-restraints excluded: chain A residue 582 ILE Chi-restraints excluded: chain A residue 661 LEU Chi-restraints excluded: chain A residue 679 THR Chi-restraints excluded: chain A residue 697 LEU Chi-restraints excluded: chain A residue 731 ILE Chi-restraints excluded: chain A residue 746 SER Chi-restraints excluded: chain A residue 747 VAL Chi-restraints excluded: chain B residue 58 LEU Chi-restraints excluded: chain B residue 70 ILE Chi-restraints excluded: chain B residue 85 ASN Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 218 GLU Chi-restraints excluded: chain B residue 281 GLU Chi-restraints excluded: chain B residue 291 GLU Chi-restraints excluded: chain B residue 321 GLU Chi-restraints excluded: chain B residue 342 ILE Chi-restraints excluded: chain B residue 371 ILE Chi-restraints excluded: chain B residue 447 VAL Chi-restraints excluded: chain B residue 448 THR Chi-restraints excluded: chain B residue 479 ILE Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain B residue 504 LEU Chi-restraints excluded: chain B residue 531 ILE Chi-restraints excluded: chain B residue 550 MET Chi-restraints excluded: chain B residue 692 GLN Chi-restraints excluded: chain B residue 697 LEU Chi-restraints excluded: chain B residue 701 GLU Chi-restraints excluded: chain B residue 746 SER Chi-restraints excluded: chain B residue 747 VAL Chi-restraints excluded: chain C residue 85 ASN Chi-restraints excluded: chain C residue 122 THR Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain C residue 198 LEU Chi-restraints excluded: chain C residue 342 ILE Chi-restraints excluded: chain C residue 371 ILE Chi-restraints excluded: chain C residue 427 MET Chi-restraints excluded: chain C residue 447 VAL Chi-restraints excluded: chain C residue 448 THR Chi-restraints excluded: chain C residue 449 MET Chi-restraints excluded: chain C residue 479 ILE Chi-restraints excluded: chain C residue 492 LEU Chi-restraints excluded: chain C residue 494 GLN Chi-restraints excluded: chain C residue 508 MET Chi-restraints excluded: chain C residue 531 ILE Chi-restraints excluded: chain C residue 582 ILE Chi-restraints excluded: chain C residue 661 LEU Chi-restraints excluded: chain C residue 692 GLN Chi-restraints excluded: chain C residue 697 LEU Chi-restraints excluded: chain C residue 746 SER Chi-restraints excluded: chain C residue 747 VAL Chi-restraints excluded: chain D residue 58 LEU Chi-restraints excluded: chain D residue 70 ILE Chi-restraints excluded: chain D residue 85 ASN Chi-restraints excluded: chain D residue 123 VAL Chi-restraints excluded: chain D residue 146 ILE Chi-restraints excluded: chain D residue 198 LEU Chi-restraints excluded: chain D residue 239 ARG Chi-restraints excluded: chain D residue 342 ILE Chi-restraints excluded: chain D residue 371 ILE Chi-restraints excluded: chain D residue 378 LEU Chi-restraints excluded: chain D residue 420 LEU Chi-restraints excluded: chain D residue 427 MET Chi-restraints excluded: chain D residue 447 VAL Chi-restraints excluded: chain D residue 448 THR Chi-restraints excluded: chain D residue 449 MET Chi-restraints excluded: chain D residue 479 ILE Chi-restraints excluded: chain D residue 492 LEU Chi-restraints excluded: chain D residue 504 LEU Chi-restraints excluded: chain D residue 531 ILE Chi-restraints excluded: chain D residue 582 ILE Chi-restraints excluded: chain D residue 661 LEU Chi-restraints excluded: chain D residue 679 THR Chi-restraints excluded: chain D residue 692 GLN Chi-restraints excluded: chain D residue 697 LEU Chi-restraints excluded: chain D residue 746 SER Chi-restraints excluded: chain E residue 58 LEU Chi-restraints excluded: chain E residue 70 ILE Chi-restraints excluded: chain E residue 85 ASN Chi-restraints excluded: chain E residue 123 VAL Chi-restraints excluded: chain E residue 198 LEU Chi-restraints excluded: chain E residue 218 GLU Chi-restraints excluded: chain E residue 291 GLU Chi-restraints excluded: chain E residue 342 ILE Chi-restraints excluded: chain E residue 371 ILE Chi-restraints excluded: chain E residue 447 VAL Chi-restraints excluded: chain E residue 448 THR Chi-restraints excluded: chain E residue 479 ILE Chi-restraints excluded: chain E residue 492 LEU Chi-restraints excluded: chain E residue 504 LEU Chi-restraints excluded: chain E residue 531 ILE Chi-restraints excluded: chain E residue 550 MET Chi-restraints excluded: chain E residue 692 GLN Chi-restraints excluded: chain E residue 697 LEU Chi-restraints excluded: chain E residue 701 GLU Chi-restraints excluded: chain E residue 746 SER Chi-restraints excluded: chain E residue 747 VAL Chi-restraints excluded: chain F residue 85 ASN Chi-restraints excluded: chain F residue 122 THR Chi-restraints excluded: chain F residue 123 VAL Chi-restraints excluded: chain F residue 198 LEU Chi-restraints excluded: chain F residue 231 LYS Chi-restraints excluded: chain F residue 285 ASN Chi-restraints excluded: chain F residue 342 ILE Chi-restraints excluded: chain F residue 371 ILE Chi-restraints excluded: chain F residue 447 VAL Chi-restraints excluded: chain F residue 448 THR Chi-restraints excluded: chain F residue 479 ILE Chi-restraints excluded: chain F residue 492 LEU Chi-restraints excluded: chain F residue 494 GLN Chi-restraints excluded: chain F residue 531 ILE Chi-restraints excluded: chain F residue 558 ASN Chi-restraints excluded: chain F residue 582 ILE Chi-restraints excluded: chain F residue 661 LEU Chi-restraints excluded: chain F residue 692 GLN Chi-restraints excluded: chain F residue 697 LEU Chi-restraints excluded: chain F residue 701 GLU Chi-restraints excluded: chain F residue 746 SER Chi-restraints excluded: chain F residue 747 VAL Chi-restraints excluded: chain F residue 757 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 164 optimal weight: 7.9990 chunk 409 optimal weight: 0.9990 chunk 103 optimal weight: 0.0570 chunk 50 optimal weight: 9.9990 chunk 186 optimal weight: 30.0000 chunk 258 optimal weight: 7.9990 chunk 256 optimal weight: 6.9990 chunk 349 optimal weight: 1.9990 chunk 407 optimal weight: 6.9990 chunk 200 optimal weight: 20.0000 chunk 314 optimal weight: 10.0000 overall best weight: 3.4106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 285 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.147162 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.114818 restraints weight = 58717.644| |-----------------------------------------------------------------------------| r_work (start): 0.3527 rms_B_bonded: 2.63 r_work: 0.3300 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.3300 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8070 moved from start: 0.4722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 35130 Z= 0.139 Angle : 0.674 7.270 47514 Z= 0.337 Chirality : 0.047 0.167 5352 Planarity : 0.005 0.049 6234 Dihedral : 8.804 130.417 4926 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 9.55 Ramachandran Plot: Outliers : 0.28 % Allowed : 7.23 % Favored : 92.50 % Rotamer: Outliers : 3.47 % Allowed : 16.75 % Favored : 79.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.28 (0.13), residues: 4344 helix: -0.43 (0.12), residues: 1788 sheet: -1.08 (0.20), residues: 618 loop : -1.03 (0.14), residues: 1938 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG F 287 TYR 0.015 0.001 TYR D 173 PHE 0.012 0.001 PHE C 152 TRP 0.008 0.001 TRP A 551 HIS 0.005 0.001 HIS F 317 Details of bonding type rmsd covalent geometry : bond 0.00320 (35130) covalent geometry : angle 0.67409 (47514) hydrogen bonds : bond 0.03602 ( 1229) hydrogen bonds : angle 5.06386 ( 3417) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8688 Ramachandran restraints generated. 4344 Oldfield, 0 Emsley, 4344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8688 Ramachandran restraints generated. 4344 Oldfield, 0 Emsley, 4344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 544 residues out of total 3714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 129 poor density : 415 time to evaluate : 1.379 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 VAL cc_start: 0.5313 (t) cc_final: 0.4988 (m) REVERT: A 83 ARG cc_start: 0.6033 (mmt90) cc_final: 0.5661 (mmm-85) REVERT: A 239 ARG cc_start: 0.8217 (OUTLIER) cc_final: 0.7943 (ptt-90) REVERT: A 449 MET cc_start: 0.7706 (OUTLIER) cc_final: 0.7339 (tpp) REVERT: A 560 ARG cc_start: 0.7723 (mtp180) cc_final: 0.7042 (mtp180) REVERT: A 599 ARG cc_start: 0.7725 (ptp90) cc_final: 0.7199 (ttp80) REVERT: A 679 THR cc_start: 0.7899 (OUTLIER) cc_final: 0.7520 (p) REVERT: A 692 GLN cc_start: 0.8040 (mm-40) cc_final: 0.7491 (mm110) REVERT: B 39 VAL cc_start: 0.5368 (t) cc_final: 0.5105 (m) REVERT: B 66 GLU cc_start: 0.6458 (mp0) cc_final: 0.6019 (mm-30) REVERT: B 83 ARG cc_start: 0.6097 (mmt90) cc_final: 0.5626 (mmm-85) REVERT: B 122 THR cc_start: 0.6555 (m) cc_final: 0.6322 (p) REVERT: B 427 MET cc_start: 0.6746 (mmp) cc_final: 0.6325 (mmm) REVERT: B 449 MET cc_start: 0.7511 (tpp) cc_final: 0.7152 (tpp) REVERT: B 560 ARG cc_start: 0.7833 (mtp180) cc_final: 0.7269 (mtp180) REVERT: B 599 ARG cc_start: 0.7651 (ptp90) cc_final: 0.7093 (ttp80) REVERT: C 39 VAL cc_start: 0.5475 (t) cc_final: 0.5190 (m) REVERT: C 66 GLU cc_start: 0.6406 (mp0) cc_final: 0.5910 (mm-30) REVERT: C 122 THR cc_start: 0.6545 (OUTLIER) cc_final: 0.6312 (p) REVERT: C 321 GLU cc_start: 0.7473 (tt0) cc_final: 0.7179 (tt0) REVERT: C 449 MET cc_start: 0.7667 (OUTLIER) cc_final: 0.7328 (tpp) REVERT: C 494 GLN cc_start: 0.8304 (OUTLIER) cc_final: 0.7967 (mm110) REVERT: C 599 ARG cc_start: 0.7893 (ptp-170) cc_final: 0.7434 (ttp80) REVERT: D 39 VAL cc_start: 0.5326 (t) cc_final: 0.4998 (m) REVERT: D 66 GLU cc_start: 0.6203 (mp0) cc_final: 0.5690 (pt0) REVERT: D 83 ARG cc_start: 0.6040 (mmt90) cc_final: 0.5666 (mmm-85) REVERT: D 239 ARG cc_start: 0.8219 (OUTLIER) cc_final: 0.7909 (ptt-90) REVERT: D 449 MET cc_start: 0.7652 (OUTLIER) cc_final: 0.6690 (ttm) REVERT: D 599 ARG cc_start: 0.7689 (ptp90) cc_final: 0.7120 (ttp80) REVERT: D 679 THR cc_start: 0.7873 (OUTLIER) cc_final: 0.7431 (p) REVERT: D 692 GLN cc_start: 0.7610 (OUTLIER) cc_final: 0.7384 (mm110) REVERT: E 39 VAL cc_start: 0.5147 (t) cc_final: 0.4889 (m) REVERT: E 66 GLU cc_start: 0.6407 (mp0) cc_final: 0.5731 (pt0) REVERT: E 83 ARG cc_start: 0.6132 (mmt90) cc_final: 0.5644 (mmm-85) REVERT: E 122 THR cc_start: 0.6542 (m) cc_final: 0.6313 (p) REVERT: E 427 MET cc_start: 0.6730 (mmp) cc_final: 0.6312 (mmm) REVERT: E 560 ARG cc_start: 0.7843 (mtp180) cc_final: 0.7230 (mtp180) REVERT: E 599 ARG cc_start: 0.7673 (ptp90) cc_final: 0.7111 (ttp80) REVERT: F 39 VAL cc_start: 0.5425 (t) cc_final: 0.5182 (m) REVERT: F 66 GLU cc_start: 0.6175 (mp0) cc_final: 0.5612 (pt0) REVERT: F 122 THR cc_start: 0.6525 (OUTLIER) cc_final: 0.6252 (p) REVERT: F 158 MET cc_start: 0.7982 (mmm) cc_final: 0.7612 (mtt) REVERT: F 427 MET cc_start: 0.6700 (mmp) cc_final: 0.6311 (mmm) REVERT: F 442 MET cc_start: 0.7141 (mmp) cc_final: 0.6512 (mmt) REVERT: F 449 MET cc_start: 0.7690 (tpp) cc_final: 0.7219 (tpp) REVERT: F 494 GLN cc_start: 0.8373 (OUTLIER) cc_final: 0.8135 (mm110) REVERT: F 560 ARG cc_start: 0.7812 (mtp180) cc_final: 0.7209 (mtp180) REVERT: F 599 ARG cc_start: 0.7890 (ptp-170) cc_final: 0.7429 (ttp80) outliers start: 129 outliers final: 105 residues processed: 489 average time/residue: 0.2488 time to fit residues: 190.5606 Evaluate side-chains 522 residues out of total 3714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 405 time to evaluate : 1.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 198 LEU Chi-restraints excluded: chain A residue 218 GLU Chi-restraints excluded: chain A residue 239 ARG Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain A residue 427 MET Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 448 THR Chi-restraints excluded: chain A residue 449 MET Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 504 LEU Chi-restraints excluded: chain A residue 531 ILE Chi-restraints excluded: chain A residue 582 ILE Chi-restraints excluded: chain A residue 661 LEU Chi-restraints excluded: chain A residue 679 THR Chi-restraints excluded: chain A residue 731 ILE Chi-restraints excluded: chain A residue 746 SER Chi-restraints excluded: chain A residue 747 VAL Chi-restraints excluded: chain B residue 58 LEU Chi-restraints excluded: chain B residue 85 ASN Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 218 GLU Chi-restraints excluded: chain B residue 281 GLU Chi-restraints excluded: chain B residue 291 GLU Chi-restraints excluded: chain B residue 321 GLU Chi-restraints excluded: chain B residue 342 ILE Chi-restraints excluded: chain B residue 371 ILE Chi-restraints excluded: chain B residue 447 VAL Chi-restraints excluded: chain B residue 448 THR Chi-restraints excluded: chain B residue 479 ILE Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain B residue 504 LEU Chi-restraints excluded: chain B residue 531 ILE Chi-restraints excluded: chain B residue 692 GLN Chi-restraints excluded: chain B residue 697 LEU Chi-restraints excluded: chain B residue 701 GLU Chi-restraints excluded: chain B residue 746 SER Chi-restraints excluded: chain B residue 747 VAL Chi-restraints excluded: chain C residue 85 ASN Chi-restraints excluded: chain C residue 122 THR Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain C residue 198 LEU Chi-restraints excluded: chain C residue 342 ILE Chi-restraints excluded: chain C residue 371 ILE Chi-restraints excluded: chain C residue 427 MET Chi-restraints excluded: chain C residue 447 VAL Chi-restraints excluded: chain C residue 448 THR Chi-restraints excluded: chain C residue 449 MET Chi-restraints excluded: chain C residue 479 ILE Chi-restraints excluded: chain C residue 494 GLN Chi-restraints excluded: chain C residue 508 MET Chi-restraints excluded: chain C residue 531 ILE Chi-restraints excluded: chain C residue 582 ILE Chi-restraints excluded: chain C residue 661 LEU Chi-restraints excluded: chain C residue 692 GLN Chi-restraints excluded: chain C residue 697 LEU Chi-restraints excluded: chain C residue 746 SER Chi-restraints excluded: chain C residue 747 VAL Chi-restraints excluded: chain D residue 58 LEU Chi-restraints excluded: chain D residue 85 ASN Chi-restraints excluded: chain D residue 123 VAL Chi-restraints excluded: chain D residue 198 LEU Chi-restraints excluded: chain D residue 239 ARG Chi-restraints excluded: chain D residue 342 ILE Chi-restraints excluded: chain D residue 378 LEU Chi-restraints excluded: chain D residue 388 MET Chi-restraints excluded: chain D residue 420 LEU Chi-restraints excluded: chain D residue 427 MET Chi-restraints excluded: chain D residue 447 VAL Chi-restraints excluded: chain D residue 448 THR Chi-restraints excluded: chain D residue 449 MET Chi-restraints excluded: chain D residue 479 ILE Chi-restraints excluded: chain D residue 492 LEU Chi-restraints excluded: chain D residue 504 LEU Chi-restraints excluded: chain D residue 531 ILE Chi-restraints excluded: chain D residue 582 ILE Chi-restraints excluded: chain D residue 661 LEU Chi-restraints excluded: chain D residue 679 THR Chi-restraints excluded: chain D residue 692 GLN Chi-restraints excluded: chain E residue 58 LEU Chi-restraints excluded: chain E residue 70 ILE Chi-restraints excluded: chain E residue 85 ASN Chi-restraints excluded: chain E residue 198 LEU Chi-restraints excluded: chain E residue 218 GLU Chi-restraints excluded: chain E residue 291 GLU Chi-restraints excluded: chain E residue 342 ILE Chi-restraints excluded: chain E residue 371 ILE Chi-restraints excluded: chain E residue 447 VAL Chi-restraints excluded: chain E residue 448 THR Chi-restraints excluded: chain E residue 479 ILE Chi-restraints excluded: chain E residue 492 LEU Chi-restraints excluded: chain E residue 504 LEU Chi-restraints excluded: chain E residue 531 ILE Chi-restraints excluded: chain E residue 692 GLN Chi-restraints excluded: chain E residue 697 LEU Chi-restraints excluded: chain E residue 701 GLU Chi-restraints excluded: chain E residue 746 SER Chi-restraints excluded: chain E residue 747 VAL Chi-restraints excluded: chain F residue 85 ASN Chi-restraints excluded: chain F residue 122 THR Chi-restraints excluded: chain F residue 123 VAL Chi-restraints excluded: chain F residue 198 LEU Chi-restraints excluded: chain F residue 231 LYS Chi-restraints excluded: chain F residue 285 ASN Chi-restraints excluded: chain F residue 447 VAL Chi-restraints excluded: chain F residue 479 ILE Chi-restraints excluded: chain F residue 492 LEU Chi-restraints excluded: chain F residue 494 GLN Chi-restraints excluded: chain F residue 531 ILE Chi-restraints excluded: chain F residue 582 ILE Chi-restraints excluded: chain F residue 661 LEU Chi-restraints excluded: chain F residue 692 GLN Chi-restraints excluded: chain F residue 697 LEU Chi-restraints excluded: chain F residue 701 GLU Chi-restraints excluded: chain F residue 746 SER Chi-restraints excluded: chain F residue 747 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 45 optimal weight: 6.9990 chunk 81 optimal weight: 7.9990 chunk 119 optimal weight: 1.9990 chunk 370 optimal weight: 0.5980 chunk 381 optimal weight: 10.0000 chunk 265 optimal weight: 0.9980 chunk 167 optimal weight: 5.9990 chunk 143 optimal weight: 10.0000 chunk 4 optimal weight: 30.0000 chunk 145 optimal weight: 8.9990 chunk 423 optimal weight: 8.9990 overall best weight: 3.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 285 ASN E 285 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.147561 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.115191 restraints weight = 58357.165| |-----------------------------------------------------------------------------| r_work (start): 0.3531 rms_B_bonded: 2.54 r_work: 0.3304 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.3304 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8060 moved from start: 0.4827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 35130 Z= 0.137 Angle : 0.666 7.235 47514 Z= 0.332 Chirality : 0.046 0.161 5352 Planarity : 0.005 0.049 6234 Dihedral : 8.680 127.117 4926 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 9.57 Ramachandran Plot: Outliers : 0.28 % Allowed : 7.60 % Favored : 92.13 % Rotamer: Outliers : 3.74 % Allowed : 16.67 % Favored : 79.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.22 (0.13), residues: 4344 helix: -0.32 (0.13), residues: 1782 sheet: -1.19 (0.19), residues: 654 loop : -0.99 (0.14), residues: 1908 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 83 TYR 0.015 0.001 TYR C 173 PHE 0.012 0.001 PHE C 152 TRP 0.006 0.001 TRP B 551 HIS 0.004 0.001 HIS B 384 Details of bonding type rmsd covalent geometry : bond 0.00316 (35130) covalent geometry : angle 0.66576 (47514) hydrogen bonds : bond 0.03472 ( 1229) hydrogen bonds : angle 4.97726 ( 3417) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8687.17 seconds wall clock time: 149 minutes 22.65 seconds (8962.65 seconds total)