Starting phenix.real_space_refine on Mon Sep 14 23:37:19 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/5ftm_3298/09_2026/5ftm_3298.cif Found real_map, /net/cci-nas-00/data/ceres_data/5ftm_3298/09_2026/5ftm_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 { restraint_files = "/net/cci-nas-00/data/ceres_data/5ftm_3298/09_2026/5ftm_3298.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/5ftm_3298/09_2026/5ftm_3298.cif" model { file = "/net/cci-nas-00/data/ceres_data/5ftm_3298/09_2026/5ftm_3298.cif" } default_model = "/net/cci-nas-00/data/ceres_data/5ftm_3298/09_2026/5ftm_3298.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/5ftm_3298/09_2026/5ftm_3298.map" default_real_map = "/net/cci-nas-00/data/ceres_data/5ftm_3298/09_2026/5ftm_3298.map" } 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-2.2.1-6174/lib/python3.11/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: 7.10, 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: 2.94 Conformation dependent library (CDL) restraints added in 1.4 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: 1.27 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: 7.29 Time building geometry restraints manager: 3.89 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: 21382 30.45 - 60.90: 272 60.90 - 91.35: 54 91.35 - 121.80: 0 121.80 - 152.24: 6 Dihedral angle restraints: 21714 sinusoidal: 9144 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 21711 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: 0.12 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: 1.480 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: 0.030 Extract box with map and model: 0.730 Check model and map are aligned: 0.110 Set scattering table: 0.090 Process input model: 31.270 Find NCS groups from input model: 0.520 Set up NCS constraints: 0.080 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:1.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.650 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8208 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.014 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 : 11.932 152.244 13566 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/Z covalent geometry : bond 0.01373 / 0.62 (35130) covalent geometry : angle 1.33939 / 0.76 (47514) hydrogen bonds : bond 0.29171 / 19.31 ( 1229) hydrogen bonds : angle 10.03316 / 6.98 ( 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 : 1.510 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: 0.2831 time to fit residues: 364.1946 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 : 1.410 ------------------------------------------------------------------------------- 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... ** 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 = 0.4000 r_free = 0.4000 target = 0.148905 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.113860 restraints weight = 58649.284| |-----------------------------------------------------------------------------| r_work (start): 0.3508 rms_B_bonded: 2.75 r_work: 0.3313 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.3313 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8177 moved from start: 0.2896 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= 0.195 Angle : 0.872 8.591 47514 Z= 0.447 Chirality : 0.051 0.172 5352 Planarity : 0.006 0.048 6234 Dihedral : 9.358 138.488 4860 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 13.53 Ramachandran Plot: Outliers : 0.28 % Allowed : 6.84 % Favored : 92.89 % Rotamer: Outliers : 1.75 % Allowed : 8.72 % Favored : 89.53 % 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: -3.06 (0.11), residues: 4344 helix: -2.30 (0.10), residues: 1698 sheet: -1.63 (0.18), residues: 666 loop : -1.76 (0.13), residues: 1980 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C 377 TYR 0.022 0.003 TYR D 244 PHE 0.017 0.002 PHE A 516 TRP 0.005 0.002 TRP C 476 HIS 0.007 0.002 HIS D 317 Details of bonding type rmsd/Z covalent geometry : bond 0.00429 / 0.19 (35130) covalent geometry : angle 0.87173 / 0.45 (47514) hydrogen bonds : bond 0.06200 / 4.10 ( 1229) hydrogen bonds : angle 6.23539 / 4.33 ( 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 617 residues out of total 3714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 552 time to evaluate : 1.161 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 36 ASN cc_start: 0.6081 (t0) cc_final: 0.5841 (t0) REVERT: A 39 VAL cc_start: 0.5528 (t) cc_final: 0.5196 (m) REVERT: A 83 ARG cc_start: 0.5851 (mmt90) cc_final: 0.5492 (mmt90) REVERT: A 93 ARG cc_start: 0.7574 (mmt90) cc_final: 0.7299 (mmt180) REVERT: A 134 TYR cc_start: 0.6097 (m-80) cc_final: 0.5858 (m-10) REVERT: A 173 TYR cc_start: 0.4549 (p90) cc_final: 0.4011 (p90) REVERT: A 440 GLU cc_start: 0.7006 (pm20) cc_final: 0.6655 (tp30) REVERT: A 449 MET cc_start: 0.7694 (tpp) cc_final: 0.6623 (ttm) REVERT: A 546 GLU cc_start: 0.8367 (tm-30) cc_final: 0.8158 (tm-30) REVERT: A 551 TRP cc_start: 0.5393 (t60) cc_final: 0.5165 (t60) REVERT: A 560 ARG cc_start: 0.7593 (mtp180) cc_final: 0.7077 (mtp180) REVERT: A 599 ARG cc_start: 0.7751 (ptp90) cc_final: 0.7168 (ptt90) REVERT: B 39 VAL cc_start: 0.5534 (t) cc_final: 0.5214 (m) REVERT: B 83 ARG cc_start: 0.5870 (mmt90) cc_final: 0.5610 (mmt90) REVERT: B 134 TYR cc_start: 0.6156 (m-80) cc_final: 0.5699 (m-10) REVERT: B 148 LYS cc_start: 0.6226 (mttt) cc_final: 0.5910 (mmtt) REVERT: B 440 GLU cc_start: 0.7138 (pm20) cc_final: 0.6786 (tp30) REVERT: B 449 MET cc_start: 0.7648 (tpp) cc_final: 0.6596 (ttm) REVERT: B 551 TRP cc_start: 0.5529 (t60) cc_final: 0.5090 (t60) REVERT: B 560 ARG cc_start: 0.7661 (mtp180) cc_final: 0.7140 (mtp180) REVERT: B 599 ARG cc_start: 0.7694 (ptp90) cc_final: 0.7167 (ptt90) REVERT: C 36 ASN cc_start: 0.6067 (t0) cc_final: 0.5816 (t0) REVERT: C 39 VAL cc_start: 0.5754 (t) cc_final: 0.5467 (m) REVERT: C 173 TYR cc_start: 0.4862 (p90) cc_final: 0.4106 (p90) REVERT: C 393 ASP cc_start: 0.6423 (p0) cc_final: 0.6211 (p0) REVERT: C 440 GLU cc_start: 0.6971 (pm20) cc_final: 0.6606 (tp30) REVERT: C 546 GLU cc_start: 0.8287 (tm-30) cc_final: 0.8034 (tm-30) REVERT: C 560 ARG cc_start: 0.7616 (mtp180) cc_final: 0.6767 (mtp180) REVERT: C 564 ASP cc_start: 0.7463 (m-30) cc_final: 0.7230 (m-30) REVERT: D 39 VAL cc_start: 0.5499 (t) cc_final: 0.5170 (m) REVERT: D 134 TYR cc_start: 0.6114 (m-80) cc_final: 0.5877 (m-10) REVERT: D 440 GLU cc_start: 0.6969 (pm20) cc_final: 0.6639 (tp30) REVERT: D 442 MET cc_start: 0.7236 (mmp) cc_final: 0.6564 (mmt) REVERT: D 449 MET cc_start: 0.7634 (tpp) cc_final: 0.6590 (ttm) REVERT: D 546 GLU cc_start: 0.8323 (tm-30) cc_final: 0.8122 (tm-30) REVERT: D 551 TRP cc_start: 0.5419 (t60) cc_final: 0.5215 (t60) REVERT: D 560 ARG cc_start: 0.7606 (mtp180) cc_final: 0.7092 (mtp180) REVERT: D 599 ARG cc_start: 0.7764 (ptp90) cc_final: 0.7187 (ptt90) REVERT: E 36 ASN cc_start: 0.6048 (t0) cc_final: 0.5707 (t0) REVERT: E 39 VAL cc_start: 0.5299 (t) cc_final: 0.5006 (m) REVERT: E 83 ARG cc_start: 0.5822 (mmt90) cc_final: 0.5568 (mmt90) REVERT: E 134 TYR cc_start: 0.6142 (m-80) cc_final: 0.5662 (m-10) REVERT: E 148 LYS cc_start: 0.6227 (mttt) cc_final: 0.5903 (mmtt) REVERT: E 440 GLU cc_start: 0.7137 (pm20) cc_final: 0.6788 (tp30) REVERT: E 449 MET cc_start: 0.7628 (tpp) cc_final: 0.6598 (ttm) REVERT: E 551 TRP cc_start: 0.5515 (t60) cc_final: 0.5085 (t60) REVERT: E 560 ARG cc_start: 0.7633 (mtp180) cc_final: 0.7130 (mtp180) REVERT: E 599 ARG cc_start: 0.7694 (ptp90) cc_final: 0.7198 (ptt90) REVERT: F 36 ASN cc_start: 0.6099 (t0) cc_final: 0.5827 (t0) REVERT: F 39 VAL cc_start: 0.5515 (t) cc_final: 0.5207 (m) REVERT: F 134 TYR cc_start: 0.6084 (m-80) cc_final: 0.5855 (m-10) REVERT: F 148 LYS cc_start: 0.6213 (mttt) cc_final: 0.5884 (mmtm) REVERT: F 440 GLU cc_start: 0.6960 (pm20) cc_final: 0.6570 (tp30) REVERT: F 442 MET cc_start: 0.7155 (mmt) cc_final: 0.6870 (mmt) REVERT: F 546 GLU cc_start: 0.8287 (tm-30) cc_final: 0.8039 (tm-30) REVERT: F 558 ASN cc_start: 0.6767 (m110) cc_final: 0.6524 (m110) REVERT: F 560 ARG cc_start: 0.7587 (mtp180) cc_final: 0.7144 (mtp180) outliers start: 65 outliers final: 47 residues processed: 592 average time/residue: 0.2649 time to fit residues: 239.4498 Evaluate side-chains 480 residues out of total 3714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 433 time to evaluate : 1.303 ------------------------------------------------------------------------------- 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 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: 8.9990 chunk 270 optimal weight: 0.9980 chunk 248 optimal weight: 10.0000 chunk 111 optimal weight: 10.0000 chunk 284 optimal weight: 7.9990 chunk 125 optimal weight: 10.0000 chunk 310 optimal weight: 5.9990 chunk 7 optimal weight: 9.9990 chunk 89 optimal weight: 30.0000 chunk 39 optimal weight: 4.9990 chunk 149 optimal weight: 9.9990 overall best weight: 5.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 348 ASN ** 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 ** E 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 348 ASN ** F 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3982 r_free = 0.3982 target = 0.147802 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.115603 restraints weight = 58903.195| |-----------------------------------------------------------------------------| r_work (start): 0.3540 rms_B_bonded: 2.52 r_work: 0.3301 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.3301 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8194 moved from start: 0.3467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 35130 Z= 0.200 Angle : 0.786 8.164 47514 Z= 0.397 Chirality : 0.050 0.159 5352 Planarity : 0.006 0.086 6234 Dihedral : 8.677 129.288 4860 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 11.59 Ramachandran Plot: Outliers : 0.28 % Allowed : 7.48 % Favored : 92.24 % Rotamer: Outliers : 3.12 % Allowed : 10.69 % Favored : 86.19 % 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: -1.37 (0.12), residues: 1716 sheet: -1.51 (0.18), residues: 666 loop : -1.43 (0.14), residues: 1962 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 599 TYR 0.019 0.002 TYR D 138 PHE 0.019 0.002 PHE A 516 TRP 0.012 0.002 TRP D 551 HIS 0.007 0.002 HIS B 340 Details of bonding type rmsd/Z covalent geometry : bond 0.00464 / 0.20 (35130) covalent geometry : angle 0.78561 / 0.40 (47514) hydrogen bonds : bond 0.04940 / 3.25 ( 1229) hydrogen bonds : angle 5.67210 / 3.93 ( 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 588 residues out of total 3714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 472 time to evaluate : 1.455 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: 0.5463 (t) cc_final: 0.5128 (m) REVERT: A 83 ARG cc_start: 0.5923 (mmt90) cc_final: 0.5722 (mmt90) REVERT: A 134 TYR cc_start: 0.6085 (m-80) cc_final: 0.5822 (m-10) REVERT: A 294 GLU cc_start: 0.7247 (tp30) cc_final: 0.6822 (tp30) REVERT: A 449 MET cc_start: 0.7628 (tpp) cc_final: 0.6632 (ttm) REVERT: A 551 TRP cc_start: 0.5424 (t60) cc_final: 0.5102 (t60) REVERT: A 599 ARG cc_start: 0.7824 (ptp90) cc_final: 0.7325 (ttp80) REVERT: A 686 ASP cc_start: 0.7677 (m-30) cc_final: 0.7243 (m-30) REVERT: B 39 VAL cc_start: 0.5378 (t) cc_final: 0.5059 (m) REVERT: B 134 TYR cc_start: 0.6157 (m-80) cc_final: 0.5628 (m-10) REVERT: B 440 GLU cc_start: 0.7010 (pm20) cc_final: 0.6809 (tp30) REVERT: B 449 MET cc_start: 0.7651 (tpp) cc_final: 0.6616 (ttm) REVERT: B 551 TRP cc_start: 0.5553 (t60) cc_final: 0.5026 (t60) REVERT: C 39 VAL cc_start: 0.5635 (t) cc_final: 0.5350 (m) REVERT: C 365 ARG cc_start: 0.8544 (mmt90) cc_final: 0.8185 (mmt90) REVERT: C 442 MET cc_start: 0.7136 (mmp) cc_final: 0.6449 (mmt) REVERT: C 449 MET cc_start: 0.7534 (OUTLIER) cc_final: 0.6537 (ttm) REVERT: C 560 ARG cc_start: 0.7818 (mtp180) cc_final: 0.6913 (mtp180) REVERT: C 599 ARG cc_start: 0.7805 (ptp-170) cc_final: 0.7206 (ttp80) REVERT: D 39 VAL cc_start: 0.5509 (t) cc_final: 0.5163 (m) REVERT: D 83 ARG cc_start: 0.5833 (mmt90) cc_final: 0.5305 (mmm-85) REVERT: D 134 TYR cc_start: 0.6125 (m-80) cc_final: 0.5841 (m-10) REVERT: D 449 MET cc_start: 0.7651 (tpp) cc_final: 0.6665 (ttm) REVERT: D 551 TRP cc_start: 0.5443 (t60) cc_final: 0.5100 (t60) REVERT: D 599 ARG cc_start: 0.7835 (ptp90) cc_final: 0.7329 (ttp80) REVERT: D 686 ASP cc_start: 0.7669 (m-30) cc_final: 0.7254 (m-30) REVERT: E 39 VAL cc_start: 0.5131 (t) cc_final: 0.4864 (m) REVERT: E 134 TYR cc_start: 0.6128 (m-80) cc_final: 0.5574 (m-10) REVERT: E 294 GLU cc_start: 0.7327 (tp30) cc_final: 0.6909 (tp30) REVERT: E 442 MET cc_start: 0.7397 (mmp) cc_final: 0.6733 (mmt) REVERT: E 449 MET cc_start: 0.7665 (tpp) cc_final: 0.6632 (ttm) REVERT: E 551 TRP cc_start: 0.5467 (t60) cc_final: 0.4991 (t60) REVERT: F 39 VAL cc_start: 0.5471 (t) cc_final: 0.5193 (m) REVERT: F 134 TYR cc_start: 0.6066 (m-80) cc_final: 0.5857 (m-10) REVERT: F 365 ARG cc_start: 0.8564 (mmt90) cc_final: 0.8190 (mmt90) REVERT: F 440 GLU cc_start: 0.6856 (pm20) cc_final: 0.6612 (tp30) REVERT: F 449 MET cc_start: 0.7678 (tpp) cc_final: 0.6514 (ttm) REVERT: F 558 ASN cc_start: 0.6658 (m110) cc_final: 0.6450 (m110) REVERT: F 599 ARG cc_start: 0.7843 (ptp-170) cc_final: 0.7259 (ttp80) outliers start: 116 outliers final: 75 residues processed: 554 average time/residue: 0.2504 time to fit residues: 217.9192 Evaluate side-chains 481 residues out of total 3714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 405 time to evaluate : 1.162 ------------------------------------------------------------------------------- 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 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 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 449 MET 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 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 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 531 ILE 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 342 ILE 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 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 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: 10.0000 chunk 386 optimal weight: 7.9990 chunk 28 optimal weight: 5.9990 chunk 122 optimal weight: 7.9990 chunk 108 optimal weight: 9.9990 chunk 180 optimal weight: 10.0000 chunk 29 optimal weight: 0.8980 chunk 245 optimal weight: 10.0000 chunk 135 optimal weight: 7.9990 overall best weight: 4.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3983 r_free = 0.3983 target = 0.148039 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.114961 restraints weight = 58556.751| |-----------------------------------------------------------------------------| r_work (start): 0.3521 rms_B_bonded: 2.66 r_work: 0.3287 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.3287 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8206 moved from start: 0.3863 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= 0.174 Angle : 0.730 7.633 47514 Z= 0.368 Chirality : 0.048 0.156 5352 Planarity : 0.006 0.047 6234 Dihedral : 8.128 123.379 4860 Min Nonbonded Distance : 2.282 Molprobity Statistics. All-atom Clashscore : 10.66 Ramachandran Plot: Outliers : 0.28 % Allowed : 7.37 % Favored : 92.36 % Rotamer: Outliers : 3.61 % Allowed : 12.41 % Favored : 83.98 % 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: -1.00 (0.12), residues: 1758 sheet: -1.39 (0.19), residues: 618 loop : -1.22 (0.14), residues: 1968 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 83 TYR 0.016 0.002 TYR B 138 PHE 0.016 0.002 PHE A 576 TRP 0.008 0.001 TRP B 551 HIS 0.007 0.001 HIS F 384 Details of bonding type rmsd/Z covalent geometry : bond 0.00401 / 0.17 (35130) covalent geometry : angle 0.73022 / 0.37 (47514) hydrogen bonds : bond 0.04274 / 2.82 ( 1229) hydrogen bonds : angle 5.38563 / 3.73 ( 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 576 residues out of total 3714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 134 poor density : 442 time to evaluate : 1.335 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: A 39 VAL cc_start: 0.5493 (t) cc_final: 0.5124 (m) REVERT: A 134 TYR cc_start: 0.6171 (m-80) cc_final: 0.5853 (m-10) REVERT: A 239 ARG cc_start: 0.8050 (OUTLIER) cc_final: 0.7650 (ptt-90) REVERT: A 294 GLU cc_start: 0.7335 (tp30) cc_final: 0.7107 (tp30) REVERT: A 449 MET cc_start: 0.7767 (tpp) cc_final: 0.7490 (tpp) REVERT: A 551 TRP cc_start: 0.5296 (t60) cc_final: 0.5074 (t60) REVERT: A 599 ARG cc_start: 0.7899 (ptp90) cc_final: 0.7480 (ttp80) REVERT: B 39 VAL cc_start: 0.5504 (t) cc_final: 0.5230 (m) REVERT: B 83 ARG cc_start: 0.6019 (mmt90) cc_final: 0.5609 (mmm-85) REVERT: B 599 ARG cc_start: 0.7801 (ptp90) cc_final: 0.7161 (ttp80) REVERT: C 39 VAL cc_start: 0.5660 (t) cc_final: 0.5371 (m) REVERT: C 158 MET cc_start: 0.7765 (mmm) cc_final: 0.7409 (mtt) REVERT: C 365 ARG cc_start: 0.8581 (mmt90) cc_final: 0.8198 (mmt90) REVERT: C 449 MET cc_start: 0.7689 (tpp) cc_final: 0.6627 (ttm) REVERT: C 599 ARG cc_start: 0.7915 (ptp-170) cc_final: 0.7395 (ttp80) REVERT: D 39 VAL cc_start: 0.5502 (t) cc_final: 0.5136 (m) REVERT: D 83 ARG cc_start: 0.6022 (mmt90) cc_final: 0.5781 (mmt90) REVERT: D 134 TYR cc_start: 0.6125 (m-80) cc_final: 0.5836 (m-10) REVERT: D 239 ARG cc_start: 0.8095 (OUTLIER) cc_final: 0.7701 (ptt-90) REVERT: D 449 MET cc_start: 0.7733 (tpp) cc_final: 0.7483 (tpp) REVERT: D 551 TRP cc_start: 0.5306 (t60) cc_final: 0.5065 (t60) REVERT: D 599 ARG cc_start: 0.7912 (ptp90) cc_final: 0.7496 (ttp80) REVERT: E 39 VAL cc_start: 0.5168 (t) cc_final: 0.4902 (m) REVERT: E 83 ARG cc_start: 0.6024 (mmt90) cc_final: 0.5581 (mmm-85) REVERT: E 134 TYR cc_start: 0.6099 (m-80) cc_final: 0.5601 (m-10) REVERT: E 294 GLU cc_start: 0.7373 (tp30) cc_final: 0.7086 (tp30) REVERT: E 449 MET cc_start: 0.7665 (tpp) cc_final: 0.7403 (tpp) REVERT: E 599 ARG cc_start: 0.7782 (ptp90) cc_final: 0.7125 (ttp80) REVERT: F 39 VAL cc_start: 0.5546 (t) cc_final: 0.5258 (m) REVERT: F 65 ARG cc_start: 0.5235 (ttp-170) cc_final: 0.4770 (ttp-170) REVERT: F 66 GLU cc_start: 0.6260 (mp0) cc_final: 0.4925 (mt-10) REVERT: F 83 ARG cc_start: 0.6145 (mmt90) cc_final: 0.5663 (mmm-85) REVERT: F 158 MET cc_start: 0.7789 (mmm) cc_final: 0.7300 (mtt) REVERT: F 442 MET cc_start: 0.7130 (mmp) cc_final: 0.6471 (mmt) REVERT: F 449 MET cc_start: 0.7715 (tpp) cc_final: 0.6543 (ttm) REVERT: F 550 MET cc_start: 0.6482 (tpt) cc_final: 0.6277 (ttp) REVERT: F 558 ASN cc_start: 0.6642 (m110) cc_final: 0.6442 (m110) REVERT: F 599 ARG cc_start: 0.7962 (ptp-170) cc_final: 0.7317 (ttp80) outliers start: 134 outliers final: 98 residues processed: 540 average time/residue: 0.2426 time to fit residues: 205.9996 Evaluate side-chains 487 residues out of total 3714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 387 time to evaluate : 1.406 ------------------------------------------------------------------------------- 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 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 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 692 GLN 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 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 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 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 469 VAL 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 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 701 GLU Chi-restraints excluded: chain E residue 84 MET 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 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 218 GLU 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 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: 0.0670 chunk 215 optimal weight: 6.9990 chunk 375 optimal weight: 30.0000 chunk 323 optimal weight: 10.0000 chunk 70 optimal weight: 30.0000 chunk 221 optimal weight: 4.9990 chunk 392 optimal weight: 6.9990 chunk 39 optimal weight: 5.9990 chunk 148 optimal weight: 3.9990 chunk 45 optimal weight: 10.0000 overall best weight: 4.4126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 285 ASN A 660 ASN ** C 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 285 ASN ** D 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 660 ASN E 285 ASN ** E 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 660 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.147997 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.114998 restraints weight = 58800.451| |-----------------------------------------------------------------------------| r_work (start): 0.3521 rms_B_bonded: 2.51 r_work: 0.3300 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.3300 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8188 moved from start: 0.4170 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= 0.158 Angle : 0.693 7.128 47514 Z= 0.347 Chirality : 0.047 0.153 5352 Planarity : 0.005 0.050 6234 Dihedral : 7.814 118.220 4860 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 9.93 Ramachandran Plot: Outliers : 0.14 % Allowed : 7.55 % Favored : 92.31 % Rotamer: Outliers : 3.90 % Allowed : 13.49 % Favored : 82.61 % 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: -1.59 (0.13), residues: 4344 helix: -0.76 (0.12), residues: 1758 sheet: -1.31 (0.19), residues: 618 loop : -1.10 (0.14), residues: 1968 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 83 TYR 0.015 0.002 TYR D 244 PHE 0.014 0.002 PHE A 516 TRP 0.010 0.001 TRP D 551 HIS 0.006 0.001 HIS B 384 Details of bonding type rmsd/Z covalent geometry : bond 0.00365 / 0.16 (35130) covalent geometry : angle 0.69349 / 0.35 (47514) hydrogen bonds : bond 0.03922 / 2.58 ( 1229) hydrogen bonds : angle 5.18614 / 3.57 ( 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 593 residues out of total 3714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 145 poor density : 448 time to evaluate : 1.471 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 VAL cc_start: 0.5495 (t) cc_final: 0.5136 (m) REVERT: A 66 GLU cc_start: 0.6470 (mp0) cc_final: 0.5723 (pt0) REVERT: A 83 ARG cc_start: 0.6076 (mmt90) cc_final: 0.5644 (mmm-85) REVERT: A 122 THR cc_start: 0.6558 (m) cc_final: 0.6312 (p) REVERT: A 134 TYR cc_start: 0.6180 (m-80) cc_final: 0.5789 (m-10) REVERT: A 239 ARG cc_start: 0.8083 (OUTLIER) cc_final: 0.7667 (ptt-90) REVERT: A 551 TRP cc_start: 0.5262 (t60) cc_final: 0.5035 (t60) REVERT: A 599 ARG cc_start: 0.7924 (ptp90) cc_final: 0.7427 (ttp80) REVERT: A 679 THR cc_start: 0.7929 (OUTLIER) cc_final: 0.7571 (p) REVERT: B 39 VAL cc_start: 0.5552 (t) cc_final: 0.5264 (m) REVERT: B 66 GLU cc_start: 0.6423 (mp0) cc_final: 0.5600 (pt0) REVERT: B 83 ARG cc_start: 0.6195 (mmt90) cc_final: 0.5749 (mmm-85) REVERT: B 93 ARG cc_start: 0.7103 (mmt90) cc_final: 0.6785 (mmt90) REVERT: B 599 ARG cc_start: 0.7901 (ptp90) cc_final: 0.7379 (ttp80) REVERT: C 39 VAL cc_start: 0.5652 (t) cc_final: 0.5375 (m) REVERT: C 83 ARG cc_start: 0.6162 (mmt90) cc_final: 0.5699 (mmm-85) REVERT: C 122 THR cc_start: 0.6623 (m) cc_final: 0.6374 (p) REVERT: C 158 MET cc_start: 0.7783 (mmm) cc_final: 0.7530 (mtt) REVERT: C 365 ARG cc_start: 0.8583 (mmt90) cc_final: 0.8197 (mmt90) REVERT: C 449 MET cc_start: 0.7657 (tpp) cc_final: 0.6693 (ttm) REVERT: C 494 GLN cc_start: 0.8329 (OUTLIER) cc_final: 0.7989 (mm110) REVERT: C 599 ARG cc_start: 0.7915 (ptp-170) cc_final: 0.7292 (ttp80) REVERT: D 39 VAL cc_start: 0.5493 (t) cc_final: 0.5121 (m) REVERT: D 66 GLU cc_start: 0.6408 (mp0) cc_final: 0.5293 (mt-10) REVERT: D 83 ARG cc_start: 0.6076 (mmt90) cc_final: 0.5826 (mmt90) REVERT: D 122 THR cc_start: 0.6525 (m) cc_final: 0.6273 (p) REVERT: D 239 ARG cc_start: 0.8108 (OUTLIER) cc_final: 0.7710 (ptt-90) REVERT: D 551 TRP cc_start: 0.5263 (t60) cc_final: 0.5039 (t60) REVERT: D 599 ARG cc_start: 0.7929 (ptp90) cc_final: 0.7413 (ttp80) REVERT: D 692 GLN cc_start: 0.7650 (OUTLIER) cc_final: 0.7233 (tp40) REVERT: E 39 VAL cc_start: 0.5290 (t) cc_final: 0.4991 (m) REVERT: E 66 GLU cc_start: 0.6423 (mp0) cc_final: 0.5649 (pt0) REVERT: E 83 ARG cc_start: 0.6167 (mmt90) cc_final: 0.5735 (mmm-85) REVERT: E 93 ARG cc_start: 0.7166 (mmt90) cc_final: 0.6755 (mmt90) REVERT: E 599 ARG cc_start: 0.7856 (ptp90) cc_final: 0.7336 (ttp80) REVERT: F 39 VAL cc_start: 0.5485 (t) cc_final: 0.5184 (m) REVERT: F 66 GLU cc_start: 0.6290 (mp0) cc_final: 0.5527 (pt0) REVERT: F 83 ARG cc_start: 0.6224 (mmt90) cc_final: 0.5722 (mmm-85) REVERT: F 122 THR cc_start: 0.6548 (m) cc_final: 0.6268 (p) REVERT: F 158 MET cc_start: 0.7802 (mmm) cc_final: 0.7437 (mtt) REVERT: F 427 MET cc_start: 0.6741 (mmp) cc_final: 0.6401 (mmm) REVERT: F 442 MET cc_start: 0.7157 (mmp) cc_final: 0.6495 (mmt) REVERT: F 494 GLN cc_start: 0.8402 (OUTLIER) cc_final: 0.8189 (mm110) REVERT: F 564 ASP cc_start: 0.7424 (m-30) cc_final: 0.7219 (m-30) REVERT: F 599 ARG cc_start: 0.7897 (ptp-170) cc_final: 0.7295 (ttp80) outliers start: 145 outliers final: 104 residues processed: 552 average time/residue: 0.2365 time to fit residues: 207.4801 Evaluate side-chains 511 residues out of total 3714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 401 time to evaluate : 1.376 ------------------------------------------------------------------------------- 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 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 492 LEU Chi-restraints excluded: chain A residue 501 ASP Chi-restraints excluded: chain A residue 531 ILE Chi-restraints excluded: chain A residue 679 THR Chi-restraints excluded: chain A residue 692 GLN Chi-restraints excluded: chain A residue 701 GLU 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 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 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 582 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 146 ILE Chi-restraints excluded: chain C residue 198 LEU 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 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 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 285 ASN 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 492 LEU Chi-restraints excluded: chain D residue 501 ASP Chi-restraints excluded: chain D residue 531 ILE Chi-restraints excluded: chain D residue 692 GLN Chi-restraints excluded: chain D residue 701 GLU 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 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 427 MET 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 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 E residue 746 SER Chi-restraints excluded: chain F residue 85 ASN Chi-restraints excluded: chain F residue 146 ILE Chi-restraints excluded: chain F residue 198 LEU Chi-restraints excluded: chain F residue 218 GLU 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 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: 2.9990 chunk 76 optimal weight: 0.8980 chunk 361 optimal weight: 20.0000 chunk 394 optimal weight: 2.9990 chunk 327 optimal weight: 10.0000 chunk 312 optimal weight: 20.0000 chunk 181 optimal weight: 4.9990 chunk 32 optimal weight: 9.9990 chunk 279 optimal weight: 20.0000 chunk 178 optimal weight: 10.0000 chunk 3 optimal weight: 0.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 660 ASN ** C 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 660 ASN E 660 ASN F 285 ASN ** F 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.148614 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.116409 restraints weight = 58491.225| |-----------------------------------------------------------------------------| r_work (start): 0.3545 rms_B_bonded: 2.67 r_work: 0.3304 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.3304 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8181 moved from start: 0.4421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 35130 Z= 0.127 Angle : 0.657 7.211 47514 Z= 0.328 Chirality : 0.046 0.151 5352 Planarity : 0.005 0.050 6234 Dihedral : 7.555 114.637 4860 Min Nonbonded Distance : 2.291 Molprobity Statistics. All-atom Clashscore : 9.31 Ramachandran Plot: Outliers : 0.14 % Allowed : 7.69 % Favored : 92.17 % Rotamer: Outliers : 3.69 % Allowed : 14.40 % Favored : 81.91 % 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: -1.43 (0.13), residues: 4344 helix: -0.60 (0.12), residues: 1788 sheet: -1.23 (0.19), residues: 636 loop : -1.02 (0.15), residues: 1920 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 465 TYR 0.015 0.001 TYR A 244 PHE 0.012 0.001 PHE D 152 TRP 0.007 0.001 TRP B 551 HIS 0.007 0.001 HIS C 317 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.13 (35130) covalent geometry : angle 0.65745 / 0.33 (47514) hydrogen bonds : bond 0.03603 / 2.37 ( 1229) hydrogen bonds : angle 5.04699 / 3.48 ( 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 563 residues out of total 3714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 137 poor density : 426 time to evaluate : 1.330 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 VAL cc_start: 0.5284 (t) cc_final: 0.4935 (m) REVERT: A 66 GLU cc_start: 0.6362 (mp0) cc_final: 0.5263 (mt-10) REVERT: A 83 ARG cc_start: 0.5988 (mmt90) cc_final: 0.5573 (mmm-85) REVERT: A 239 ARG cc_start: 0.8098 (OUTLIER) cc_final: 0.7757 (ptt-90) REVERT: A 449 MET cc_start: 0.7747 (tpp) cc_final: 0.6665 (ttm) REVERT: A 561 GLU cc_start: 0.8463 (OUTLIER) cc_final: 0.8241 (mp0) REVERT: A 599 ARG cc_start: 0.7895 (ptp90) cc_final: 0.7412 (ttp80) REVERT: A 679 THR cc_start: 0.7901 (OUTLIER) cc_final: 0.7546 (p) REVERT: B 39 VAL cc_start: 0.5361 (t) cc_final: 0.5088 (m) REVERT: B 66 GLU cc_start: 0.6449 (mp0) cc_final: 0.5335 (mt-10) REVERT: B 83 ARG cc_start: 0.6003 (mmt90) cc_final: 0.5581 (mmm-85) REVERT: B 317 HIS cc_start: 0.4134 (t70) cc_final: 0.3613 (m170) REVERT: B 321 GLU cc_start: 0.7430 (tt0) cc_final: 0.7155 (tt0) REVERT: B 440 GLU cc_start: 0.7225 (tp30) cc_final: 0.7024 (tp30) REVERT: B 494 GLN cc_start: 0.8276 (OUTLIER) cc_final: 0.8076 (mm110) REVERT: B 599 ARG cc_start: 0.7871 (ptp90) cc_final: 0.7214 (ttp80) REVERT: B 661 LEU cc_start: 0.8380 (OUTLIER) cc_final: 0.8174 (pp) REVERT: B 679 THR cc_start: 0.7917 (OUTLIER) cc_final: 0.7504 (p) REVERT: C 39 VAL cc_start: 0.5537 (t) cc_final: 0.5258 (m) REVERT: C 66 GLU cc_start: 0.6468 (mp0) cc_final: 0.5244 (mt-10) REVERT: C 83 ARG cc_start: 0.6078 (mmt90) cc_final: 0.5649 (mmm-85) REVERT: C 122 THR cc_start: 0.6606 (m) cc_final: 0.6357 (p) REVERT: C 158 MET cc_start: 0.7774 (mmm) cc_final: 0.7567 (mtt) REVERT: C 449 MET cc_start: 0.7639 (tpp) cc_final: 0.7268 (tpp) REVERT: C 599 ARG cc_start: 0.7876 (ptp-170) cc_final: 0.7346 (ttp80) REVERT: D 39 VAL cc_start: 0.5343 (t) cc_final: 0.4980 (m) REVERT: D 66 GLU cc_start: 0.6337 (mp0) cc_final: 0.5239 (mt-10) REVERT: D 239 ARG cc_start: 0.8150 (OUTLIER) cc_final: 0.7761 (ptt-90) REVERT: D 449 MET cc_start: 0.7695 (tpp) cc_final: 0.6646 (ttm) REVERT: D 561 GLU cc_start: 0.8479 (OUTLIER) cc_final: 0.8257 (mp0) REVERT: D 599 ARG cc_start: 0.7905 (ptp90) cc_final: 0.7419 (ttp80) REVERT: D 679 THR cc_start: 0.7872 (OUTLIER) cc_final: 0.7449 (p) REVERT: D 692 GLN cc_start: 0.7645 (OUTLIER) cc_final: 0.7363 (mm110) REVERT: E 39 VAL cc_start: 0.5143 (t) cc_final: 0.4867 (m) REVERT: E 66 GLU cc_start: 0.6441 (mp0) cc_final: 0.5315 (mt-10) REVERT: E 83 ARG cc_start: 0.6041 (mmt90) cc_final: 0.5607 (mmm-85) REVERT: E 317 HIS cc_start: 0.4231 (t70) cc_final: 0.3701 (m170) REVERT: E 427 MET cc_start: 0.6061 (OUTLIER) cc_final: 0.5822 (mmp) REVERT: E 599 ARG cc_start: 0.7839 (ptp90) cc_final: 0.7172 (ttp80) REVERT: E 661 LEU cc_start: 0.8381 (OUTLIER) cc_final: 0.8174 (pp) REVERT: E 679 THR cc_start: 0.7908 (OUTLIER) cc_final: 0.7485 (p) REVERT: F 39 VAL cc_start: 0.5492 (t) cc_final: 0.5231 (m) REVERT: F 66 GLU cc_start: 0.6268 (mp0) cc_final: 0.5182 (mt-10) REVERT: F 83 ARG cc_start: 0.6117 (mmt90) cc_final: 0.5674 (mmm-85) REVERT: F 122 THR cc_start: 0.6520 (OUTLIER) cc_final: 0.6256 (p) REVERT: F 321 GLU cc_start: 0.7482 (tt0) cc_final: 0.7262 (tt0) REVERT: F 427 MET cc_start: 0.6803 (mmp) cc_final: 0.6420 (mmm) REVERT: F 449 MET cc_start: 0.7725 (tpp) cc_final: 0.6543 (ttm) REVERT: F 494 GLN cc_start: 0.8378 (OUTLIER) cc_final: 0.8137 (mm110) REVERT: F 599 ARG cc_start: 0.7883 (ptp-170) cc_final: 0.7363 (ttp80) REVERT: F 679 THR cc_start: 0.7873 (OUTLIER) cc_final: 0.7441 (p) outliers start: 137 outliers final: 97 residues processed: 521 average time/residue: 0.2355 time to fit residues: 194.8198 Evaluate side-chains 516 residues out of total 3714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 403 time to evaluate : 1.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 LEU 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 492 LEU Chi-restraints excluded: chain A residue 501 ASP Chi-restraints excluded: chain A residue 531 ILE Chi-restraints excluded: chain A residue 561 GLU Chi-restraints excluded: chain A residue 582 ILE 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 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 378 LEU 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 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 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 123 VAL Chi-restraints excluded: chain C residue 198 LEU Chi-restraints excluded: chain C residue 427 MET 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 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 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 492 LEU Chi-restraints excluded: chain D residue 501 ASP Chi-restraints excluded: chain D residue 531 ILE Chi-restraints excluded: chain D residue 561 GLU Chi-restraints excluded: chain D residue 582 ILE 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 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 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 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 123 VAL Chi-restraints excluded: chain F residue 218 GLU 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: 1.9990 chunk 260 optimal weight: 6.9990 chunk 212 optimal weight: 6.9990 chunk 150 optimal weight: 9.9990 chunk 217 optimal weight: 20.0000 chunk 120 optimal weight: 10.0000 chunk 171 optimal weight: 10.0000 chunk 149 optimal weight: 5.9990 chunk 73 optimal weight: 20.0000 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 285 ASN ** F 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.146536 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.113629 restraints weight = 58864.307| |-----------------------------------------------------------------------------| r_work (start): 0.3508 rms_B_bonded: 2.45 r_work: 0.3283 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.3283 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 moved from start: 0.4428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 35130 Z= 0.198 Angle : 0.723 8.801 47514 Z= 0.360 Chirality : 0.049 0.158 5352 Planarity : 0.006 0.081 6234 Dihedral : 7.836 119.866 4860 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 9.78 Ramachandran Plot: Outliers : 0.28 % Allowed : 8.13 % Favored : 91.60 % Rotamer: Outliers : 4.33 % Allowed : 14.46 % Favored : 81.21 % 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: -1.49 (0.13), residues: 4344 helix: -0.68 (0.12), residues: 1782 sheet: -1.14 (0.20), residues: 618 loop : -1.07 (0.14), residues: 1944 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG F 465 TYR 0.016 0.002 TYR E 138 PHE 0.017 0.002 PHE A 576 TRP 0.014 0.002 TRP D 551 HIS 0.007 0.002 HIS B 384 Details of bonding type rmsd/Z covalent geometry : bond 0.00467 / 0.20 (35130) covalent geometry : angle 0.72301 / 0.36 (47514) hydrogen bonds : bond 0.04083 / 2.68 ( 1229) hydrogen bonds : angle 5.21382 / 3.59 ( 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 566 residues out of total 3714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 161 poor density : 405 time to evaluate : 1.696 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: 0.5429 (t) cc_final: 0.5070 (m) REVERT: A 66 GLU cc_start: 0.6376 (mp0) cc_final: 0.5264 (mt-10) REVERT: A 83 ARG cc_start: 0.6029 (mmt90) cc_final: 0.5571 (mmm-85) REVERT: A 239 ARG cc_start: 0.8176 (OUTLIER) cc_final: 0.7807 (ptt-90) REVERT: A 449 MET cc_start: 0.7778 (tpp) cc_final: 0.6741 (ttm) REVERT: A 561 GLU cc_start: 0.8454 (OUTLIER) cc_final: 0.8183 (mp0) REVERT: A 599 ARG cc_start: 0.7666 (ptp90) cc_final: 0.7229 (ptt90) REVERT: A 679 THR cc_start: 0.7912 (OUTLIER) cc_final: 0.7542 (p) REVERT: B 39 VAL cc_start: 0.5326 (t) cc_final: 0.5023 (m) REVERT: B 65 ARG cc_start: 0.5117 (ttp-170) cc_final: 0.4873 (ttp-170) REVERT: B 66 GLU cc_start: 0.6338 (mp0) cc_final: 0.5590 (pt0) REVERT: B 83 ARG cc_start: 0.6021 (mmt90) cc_final: 0.5547 (mmm-85) REVERT: B 122 THR cc_start: 0.6576 (m) cc_final: 0.6356 (p) REVERT: B 317 HIS cc_start: 0.4002 (t70) cc_final: 0.3758 (m-70) REVERT: B 427 MET cc_start: 0.6802 (mmp) cc_final: 0.6495 (mmm) REVERT: B 449 MET cc_start: 0.7618 (tpp) cc_final: 0.7283 (tpp) REVERT: B 494 GLN cc_start: 0.8286 (OUTLIER) cc_final: 0.8081 (mm110) REVERT: B 599 ARG cc_start: 0.7929 (ptp90) cc_final: 0.7352 (ttp80) REVERT: B 661 LEU cc_start: 0.8442 (OUTLIER) cc_final: 0.8219 (pp) REVERT: B 679 THR cc_start: 0.7979 (OUTLIER) cc_final: 0.7549 (p) REVERT: C 39 VAL cc_start: 0.5572 (t) cc_final: 0.5290 (m) REVERT: C 66 GLU cc_start: 0.6497 (mp0) cc_final: 0.5667 (pt0) REVERT: C 83 ARG cc_start: 0.6033 (mmt90) cc_final: 0.5532 (mmm-85) REVERT: C 122 THR cc_start: 0.6601 (OUTLIER) cc_final: 0.6364 (p) REVERT: C 158 MET cc_start: 0.7932 (mmm) cc_final: 0.7679 (mtt) REVERT: C 449 MET cc_start: 0.7762 (tpp) cc_final: 0.7247 (tpp) REVERT: C 494 GLN cc_start: 0.8327 (OUTLIER) cc_final: 0.7937 (mm110) REVERT: C 599 ARG cc_start: 0.7941 (ptp-170) cc_final: 0.7511 (ttp80) REVERT: C 679 THR cc_start: 0.7906 (OUTLIER) cc_final: 0.7468 (p) REVERT: D 39 VAL cc_start: 0.5441 (t) cc_final: 0.5086 (m) REVERT: D 66 GLU cc_start: 0.6311 (mp0) cc_final: 0.5297 (mt-10) REVERT: D 83 ARG cc_start: 0.5918 (mmt90) cc_final: 0.5515 (mmm-85) REVERT: D 239 ARG cc_start: 0.8188 (OUTLIER) cc_final: 0.7841 (ptt-90) REVERT: D 449 MET cc_start: 0.7747 (tpp) cc_final: 0.6728 (ttm) REVERT: D 561 GLU cc_start: 0.8459 (OUTLIER) cc_final: 0.8203 (mp0) REVERT: D 599 ARG cc_start: 0.7653 (ptp90) cc_final: 0.7203 (ptt90) REVERT: D 679 THR cc_start: 0.7942 (OUTLIER) cc_final: 0.7518 (p) REVERT: D 692 GLN cc_start: 0.7652 (OUTLIER) cc_final: 0.7181 (tp40) REVERT: E 39 VAL cc_start: 0.5218 (t) cc_final: 0.4941 (m) REVERT: E 65 ARG cc_start: 0.5125 (ttp-170) cc_final: 0.4894 (ttp-170) REVERT: E 66 GLU cc_start: 0.6370 (mp0) cc_final: 0.5637 (pt0) REVERT: E 83 ARG cc_start: 0.6026 (mmt90) cc_final: 0.5529 (mmm-85) REVERT: E 122 THR cc_start: 0.6575 (m) cc_final: 0.6346 (p) REVERT: E 317 HIS cc_start: 0.4021 (t70) cc_final: 0.3784 (m-70) REVERT: E 449 MET cc_start: 0.7585 (tpp) cc_final: 0.7260 (tpp) REVERT: E 599 ARG cc_start: 0.7900 (ptp90) cc_final: 0.7316 (ttp80) REVERT: E 661 LEU cc_start: 0.8439 (OUTLIER) cc_final: 0.8212 (pp) REVERT: E 679 THR cc_start: 0.7990 (OUTLIER) cc_final: 0.7570 (p) REVERT: F 39 VAL cc_start: 0.5450 (t) cc_final: 0.5188 (m) REVERT: F 66 GLU cc_start: 0.6287 (mp0) cc_final: 0.5661 (pt0) REVERT: F 122 THR cc_start: 0.6559 (OUTLIER) cc_final: 0.6293 (p) REVERT: F 427 MET cc_start: 0.6825 (mmp) cc_final: 0.6424 (mmm) REVERT: F 449 MET cc_start: 0.7726 (tpp) cc_final: 0.6593 (ttm) REVERT: F 494 GLN cc_start: 0.8392 (OUTLIER) cc_final: 0.8158 (mm110) REVERT: F 599 ARG cc_start: 0.7958 (ptp-170) cc_final: 0.7550 (ttp80) REVERT: F 679 THR cc_start: 0.7930 (OUTLIER) cc_final: 0.7479 (p) outliers start: 161 outliers final: 118 residues processed: 513 average time/residue: 0.2452 time to fit residues: 200.4597 Evaluate side-chains 527 residues out of total 3714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 136 poor density : 391 time to evaluate : 1.388 ------------------------------------------------------------------------------- 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 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 479 ILE Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 531 ILE Chi-restraints excluded: chain A residue 561 GLU 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 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 378 LEU 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 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 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 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 479 ILE Chi-restraints excluded: chain D residue 492 LEU Chi-restraints excluded: chain D residue 531 ILE Chi-restraints excluded: chain D residue 561 GLU 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 701 GLU 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 342 ILE Chi-restraints excluded: chain E residue 371 ILE 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 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 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 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 508 MET Chi-restraints excluded: chain F residue 531 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: 5.9990 chunk 212 optimal weight: 10.0000 chunk 40 optimal weight: 8.9990 chunk 232 optimal weight: 7.9990 chunk 76 optimal weight: 7.9990 chunk 327 optimal weight: 6.9990 chunk 66 optimal weight: 5.9990 chunk 79 optimal weight: 8.9990 chunk 395 optimal weight: 6.9990 chunk 30 optimal weight: 3.9990 chunk 80 optimal weight: 1.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3976 r_free = 0.3976 target = 0.147033 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.114433 restraints weight = 58736.650| |-----------------------------------------------------------------------------| r_work (start): 0.3520 rms_B_bonded: 2.59 r_work: 0.3291 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.3291 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8202 moved from start: 0.4564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 35130 Z= 0.166 Angle : 0.689 7.985 47514 Z= 0.344 Chirality : 0.047 0.175 5352 Planarity : 0.005 0.050 6234 Dihedral : 7.723 117.982 4860 Min Nonbonded Distance : 2.308 Molprobity Statistics. All-atom Clashscore : 9.58 Ramachandran Plot: Outliers : 0.28 % Allowed : 7.60 % Favored : 92.13 % Rotamer: Outliers : 4.15 % Allowed : 15.24 % Favored : 80.61 % 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: -1.43 (0.12), residues: 4344 helix: -0.58 (0.12), residues: 1788 sheet: -1.10 (0.20), residues: 618 loop : -1.11 (0.14), residues: 1938 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG F 83 TYR 0.015 0.002 TYR E 138 PHE 0.013 0.002 PHE A 516 TRP 0.010 0.001 TRP E 551 HIS 0.006 0.001 HIS B 384 Details of bonding type rmsd/Z covalent geometry : bond 0.00390 / 0.17 (35130) covalent geometry : angle 0.68924 / 0.34 (47514) hydrogen bonds : bond 0.03780 / 2.48 ( 1229) hydrogen bonds : angle 5.14359 / 3.54 ( 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 571 residues out of total 3714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 154 poor density : 417 time to evaluate : 1.643 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: 0.5339 (t) cc_final: 0.4994 (m) REVERT: A 66 GLU cc_start: 0.6394 (mp0) cc_final: 0.5733 (pt0) REVERT: A 83 ARG cc_start: 0.6005 (mmt90) cc_final: 0.5581 (mmm-85) REVERT: A 239 ARG cc_start: 0.8174 (OUTLIER) cc_final: 0.7880 (ptt-90) REVERT: A 449 MET cc_start: 0.7749 (tpp) cc_final: 0.6763 (ttm) REVERT: A 550 MET cc_start: 0.5628 (ptt) cc_final: 0.4800 (mtp) REVERT: A 599 ARG cc_start: 0.7760 (ptp90) cc_final: 0.7245 (ttp80) REVERT: A 679 THR cc_start: 0.7889 (OUTLIER) cc_final: 0.7511 (p) REVERT: B 39 VAL cc_start: 0.5282 (t) cc_final: 0.4991 (m) REVERT: B 66 GLU cc_start: 0.6294 (mp0) cc_final: 0.5988 (mm-30) REVERT: B 83 ARG cc_start: 0.6077 (mmt90) cc_final: 0.5605 (mmm-85) REVERT: B 122 THR cc_start: 0.6557 (m) cc_final: 0.6339 (p) REVERT: B 427 MET cc_start: 0.6871 (mmp) cc_final: 0.6504 (mmm) REVERT: B 442 MET cc_start: 0.7359 (mmp) cc_final: 0.6679 (mmt) REVERT: B 449 MET cc_start: 0.7582 (tpp) cc_final: 0.7242 (tpp) REVERT: B 546 GLU cc_start: 0.8237 (tm-30) cc_final: 0.8001 (tp30) REVERT: B 560 ARG cc_start: 0.7803 (mtp180) cc_final: 0.7158 (mtp180) REVERT: B 599 ARG cc_start: 0.7910 (ptp90) cc_final: 0.7321 (ttp80) REVERT: C 39 VAL cc_start: 0.5477 (t) cc_final: 0.5201 (m) REVERT: C 66 GLU cc_start: 0.6484 (mp0) cc_final: 0.5279 (mt-10) REVERT: C 83 ARG cc_start: 0.6048 (mmt90) cc_final: 0.5564 (mmm-85) REVERT: C 122 THR cc_start: 0.6572 (OUTLIER) cc_final: 0.6348 (p) REVERT: C 158 MET cc_start: 0.7917 (mmm) cc_final: 0.7684 (mtt) REVERT: C 285 ASN cc_start: 0.7900 (OUTLIER) cc_final: 0.7552 (m-40) REVERT: C 449 MET cc_start: 0.7733 (tpp) cc_final: 0.7250 (tpp) REVERT: C 494 GLN cc_start: 0.8329 (OUTLIER) cc_final: 0.7967 (mm110) REVERT: C 599 ARG cc_start: 0.7904 (ptp-170) cc_final: 0.7448 (ttp80) REVERT: C 679 THR cc_start: 0.7874 (OUTLIER) cc_final: 0.7425 (p) REVERT: D 39 VAL cc_start: 0.5373 (t) cc_final: 0.5023 (m) REVERT: D 66 GLU cc_start: 0.6345 (mp0) cc_final: 0.5773 (pt0) REVERT: D 83 ARG cc_start: 0.6072 (mmt90) cc_final: 0.5689 (mmm-85) REVERT: D 239 ARG cc_start: 0.8207 (OUTLIER) cc_final: 0.7861 (ptt-90) REVERT: D 449 MET cc_start: 0.7681 (tpp) cc_final: 0.6723 (ttm) REVERT: D 550 MET cc_start: 0.5599 (ptt) cc_final: 0.4768 (mtp) REVERT: D 599 ARG cc_start: 0.7752 (ptp90) cc_final: 0.7233 (ttp80) REVERT: D 679 THR cc_start: 0.7876 (OUTLIER) cc_final: 0.7442 (p) REVERT: D 692 GLN cc_start: 0.7652 (OUTLIER) cc_final: 0.7176 (tp40) REVERT: E 39 VAL cc_start: 0.5194 (t) cc_final: 0.4920 (m) REVERT: E 66 GLU cc_start: 0.6322 (mp0) cc_final: 0.6026 (mm-30) REVERT: E 83 ARG cc_start: 0.6036 (mmt90) cc_final: 0.5571 (mmm-85) REVERT: E 122 THR cc_start: 0.6594 (m) cc_final: 0.6361 (p) REVERT: E 317 HIS cc_start: 0.4113 (t70) cc_final: 0.3854 (m170) REVERT: E 449 MET cc_start: 0.7571 (tpp) cc_final: 0.7234 (tpp) REVERT: E 599 ARG cc_start: 0.7890 (ptp90) cc_final: 0.7312 (ttp80) REVERT: E 679 THR cc_start: 0.7961 (OUTLIER) cc_final: 0.7512 (p) REVERT: F 39 VAL cc_start: 0.5419 (t) cc_final: 0.5158 (m) REVERT: F 122 THR cc_start: 0.6525 (OUTLIER) cc_final: 0.6252 (p) REVERT: F 427 MET cc_start: 0.6781 (mmp) cc_final: 0.6334 (mmm) REVERT: F 449 MET cc_start: 0.7796 (tpp) cc_final: 0.6617 (ttm) REVERT: F 494 GLN cc_start: 0.8379 (OUTLIER) cc_final: 0.8144 (mm110) REVERT: F 599 ARG cc_start: 0.7948 (ptp-170) cc_final: 0.7493 (ttp80) REVERT: F 679 THR cc_start: 0.7893 (OUTLIER) cc_final: 0.7428 (p) outliers start: 154 outliers final: 112 residues processed: 517 average time/residue: 0.2340 time to fit residues: 192.3827 Evaluate side-chains 527 residues out of total 3714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 125 poor density : 402 time to evaluate : 0.932 ------------------------------------------------------------------------------- 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 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 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 679 THR Chi-restraints excluded: chain A residue 731 ILE Chi-restraints excluded: chain A residue 746 SER 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 378 LEU 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 582 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 285 ASN 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 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 479 ILE 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 582 ILE 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 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 427 MET 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 582 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 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 508 MET Chi-restraints excluded: chain F residue 531 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 277 optimal weight: 6.9990 chunk 266 optimal weight: 8.9990 chunk 40 optimal weight: 5.9990 chunk 9 optimal weight: 8.9990 chunk 365 optimal weight: 30.0000 chunk 281 optimal weight: 9.9990 chunk 87 optimal weight: 30.0000 chunk 191 optimal weight: 5.9990 chunk 412 optimal weight: 0.9980 chunk 45 optimal weight: 10.0000 chunk 415 optimal weight: 0.9990 overall best weight: 4.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 285 ASN F 285 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.147294 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.114570 restraints weight = 58563.423| |-----------------------------------------------------------------------------| r_work (start): 0.3522 rms_B_bonded: 2.54 r_work: 0.3296 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.3296 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8197 moved from start: 0.4659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 35130 Z= 0.152 Angle : 0.681 7.631 47514 Z= 0.339 Chirality : 0.047 0.163 5352 Planarity : 0.005 0.049 6234 Dihedral : 7.618 116.378 4860 Min Nonbonded Distance : 2.310 Molprobity Statistics. All-atom Clashscore : 9.48 Ramachandran Plot: Outliers : 0.28 % Allowed : 7.97 % Favored : 91.76 % Rotamer: Outliers : 3.55 % Allowed : 16.34 % Favored : 80.10 % 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: -1.35 (0.13), residues: 4344 helix: -0.50 (0.12), residues: 1788 sheet: -1.05 (0.20), residues: 618 loop : -1.08 (0.14), residues: 1938 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 287 TYR 0.015 0.002 TYR E 138 PHE 0.013 0.002 PHE C 152 TRP 0.011 0.001 TRP B 551 HIS 0.006 0.001 HIS D 317 Details of bonding type rmsd/Z covalent geometry : bond 0.00353 / 0.15 (35130) covalent geometry : angle 0.68083 / 0.34 (47514) hydrogen bonds : bond 0.03665 / 2.41 ( 1229) hydrogen bonds : angle 5.08969 / 3.51 ( 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 542 residues out of total 3714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 132 poor density : 410 time to evaluate : 1.342 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 VAL cc_start: 0.5306 (t) cc_final: 0.4971 (m) REVERT: A 66 GLU cc_start: 0.6333 (mp0) cc_final: 0.5785 (pt0) REVERT: A 83 ARG cc_start: 0.5993 (mmt90) cc_final: 0.5581 (mmm-85) REVERT: A 239 ARG cc_start: 0.8208 (OUTLIER) cc_final: 0.7912 (ptt-90) REVERT: A 449 MET cc_start: 0.7742 (tpp) cc_final: 0.6766 (ttm) REVERT: A 550 MET cc_start: 0.5434 (ptt) cc_final: 0.4889 (mtp) REVERT: A 599 ARG cc_start: 0.7742 (ptp90) cc_final: 0.7236 (ttp80) REVERT: A 679 THR cc_start: 0.7888 (OUTLIER) cc_final: 0.7497 (p) REVERT: B 39 VAL cc_start: 0.5367 (t) cc_final: 0.5089 (m) REVERT: B 65 ARG cc_start: 0.5204 (ttp-170) cc_final: 0.4752 (ttp-170) REVERT: B 66 GLU cc_start: 0.6302 (mp0) cc_final: 0.5685 (pt0) REVERT: B 83 ARG cc_start: 0.6114 (mmt90) cc_final: 0.5643 (mmm-85) REVERT: B 122 THR cc_start: 0.6552 (m) cc_final: 0.6339 (p) REVERT: B 427 MET cc_start: 0.6758 (mmp) cc_final: 0.6376 (mmm) REVERT: B 449 MET cc_start: 0.7556 (tpp) cc_final: 0.7204 (tpp) REVERT: B 560 ARG cc_start: 0.7823 (mtp180) cc_final: 0.7137 (mtp180) REVERT: B 599 ARG cc_start: 0.7918 (ptp90) cc_final: 0.7348 (ttp80) REVERT: C 39 VAL cc_start: 0.5472 (t) cc_final: 0.5196 (m) REVERT: C 66 GLU cc_start: 0.6440 (mp0) cc_final: 0.5767 (pt0) REVERT: C 83 ARG cc_start: 0.6087 (mmt90) cc_final: 0.5618 (mmm-85) REVERT: C 122 THR cc_start: 0.6553 (OUTLIER) cc_final: 0.6329 (p) REVERT: C 158 MET cc_start: 0.7942 (mmm) cc_final: 0.7719 (mtt) REVERT: C 449 MET cc_start: 0.7695 (tpp) cc_final: 0.7226 (tpp) REVERT: C 494 GLN cc_start: 0.8328 (OUTLIER) cc_final: 0.7953 (mm110) REVERT: C 560 ARG cc_start: 0.7882 (mtp180) cc_final: 0.7174 (mtp180) REVERT: C 599 ARG cc_start: 0.7916 (ptp-170) cc_final: 0.7435 (ttp80) REVERT: C 679 THR cc_start: 0.7888 (OUTLIER) cc_final: 0.7421 (p) REVERT: D 39 VAL cc_start: 0.5309 (t) cc_final: 0.4977 (m) REVERT: D 66 GLU cc_start: 0.6328 (mp0) cc_final: 0.5803 (pt0) REVERT: D 83 ARG cc_start: 0.6058 (mmt90) cc_final: 0.5679 (mmm-85) REVERT: D 239 ARG cc_start: 0.8215 (OUTLIER) cc_final: 0.7883 (ptt-90) REVERT: D 449 MET cc_start: 0.7699 (tpp) cc_final: 0.6744 (ttm) REVERT: D 550 MET cc_start: 0.5430 (ptt) cc_final: 0.4901 (mtp) REVERT: D 599 ARG cc_start: 0.7730 (ptp90) cc_final: 0.7220 (ttp80) REVERT: D 679 THR cc_start: 0.7871 (OUTLIER) cc_final: 0.7430 (p) REVERT: D 692 GLN cc_start: 0.7643 (OUTLIER) cc_final: 0.7371 (mm110) REVERT: E 39 VAL cc_start: 0.5149 (t) cc_final: 0.4880 (m) REVERT: E 65 ARG cc_start: 0.5179 (ttp-170) cc_final: 0.4740 (ttp-170) REVERT: E 66 GLU cc_start: 0.6317 (mp0) cc_final: 0.5707 (pt0) REVERT: E 83 ARG cc_start: 0.6030 (mmt90) cc_final: 0.5587 (mmm-85) REVERT: E 122 THR cc_start: 0.6555 (m) cc_final: 0.6319 (p) REVERT: E 449 MET cc_start: 0.7549 (tpp) cc_final: 0.7200 (tpp) REVERT: E 560 ARG cc_start: 0.7870 (mtp180) cc_final: 0.7166 (mtp180) REVERT: E 599 ARG cc_start: 0.7902 (ptp90) cc_final: 0.7332 (ttp80) REVERT: F 39 VAL cc_start: 0.5398 (t) cc_final: 0.5124 (m) REVERT: F 66 GLU cc_start: 0.6264 (mp0) cc_final: 0.5882 (mm-30) REVERT: F 122 THR cc_start: 0.6539 (OUTLIER) cc_final: 0.6270 (p) REVERT: F 427 MET cc_start: 0.6807 (mmp) cc_final: 0.6356 (mmm) REVERT: F 449 MET cc_start: 0.7789 (tpp) cc_final: 0.6617 (ttm) REVERT: F 494 GLN cc_start: 0.8373 (OUTLIER) cc_final: 0.8138 (mm110) REVERT: F 560 ARG cc_start: 0.7917 (mtp180) cc_final: 0.7193 (mtp180) REVERT: F 599 ARG cc_start: 0.7915 (ptp-170) cc_final: 0.7446 (ttp80) outliers start: 132 outliers final: 107 residues processed: 494 average time/residue: 0.2524 time to fit residues: 196.2039 Evaluate side-chains 523 residues out of total 3714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 406 time to evaluate : 1.401 ------------------------------------------------------------------------------- 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 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 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 492 LEU Chi-restraints excluded: chain A residue 531 ILE Chi-restraints excluded: chain A residue 582 ILE 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 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 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 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 582 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 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 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 492 LEU Chi-restraints excluded: chain D residue 501 ASP Chi-restraints excluded: chain D residue 531 ILE Chi-restraints excluded: chain D residue 582 ILE 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 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 427 MET 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 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 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 285 ASN 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 508 MET 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 164 optimal weight: 7.9990 chunk 409 optimal weight: 4.9990 chunk 103 optimal weight: 8.9990 chunk 50 optimal weight: 6.9990 chunk 186 optimal weight: 30.0000 chunk 258 optimal weight: 7.9990 chunk 256 optimal weight: 9.9990 chunk 349 optimal weight: 8.9990 chunk 407 optimal weight: 5.9990 chunk 200 optimal weight: 30.0000 chunk 314 optimal weight: 9.9990 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 285 ASN C 384 HIS ** D 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 285 ASN ** E 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 285 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.145915 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.113420 restraints weight = 58709.188| |-----------------------------------------------------------------------------| r_work (start): 0.3502 rms_B_bonded: 2.55 r_work: 0.3276 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.3276 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8220 moved from start: 0.4646 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= 0.208 Angle : 0.737 7.601 47514 Z= 0.368 Chirality : 0.049 0.179 5352 Planarity : 0.006 0.051 6234 Dihedral : 7.865 120.519 4860 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 10.01 Ramachandran Plot: Outliers : 0.28 % Allowed : 8.10 % Favored : 91.62 % Rotamer: Outliers : 3.82 % Allowed : 16.07 % Favored : 80.10 % 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 (0.12), residues: 4344 helix: -0.63 (0.12), residues: 1782 sheet: -1.14 (0.20), residues: 618 loop : -1.15 (0.14), residues: 1944 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 586 TYR 0.018 0.002 TYR E 138 PHE 0.018 0.002 PHE D 576 TRP 0.011 0.002 TRP D 551 HIS 0.009 0.002 HIS E 317 Details of bonding type rmsd/Z covalent geometry : bond 0.00492 / 0.21 (35130) covalent geometry : angle 0.73700 / 0.37 (47514) hydrogen bonds : bond 0.04056 / 2.65 ( 1229) hydrogen bonds : angle 5.23778 / 3.61 ( 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 551 residues out of total 3714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 142 poor density : 409 time to evaluate : 1.416 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 VAL cc_start: 0.5400 (t) cc_final: 0.5045 (m) REVERT: A 66 GLU cc_start: 0.6290 (mp0) cc_final: 0.5700 (pt0) REVERT: A 239 ARG cc_start: 0.8228 (OUTLIER) cc_final: 0.7920 (ptt-90) REVERT: A 449 MET cc_start: 0.7770 (tpp) cc_final: 0.6812 (ttm) REVERT: A 550 MET cc_start: 0.5601 (ptt) cc_final: 0.4867 (mtp) REVERT: A 560 ARG cc_start: 0.7815 (mtp180) cc_final: 0.7211 (mtp180) REVERT: A 599 ARG cc_start: 0.7904 (ptp90) cc_final: 0.7415 (ttp80) REVERT: A 679 THR cc_start: 0.7924 (OUTLIER) cc_final: 0.7535 (p) REVERT: B 39 VAL cc_start: 0.5362 (t) cc_final: 0.5064 (m) REVERT: B 65 ARG cc_start: 0.5272 (ttp-170) cc_final: 0.4827 (ttp-170) REVERT: B 66 GLU cc_start: 0.6250 (mp0) cc_final: 0.5666 (pt0) REVERT: B 83 ARG cc_start: 0.6091 (mmt90) cc_final: 0.5752 (mmm-85) REVERT: B 122 THR cc_start: 0.6563 (m) cc_final: 0.6326 (p) REVERT: B 321 GLU cc_start: 0.7498 (tt0) cc_final: 0.7159 (tt0) REVERT: B 427 MET cc_start: 0.6804 (mmp) cc_final: 0.6406 (mmm) REVERT: B 442 MET cc_start: 0.7242 (mmt) cc_final: 0.6679 (mmt) REVERT: B 449 MET cc_start: 0.7589 (tpp) cc_final: 0.7241 (tpp) REVERT: B 546 GLU cc_start: 0.8264 (tm-30) cc_final: 0.8033 (tp30) REVERT: B 550 MET cc_start: 0.6935 (ptp) cc_final: 0.6708 (ptp) REVERT: B 560 ARG cc_start: 0.7878 (mtp180) cc_final: 0.7233 (mtp180) REVERT: B 599 ARG cc_start: 0.7958 (ptp90) cc_final: 0.7524 (ttp80) REVERT: C 39 VAL cc_start: 0.5512 (t) cc_final: 0.5228 (m) REVERT: C 66 GLU cc_start: 0.6498 (mp0) cc_final: 0.5778 (pt0) REVERT: C 122 THR cc_start: 0.6609 (OUTLIER) cc_final: 0.6404 (p) REVERT: C 158 MET cc_start: 0.8022 (mmm) cc_final: 0.7721 (mtt) REVERT: C 449 MET cc_start: 0.7654 (tpp) cc_final: 0.7153 (tpp) REVERT: C 492 LEU cc_start: 0.9086 (OUTLIER) cc_final: 0.8870 (mp) REVERT: C 494 GLN cc_start: 0.8335 (OUTLIER) cc_final: 0.7963 (mm110) REVERT: C 560 ARG cc_start: 0.7900 (mtp180) cc_final: 0.7242 (mtp180) REVERT: C 599 ARG cc_start: 0.7923 (ptp-170) cc_final: 0.7482 (ttp80) REVERT: D 39 VAL cc_start: 0.5429 (t) cc_final: 0.5067 (m) REVERT: D 66 GLU cc_start: 0.6341 (mp0) cc_final: 0.5781 (pt0) REVERT: D 83 ARG cc_start: 0.6124 (mmt90) cc_final: 0.5707 (mmm-85) REVERT: D 239 ARG cc_start: 0.8206 (OUTLIER) cc_final: 0.7918 (ptt-90) REVERT: D 449 MET cc_start: 0.7703 (tpp) cc_final: 0.6769 (ttm) REVERT: D 550 MET cc_start: 0.5551 (ptt) cc_final: 0.4835 (mtp) REVERT: D 560 ARG cc_start: 0.7825 (mtp180) cc_final: 0.7203 (mtp180) REVERT: D 599 ARG cc_start: 0.7891 (ptp90) cc_final: 0.7400 (ttp80) REVERT: D 679 THR cc_start: 0.7944 (OUTLIER) cc_final: 0.7509 (p) REVERT: D 692 GLN cc_start: 0.7674 (OUTLIER) cc_final: 0.7199 (tp40) REVERT: E 36 ASN cc_start: 0.6281 (t0) cc_final: 0.6057 (t0) REVERT: E 39 VAL cc_start: 0.5243 (t) cc_final: 0.4985 (m) REVERT: E 65 ARG cc_start: 0.5238 (ttp-170) cc_final: 0.4790 (ttp-170) REVERT: E 66 GLU cc_start: 0.6336 (mp0) cc_final: 0.5728 (pt0) REVERT: E 83 ARG cc_start: 0.6052 (mmt90) cc_final: 0.5710 (mmm-85) REVERT: E 122 THR cc_start: 0.6579 (m) cc_final: 0.6342 (p) REVERT: E 449 MET cc_start: 0.7550 (tpp) cc_final: 0.7201 (tpp) REVERT: E 546 GLU cc_start: 0.8258 (tm-30) cc_final: 0.8045 (tp30) REVERT: E 560 ARG cc_start: 0.7888 (mtp180) cc_final: 0.7195 (mtp180) REVERT: E 599 ARG cc_start: 0.7944 (ptp90) cc_final: 0.7512 (ttp80) REVERT: F 39 VAL cc_start: 0.5382 (t) cc_final: 0.5090 (m) REVERT: F 66 GLU cc_start: 0.6335 (mp0) cc_final: 0.5883 (mm-30) REVERT: F 122 THR cc_start: 0.6592 (OUTLIER) cc_final: 0.6308 (p) REVERT: F 427 MET cc_start: 0.6855 (mmp) cc_final: 0.6382 (mmm) REVERT: F 449 MET cc_start: 0.7794 (tpp) cc_final: 0.6682 (ttm) REVERT: F 492 LEU cc_start: 0.9069 (OUTLIER) cc_final: 0.8854 (mp) REVERT: F 494 GLN cc_start: 0.8396 (OUTLIER) cc_final: 0.8182 (mm110) REVERT: F 560 ARG cc_start: 0.7952 (mtp180) cc_final: 0.7234 (mtp180) REVERT: F 599 ARG cc_start: 0.7971 (ptp-170) cc_final: 0.7498 (ttp80) outliers start: 142 outliers final: 116 residues processed: 504 average time/residue: 0.2439 time to fit residues: 193.5366 Evaluate side-chains 531 residues out of total 3714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 127 poor density : 404 time to evaluate : 1.404 ------------------------------------------------------------------------------- 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 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 479 ILE 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 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 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 342 ILE Chi-restraints excluded: chain B residue 371 ILE 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 504 LEU 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 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 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 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 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 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 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 531 ILE Chi-restraints excluded: chain D residue 582 ILE 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 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 291 GLU Chi-restraints excluded: chain E residue 342 ILE Chi-restraints excluded: chain E residue 371 ILE 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 471 VAL 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 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 E residue 746 SER Chi-restraints excluded: chain E residue 747 VAL 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 285 ASN 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 508 MET 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: 8.9990 chunk 119 optimal weight: 1.9990 chunk 370 optimal weight: 0.1980 chunk 381 optimal weight: 0.0170 chunk 265 optimal weight: 3.9990 chunk 167 optimal weight: 5.9990 chunk 143 optimal weight: 10.0000 chunk 4 optimal weight: 9.9990 chunk 145 optimal weight: 20.0000 chunk 423 optimal weight: 9.9990 overall best weight: 2.4424 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 285 ASN E 285 ASN ** F 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.148111 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.115644 restraints weight = 58549.571| |-----------------------------------------------------------------------------| r_work (start): 0.3534 rms_B_bonded: 2.66 r_work: 0.3309 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.3309 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8180 moved from start: 0.4837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 35130 Z= 0.123 Angle : 0.659 7.092 47514 Z= 0.328 Chirality : 0.046 0.152 5352 Planarity : 0.005 0.051 6234 Dihedral : 7.495 113.852 4860 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 9.06 Ramachandran Plot: Outliers : 0.28 % Allowed : 6.93 % Favored : 92.79 % Rotamer: Outliers : 2.88 % Allowed : 17.15 % Favored : 79.97 % 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: -1.27 (0.13), residues: 4344 helix: -0.35 (0.13), residues: 1782 sheet: -1.18 (0.19), residues: 654 loop : -1.06 (0.14), residues: 1908 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 83 TYR 0.014 0.001 TYR C 173 PHE 0.013 0.001 PHE C 152 TRP 0.011 0.001 TRP D 551 HIS 0.008 0.001 HIS B 317 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.12 (35130) covalent geometry : angle 0.65887 / 0.33 (47514) hydrogen bonds : bond 0.03424 / 2.25 ( 1229) hydrogen bonds : angle 5.01092 / 3.45 ( 3417) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8694.58 seconds wall clock time: 149 minutes 35.98 seconds (8975.98 seconds total)