Starting phenix.real_space_refine on Fri Mar 6 22:02:11 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ln3_23447/03_2026/7ln3_23447.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ln3_23447/03_2026/7ln3_23447.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.45 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7ln3_23447/03_2026/7ln3_23447.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ln3_23447/03_2026/7ln3_23447.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7ln3_23447/03_2026/7ln3_23447.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ln3_23447/03_2026/7ln3_23447.map" } resolution = 3.45 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= 0.002 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 31 5.49 5 Mg 7 5.21 5 S 178 5.16 5 C 21867 2.51 5 N 6194 2.21 5 O 6643 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 115 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 34920 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 5720 Number of conformers: 1 Conformer: "" Number of residues, atoms: 732, 5720 Classifications: {'peptide': 732} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PCIS': 3, 'PTRANS': 37, 'TRANS': 691} Chain breaks: 2 Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 23 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 3, 'GLN:plan1': 3} Unresolved non-hydrogen planarities: 24 Chain: "B" Number of atoms: 5784 Number of conformers: 1 Conformer: "" Number of residues, atoms: 741, 5784 Classifications: {'peptide': 741} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PCIS': 3, 'PTRANS': 37, 'TRANS': 700} Chain breaks: 1 Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 44 Unresolved non-hydrogen dihedrals: 26 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1, 'GLN:plan1': 2} Unresolved non-hydrogen planarities: 31 Chain: "C" Number of atoms: 5866 Number of conformers: 1 Conformer: "" Number of residues, atoms: 752, 5866 Classifications: {'peptide': 752} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PCIS': 4, 'PTRANS': 37, 'TRANS': 710} Chain breaks: 1 Unresolved non-hydrogen bonds: 42 Unresolved non-hydrogen angles: 53 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 1, 'GLN:plan1': 3, 'ARG:plan': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 37 Chain: "D" Number of atoms: 5865 Number of conformers: 1 Conformer: "" Number of residues, atoms: 752, 5865 Classifications: {'peptide': 752} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PCIS': 3, 'PTRANS': 38, 'TRANS': 710} Chain breaks: 1 Unresolved non-hydrogen bonds: 43 Unresolved non-hydrogen angles: 54 Unresolved non-hydrogen dihedrals: 34 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 1, 'GLN:plan1': 3, 'ARG:plan': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 37 Chain: "E" Number of atoms: 5712 Number of conformers: 1 Conformer: "" Number of residues, atoms: 732, 5712 Classifications: {'peptide': 732} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PCIS': 4, 'PTRANS': 35, 'TRANS': 692} Chain breaks: 1 Unresolved non-hydrogen bonds: 36 Unresolved non-hydrogen angles: 45 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 1, 'GLN:plan1': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 31 Chain: "F" Number of atoms: 5504 Number of conformers: 1 Conformer: "" Number of residues, atoms: 700, 5504 Classifications: {'peptide': 700} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 3, 'PTRANS': 37, 'TRANS': 659} Chain breaks: 5 Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 10 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 12 Chain: "G" Number of atoms: 110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 110 Classifications: {'peptide': 22} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'TRANS': 21} Unresolved non-hydrogen bonds: 44 Unresolved non-hydrogen angles: 66 Unresolved non-hydrogen dihedrals: 22 Planarities with less than four sites: {'UNK:plan-1': 22} Unresolved non-hydrogen planarities: 22 Chain: "A" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 54 Unusual residues: {'ADP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 59 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 59 Unusual residues: {' MG': 1, 'ADP': 1, 'ATP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 64 Unusual residues: {' MG': 2, 'ATP': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "D" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 64 Unusual residues: {' MG': 2, 'ATP': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "E" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 64 Unusual residues: {' MG': 2, 'ATP': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "F" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 54 Unusual residues: {'ADP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 8.64, per 1000 atoms: 0.25 Number of scatterers: 34920 At special positions: 0 Unit cell: (165.148, 170.545, 138.163, 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 178 16.00 P 31 15.00 Mg 7 11.99 O 6643 8.00 N 6194 7.00 C 21867 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: 3.06 Conformation dependent library (CDL) restraints added in 1.7 seconds 8750 Ramachandran restraints generated. 4375 Oldfield, 0 Emsley, 4375 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8284 Finding SS restraints... Secondary structure from input PDB file: 197 helices and 32 sheets defined 51.3% alpha, 12.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.39 Creating SS restraints... Processing helix chain 'A' and resid 42 through 50 Processing helix chain 'A' and resid 61 through 65 Processing helix chain 'A' and resid 85 through 93 removed outlier: 3.531A pdb=" N ARG A 89 " --> pdb=" O ASN A 85 " (cutoff:3.500A) Processing helix chain 'A' and resid 119 through 124 removed outlier: 3.911A pdb=" N GLU A 124 " --> pdb=" O ASP A 120 " (cutoff:3.500A) Processing helix chain 'A' and resid 129 through 134 Processing helix chain 'A' and resid 134 through 139 Processing helix chain 'A' and resid 190 through 200 removed outlier: 3.589A pdb=" N GLU A 194 " --> pdb=" O LYS A 190 " (cutoff:3.500A) Processing helix chain 'A' and resid 209 through 226 removed outlier: 3.907A 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 234 removed outlier: 4.089A pdb=" N PHE A 230 " --> pdb=" O HIS A 226 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N ILE A 233 " --> pdb=" O LEU A 229 " (cutoff:3.500A) Processing helix chain 'A' and resid 250 through 262 Processing helix chain 'A' and resid 271 through 276 Processing helix chain 'A' and resid 280 through 296 Processing helix chain 'A' and resid 319 through 335 Processing helix chain 'A' and resid 373 through 386 Processing helix chain 'A' and resid 395 through 403 removed outlier: 3.751A pdb=" N VAL A 399 " --> pdb=" O ASP A 395 " (cutoff:3.500A) Processing helix chain 'A' and resid 407 through 425 Processing helix chain 'A' and resid 438 through 444 removed outlier: 4.105A pdb=" N MET A 442 " --> pdb=" O ASP A 438 " (cutoff:3.500A) Processing helix chain 'A' and resid 448 through 459 Processing helix chain 'A' and resid 482 through 499 removed outlier: 3.823A pdb=" N VAL A 493 " --> pdb=" O LEU A 489 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLN A 494 " --> pdb=" O GLN A 490 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N TYR A 495 " --> pdb=" O GLU A 491 " (cutoff:3.500A) Proline residue: A 496 - end of helix Processing helix chain 'A' and resid 499 through 507 removed outlier: 3.843A pdb=" N PHE A 503 " --> pdb=" O HIS A 499 " (cutoff:3.500A) Processing helix chain 'A' and resid 523 through 535 Processing helix chain 'A' and resid 544 through 549 removed outlier: 4.403A pdb=" N THR A 549 " --> pdb=" O PRO A 545 " (cutoff:3.500A) Processing helix chain 'A' and resid 553 through 569 removed outlier: 3.514A pdb=" N ALA A 557 " --> pdb=" O GLY A 553 " (cutoff:3.500A) Processing helix chain 'A' and resid 578 through 583 removed outlier: 4.079A pdb=" N ILE A 582 " --> pdb=" O GLN A 578 " (cutoff:3.500A) Processing helix chain 'A' and resid 591 through 612 Processing helix chain 'A' and resid 630 through 635 removed outlier: 3.528A pdb=" N LEU A 634 " --> pdb=" O ASP A 630 " (cutoff:3.500A) Processing helix chain 'A' and resid 649 through 661 Processing helix chain 'A' and resid 671 through 679 Processing helix chain 'A' and resid 683 through 714 removed outlier: 3.687A pdb=" N GLU A 704 " --> pdb=" O ARG A 700 " (cutoff:3.500A) Processing helix chain 'A' and resid 732 through 743 Processing helix chain 'A' and resid 748 through 766 removed outlier: 3.734A pdb=" N ILE A 752 " --> pdb=" O SER A 748 " (cutoff:3.500A) Processing helix chain 'B' and resid 42 through 50 Processing helix chain 'B' and resid 61 through 65 removed outlier: 3.569A pdb=" N ARG B 64 " --> pdb=" O GLY B 61 " (cutoff:3.500A) Processing helix chain 'B' and resid 85 through 93 Processing helix chain 'B' and resid 119 through 124 Processing helix chain 'B' and resid 129 through 134 Processing helix chain 'B' and resid 134 through 139 Processing helix chain 'B' and resid 190 through 199 removed outlier: 3.560A pdb=" N GLU B 194 " --> pdb=" O LYS B 190 " (cutoff:3.500A) Processing helix chain 'B' and resid 202 through 206 Processing helix chain 'B' and resid 209 through 226 removed outlier: 4.185A 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 234 removed outlier: 3.935A pdb=" N PHE B 230 " --> pdb=" O HIS B 226 " (cutoff:3.500A) Processing helix chain 'B' and resid 250 through 262 Processing helix chain 'B' and resid 271 through 275 removed outlier: 4.059A pdb=" N MET B 275 " --> pdb=" O GLY B 271 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 271 through 275' Processing helix chain 'B' and resid 280 through 296 removed outlier: 3.594A pdb=" N SER B 284 " --> pdb=" O GLY B 280 " (cutoff:3.500A) Processing helix chain 'B' and resid 305 through 310 removed outlier: 3.503A pdb=" N ILE B 309 " --> pdb=" O GLU B 305 " (cutoff:3.500A) Processing helix chain 'B' and resid 318 through 333 removed outlier: 3.833A pdb=" N ARG B 322 " --> pdb=" O GLY B 318 " (cutoff:3.500A) Processing helix chain 'B' and resid 349 through 353 removed outlier: 3.526A pdb=" N SER B 352 " --> pdb=" O ARG B 349 " (cutoff:3.500A) Processing helix chain 'B' and resid 354 through 359 removed outlier: 3.616A pdb=" N ARG B 359 " --> pdb=" O ALA B 356 " (cutoff:3.500A) Processing helix chain 'B' and resid 373 through 388 removed outlier: 4.264A pdb=" N ASN B 387 " --> pdb=" O ILE B 383 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N MET B 388 " --> pdb=" O HIS B 384 " (cutoff:3.500A) Processing helix chain 'B' and resid 395 through 403 removed outlier: 3.689A pdb=" N VAL B 399 " --> pdb=" O ASP B 395 " (cutoff:3.500A) Processing helix chain 'B' and resid 407 through 428 removed outlier: 4.121A pdb=" N ASP B 428 " --> pdb=" O ARG B 424 " (cutoff:3.500A) Processing helix chain 'B' and resid 438 through 445 Processing helix chain 'B' and resid 448 through 459 removed outlier: 3.528A pdb=" N PHE B 452 " --> pdb=" O THR B 448 " (cutoff:3.500A) Processing helix chain 'B' and resid 482 through 499 Proline residue: B 496 - end of helix Processing helix chain 'B' and resid 499 through 507 removed outlier: 3.849A pdb=" N PHE B 503 " --> pdb=" O HIS B 499 " (cutoff:3.500A) Processing helix chain 'B' and resid 523 through 535 removed outlier: 3.542A pdb=" N CYS B 535 " --> pdb=" O ILE B 531 " (cutoff:3.500A) Processing helix chain 'B' and resid 543 through 547 removed outlier: 4.374A pdb=" N LEU B 547 " --> pdb=" O GLY B 544 " (cutoff:3.500A) Processing helix chain 'B' and resid 553 through 569 removed outlier: 3.631A pdb=" N ALA B 557 " --> pdb=" O GLY B 553 " (cutoff:3.500A) Processing helix chain 'B' and resid 578 through 583 removed outlier: 4.390A pdb=" N ILE B 582 " --> pdb=" O GLN B 578 " (cutoff:3.500A) Processing helix chain 'B' and resid 595 through 609 Processing helix chain 'B' and resid 630 through 635 removed outlier: 3.560A pdb=" N LEU B 634 " --> pdb=" O ASP B 630 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ARG B 635 " --> pdb=" O PRO B 631 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 630 through 635' Processing helix chain 'B' and resid 649 through 662 Processing helix chain 'B' and resid 671 through 679 removed outlier: 3.987A pdb=" N LEU B 675 " --> pdb=" O ASP B 671 " (cutoff:3.500A) Processing helix chain 'B' and resid 683 through 714 Processing helix chain 'B' and resid 732 through 742 removed outlier: 3.736A pdb=" N PHE B 736 " --> pdb=" O ARG B 732 " (cutoff:3.500A) Processing helix chain 'B' and resid 748 through 767 removed outlier: 3.638A pdb=" N ILE B 752 " --> pdb=" O SER B 748 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N GLY B 767 " --> pdb=" O GLN B 763 " (cutoff:3.500A) Processing helix chain 'C' and resid 12 through 16 removed outlier: 4.109A pdb=" N ILE C 16 " --> pdb=" O SER C 13 " (cutoff:3.500A) Processing helix chain 'C' and resid 43 through 50 Processing helix chain 'C' and resid 61 through 65 removed outlier: 3.862A pdb=" N ARG C 64 " --> pdb=" O GLY C 61 " (cutoff:3.500A) Processing helix chain 'C' and resid 85 through 93 Processing helix chain 'C' and resid 119 through 124 Processing helix chain 'C' and resid 129 through 134 Processing helix chain 'C' and resid 134 through 139 Processing helix chain 'C' and resid 190 through 200 Processing helix chain 'C' and resid 202 through 206 Processing helix chain 'C' and resid 209 through 226 removed outlier: 4.231A 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 234 removed outlier: 4.085A pdb=" N PHE C 230 " --> pdb=" O HIS C 226 " (cutoff:3.500A) Processing helix chain 'C' and resid 250 through 262 Processing helix chain 'C' and resid 281 through 296 Processing helix chain 'C' and resid 305 through 310 removed outlier: 3.930A pdb=" N ILE C 309 " --> pdb=" O GLU C 305 " (cutoff:3.500A) Processing helix chain 'C' and resid 318 through 333 removed outlier: 3.698A pdb=" N ARG C 322 " --> pdb=" O GLY C 318 " (cutoff:3.500A) Processing helix chain 'C' and resid 349 through 353 removed outlier: 3.664A pdb=" N SER C 352 " --> pdb=" O ARG C 349 " (cutoff:3.500A) Processing helix chain 'C' and resid 373 through 386 Processing helix chain 'C' and resid 395 through 403 Processing helix chain 'C' and resid 408 through 430 removed outlier: 3.541A pdb=" N ALA C 412 " --> pdb=" O GLY C 408 " (cutoff:3.500A) Processing helix chain 'C' and resid 438 through 445 Processing helix chain 'C' and resid 448 through 459 Processing helix chain 'C' and resid 462 through 466 removed outlier: 4.389A pdb=" N GLU C 466 " --> pdb=" O ALA C 463 " (cutoff:3.500A) Processing helix chain 'C' and resid 482 through 499 Proline residue: C 496 - end of helix Processing helix chain 'C' and resid 499 through 507 removed outlier: 3.999A pdb=" N PHE C 503 " --> pdb=" O HIS C 499 " (cutoff:3.500A) Processing helix chain 'C' and resid 523 through 534 Processing helix chain 'C' and resid 543 through 548 removed outlier: 4.182A pdb=" N LEU C 547 " --> pdb=" O GLY C 544 " (cutoff:3.500A) Processing helix chain 'C' and resid 553 through 569 Processing helix chain 'C' and resid 579 through 582 Processing helix chain 'C' and resid 595 through 609 removed outlier: 3.541A pdb=" N ARG C 599 " --> pdb=" O GLY C 595 " (cutoff:3.500A) Processing helix chain 'C' and resid 649 through 662 Processing helix chain 'C' and resid 671 through 679 removed outlier: 3.609A pdb=" N LEU C 675 " --> pdb=" O ASP C 671 " (cutoff:3.500A) Processing helix chain 'C' and resid 683 through 714 Processing helix chain 'C' and resid 732 through 743 removed outlier: 3.596A pdb=" N PHE C 736 " --> pdb=" O ARG C 732 " (cutoff:3.500A) Processing helix chain 'C' and resid 748 through 767 removed outlier: 3.537A pdb=" N GLY C 767 " --> pdb=" O GLN C 763 " (cutoff:3.500A) Processing helix chain 'D' and resid 13 through 17 removed outlier: 4.118A pdb=" N ILE D 16 " --> pdb=" O SER D 13 " (cutoff:3.500A) Processing helix chain 'D' and resid 42 through 50 Processing helix chain 'D' and resid 85 through 93 Processing helix chain 'D' and resid 119 through 124 removed outlier: 3.540A pdb=" N GLU D 124 " --> pdb=" O ASP D 120 " (cutoff:3.500A) Processing helix chain 'D' and resid 129 through 134 Processing helix chain 'D' and resid 134 through 139 Processing helix chain 'D' and resid 190 through 199 Processing helix chain 'D' and resid 209 through 226 removed outlier: 4.018A 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 234 removed outlier: 4.113A pdb=" N PHE D 230 " --> pdb=" O HIS D 226 " (cutoff:3.500A) Processing helix chain 'D' and resid 250 through 261 Processing helix chain 'D' and resid 272 through 275 Processing helix chain 'D' and resid 280 through 296 removed outlier: 3.603A pdb=" N ASN D 296 " --> pdb=" O GLU D 292 " (cutoff:3.500A) Processing helix chain 'D' and resid 305 through 310 removed outlier: 4.222A pdb=" N ILE D 309 " --> pdb=" O GLU D 305 " (cutoff:3.500A) Processing helix chain 'D' and resid 318 through 333 Processing helix chain 'D' and resid 349 through 353 Processing helix chain 'D' and resid 373 through 386 Processing helix chain 'D' and resid 395 through 403 removed outlier: 3.596A pdb=" N VAL D 399 " --> pdb=" O ASP D 395 " (cutoff:3.500A) Processing helix chain 'D' and resid 408 through 425 Processing helix chain 'D' and resid 438 through 445 Processing helix chain 'D' and resid 448 through 459 Processing helix chain 'D' and resid 482 through 499 Proline residue: D 496 - end of helix Processing helix chain 'D' and resid 499 through 507 removed outlier: 3.938A pdb=" N PHE D 503 " --> pdb=" O HIS D 499 " (cutoff:3.500A) Processing helix chain 'D' and resid 523 through 535 Processing helix chain 'D' and resid 543 through 547 removed outlier: 3.852A pdb=" N LEU D 547 " --> pdb=" O GLY D 544 " (cutoff:3.500A) Processing helix chain 'D' and resid 553 through 569 removed outlier: 3.570A pdb=" N ALA D 557 " --> pdb=" O GLY D 553 " (cutoff:3.500A) Processing helix chain 'D' and resid 578 through 583 removed outlier: 4.199A pdb=" N ILE D 582 " --> pdb=" O GLN D 578 " (cutoff:3.500A) Processing helix chain 'D' and resid 591 through 609 removed outlier: 4.072A pdb=" N GLY D 595 " --> pdb=" O GLY D 591 " (cutoff:3.500A) removed outlier: 7.255A pdb=" N ALA D 597 " --> pdb=" O GLY D 593 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N ASP D 598 " --> pdb=" O GLY D 594 " (cutoff:3.500A) Processing helix chain 'D' and resid 649 through 661 Processing helix chain 'D' and resid 671 through 679 Processing helix chain 'D' and resid 683 through 714 Processing helix chain 'D' and resid 732 through 743 removed outlier: 3.651A pdb=" N PHE D 736 " --> pdb=" O ARG D 732 " (cutoff:3.500A) Processing helix chain 'D' and resid 748 through 767 removed outlier: 3.662A pdb=" N GLY D 767 " --> pdb=" O GLN D 763 " (cutoff:3.500A) Processing helix chain 'E' and resid 42 through 50 Processing helix chain 'E' and resid 61 through 65 removed outlier: 3.667A pdb=" N ARG E 64 " --> pdb=" O GLY E 61 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 92 Processing helix chain 'E' and resid 119 through 124 Processing helix chain 'E' and resid 129 through 134 Processing helix chain 'E' and resid 134 through 140 Processing helix chain 'E' and resid 190 through 199 Processing helix chain 'E' and resid 209 through 220 Processing helix chain 'E' and resid 220 through 226 Processing helix chain 'E' and resid 226 through 234 removed outlier: 3.724A pdb=" N PHE E 230 " --> pdb=" O HIS E 226 " (cutoff:3.500A) Processing helix chain 'E' and resid 250 through 262 Processing helix chain 'E' and resid 271 through 275 removed outlier: 4.224A pdb=" N MET E 275 " --> pdb=" O GLY E 271 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 271 through 275' Processing helix chain 'E' and resid 280 through 296 Processing helix chain 'E' and resid 305 through 310 removed outlier: 3.751A pdb=" N ILE E 309 " --> pdb=" O GLU E 305 " (cutoff:3.500A) Processing helix chain 'E' and resid 318 through 338 removed outlier: 3.859A pdb=" N GLN E 337 " --> pdb=" O ASP E 333 " (cutoff:3.500A) Processing helix chain 'E' and resid 373 through 385 Processing helix chain 'E' and resid 395 through 403 removed outlier: 4.025A pdb=" N VAL E 399 " --> pdb=" O ASP E 395 " (cutoff:3.500A) Processing helix chain 'E' and resid 408 through 426 removed outlier: 3.673A pdb=" N ALA E 412 " --> pdb=" O GLY E 408 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LYS E 426 " --> pdb=" O ALA E 422 " (cutoff:3.500A) Processing helix chain 'E' and resid 438 through 445 Processing helix chain 'E' and resid 448 through 459 removed outlier: 3.572A pdb=" N PHE E 452 " --> pdb=" O THR E 448 " (cutoff:3.500A) Processing helix chain 'E' and resid 462 through 466 removed outlier: 3.574A pdb=" N GLU E 466 " --> pdb=" O ALA E 463 " (cutoff:3.500A) Processing helix chain 'E' and resid 482 through 499 Proline residue: E 496 - end of helix Processing helix chain 'E' and resid 499 through 507 removed outlier: 4.111A pdb=" N PHE E 503 " --> pdb=" O HIS E 499 " (cutoff:3.500A) Processing helix chain 'E' and resid 523 through 535 Processing helix chain 'E' and resid 553 through 568 Processing helix chain 'E' and resid 578 through 582 Processing helix chain 'E' and resid 587 through 592 Processing helix chain 'E' and resid 595 through 611 removed outlier: 3.916A pdb=" N ARG E 599 " --> pdb=" O GLY E 595 " (cutoff:3.500A) Processing helix chain 'E' and resid 625 through 629 removed outlier: 3.571A pdb=" N ILE E 628 " --> pdb=" O ARG E 625 " (cutoff:3.500A) Processing helix chain 'E' and resid 630 through 635 Processing helix chain 'E' and resid 649 through 661 Processing helix chain 'E' and resid 671 through 679 removed outlier: 3.605A pdb=" N LEU E 675 " --> pdb=" O ASP E 671 " (cutoff:3.500A) Processing helix chain 'E' and resid 683 through 714 Processing helix chain 'E' and resid 732 through 742 removed outlier: 3.654A pdb=" N PHE E 736 " --> pdb=" O ARG E 732 " (cutoff:3.500A) Processing helix chain 'E' and resid 748 through 766 removed outlier: 3.691A pdb=" N ILE E 752 " --> pdb=" O SER E 748 " (cutoff:3.500A) Processing helix chain 'F' and resid 43 through 50 Processing helix chain 'F' and resid 85 through 93 Processing helix chain 'F' and resid 129 through 134 Processing helix chain 'F' and resid 190 through 200 Processing helix chain 'F' and resid 209 through 220 Processing helix chain 'F' and resid 220 through 226 Processing helix chain 'F' and resid 226 through 234 removed outlier: 3.646A pdb=" N PHE F 230 " --> pdb=" O HIS F 226 " (cutoff:3.500A) Processing helix chain 'F' and resid 250 through 262 Processing helix chain 'F' and resid 271 through 277 Processing helix chain 'F' and resid 280 through 296 removed outlier: 3.673A pdb=" N ASN F 296 " --> pdb=" O GLU F 292 " (cutoff:3.500A) Processing helix chain 'F' and resid 305 through 310 Processing helix chain 'F' and resid 318 through 335 Processing helix chain 'F' and resid 354 through 359 removed outlier: 3.623A pdb=" N ARG F 358 " --> pdb=" O ASP F 354 " (cutoff:3.500A) Processing helix chain 'F' and resid 373 through 388 removed outlier: 3.990A pdb=" N ASN F 387 " --> pdb=" O ILE F 383 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N MET F 388 " --> pdb=" O HIS F 384 " (cutoff:3.500A) Processing helix chain 'F' and resid 395 through 403 removed outlier: 4.335A pdb=" N VAL F 399 " --> pdb=" O ASP F 395 " (cutoff:3.500A) Processing helix chain 'F' and resid 408 through 426 Processing helix chain 'F' and resid 438 through 445 Processing helix chain 'F' and resid 448 through 459 removed outlier: 3.537A pdb=" N PHE F 452 " --> pdb=" O THR F 448 " (cutoff:3.500A) Processing helix chain 'F' and resid 482 through 499 Proline residue: F 496 - end of helix Processing helix chain 'F' and resid 499 through 506 Processing helix chain 'F' and resid 523 through 536 Processing helix chain 'F' and resid 559 through 569 Processing helix chain 'F' and resid 578 through 583 removed outlier: 3.618A pdb=" N ILE F 582 " --> pdb=" O GLN F 578 " (cutoff:3.500A) Processing helix chain 'F' and resid 598 through 614 removed outlier: 3.868A pdb=" N LYS F 614 " --> pdb=" O GLY F 610 " (cutoff:3.500A) Processing helix chain 'F' and resid 630 through 635 removed outlier: 3.822A pdb=" N LEU F 634 " --> pdb=" O ASP F 630 " (cutoff:3.500A) Processing helix chain 'F' and resid 649 through 662 Processing helix chain 'F' and resid 671 through 679 Processing helix chain 'F' and resid 683 through 714 Processing helix chain 'F' and resid 732 through 743 removed outlier: 3.926A pdb=" N PHE F 736 " --> pdb=" O ARG F 732 " (cutoff:3.500A) Processing helix chain 'F' and resid 748 through 762 Processing sheet with id=AA1, first strand: chain 'A' and resid 25 through 30 removed outlier: 7.698A pdb=" N ILE A 82 " --> pdb=" O ARG A 25 " (cutoff:3.500A) removed outlier: 5.952A pdb=" N ILE A 27 " --> pdb=" O ILE A 82 " (cutoff:3.500A) removed outlier: 7.167A pdb=" N MET A 84 " --> pdb=" O ILE A 27 " (cutoff:3.500A) removed outlier: 5.763A pdb=" N ASP A 29 " --> pdb=" O MET A 84 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 151 through 154 removed outlier: 3.597A pdb=" N VAL A 154 " --> pdb=" O VAL A 161 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N VAL A 161 " --> pdb=" O VAL A 154 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N VAL A 166 " --> pdb=" O HIS A 115 " (cutoff:3.500A) removed outlier: 7.408A pdb=" N HIS A 115 " --> pdb=" O VAL A 166 " (cutoff:3.500A) removed outlier: 5.562A pdb=" N THR A 168 " --> pdb=" O ARG A 113 " (cutoff:3.500A) removed outlier: 7.502A pdb=" N ARG A 113 " --> pdb=" O THR A 168 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N HIS A 183 " --> pdb=" O ILE A 114 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N VAL A 116 " --> pdb=" O HIS A 183 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 144 through 147 removed outlier: 3.697A pdb=" N ARG A 144 " --> pdb=" O VAL A 176 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 265 through 270 removed outlier: 6.228A pdb=" N PHE A 265 " --> pdb=" O ILE A 300 " (cutoff:3.500A) removed outlier: 7.858A pdb=" N PHE A 302 " --> pdb=" O PHE A 265 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N PHE A 267 " --> pdb=" O PHE A 302 " (cutoff:3.500A) removed outlier: 7.868A pdb=" N ASP A 304 " --> pdb=" O PHE A 267 " (cutoff:3.500A) removed outlier: 7.203A pdb=" N ILE A 269 " --> pdb=" O ASP A 304 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N ALA A 299 " --> pdb=" O ILE A 342 " (cutoff:3.500A) removed outlier: 8.025A pdb=" N MET A 344 " --> pdb=" O ALA A 299 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N ILE A 301 " --> pdb=" O MET A 344 " (cutoff:3.500A) removed outlier: 7.925A pdb=" N ALA A 346 " --> pdb=" O ILE A 301 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N ILE A 303 " --> pdb=" O ALA A 346 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N ILE A 241 " --> pdb=" O ALA A 345 " (cutoff:3.500A) removed outlier: 7.606A pdb=" N THR A 347 " --> pdb=" O ILE A 241 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N LEU A 243 " --> pdb=" O THR A 347 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 538 through 543 removed outlier: 6.293A pdb=" N ASN A 538 " --> pdb=" O VAL A 573 " (cutoff:3.500A) removed outlier: 7.370A pdb=" N PHE A 575 " --> pdb=" O ASN A 538 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N ILE A 540 " --> pdb=" O PHE A 575 " (cutoff:3.500A) removed outlier: 7.453A pdb=" N ASP A 577 " --> pdb=" O ILE A 540 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N ILE A 542 " --> pdb=" O ASP A 577 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N CYS A 572 " --> pdb=" O PHE A 618 " (cutoff:3.500A) removed outlier: 7.658A pdb=" N ILE A 620 " --> pdb=" O CYS A 572 " (cutoff:3.500A) removed outlier: 6.047A pdb=" N LEU A 574 " --> pdb=" O ILE A 620 " (cutoff:3.500A) removed outlier: 7.623A pdb=" N ALA A 622 " --> pdb=" O LEU A 574 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N PHE A 576 " --> pdb=" O ALA A 622 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N GLY A 513 " --> pdb=" O GLN A 641 " (cutoff:3.500A) removed outlier: 7.609A pdb=" N ILE A 643 " --> pdb=" O GLY A 513 " (cutoff:3.500A) removed outlier: 5.841A pdb=" N LEU A 515 " --> pdb=" O ILE A 643 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 81 through 84 Processing sheet with id=AA7, first strand: chain 'B' and resid 38 through 41 removed outlier: 3.633A pdb=" N ALA B 67 " --> pdb=" O LEU B 59 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 113 through 118 removed outlier: 7.865A pdb=" N ARG B 113 " --> pdb=" O THR B 168 " (cutoff:3.500A) removed outlier: 5.846A pdb=" N THR B 168 " --> pdb=" O ARG B 113 " (cutoff:3.500A) removed outlier: 7.365A pdb=" N HIS B 115 " --> pdb=" O VAL B 166 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N VAL B 166 " --> pdb=" O HIS B 115 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N VAL B 161 " --> pdb=" O VAL B 154 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N VAL B 154 " --> pdb=" O VAL B 161 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N ASP B 150 " --> pdb=" O VAL B 165 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 145 through 147 Processing sheet with id=AB1, first strand: chain 'B' and resid 265 through 270 removed outlier: 6.141A pdb=" N PHE B 265 " --> pdb=" O ILE B 300 " (cutoff:3.500A) removed outlier: 7.093A pdb=" N PHE B 302 " --> pdb=" O PHE B 265 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N PHE B 267 " --> pdb=" O PHE B 302 " (cutoff:3.500A) removed outlier: 7.261A pdb=" N ASP B 304 " --> pdb=" O PHE B 267 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N ILE B 269 " --> pdb=" O ASP B 304 " (cutoff:3.500A) removed outlier: 6.188A pdb=" N ALA B 299 " --> pdb=" O ILE B 342 " (cutoff:3.500A) removed outlier: 7.410A pdb=" N MET B 344 " --> pdb=" O ALA B 299 " (cutoff:3.500A) removed outlier: 5.670A pdb=" N ILE B 301 " --> pdb=" O MET B 344 " (cutoff:3.500A) removed outlier: 7.418A pdb=" N ALA B 346 " --> pdb=" O ILE B 301 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N ILE B 303 " --> pdb=" O ALA B 346 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N GLY B 240 " --> pdb=" O ARG B 365 " (cutoff:3.500A) removed outlier: 7.684A pdb=" N VAL B 367 " --> pdb=" O GLY B 240 " (cutoff:3.500A) removed outlier: 6.133A pdb=" N LEU B 242 " --> pdb=" O VAL B 367 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 538 through 542 removed outlier: 6.572A pdb=" N ASN B 538 " --> pdb=" O VAL B 573 " (cutoff:3.500A) removed outlier: 7.606A pdb=" N PHE B 575 " --> pdb=" O ASN B 538 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N ILE B 540 " --> pdb=" O PHE B 575 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N GLY B 513 " --> pdb=" O GLN B 641 " (cutoff:3.500A) removed outlier: 7.504A pdb=" N ILE B 643 " --> pdb=" O GLY B 513 " (cutoff:3.500A) removed outlier: 5.916A pdb=" N LEU B 515 " --> pdb=" O ILE B 643 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 99 through 100 removed outlier: 6.041A pdb=" N ILE C 27 " --> pdb=" O ILE C 82 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N MET C 84 " --> pdb=" O ILE C 27 " (cutoff:3.500A) removed outlier: 5.612A pdb=" N ASP C 29 " --> pdb=" O MET C 84 " (cutoff:3.500A) removed outlier: 8.415A pdb=" N LYS C 81 " --> pdb=" O SER C 42 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N SER C 42 " --> pdb=" O LYS C 81 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N SER C 40 " --> pdb=" O ARG C 83 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ALA C 67 " --> pdb=" O LEU C 59 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N CYS C 69 " --> pdb=" O VAL C 57 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 109 through 110 removed outlier: 7.411A pdb=" N LYS C 109 " --> pdb=" O ILE C 175 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N CYS C 174 " --> pdb=" O ILE C 146 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 115 through 118 removed outlier: 6.598A pdb=" N HIS C 115 " --> pdb=" O VAL C 166 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N VAL C 161 " --> pdb=" O VAL C 154 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 265 through 270 removed outlier: 6.435A pdb=" N ALA C 299 " --> pdb=" O ILE C 342 " (cutoff:3.500A) removed outlier: 7.557A pdb=" N MET C 344 " --> pdb=" O ALA C 299 " (cutoff:3.500A) removed outlier: 5.780A pdb=" N ILE C 301 " --> pdb=" O MET C 344 " (cutoff:3.500A) removed outlier: 7.618A pdb=" N ALA C 346 " --> pdb=" O ILE C 301 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N ILE C 303 " --> pdb=" O ALA C 346 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N GLY C 240 " --> pdb=" O ARG C 365 " (cutoff:3.500A) removed outlier: 7.495A pdb=" N VAL C 367 " --> pdb=" O GLY C 240 " (cutoff:3.500A) removed outlier: 6.018A pdb=" N LEU C 242 " --> pdb=" O VAL C 367 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 538 through 542 removed outlier: 6.477A pdb=" N CYS C 572 " --> pdb=" O PHE C 618 " (cutoff:3.500A) removed outlier: 7.565A pdb=" N ILE C 620 " --> pdb=" O CYS C 572 " (cutoff:3.500A) removed outlier: 6.135A pdb=" N LEU C 574 " --> pdb=" O ILE C 620 " (cutoff:3.500A) removed outlier: 7.862A pdb=" N ALA C 622 " --> pdb=" O LEU C 574 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N PHE C 576 " --> pdb=" O ALA C 622 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N GLY C 513 " --> pdb=" O GLN C 641 " (cutoff:3.500A) removed outlier: 7.499A pdb=" N ILE C 643 " --> pdb=" O GLY C 513 " (cutoff:3.500A) removed outlier: 5.902A pdb=" N LEU C 515 " --> pdb=" O ILE C 643 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 81 through 84 removed outlier: 6.014A pdb=" N ILE D 27 " --> pdb=" O ILE D 82 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N MET D 84 " --> pdb=" O ILE D 27 " (cutoff:3.500A) removed outlier: 5.714A pdb=" N ASP D 29 " --> pdb=" O MET D 84 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 38 through 41 removed outlier: 3.631A pdb=" N CYS D 69 " --> pdb=" O VAL D 57 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 150 through 154 removed outlier: 4.372A pdb=" N ASP D 150 " --> pdb=" O VAL D 165 " (cutoff:3.500A) removed outlier: 7.048A pdb=" N HIS D 115 " --> pdb=" O VAL D 166 " (cutoff:3.500A) removed outlier: 5.160A pdb=" N THR D 168 " --> pdb=" O ARG D 113 " (cutoff:3.500A) removed outlier: 7.241A pdb=" N ARG D 113 " --> pdb=" O THR D 168 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N HIS D 183 " --> pdb=" O ILE D 114 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N VAL D 116 " --> pdb=" O HIS D 183 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 145 through 146 removed outlier: 3.649A pdb=" N CYS D 174 " --> pdb=" O ILE D 146 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 265 through 270 removed outlier: 6.244A pdb=" N PHE D 265 " --> pdb=" O ILE D 300 " (cutoff:3.500A) removed outlier: 7.464A pdb=" N PHE D 302 " --> pdb=" O PHE D 265 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N PHE D 267 " --> pdb=" O PHE D 302 " (cutoff:3.500A) removed outlier: 7.623A pdb=" N ASP D 304 " --> pdb=" O PHE D 267 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N ILE D 269 " --> pdb=" O ASP D 304 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N ALA D 299 " --> pdb=" O ILE D 342 " (cutoff:3.500A) removed outlier: 7.640A pdb=" N MET D 344 " --> pdb=" O ALA D 299 " (cutoff:3.500A) removed outlier: 5.995A pdb=" N ILE D 301 " --> pdb=" O MET D 344 " (cutoff:3.500A) removed outlier: 7.856A pdb=" N ALA D 346 " --> pdb=" O ILE D 301 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N ILE D 303 " --> pdb=" O ALA D 346 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N GLY D 240 " --> pdb=" O ARG D 365 " (cutoff:3.500A) removed outlier: 7.339A pdb=" N VAL D 367 " --> pdb=" O GLY D 240 " (cutoff:3.500A) removed outlier: 6.073A pdb=" N LEU D 242 " --> pdb=" O VAL D 367 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 538 through 542 removed outlier: 6.432A pdb=" N ASN D 538 " --> pdb=" O VAL D 573 " (cutoff:3.500A) removed outlier: 7.646A pdb=" N PHE D 575 " --> pdb=" O ASN D 538 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N ILE D 540 " --> pdb=" O PHE D 575 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N CYS D 572 " --> pdb=" O PHE D 618 " (cutoff:3.500A) removed outlier: 7.586A pdb=" N ILE D 620 " --> pdb=" O CYS D 572 " (cutoff:3.500A) removed outlier: 5.958A pdb=" N LEU D 574 " --> pdb=" O ILE D 620 " (cutoff:3.500A) removed outlier: 7.773A pdb=" N ALA D 622 " --> pdb=" O LEU D 574 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N PHE D 576 " --> pdb=" O ALA D 622 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N GLY D 513 " --> pdb=" O GLN D 641 " (cutoff:3.500A) removed outlier: 7.520A pdb=" N ILE D 643 " --> pdb=" O GLY D 513 " (cutoff:3.500A) removed outlier: 5.900A pdb=" N LEU D 515 " --> pdb=" O ILE D 643 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 25 through 29 removed outlier: 3.501A pdb=" N SER E 40 " --> pdb=" O ARG E 83 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 109 through 111 Processing sheet with id=AC7, first strand: chain 'E' and resid 151 through 154 removed outlier: 3.593A pdb=" N VAL E 161 " --> pdb=" O VAL E 154 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N VAL E 166 " --> pdb=" O HIS E 115 " (cutoff:3.500A) removed outlier: 7.848A pdb=" N HIS E 115 " --> pdb=" O VAL E 166 " (cutoff:3.500A) removed outlier: 6.192A pdb=" N THR E 168 " --> pdb=" O ARG E 113 " (cutoff:3.500A) removed outlier: 8.157A pdb=" N ARG E 113 " --> pdb=" O THR E 168 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N HIS E 183 " --> pdb=" O ILE E 114 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N VAL E 116 " --> pdb=" O HIS E 183 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'E' and resid 265 through 270 removed outlier: 6.195A pdb=" N PHE E 265 " --> pdb=" O ILE E 300 " (cutoff:3.500A) removed outlier: 7.287A pdb=" N PHE E 302 " --> pdb=" O PHE E 265 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N PHE E 267 " --> pdb=" O PHE E 302 " (cutoff:3.500A) removed outlier: 7.394A pdb=" N ASP E 304 " --> pdb=" O PHE E 267 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N ILE E 269 " --> pdb=" O ASP E 304 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N ALA E 299 " --> pdb=" O ILE E 342 " (cutoff:3.500A) removed outlier: 7.770A pdb=" N MET E 344 " --> pdb=" O ALA E 299 " (cutoff:3.500A) removed outlier: 6.012A pdb=" N ILE E 301 " --> pdb=" O MET E 344 " (cutoff:3.500A) removed outlier: 7.805A pdb=" N ALA E 346 " --> pdb=" O ILE E 301 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N ILE E 303 " --> pdb=" O ALA E 346 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N GLY E 240 " --> pdb=" O ARG E 365 " (cutoff:3.500A) removed outlier: 7.554A pdb=" N VAL E 367 " --> pdb=" O GLY E 240 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N LEU E 242 " --> pdb=" O VAL E 367 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'E' and resid 538 through 542 removed outlier: 6.416A pdb=" N ASN E 538 " --> pdb=" O VAL E 573 " (cutoff:3.500A) removed outlier: 7.408A pdb=" N PHE E 575 " --> pdb=" O ASN E 538 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N ILE E 540 " --> pdb=" O PHE E 575 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N GLY E 513 " --> pdb=" O GLN E 641 " (cutoff:3.500A) removed outlier: 7.564A pdb=" N ILE E 643 " --> pdb=" O GLY E 513 " (cutoff:3.500A) removed outlier: 5.963A pdb=" N LEU E 515 " --> pdb=" O ILE E 643 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'F' and resid 99 through 100 removed outlier: 3.523A pdb=" N LEU F 26 " --> pdb=" O ILE F 100 " (cutoff:3.500A) removed outlier: 5.902A pdb=" N ILE F 27 " --> pdb=" O ILE F 82 " (cutoff:3.500A) removed outlier: 8.600A pdb=" N LYS F 81 " --> pdb=" O SER F 42 " (cutoff:3.500A) removed outlier: 4.965A pdb=" N SER F 42 " --> pdb=" O LYS F 81 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ALA F 67 " --> pdb=" O LEU F 59 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'F' and resid 150 through 154 removed outlier: 4.553A pdb=" N VAL F 166 " --> pdb=" O HIS F 115 " (cutoff:3.500A) removed outlier: 8.592A pdb=" N HIS F 115 " --> pdb=" O VAL F 166 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'F' and resid 145 through 147 Processing sheet with id=AD4, first strand: chain 'F' and resid 266 through 270 removed outlier: 6.395A pdb=" N ILE F 301 " --> pdb=" O MET F 344 " (cutoff:3.500A) removed outlier: 8.208A pdb=" N ALA F 346 " --> pdb=" O ILE F 301 " (cutoff:3.500A) removed outlier: 7.139A pdb=" N ILE F 303 " --> pdb=" O ALA F 346 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N GLY F 240 " --> pdb=" O ARG F 365 " (cutoff:3.500A) removed outlier: 7.930A pdb=" N VAL F 367 " --> pdb=" O GLY F 240 " (cutoff:3.500A) removed outlier: 6.096A pdb=" N LEU F 242 " --> pdb=" O VAL F 367 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'F' and resid 538 through 542 removed outlier: 6.026A pdb=" N CYS F 572 " --> pdb=" O PHE F 618 " (cutoff:3.500A) removed outlier: 7.656A pdb=" N ILE F 620 " --> pdb=" O CYS F 572 " (cutoff:3.500A) removed outlier: 6.088A pdb=" N LEU F 574 " --> pdb=" O ILE F 620 " (cutoff:3.500A) removed outlier: 7.851A pdb=" N ALA F 622 " --> pdb=" O LEU F 574 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N PHE F 576 " --> pdb=" O ALA F 622 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N GLY F 513 " --> pdb=" O GLN F 641 " (cutoff:3.500A) removed outlier: 7.750A pdb=" N ILE F 643 " --> pdb=" O GLY F 513 " (cutoff:3.500A) removed outlier: 6.017A pdb=" N LEU F 515 " --> pdb=" O ILE F 643 " (cutoff:3.500A) 1571 hydrogen bonds defined for protein. 4587 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: 8.17 Time building geometry restraints manager: 4.08 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 11907 1.34 - 1.46: 5916 1.46 - 1.58: 17370 1.58 - 1.70: 26 1.70 - 1.82: 284 Bond restraints: 35503 Sorted by residual: bond pdb=" CB PRO A 238 " pdb=" CG PRO A 238 " ideal model delta sigma weight residual 1.492 1.595 -0.103 5.00e-02 4.00e+02 4.21e+00 bond pdb=" N THR A 549 " pdb=" CA THR A 549 " ideal model delta sigma weight residual 1.457 1.481 -0.024 1.29e-02 6.01e+03 3.38e+00 bond pdb=" CB MET E 84 " pdb=" CG MET E 84 " ideal model delta sigma weight residual 1.520 1.474 0.046 3.00e-02 1.11e+03 2.37e+00 bond pdb=" CA ALA A 297 " pdb=" C ALA A 297 " ideal model delta sigma weight residual 1.524 1.543 -0.019 1.26e-02 6.30e+03 2.22e+00 bond pdb=" CB PRO F 727 " pdb=" CG PRO F 727 " ideal model delta sigma weight residual 1.492 1.561 -0.069 5.00e-02 4.00e+02 1.88e+00 ... (remaining 35498 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.21: 47710 3.21 - 6.42: 283 6.42 - 9.63: 10 9.63 - 12.84: 1 12.84 - 16.06: 1 Bond angle restraints: 48005 Sorted by residual: angle pdb=" CB MET E 84 " pdb=" CG MET E 84 " pdb=" SD MET E 84 " ideal model delta sigma weight residual 112.70 96.64 16.06 3.00e+00 1.11e-01 2.86e+01 angle pdb=" CA PRO A 298 " pdb=" N PRO A 298 " pdb=" CD PRO A 298 " ideal model delta sigma weight residual 112.00 106.09 5.91 1.40e+00 5.10e-01 1.78e+01 angle pdb=" CA PRO A 238 " pdb=" N PRO A 238 " pdb=" CD PRO A 238 " ideal model delta sigma weight residual 112.00 106.24 5.76 1.40e+00 5.10e-01 1.69e+01 angle pdb=" C LYS F 336 " pdb=" N GLN F 337 " pdb=" CA GLN F 337 " ideal model delta sigma weight residual 121.54 128.96 -7.42 1.91e+00 2.74e-01 1.51e+01 angle pdb=" CA ALA A 297 " pdb=" C ALA A 297 " pdb=" N PRO A 298 " ideal model delta sigma weight residual 118.44 124.56 -6.12 1.59e+00 3.96e-01 1.48e+01 ... (remaining 48000 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.74: 21498 31.74 - 63.48: 568 63.48 - 95.21: 65 95.21 - 126.95: 4 126.95 - 158.69: 4 Dihedral angle restraints: 22139 sinusoidal: 9376 harmonic: 12763 Sorted by residual: dihedral pdb=" C5' ADP F 902 " pdb=" O5' ADP F 902 " pdb=" PA ADP F 902 " pdb=" O2A ADP F 902 " ideal model delta sinusoidal sigma weight residual -60.00 98.69 -158.69 1 2.00e+01 2.50e-03 4.64e+01 dihedral pdb=" C5' ADP B 902 " pdb=" O5' ADP B 902 " pdb=" PA ADP B 902 " pdb=" O2A ADP B 902 " ideal model delta sinusoidal sigma weight residual -60.00 77.77 -137.77 1 2.00e+01 2.50e-03 4.18e+01 dihedral pdb=" O2A ADP F 902 " pdb=" O3A ADP F 902 " pdb=" PA ADP F 902 " pdb=" PB ADP F 902 " ideal model delta sinusoidal sigma weight residual -60.00 72.72 -132.72 1 2.00e+01 2.50e-03 4.03e+01 ... (remaining 22136 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 3611 0.037 - 0.074: 1184 0.074 - 0.110: 476 0.110 - 0.147: 123 0.147 - 0.184: 3 Chirality restraints: 5397 Sorted by residual: chirality pdb=" CB ILE E 82 " pdb=" CA ILE E 82 " pdb=" CG1 ILE E 82 " pdb=" CG2 ILE E 82 " both_signs ideal model delta sigma weight residual False 2.64 2.46 0.18 2.00e-01 2.50e+01 8.44e-01 chirality pdb=" CA GLU D 261 " pdb=" N GLU D 261 " pdb=" C GLU D 261 " pdb=" CB GLU D 261 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.18e-01 chirality pdb=" CB THR C 467 " pdb=" CA THR C 467 " pdb=" OG1 THR C 467 " pdb=" CG2 THR C 467 " both_signs ideal model delta sigma weight residual False 2.55 2.40 0.15 2.00e-01 2.50e+01 5.48e-01 ... (remaining 5394 not shown) Planarity restraints: 6286 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO A 237 " -0.062 5.00e-02 4.00e+02 9.14e-02 1.34e+01 pdb=" N PRO A 238 " 0.158 5.00e-02 4.00e+02 pdb=" CA PRO A 238 " -0.045 5.00e-02 4.00e+02 pdb=" CD PRO A 238 " -0.050 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG F 635 " 0.054 5.00e-02 4.00e+02 8.22e-02 1.08e+01 pdb=" N PRO F 636 " -0.142 5.00e-02 4.00e+02 pdb=" CA PRO F 636 " 0.043 5.00e-02 4.00e+02 pdb=" CD PRO F 636 " 0.045 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER F 171 " -0.044 5.00e-02 4.00e+02 6.68e-02 7.14e+00 pdb=" N PRO F 172 " 0.116 5.00e-02 4.00e+02 pdb=" CA PRO F 172 " -0.037 5.00e-02 4.00e+02 pdb=" CD PRO F 172 " -0.034 5.00e-02 4.00e+02 ... (remaining 6283 not shown) Histogram of nonbonded interaction distances: 1.95 - 2.54: 197 2.54 - 3.13: 27159 3.13 - 3.72: 55398 3.72 - 4.31: 76647 4.31 - 4.90: 126657 Nonbonded interactions: 286058 Sorted by model distance: nonbonded pdb=" O1G ATP B 901 " pdb="MG MG B 903 " model vdw 1.950 2.170 nonbonded pdb=" OG1 THR C 252 " pdb="MG MG C 903 " model vdw 2.039 2.170 nonbonded pdb=" OG1 THR E 525 " pdb="MG MG E 904 " model vdw 2.043 2.170 nonbonded pdb=" O1B ATP E 902 " pdb="MG MG E 904 " model vdw 2.050 2.170 nonbonded pdb=" OG1 THR D 252 " pdb="MG MG D 903 " model vdw 2.057 2.170 ... (remaining 286053 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 23 through 238 or (resid 239 and (name N or name CA or nam \ e C or name O or name CB )) or resid 240 through 406 or (resid 407 and (name N o \ r name CA or name C or name O or name CB )) or resid 408 through 461 or resid 47 \ 2 through 533 or (resid 534 and (name N or name CA or name C or name O or name C \ B )) or resid 535 through 545 or resid 558 through 583 or resid 596 through 762) \ ) selection = (chain 'B' and (resid 23 through 406 or (resid 407 and (name N or name CA or nam \ e C or name O or name CB )) or resid 408 through 461 or resid 472 through 507 or \ (resid 508 and (name N or name CA or name C or name O or name CB )) or resid 50 \ 9 through 545 or resid 558 through 583 or resid 596 through 762)) selection = (chain 'C' and (resid 23 through 238 or (resid 239 and (name N or name CA or nam \ e C or name O or name CB )) or resid 240 through 406 or (resid 407 and (name N o \ r name CA or name C or name O or name CB )) or resid 408 through 461 or resid 47 \ 2 through 507 or (resid 508 and (name N or name CA or name C or name O or name C \ B )) or resid 509 through 533 or (resid 534 and (name N or name CA or name C or \ name O or name CB )) or resid 535 through 545 or resid 558 through 583 or resid \ 596 through 762)) selection = (chain 'D' and (resid 23 through 238 or (resid 239 and (name N or name CA or nam \ e C or name O or name CB )) or resid 240 through 406 or (resid 407 and (name N o \ r name CA or name C or name O or name CB )) or resid 408 through 461 or resid 47 \ 2 through 507 or (resid 508 and (name N or name CA or name C or name O or name C \ B )) or resid 509 through 533 or (resid 534 and (name N or name CA or name C or \ name O or name CB )) or resid 535 through 545 or resid 558 through 583 or resid \ 596 through 762)) selection = (chain 'E' and (resid 23 through 238 or (resid 239 and (name N or name CA or nam \ e C or name O or name CB )) or resid 240 through 406 or (resid 407 and (name N o \ r name CA or name C or name O or name CB )) or resid 408 through 461 or resid 47 \ 2 through 507 or (resid 508 and (name N or name CA or name C or name O or name C \ B )) or resid 509 through 533 or (resid 534 and (name N or name CA or name C or \ name O or name CB )) or resid 535 through 545 or resid 558 through 583 or resid \ 596 through 762)) selection = (chain 'F' and (resid 23 through 238 or (resid 239 and (name N or name CA or nam \ e C or name O or name CB )) or resid 240 through 507 or (resid 508 and (name N o \ r name CA or name C or name O or name CB )) or resid 509 through 533 or (resid 5 \ 34 and (name N or name CA or name C or name O or name CB )) or resid 535 through \ 762)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.43 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: 2.160 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.030 Extract box with map and model: 0.560 Check model and map are aligned: 0.110 Set scattering table: 0.090 Process input model: 34.090 Find NCS groups from input model: 1.000 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.500 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6137 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 : 0.005 0.103 35503 Z= 0.197 Angle : 0.674 16.056 48005 Z= 0.359 Chirality : 0.044 0.184 5397 Planarity : 0.005 0.091 6286 Dihedral : 14.414 158.690 13855 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 10.73 Ramachandran Plot: Outliers : 0.07 % Allowed : 1.76 % Favored : 98.17 % Rotamer: Outliers : 0.00 % Allowed : 0.32 % Favored : 99.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.55 % 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: 1.48 (0.12), residues: 4375 helix: 1.52 (0.12), residues: 1936 sheet: 1.30 (0.21), residues: 590 loop : 0.42 (0.14), residues: 1849 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG F 313 TYR 0.018 0.002 TYR C 644 PHE 0.022 0.002 PHE A 768 TRP 0.019 0.001 TRP C 454 HIS 0.006 0.001 HIS F 406 Details of bonding type rmsd covalent geometry : bond 0.00464 (35503) covalent geometry : angle 0.67402 (48005) hydrogen bonds : bond 0.17020 ( 1571) hydrogen bonds : angle 6.24537 ( 4587) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8750 Ramachandran restraints generated. 4375 Oldfield, 0 Emsley, 4375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8750 Ramachandran restraints generated. 4375 Oldfield, 0 Emsley, 4375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 3768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 244 time to evaluate : 1.511 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 508 MET cc_start: 0.7861 (mmm) cc_final: 0.7500 (mmm) outliers start: 0 outliers final: 0 residues processed: 244 average time/residue: 0.2556 time to fit residues: 97.7488 Evaluate side-chains 153 residues out of total 3768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 153 time to evaluate : 1.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 442 random chunks: chunk 432 optimal weight: 6.9990 chunk 197 optimal weight: 0.9980 chunk 388 optimal weight: 20.0000 chunk 215 optimal weight: 6.9990 chunk 20 optimal weight: 9.9990 chunk 132 optimal weight: 0.6980 chunk 261 optimal weight: 1.9990 chunk 248 optimal weight: 9.9990 chunk 207 optimal weight: 0.9990 chunk 401 optimal weight: 10.0000 chunk 424 optimal weight: 20.0000 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 735 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 103 GLN C 327 GLN ** C 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 226 HIS ** D 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 260 ASN ** E 538 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 382 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 458 GLN F 578 GLN F 603 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4019 r_free = 0.4019 target = 0.093418 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.062074 restraints weight = 169570.778| |-----------------------------------------------------------------------------| r_work (start): 0.3058 rms_B_bonded: 5.04 r_work (final): 0.3058 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3060 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3060 r_free = 0.3060 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3060 r_free = 0.3060 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3060 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7902 moved from start: 0.1345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 35503 Z= 0.160 Angle : 0.601 10.095 48005 Z= 0.304 Chirality : 0.043 0.162 5397 Planarity : 0.005 0.058 6286 Dihedral : 10.233 158.048 5107 Min Nonbonded Distance : 1.892 Molprobity Statistics. All-atom Clashscore : 10.02 Ramachandran Plot: Outliers : 0.07 % Allowed : 1.49 % Favored : 98.45 % Rotamer: Outliers : 0.32 % Allowed : 5.01 % Favored : 94.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.55 % 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: 1.70 (0.13), residues: 4375 helix: 1.77 (0.12), residues: 1987 sheet: 1.09 (0.20), residues: 611 loop : 0.54 (0.15), residues: 1777 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 86 TYR 0.012 0.001 TYR C 173 PHE 0.014 0.001 PHE D 506 TRP 0.009 0.001 TRP C 454 HIS 0.006 0.001 HIS A 404 Details of bonding type rmsd covalent geometry : bond 0.00356 (35503) covalent geometry : angle 0.60091 (48005) hydrogen bonds : bond 0.04431 ( 1571) hydrogen bonds : angle 4.82742 ( 4587) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8750 Ramachandran restraints generated. 4375 Oldfield, 0 Emsley, 4375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8750 Ramachandran restraints generated. 4375 Oldfield, 0 Emsley, 4375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 3768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 169 time to evaluate : 1.310 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: B 90 ASN cc_start: 0.8490 (m110) cc_final: 0.8028 (p0) REVERT: B 198 LEU cc_start: 0.9503 (tp) cc_final: 0.9240 (mt) REVERT: B 442 MET cc_start: 0.8777 (mmm) cc_final: 0.8091 (mmm) REVERT: B 508 MET cc_start: 0.8432 (OUTLIER) cc_final: 0.8053 (mtp) REVERT: C 84 MET cc_start: 0.8840 (tpp) cc_final: 0.8128 (mmm) REVERT: C 163 PHE cc_start: 0.8674 (m-80) cc_final: 0.8236 (m-80) REVERT: C 508 MET cc_start: 0.9302 (mmm) cc_final: 0.8540 (mmm) REVERT: C 678 MET cc_start: 0.9443 (mmm) cc_final: 0.9212 (mmm) REVERT: D 84 MET cc_start: 0.8486 (ttm) cc_final: 0.8081 (ttm) REVERT: D 134 TYR cc_start: 0.5824 (m-10) cc_final: 0.5335 (m-80) REVERT: D 332 MET cc_start: 0.9055 (OUTLIER) cc_final: 0.8851 (mtp) REVERT: D 442 MET cc_start: 0.8603 (mmm) cc_final: 0.8385 (mmp) REVERT: E 46 MET cc_start: -0.0038 (ptp) cc_final: -0.1289 (tpp) REVERT: E 427 MET cc_start: 0.9055 (mtm) cc_final: 0.8368 (ptp) outliers start: 12 outliers final: 2 residues processed: 174 average time/residue: 0.2329 time to fit residues: 65.4828 Evaluate side-chains 152 residues out of total 3768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 148 time to evaluate : 1.155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 508 MET Chi-restraints excluded: chain B residue 666 VAL Chi-restraints excluded: chain D residue 99 VAL Chi-restraints excluded: chain D residue 332 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 442 random chunks: chunk 153 optimal weight: 0.9980 chunk 86 optimal weight: 30.0000 chunk 159 optimal weight: 20.0000 chunk 382 optimal weight: 10.0000 chunk 386 optimal weight: 7.9990 chunk 368 optimal weight: 9.9990 chunk 254 optimal weight: 9.9990 chunk 360 optimal weight: 9.9990 chunk 248 optimal weight: 8.9990 chunk 404 optimal weight: 8.9990 chunk 253 optimal weight: 4.9990 overall best weight: 6.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 735 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 270 ASN ** B 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 404 HIS B 533 ASN ** C 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 603 GLN D 103 GLN D 327 GLN ** D 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 538 ASN E 296 ASN E 384 HIS ** F 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 226 HIS ** F 382 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.089952 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.058118 restraints weight = 178711.542| |-----------------------------------------------------------------------------| r_work (start): 0.2950 rms_B_bonded: 4.89 r_work (final): 0.2950 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8076 moved from start: 0.2273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.071 35503 Z= 0.342 Angle : 0.740 9.696 48005 Z= 0.370 Chirality : 0.045 0.160 5397 Planarity : 0.005 0.055 6286 Dihedral : 10.272 173.254 5107 Min Nonbonded Distance : 1.660 Molprobity Statistics. All-atom Clashscore : 12.68 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.10 % Favored : 97.83 % Rotamer: Outliers : 0.89 % Allowed : 7.62 % Favored : 91.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.55 % 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: 4375 helix: 1.58 (0.12), residues: 2000 sheet: 0.86 (0.20), residues: 608 loop : 0.51 (0.15), residues: 1767 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG B 89 TYR 0.020 0.002 TYR B 134 PHE 0.018 0.002 PHE F 363 TRP 0.012 0.002 TRP E 454 HIS 0.008 0.002 HIS F 406 Details of bonding type rmsd covalent geometry : bond 0.00757 (35503) covalent geometry : angle 0.74039 (48005) hydrogen bonds : bond 0.04724 ( 1571) hydrogen bonds : angle 4.99338 ( 4587) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8750 Ramachandran restraints generated. 4375 Oldfield, 0 Emsley, 4375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8750 Ramachandran restraints generated. 4375 Oldfield, 0 Emsley, 4375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 3768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 149 time to evaluate : 1.387 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: A 219 MET cc_start: 0.9426 (mpp) cc_final: 0.9194 (mpp) REVERT: A 611 MET cc_start: 0.7358 (mmm) cc_final: 0.7101 (mmm) REVERT: B 138 TYR cc_start: 0.6425 (t80) cc_final: 0.6224 (t80) REVERT: B 198 LEU cc_start: 0.9545 (tp) cc_final: 0.9287 (mt) REVERT: B 270 ASN cc_start: 0.9170 (OUTLIER) cc_final: 0.8831 (m-40) REVERT: B 323 ARG cc_start: 0.9412 (OUTLIER) cc_final: 0.8852 (ttm110) REVERT: B 740 MET cc_start: 0.9456 (tpp) cc_final: 0.9156 (tpp) REVERT: C 163 PHE cc_start: 0.8708 (m-80) cc_final: 0.8216 (m-80) REVERT: C 508 MET cc_start: 0.9354 (mmm) cc_final: 0.8399 (mmm) REVERT: D 84 MET cc_start: 0.8646 (ttm) cc_final: 0.8272 (tmm) REVERT: D 442 MET cc_start: 0.8750 (mmm) cc_final: 0.8508 (mmp) REVERT: D 561 GLU cc_start: 0.8897 (tm-30) cc_final: 0.8695 (tm-30) REVERT: E 219 MET cc_start: 0.9555 (mmm) cc_final: 0.8979 (mmm) REVERT: E 757 MET cc_start: 0.8889 (tmm) cc_final: 0.8673 (tmm) REVERT: F 508 MET cc_start: 0.3241 (mmt) cc_final: 0.2775 (mmp) REVERT: F 608 MET cc_start: 0.8942 (ppp) cc_final: 0.8702 (ppp) outliers start: 33 outliers final: 7 residues processed: 179 average time/residue: 0.2348 time to fit residues: 68.1874 Evaluate side-chains 149 residues out of total 3768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 140 time to evaluate : 1.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 270 ASN Chi-restraints excluded: chain B residue 323 ARG Chi-restraints excluded: chain B residue 404 HIS Chi-restraints excluded: chain B residue 666 VAL Chi-restraints excluded: chain C residue 295 LYS Chi-restraints excluded: chain C residue 601 ILE Chi-restraints excluded: chain C residue 728 VAL Chi-restraints excluded: chain D residue 99 VAL Chi-restraints excluded: chain E residue 220 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 442 random chunks: chunk 113 optimal weight: 0.2980 chunk 98 optimal weight: 0.8980 chunk 206 optimal weight: 0.9980 chunk 350 optimal weight: 4.9990 chunk 77 optimal weight: 7.9990 chunk 301 optimal weight: 30.0000 chunk 348 optimal weight: 1.9990 chunk 367 optimal weight: 0.9980 chunk 18 optimal weight: 20.0000 chunk 264 optimal weight: 7.9990 chunk 89 optimal weight: 50.0000 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 199 ASN ** A 735 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 538 ASN E 384 HIS E 404 HIS E 538 ASN ** F 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 382 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3992 r_free = 0.3992 target = 0.091212 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.059855 restraints weight = 172158.455| |-----------------------------------------------------------------------------| r_work (start): 0.3028 rms_B_bonded: 4.98 r_work (final): 0.3028 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7976 moved from start: 0.2334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 35503 Z= 0.113 Angle : 0.548 9.489 48005 Z= 0.275 Chirality : 0.042 0.238 5397 Planarity : 0.004 0.051 6286 Dihedral : 9.626 177.228 5107 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.07 % Allowed : 1.37 % Favored : 98.56 % Rotamer: Outliers : 0.62 % Allowed : 8.50 % Favored : 90.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.55 % 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: 1.81 (0.13), residues: 4375 helix: 1.92 (0.12), residues: 1996 sheet: 0.87 (0.20), residues: 613 loop : 0.62 (0.15), residues: 1766 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 65 TYR 0.009 0.001 TYR A 134 PHE 0.011 0.001 PHE F 506 TRP 0.007 0.001 TRP F 454 HIS 0.015 0.001 HIS B 404 Details of bonding type rmsd covalent geometry : bond 0.00250 (35503) covalent geometry : angle 0.54795 (48005) hydrogen bonds : bond 0.03768 ( 1571) hydrogen bonds : angle 4.39633 ( 4587) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8750 Ramachandran restraints generated. 4375 Oldfield, 0 Emsley, 4375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8750 Ramachandran restraints generated. 4375 Oldfield, 0 Emsley, 4375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 3768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 144 time to evaluate : 1.332 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: A 242 LEU cc_start: 0.8715 (OUTLIER) cc_final: 0.8287 (pp) REVERT: A 489 LEU cc_start: 0.9471 (tp) cc_final: 0.9257 (tp) REVERT: B 138 TYR cc_start: 0.6479 (t80) cc_final: 0.6263 (t80) REVERT: B 198 LEU cc_start: 0.9523 (tp) cc_final: 0.9258 (mt) REVERT: B 323 ARG cc_start: 0.9183 (OUTLIER) cc_final: 0.8693 (ttp-110) REVERT: B 442 MET cc_start: 0.8944 (mmm) cc_final: 0.8309 (mmm) REVERT: B 740 MET cc_start: 0.9416 (tpp) cc_final: 0.9001 (tpp) REVERT: C 163 PHE cc_start: 0.8738 (m-80) cc_final: 0.8257 (m-80) REVERT: C 442 MET cc_start: 0.9070 (tmm) cc_final: 0.8861 (tmm) REVERT: C 508 MET cc_start: 0.9332 (mmm) cc_final: 0.8350 (mmm) REVERT: D 84 MET cc_start: 0.8581 (ttm) cc_final: 0.8218 (tmm) REVERT: D 332 MET cc_start: 0.8930 (mtp) cc_final: 0.8450 (ttm) REVERT: D 388 MET cc_start: 0.8327 (mtt) cc_final: 0.7859 (ptp) REVERT: D 442 MET cc_start: 0.8742 (mmm) cc_final: 0.8460 (mmp) REVERT: D 561 GLU cc_start: 0.8837 (tm-30) cc_final: 0.8601 (tm-30) REVERT: E 219 MET cc_start: 0.9601 (mmm) cc_final: 0.9345 (mtp) REVERT: E 427 MET cc_start: 0.9155 (mtp) cc_final: 0.8884 (ptp) REVERT: E 757 MET cc_start: 0.8915 (tmm) cc_final: 0.8640 (tmm) REVERT: F 608 MET cc_start: 0.9028 (ppp) cc_final: 0.8702 (ppp) REVERT: F 738 GLU cc_start: 0.9507 (OUTLIER) cc_final: 0.9250 (pp20) outliers start: 23 outliers final: 6 residues processed: 164 average time/residue: 0.2264 time to fit residues: 61.4569 Evaluate side-chains 147 residues out of total 3768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 138 time to evaluate : 1.435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 479 ILE Chi-restraints excluded: chain B residue 323 ARG Chi-restraints excluded: chain B residue 666 VAL Chi-restraints excluded: chain C residue 492 LEU Chi-restraints excluded: chain C residue 728 VAL Chi-restraints excluded: chain D residue 99 VAL Chi-restraints excluded: chain F residue 738 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 442 random chunks: chunk 82 optimal weight: 50.0000 chunk 332 optimal weight: 9.9990 chunk 111 optimal weight: 3.9990 chunk 420 optimal weight: 8.9990 chunk 17 optimal weight: 40.0000 chunk 243 optimal weight: 4.9990 chunk 294 optimal weight: 7.9990 chunk 97 optimal weight: 9.9990 chunk 281 optimal weight: 1.9990 chunk 44 optimal weight: 2.9990 chunk 338 optimal weight: 0.6980 overall best weight: 2.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 226 HIS ** A 735 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 538 ASN E 384 HIS ** F 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 382 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.090735 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.059495 restraints weight = 173383.365| |-----------------------------------------------------------------------------| r_work (start): 0.2995 rms_B_bonded: 4.93 r_work (final): 0.2995 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8022 moved from start: 0.2548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 35503 Z= 0.171 Angle : 0.564 9.642 48005 Z= 0.281 Chirality : 0.042 0.191 5397 Planarity : 0.004 0.050 6286 Dihedral : 9.370 171.934 5107 Min Nonbonded Distance : 1.850 Molprobity Statistics. All-atom Clashscore : 9.54 Ramachandran Plot: Outliers : 0.07 % Allowed : 1.81 % Favored : 98.13 % Rotamer: Outliers : 0.75 % Allowed : 9.58 % Favored : 89.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.55 % 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: 1.85 (0.13), residues: 4375 helix: 2.03 (0.12), residues: 1977 sheet: 0.89 (0.20), residues: 601 loop : 0.57 (0.15), residues: 1797 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 638 TYR 0.019 0.001 TYR B 134 PHE 0.013 0.001 PHE C 52 TRP 0.006 0.001 TRP B 454 HIS 0.004 0.001 HIS B 317 Details of bonding type rmsd covalent geometry : bond 0.00383 (35503) covalent geometry : angle 0.56442 (48005) hydrogen bonds : bond 0.03606 ( 1571) hydrogen bonds : angle 4.36305 ( 4587) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8750 Ramachandran restraints generated. 4375 Oldfield, 0 Emsley, 4375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8750 Ramachandran restraints generated. 4375 Oldfield, 0 Emsley, 4375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 3768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 138 time to evaluate : 1.304 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: A 219 MET cc_start: 0.9479 (mpp) cc_final: 0.9269 (mpp) REVERT: A 242 LEU cc_start: 0.8715 (OUTLIER) cc_final: 0.8271 (pp) REVERT: A 489 LEU cc_start: 0.9482 (tp) cc_final: 0.9263 (tp) REVERT: A 550 MET cc_start: 0.8608 (ppp) cc_final: 0.8392 (ppp) REVERT: B 138 TYR cc_start: 0.6469 (t80) cc_final: 0.6260 (t80) REVERT: B 158 MET cc_start: 0.2434 (pmm) cc_final: 0.2025 (pmm) REVERT: B 198 LEU cc_start: 0.9542 (tp) cc_final: 0.9286 (mt) REVERT: B 442 MET cc_start: 0.9021 (mmm) cc_final: 0.8404 (mmm) REVERT: B 740 MET cc_start: 0.9407 (tpp) cc_final: 0.9036 (tpp) REVERT: C 163 PHE cc_start: 0.8762 (m-80) cc_final: 0.8327 (m-80) REVERT: C 508 MET cc_start: 0.9362 (mmm) cc_final: 0.8437 (mmm) REVERT: D 84 MET cc_start: 0.8592 (ttm) cc_final: 0.8238 (tmm) REVERT: D 332 MET cc_start: 0.9083 (mtp) cc_final: 0.8477 (ttm) REVERT: D 388 MET cc_start: 0.8327 (mtt) cc_final: 0.7847 (ptp) REVERT: D 442 MET cc_start: 0.8818 (mmm) cc_final: 0.8539 (mmp) REVERT: D 561 GLU cc_start: 0.8834 (tm-30) cc_final: 0.8605 (tm-30) REVERT: E 219 MET cc_start: 0.9609 (mmm) cc_final: 0.9358 (mtp) REVERT: E 427 MET cc_start: 0.9180 (mtp) cc_final: 0.8879 (ptp) REVERT: E 442 MET cc_start: 0.9097 (mmm) cc_final: 0.8571 (tmm) REVERT: E 757 MET cc_start: 0.8941 (tmm) cc_final: 0.8644 (tmm) REVERT: F 84 MET cc_start: 0.0661 (mmt) cc_final: 0.0402 (tpp) REVERT: F 608 MET cc_start: 0.8984 (ppp) cc_final: 0.8688 (ppp) outliers start: 28 outliers final: 13 residues processed: 161 average time/residue: 0.2080 time to fit residues: 55.8352 Evaluate side-chains 151 residues out of total 3768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 137 time to evaluate : 1.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 394 VAL Chi-restraints excluded: chain A residue 479 ILE Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain B residue 323 ARG Chi-restraints excluded: chain B residue 336 LYS Chi-restraints excluded: chain B residue 666 VAL Chi-restraints excluded: chain C residue 492 LEU Chi-restraints excluded: chain C residue 728 VAL Chi-restraints excluded: chain D residue 99 VAL Chi-restraints excluded: chain D residue 475 THR Chi-restraints excluded: chain D residue 601 ILE Chi-restraints excluded: chain F residue 332 MET Chi-restraints excluded: chain F residue 728 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 442 random chunks: chunk 277 optimal weight: 2.9990 chunk 371 optimal weight: 50.0000 chunk 117 optimal weight: 7.9990 chunk 310 optimal weight: 5.9990 chunk 83 optimal weight: 50.0000 chunk 425 optimal weight: 5.9990 chunk 396 optimal weight: 1.9990 chunk 320 optimal weight: 10.0000 chunk 67 optimal weight: 20.0000 chunk 436 optimal weight: 8.9990 chunk 432 optimal weight: 7.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 404 HIS B 406 HIS B 460 ASN ** C 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 103 GLN ** D 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 603 GLN F 91 ASN F 212 GLN ** F 382 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.089808 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.057951 restraints weight = 176036.020| |-----------------------------------------------------------------------------| r_work (start): 0.2943 rms_B_bonded: 4.91 r_work (final): 0.2943 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8091 moved from start: 0.2878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 35503 Z= 0.258 Angle : 0.623 9.877 48005 Z= 0.311 Chirality : 0.043 0.148 5397 Planarity : 0.004 0.051 6286 Dihedral : 9.382 160.270 5107 Min Nonbonded Distance : 1.789 Molprobity Statistics. All-atom Clashscore : 10.86 Ramachandran Plot: Outliers : 0.07 % Allowed : 1.97 % Favored : 97.97 % Rotamer: Outliers : 1.13 % Allowed : 10.20 % Favored : 88.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.55 % 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: 1.74 (0.13), residues: 4375 helix: 1.93 (0.12), residues: 1968 sheet: 0.81 (0.20), residues: 599 loop : 0.54 (0.15), residues: 1808 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 733 TYR 0.010 0.001 TYR F 495 PHE 0.012 0.002 PHE A 152 TRP 0.009 0.001 TRP C 454 HIS 0.006 0.001 HIS C 735 Details of bonding type rmsd covalent geometry : bond 0.00572 (35503) covalent geometry : angle 0.62256 (48005) hydrogen bonds : bond 0.03856 ( 1571) hydrogen bonds : angle 4.52330 ( 4587) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8750 Ramachandran restraints generated. 4375 Oldfield, 0 Emsley, 4375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8750 Ramachandran restraints generated. 4375 Oldfield, 0 Emsley, 4375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 3768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 135 time to evaluate : 0.939 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 550 MET cc_start: 0.8655 (ppp) cc_final: 0.8421 (ppp) REVERT: B 158 MET cc_start: 0.2531 (pmm) cc_final: 0.2087 (pmm) REVERT: B 198 LEU cc_start: 0.9565 (tp) cc_final: 0.9311 (mt) REVERT: B 323 ARG cc_start: 0.9257 (OUTLIER) cc_final: 0.8835 (mtm-85) REVERT: B 442 MET cc_start: 0.9079 (mmm) cc_final: 0.8457 (mmm) REVERT: B 740 MET cc_start: 0.9418 (tpp) cc_final: 0.9159 (tpp) REVERT: C 18 LYS cc_start: 0.8440 (tmtt) cc_final: 0.8113 (tptp) REVERT: C 84 MET cc_start: 0.8118 (tpp) cc_final: 0.7793 (tpp) REVERT: C 163 PHE cc_start: 0.8788 (m-80) cc_final: 0.8401 (m-80) REVERT: C 427 MET cc_start: 0.8137 (tmm) cc_final: 0.7908 (tmm) REVERT: C 442 MET cc_start: 0.8993 (tmm) cc_final: 0.8754 (tmm) REVERT: D 84 MET cc_start: 0.8689 (ttm) cc_final: 0.8317 (tmm) REVERT: D 388 MET cc_start: 0.8423 (mtt) cc_final: 0.7868 (ptp) REVERT: D 442 MET cc_start: 0.8832 (mmm) cc_final: 0.8571 (mmp) REVERT: D 561 GLU cc_start: 0.8862 (tm-30) cc_final: 0.8629 (tm-30) REVERT: E 219 MET cc_start: 0.9617 (mmm) cc_final: 0.9363 (mtp) REVERT: E 427 MET cc_start: 0.9179 (mtp) cc_final: 0.8970 (ptm) REVERT: E 466 GLU cc_start: 0.9303 (tm-30) cc_final: 0.8937 (tm-30) REVERT: E 757 MET cc_start: 0.8960 (tmm) cc_final: 0.8714 (tmm) outliers start: 42 outliers final: 22 residues processed: 170 average time/residue: 0.2143 time to fit residues: 60.1608 Evaluate side-chains 157 residues out of total 3768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 134 time to evaluate : 1.084 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 394 VAL Chi-restraints excluded: chain A residue 479 ILE Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain B residue 323 ARG Chi-restraints excluded: chain B residue 336 LYS Chi-restraints excluded: chain B residue 404 HIS Chi-restraints excluded: chain B residue 475 THR Chi-restraints excluded: chain B residue 525 THR Chi-restraints excluded: chain B residue 666 VAL Chi-restraints excluded: chain C residue 295 LYS Chi-restraints excluded: chain C residue 492 LEU Chi-restraints excluded: chain C residue 728 VAL Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 475 THR Chi-restraints excluded: chain D residue 492 LEU Chi-restraints excluded: chain D residue 601 ILE Chi-restraints excluded: chain E residue 59 LEU Chi-restraints excluded: chain E residue 224 LEU Chi-restraints excluded: chain E residue 388 MET Chi-restraints excluded: chain E residue 448 THR Chi-restraints excluded: chain E residue 467 THR Chi-restraints excluded: chain F residue 332 MET Chi-restraints excluded: chain F residue 728 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 442 random chunks: chunk 141 optimal weight: 9.9990 chunk 41 optimal weight: 20.0000 chunk 164 optimal weight: 40.0000 chunk 360 optimal weight: 7.9990 chunk 165 optimal weight: 2.9990 chunk 238 optimal weight: 50.0000 chunk 317 optimal weight: 2.9990 chunk 273 optimal weight: 1.9990 chunk 72 optimal weight: 0.7980 chunk 393 optimal weight: 10.0000 chunk 113 optimal weight: 0.2980 overall best weight: 1.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 735 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 382 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.090431 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.059336 restraints weight = 172916.705| |-----------------------------------------------------------------------------| r_work (start): 0.2999 rms_B_bonded: 4.90 r_work (final): 0.2999 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8023 moved from start: 0.2949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 35503 Z= 0.127 Angle : 0.550 9.703 48005 Z= 0.273 Chirality : 0.042 0.181 5397 Planarity : 0.004 0.049 6286 Dihedral : 9.084 160.627 5107 Min Nonbonded Distance : 1.873 Molprobity Statistics. All-atom Clashscore : 9.52 Ramachandran Plot: Outliers : 0.07 % Allowed : 1.74 % Favored : 98.19 % Rotamer: Outliers : 0.94 % Allowed : 10.71 % Favored : 88.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.55 % 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: 1.88 (0.13), residues: 4375 helix: 2.07 (0.12), residues: 1970 sheet: 0.87 (0.20), residues: 597 loop : 0.58 (0.15), residues: 1808 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 567 TYR 0.018 0.001 TYR B 134 PHE 0.012 0.001 PHE A 152 TRP 0.009 0.001 TRP C 454 HIS 0.012 0.001 HIS B 404 Details of bonding type rmsd covalent geometry : bond 0.00285 (35503) covalent geometry : angle 0.54965 (48005) hydrogen bonds : bond 0.03475 ( 1571) hydrogen bonds : angle 4.24584 ( 4587) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8750 Ramachandran restraints generated. 4375 Oldfield, 0 Emsley, 4375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8750 Ramachandran restraints generated. 4375 Oldfield, 0 Emsley, 4375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 3768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 136 time to evaluate : 1.388 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: A 242 LEU cc_start: 0.8946 (OUTLIER) cc_final: 0.8636 (pp) REVERT: A 550 MET cc_start: 0.8575 (ppp) cc_final: 0.8338 (ppp) REVERT: A 611 MET cc_start: 0.7312 (mmm) cc_final: 0.6782 (mmm) REVERT: B 158 MET cc_start: 0.2399 (pmm) cc_final: 0.2014 (pmm) REVERT: B 198 LEU cc_start: 0.9562 (tp) cc_final: 0.9306 (mt) REVERT: B 323 ARG cc_start: 0.9226 (OUTLIER) cc_final: 0.8532 (ttm110) REVERT: B 442 MET cc_start: 0.9041 (mmm) cc_final: 0.8410 (mmm) REVERT: B 740 MET cc_start: 0.9361 (tpp) cc_final: 0.9074 (tpp) REVERT: C 18 LYS cc_start: 0.8425 (tmtt) cc_final: 0.8087 (tptp) REVERT: C 84 MET cc_start: 0.8207 (tpp) cc_final: 0.7638 (tpp) REVERT: C 163 PHE cc_start: 0.8854 (m-80) cc_final: 0.8502 (m-80) REVERT: C 427 MET cc_start: 0.8160 (tmm) cc_final: 0.7919 (tmm) REVERT: D 84 MET cc_start: 0.8722 (ttm) cc_final: 0.8318 (tmm) REVERT: D 442 MET cc_start: 0.8772 (mmm) cc_final: 0.8486 (mmp) REVERT: D 561 GLU cc_start: 0.8845 (tm-30) cc_final: 0.8589 (tm-30) REVERT: E 173 TYR cc_start: 0.6829 (OUTLIER) cc_final: 0.5945 (m-80) REVERT: E 219 MET cc_start: 0.9616 (mmm) cc_final: 0.9338 (mtp) REVERT: E 427 MET cc_start: 0.9216 (mtp) cc_final: 0.9011 (ptm) REVERT: E 466 GLU cc_start: 0.9264 (tm-30) cc_final: 0.8864 (tm-30) REVERT: E 757 MET cc_start: 0.8979 (tmm) cc_final: 0.8711 (tmm) REVERT: F 608 MET cc_start: 0.8798 (ppp) cc_final: 0.8585 (ppp) outliers start: 35 outliers final: 19 residues processed: 166 average time/residue: 0.2221 time to fit residues: 61.7555 Evaluate side-chains 158 residues out of total 3768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 136 time to evaluate : 1.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 479 ILE Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain B residue 323 ARG Chi-restraints excluded: chain B residue 336 LYS Chi-restraints excluded: chain B residue 460 ASN Chi-restraints excluded: chain B residue 666 VAL Chi-restraints excluded: chain C residue 492 LEU Chi-restraints excluded: chain C residue 728 VAL Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 59 LEU Chi-restraints excluded: chain D residue 96 LEU Chi-restraints excluded: chain D residue 492 LEU Chi-restraints excluded: chain D residue 601 ILE Chi-restraints excluded: chain E residue 59 LEU Chi-restraints excluded: chain E residue 173 TYR Chi-restraints excluded: chain E residue 220 VAL Chi-restraints excluded: chain E residue 224 LEU Chi-restraints excluded: chain E residue 388 MET Chi-restraints excluded: chain E residue 467 THR Chi-restraints excluded: chain F residue 728 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 442 random chunks: chunk 431 optimal weight: 6.9990 chunk 191 optimal weight: 0.9980 chunk 347 optimal weight: 7.9990 chunk 28 optimal weight: 4.9990 chunk 158 optimal weight: 3.9990 chunk 52 optimal weight: 4.9990 chunk 122 optimal weight: 1.9990 chunk 318 optimal weight: 0.9990 chunk 105 optimal weight: 7.9990 chunk 199 optimal weight: 6.9990 chunk 110 optimal weight: 2.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 103 GLN ** A 735 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 624 ASN ** D 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 382 GLN ** 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 = 0.3970 r_free = 0.3970 target = 0.090378 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.059419 restraints weight = 174618.811| |-----------------------------------------------------------------------------| r_work (start): 0.3000 rms_B_bonded: 4.88 r_work (final): 0.3000 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8030 moved from start: 0.3068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 35503 Z= 0.140 Angle : 0.557 11.062 48005 Z= 0.274 Chirality : 0.042 0.190 5397 Planarity : 0.004 0.049 6286 Dihedral : 8.926 157.472 5107 Min Nonbonded Distance : 1.858 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.07 % Allowed : 1.87 % Favored : 98.06 % Rotamer: Outliers : 0.81 % Allowed : 11.17 % Favored : 88.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.55 % 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: 1.91 (0.13), residues: 4375 helix: 2.10 (0.12), residues: 1973 sheet: 0.86 (0.20), residues: 601 loop : 0.60 (0.15), residues: 1801 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 83 TYR 0.008 0.001 TYR F 495 PHE 0.012 0.001 PHE A 152 TRP 0.008 0.001 TRP C 454 HIS 0.004 0.001 HIS D 384 Details of bonding type rmsd covalent geometry : bond 0.00315 (35503) covalent geometry : angle 0.55655 (48005) hydrogen bonds : bond 0.03360 ( 1571) hydrogen bonds : angle 4.21652 ( 4587) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8750 Ramachandran restraints generated. 4375 Oldfield, 0 Emsley, 4375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8750 Ramachandran restraints generated. 4375 Oldfield, 0 Emsley, 4375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 3768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 138 time to evaluate : 1.386 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 550 MET cc_start: 0.8563 (ppp) cc_final: 0.8313 (ppp) REVERT: B 90 ASN cc_start: 0.8601 (m110) cc_final: 0.8243 (t0) REVERT: B 158 MET cc_start: 0.2400 (pmm) cc_final: 0.2009 (pmm) REVERT: B 323 ARG cc_start: 0.9225 (OUTLIER) cc_final: 0.8356 (ttm110) REVERT: B 442 MET cc_start: 0.9064 (mmm) cc_final: 0.8445 (mmm) REVERT: B 740 MET cc_start: 0.9332 (tpp) cc_final: 0.8846 (tpp) REVERT: C 18 LYS cc_start: 0.8469 (tmtt) cc_final: 0.8071 (tmtt) REVERT: C 163 PHE cc_start: 0.8863 (m-80) cc_final: 0.8518 (m-80) REVERT: C 427 MET cc_start: 0.8163 (tmm) cc_final: 0.7916 (tmm) REVERT: D 84 MET cc_start: 0.8708 (ttm) cc_final: 0.8291 (tmm) REVERT: D 442 MET cc_start: 0.8772 (mmm) cc_final: 0.8484 (mmp) REVERT: D 561 GLU cc_start: 0.8856 (tm-30) cc_final: 0.8597 (tm-30) REVERT: E 173 TYR cc_start: 0.6831 (OUTLIER) cc_final: 0.5987 (m-80) REVERT: E 219 MET cc_start: 0.9629 (mmm) cc_final: 0.9344 (mtp) REVERT: E 466 GLU cc_start: 0.9260 (tm-30) cc_final: 0.8862 (tm-30) REVERT: E 757 MET cc_start: 0.8996 (tmm) cc_final: 0.8731 (tmm) REVERT: F 332 MET cc_start: 0.9220 (OUTLIER) cc_final: 0.8968 (ttm) outliers start: 30 outliers final: 22 residues processed: 163 average time/residue: 0.2262 time to fit residues: 61.7575 Evaluate side-chains 161 residues out of total 3768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 136 time to evaluate : 1.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 479 ILE Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain B residue 323 ARG Chi-restraints excluded: chain B residue 336 LYS Chi-restraints excluded: chain B residue 460 ASN Chi-restraints excluded: chain B residue 475 THR Chi-restraints excluded: chain B residue 489 LEU Chi-restraints excluded: chain B residue 666 VAL Chi-restraints excluded: chain C residue 492 LEU Chi-restraints excluded: chain C residue 728 VAL Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 59 LEU Chi-restraints excluded: chain D residue 96 LEU Chi-restraints excluded: chain D residue 388 MET Chi-restraints excluded: chain D residue 492 LEU Chi-restraints excluded: chain D residue 601 ILE Chi-restraints excluded: chain E residue 59 LEU Chi-restraints excluded: chain E residue 173 TYR Chi-restraints excluded: chain E residue 220 VAL Chi-restraints excluded: chain E residue 224 LEU Chi-restraints excluded: chain E residue 388 MET Chi-restraints excluded: chain E residue 467 THR Chi-restraints excluded: chain F residue 332 MET Chi-restraints excluded: chain F residue 728 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 442 random chunks: chunk 152 optimal weight: 20.0000 chunk 109 optimal weight: 9.9990 chunk 8 optimal weight: 0.9980 chunk 338 optimal weight: 9.9990 chunk 199 optimal weight: 4.9990 chunk 244 optimal weight: 3.9990 chunk 77 optimal weight: 8.9990 chunk 245 optimal weight: 0.7980 chunk 121 optimal weight: 0.9990 chunk 72 optimal weight: 1.9990 chunk 147 optimal weight: 7.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 735 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 382 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3993 r_free = 0.3993 target = 0.090803 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.060928 restraints weight = 172620.131| |-----------------------------------------------------------------------------| r_work (start): 0.3003 rms_B_bonded: 6.17 r_work (final): 0.3003 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8132 moved from start: 0.3163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 35503 Z= 0.123 Angle : 0.557 12.416 48005 Z= 0.273 Chirality : 0.041 0.192 5397 Planarity : 0.004 0.050 6286 Dihedral : 8.733 156.071 5107 Min Nonbonded Distance : 1.876 Molprobity Statistics. All-atom Clashscore : 9.17 Ramachandran Plot: Outliers : 0.07 % Allowed : 1.85 % Favored : 98.08 % Rotamer: Outliers : 0.97 % Allowed : 11.22 % Favored : 87.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.55 % 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: 1.96 (0.13), residues: 4375 helix: 2.15 (0.12), residues: 1970 sheet: 0.92 (0.20), residues: 602 loop : 0.59 (0.15), residues: 1803 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 53 TYR 0.019 0.001 TYR B 134 PHE 0.012 0.001 PHE A 152 TRP 0.008 0.001 TRP C 454 HIS 0.004 0.001 HIS B 317 Details of bonding type rmsd covalent geometry : bond 0.00276 (35503) covalent geometry : angle 0.55671 (48005) hydrogen bonds : bond 0.03242 ( 1571) hydrogen bonds : angle 4.14131 ( 4587) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8750 Ramachandran restraints generated. 4375 Oldfield, 0 Emsley, 4375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8750 Ramachandran restraints generated. 4375 Oldfield, 0 Emsley, 4375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 3768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 137 time to evaluate : 1.320 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: A 242 LEU cc_start: 0.8943 (OUTLIER) cc_final: 0.8706 (pp) REVERT: A 275 MET cc_start: -0.1263 (mtm) cc_final: -0.1520 (mtm) REVERT: A 611 MET cc_start: 0.7560 (mmm) cc_final: 0.6942 (mmm) REVERT: B 158 MET cc_start: 0.2669 (pmm) cc_final: 0.2376 (pmm) REVERT: B 323 ARG cc_start: 0.9207 (OUTLIER) cc_final: 0.8402 (mtm110) REVERT: B 442 MET cc_start: 0.9074 (mmm) cc_final: 0.8562 (mmm) REVERT: B 740 MET cc_start: 0.9488 (tpp) cc_final: 0.8863 (tpp) REVERT: C 18 LYS cc_start: 0.8316 (tmtt) cc_final: 0.7979 (tmtt) REVERT: C 163 PHE cc_start: 0.8883 (m-80) cc_final: 0.8566 (m-80) REVERT: C 427 MET cc_start: 0.8279 (tmm) cc_final: 0.8037 (tmm) REVERT: C 508 MET cc_start: 0.9203 (mmm) cc_final: 0.8516 (mmm) REVERT: D 46 MET cc_start: 0.5613 (ptp) cc_final: 0.4747 (ptp) REVERT: D 84 MET cc_start: 0.8640 (ttm) cc_final: 0.8221 (tmm) REVERT: D 442 MET cc_start: 0.8733 (mmm) cc_final: 0.8452 (mmp) REVERT: D 561 GLU cc_start: 0.8873 (tm-30) cc_final: 0.8615 (tm-30) REVERT: E 46 MET cc_start: -0.0343 (ptp) cc_final: -0.1252 (ttp) REVERT: E 173 TYR cc_start: 0.6625 (OUTLIER) cc_final: 0.5902 (m-80) REVERT: E 219 MET cc_start: 0.9602 (mmm) cc_final: 0.9344 (mtp) REVERT: E 427 MET cc_start: 0.9323 (OUTLIER) cc_final: 0.9118 (ptp) REVERT: E 466 GLU cc_start: 0.9130 (tm-30) cc_final: 0.8746 (tm-30) REVERT: E 757 MET cc_start: 0.9058 (tmm) cc_final: 0.8814 (tmm) REVERT: F 84 MET cc_start: 0.2339 (mmt) cc_final: 0.1424 (mpp) REVERT: F 219 MET cc_start: 0.8756 (mmt) cc_final: 0.8401 (mpp) REVERT: F 332 MET cc_start: 0.9204 (OUTLIER) cc_final: 0.8930 (ttm) REVERT: F 608 MET cc_start: 0.8705 (ppp) cc_final: 0.8459 (ppp) outliers start: 36 outliers final: 22 residues processed: 167 average time/residue: 0.2157 time to fit residues: 60.8435 Evaluate side-chains 161 residues out of total 3768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 134 time to evaluate : 1.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 394 VAL Chi-restraints excluded: chain A residue 479 ILE Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain B residue 323 ARG Chi-restraints excluded: chain B residue 336 LYS Chi-restraints excluded: chain B residue 460 ASN Chi-restraints excluded: chain B residue 475 THR Chi-restraints excluded: chain B residue 489 LEU Chi-restraints excluded: chain B residue 666 VAL Chi-restraints excluded: chain C residue 492 LEU Chi-restraints excluded: chain C residue 728 VAL Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 59 LEU Chi-restraints excluded: chain D residue 96 LEU Chi-restraints excluded: chain D residue 388 MET Chi-restraints excluded: chain D residue 475 THR Chi-restraints excluded: chain D residue 492 LEU Chi-restraints excluded: chain E residue 59 LEU Chi-restraints excluded: chain E residue 173 TYR Chi-restraints excluded: chain E residue 220 VAL Chi-restraints excluded: chain E residue 224 LEU Chi-restraints excluded: chain E residue 388 MET Chi-restraints excluded: chain E residue 427 MET Chi-restraints excluded: chain E residue 467 THR Chi-restraints excluded: chain F residue 332 MET Chi-restraints excluded: chain F residue 728 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 442 random chunks: chunk 340 optimal weight: 1.9990 chunk 87 optimal weight: 8.9990 chunk 250 optimal weight: 1.9990 chunk 311 optimal weight: 9.9990 chunk 45 optimal weight: 0.3980 chunk 37 optimal weight: 0.5980 chunk 195 optimal weight: 3.9990 chunk 379 optimal weight: 30.0000 chunk 429 optimal weight: 6.9990 chunk 320 optimal weight: 2.9990 chunk 48 optimal weight: 2.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 735 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 226 HIS B 384 HIS C 348 ASN ** D 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 382 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3994 r_free = 0.3994 target = 0.090788 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.060237 restraints weight = 174575.432| |-----------------------------------------------------------------------------| r_work (start): 0.3059 rms_B_bonded: 4.81 r_work (final): 0.3059 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8046 moved from start: 0.3255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 35503 Z= 0.118 Angle : 0.564 11.751 48005 Z= 0.273 Chirality : 0.042 0.203 5397 Planarity : 0.004 0.049 6286 Dihedral : 8.581 154.542 5107 Min Nonbonded Distance : 1.888 Molprobity Statistics. All-atom Clashscore : 9.22 Ramachandran Plot: Outliers : 0.07 % Allowed : 1.74 % Favored : 98.19 % Rotamer: Outliers : 0.81 % Allowed : 11.63 % Favored : 87.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.55 % 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: 1.98 (0.13), residues: 4375 helix: 2.17 (0.12), residues: 1973 sheet: 0.93 (0.20), residues: 612 loop : 0.59 (0.15), residues: 1790 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 25 TYR 0.008 0.001 TYR A 134 PHE 0.016 0.001 PHE E 163 TRP 0.007 0.001 TRP C 454 HIS 0.004 0.001 HIS B 317 Details of bonding type rmsd covalent geometry : bond 0.00267 (35503) covalent geometry : angle 0.56436 (48005) hydrogen bonds : bond 0.03184 ( 1571) hydrogen bonds : angle 4.09197 ( 4587) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8750 Ramachandran restraints generated. 4375 Oldfield, 0 Emsley, 4375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8750 Ramachandran restraints generated. 4375 Oldfield, 0 Emsley, 4375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 3768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 138 time to evaluate : 1.160 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: A 275 MET cc_start: -0.1489 (mtm) cc_final: -0.1772 (mtm) REVERT: B 84 MET cc_start: 0.7827 (tmm) cc_final: 0.7525 (tmm) REVERT: B 90 ASN cc_start: 0.8553 (m110) cc_final: 0.8216 (t0) REVERT: B 158 MET cc_start: 0.2517 (pmm) cc_final: 0.2220 (pmm) REVERT: B 323 ARG cc_start: 0.9244 (OUTLIER) cc_final: 0.8329 (mtm110) REVERT: B 442 MET cc_start: 0.9072 (mmm) cc_final: 0.8441 (mmm) REVERT: B 740 MET cc_start: 0.9318 (tpp) cc_final: 0.8793 (tpp) REVERT: C 18 LYS cc_start: 0.8461 (tmtt) cc_final: 0.8066 (tmtt) REVERT: C 84 MET cc_start: 0.7688 (tpp) cc_final: 0.7322 (tpp) REVERT: C 163 PHE cc_start: 0.8886 (m-80) cc_final: 0.8557 (m-80) REVERT: C 296 ASN cc_start: 0.8406 (OUTLIER) cc_final: 0.7836 (m-40) REVERT: C 427 MET cc_start: 0.8183 (tmm) cc_final: 0.7926 (tmm) REVERT: C 508 MET cc_start: 0.9255 (mmm) cc_final: 0.8677 (mmm) REVERT: D 84 MET cc_start: 0.8696 (ttm) cc_final: 0.8257 (tmm) REVERT: D 442 MET cc_start: 0.8772 (mmm) cc_final: 0.8471 (mmp) REVERT: D 561 GLU cc_start: 0.8817 (tm-30) cc_final: 0.8594 (tm-30) REVERT: E 173 TYR cc_start: 0.6972 (OUTLIER) cc_final: 0.6197 (m-80) REVERT: E 219 MET cc_start: 0.9628 (mmm) cc_final: 0.9346 (mtp) REVERT: E 427 MET cc_start: 0.9188 (ptm) cc_final: 0.8965 (ptp) REVERT: E 466 GLU cc_start: 0.9263 (tm-30) cc_final: 0.8803 (tm-30) REVERT: E 757 MET cc_start: 0.8992 (tmm) cc_final: 0.8745 (tmm) REVERT: F 84 MET cc_start: 0.2422 (mmt) cc_final: 0.1448 (mpp) REVERT: F 219 MET cc_start: 0.8806 (mmt) cc_final: 0.8477 (mpp) REVERT: F 306 LEU cc_start: 0.9600 (tp) cc_final: 0.9388 (mp) REVERT: F 332 MET cc_start: 0.9222 (OUTLIER) cc_final: 0.8961 (ttm) REVERT: F 608 MET cc_start: 0.8725 (ppp) cc_final: 0.8521 (ppp) outliers start: 30 outliers final: 22 residues processed: 164 average time/residue: 0.2201 time to fit residues: 60.3900 Evaluate side-chains 163 residues out of total 3768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 137 time to evaluate : 1.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 394 VAL Chi-restraints excluded: chain A residue 479 ILE Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain B residue 323 ARG Chi-restraints excluded: chain B residue 460 ASN Chi-restraints excluded: chain B residue 475 THR Chi-restraints excluded: chain B residue 489 LEU Chi-restraints excluded: chain B residue 666 VAL Chi-restraints excluded: chain C residue 296 ASN Chi-restraints excluded: chain C residue 492 LEU Chi-restraints excluded: chain C residue 728 VAL Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 59 LEU Chi-restraints excluded: chain D residue 96 LEU Chi-restraints excluded: chain D residue 388 MET Chi-restraints excluded: chain D residue 475 THR Chi-restraints excluded: chain D residue 492 LEU Chi-restraints excluded: chain E residue 59 LEU Chi-restraints excluded: chain E residue 173 TYR Chi-restraints excluded: chain E residue 220 VAL Chi-restraints excluded: chain E residue 224 LEU Chi-restraints excluded: chain E residue 388 MET Chi-restraints excluded: chain E residue 467 THR Chi-restraints excluded: chain F residue 46 MET Chi-restraints excluded: chain F residue 332 MET Chi-restraints excluded: chain F residue 728 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 442 random chunks: chunk 291 optimal weight: 2.9990 chunk 202 optimal weight: 3.9990 chunk 131 optimal weight: 0.9980 chunk 45 optimal weight: 0.1980 chunk 380 optimal weight: 50.0000 chunk 376 optimal weight: 9.9990 chunk 388 optimal weight: 10.0000 chunk 155 optimal weight: 5.9990 chunk 59 optimal weight: 7.9990 chunk 98 optimal weight: 10.0000 chunk 64 optimal weight: 3.9990 overall best weight: 2.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 735 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 382 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.090503 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.059766 restraints weight = 175432.853| |-----------------------------------------------------------------------------| r_work (start): 0.3037 rms_B_bonded: 4.74 r_work (final): 0.3037 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8076 moved from start: 0.3355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 35503 Z= 0.149 Angle : 0.570 11.420 48005 Z= 0.277 Chirality : 0.042 0.235 5397 Planarity : 0.004 0.049 6286 Dihedral : 8.557 150.546 5107 Min Nonbonded Distance : 1.876 Molprobity Statistics. All-atom Clashscore : 9.49 Ramachandran Plot: Outliers : 0.07 % Allowed : 1.78 % Favored : 98.15 % Rotamer: Outliers : 0.78 % Allowed : 11.68 % Favored : 87.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.55 % 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: 1.99 (0.13), residues: 4375 helix: 2.20 (0.12), residues: 1968 sheet: 0.86 (0.20), residues: 620 loop : 0.61 (0.15), residues: 1787 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 22 TYR 0.019 0.001 TYR B 134 PHE 0.012 0.001 PHE A 152 TRP 0.007 0.001 TRP C 454 HIS 0.004 0.001 HIS B 317 Details of bonding type rmsd covalent geometry : bond 0.00335 (35503) covalent geometry : angle 0.57044 (48005) hydrogen bonds : bond 0.03237 ( 1571) hydrogen bonds : angle 4.11883 ( 4587) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7518.99 seconds wall clock time: 129 minutes 54.51 seconds (7794.51 seconds total)