Starting phenix.real_space_refine on Sat Jun 6 05:52:44 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9y0b_72390/06_2026/9y0b_72390.cif Found real_map, /net/cci-nas-00/data/ceres_data/9y0b_72390/06_2026/9y0b_72390.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.61 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9y0b_72390/06_2026/9y0b_72390.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9y0b_72390/06_2026/9y0b_72390.map" model { file = "/net/cci-nas-00/data/ceres_data/9y0b_72390/06_2026/9y0b_72390.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9y0b_72390/06_2026/9y0b_72390.cif" } resolution = 2.61 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= 0.018 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: 5 Type Number sf(0) Gaussians P 24 5.49 5 S 132 5.16 5 C 16104 2.51 5 N 4512 2.21 5 O 4920 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6079/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 25692 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 4228 Number of conformers: 1 Conformer: "" Number of residues, atoms: 544, 4228 Classifications: {'peptide': 544} Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 26, 'TRANS': 514} Chain breaks: 1 Chain: "B" Number of atoms: 4228 Number of conformers: 1 Conformer: "" Number of residues, atoms: 544, 4228 Classifications: {'peptide': 544} Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 26, 'TRANS': 514} Chain breaks: 1 Chain: "C" Number of atoms: 4228 Number of conformers: 1 Conformer: "" Number of residues, atoms: 544, 4228 Classifications: {'peptide': 544} Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 26, 'TRANS': 514} Chain breaks: 1 Chain: "D" Number of atoms: 4228 Number of conformers: 1 Conformer: "" Number of residues, atoms: 544, 4228 Classifications: {'peptide': 544} Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 26, 'TRANS': 514} Chain breaks: 1 Chain: "E" Number of atoms: 4228 Number of conformers: 1 Conformer: "" Number of residues, atoms: 544, 4228 Classifications: {'peptide': 544} Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 26, 'TRANS': 514} Chain breaks: 1 Chain: "F" Number of atoms: 4228 Number of conformers: 1 Conformer: "" Number of residues, atoms: 544, 4228 Classifications: {'peptide': 544} Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 26, 'TRANS': 514} Chain breaks: 1 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: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 54 Unusual residues: {'ADP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" 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: "D" 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: "E" 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: "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: 6.54, per 1000 atoms: 0.25 Number of scatterers: 25692 At special positions: 0 Unit cell: (141, 143, 96, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 132 16.00 P 24 15.00 O 4920 8.00 N 4512 7.00 C 16104 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.35 Conformation dependent library (CDL) restraints added in 1.1 seconds 6480 Ramachandran restraints generated. 3240 Oldfield, 0 Emsley, 3240 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6072 Finding SS restraints... Secondary structure from input PDB file: 192 helices and 12 sheets defined 61.1% alpha, 7.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.79 Creating SS restraints... Processing helix chain 'A' and resid 202 through 206 Processing helix chain 'A' and resid 211 through 226 removed outlier: 5.396A pdb=" N LEU A 222 " --> pdb=" O GLU A 218 " (cutoff:3.500A) Proline residue: A 223 - end of helix Processing helix chain 'A' and resid 226 through 233 removed outlier: 3.533A pdb=" N PHE A 230 " --> pdb=" O HIS A 226 " (cutoff:3.500A) Processing helix chain 'A' and resid 250 through 263 Processing helix chain 'A' and resid 270 through 276 Processing helix chain 'A' and resid 280 through 296 removed outlier: 3.528A pdb=" N LYS A 295 " --> pdb=" O GLU A 291 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ASN A 296 " --> pdb=" O GLU A 292 " (cutoff:3.500A) Processing helix chain 'A' and resid 305 through 310 removed outlier: 3.905A pdb=" N ILE A 309 " --> pdb=" O GLU A 305 " (cutoff:3.500A) Processing helix chain 'A' and resid 318 through 326 Processing helix chain 'A' and resid 328 through 334 Processing helix chain 'A' and resid 349 through 353 removed outlier: 4.152A pdb=" N ILE A 353 " --> pdb=" O PRO A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 354 through 359 removed outlier: 3.618A pdb=" N ARG A 359 " --> pdb=" O ALA A 356 " (cutoff:3.500A) Processing helix chain 'A' and resid 373 through 385 Processing helix chain 'A' and resid 398 through 403 Processing helix chain 'A' and resid 407 through 426 Processing helix chain 'A' and resid 439 through 445 removed outlier: 3.901A pdb=" N ASN A 443 " --> pdb=" O ALA A 439 " (cutoff:3.500A) Processing helix chain 'A' and resid 448 through 457 Processing helix chain 'A' and resid 475 through 479 Processing helix chain 'A' and resid 482 through 499 Proline residue: A 496 - end of helix Processing helix chain 'A' and resid 499 through 507 removed outlier: 3.554A pdb=" N PHE A 506 " --> pdb=" O LYS A 502 " (cutoff:3.500A) Processing helix chain 'A' and resid 523 through 536 Processing helix chain 'A' and resid 543 through 553 Processing helix chain 'A' and resid 557 through 569 removed outlier: 3.855A pdb=" N GLU A 561 " --> pdb=" O ALA A 557 " (cutoff:3.500A) Processing helix chain 'A' and resid 580 through 586 Processing helix chain 'A' and resid 598 through 610 Processing helix chain 'A' and resid 625 through 629 Processing helix chain 'A' and resid 630 through 634 Processing helix chain 'A' and resid 649 through 661 removed outlier: 3.583A pdb=" N ALA A 655 " --> pdb=" O LYS A 651 " (cutoff:3.500A) Processing helix chain 'A' and resid 662 through 664 No H-bonds generated for 'chain 'A' and resid 662 through 664' Processing helix chain 'A' and resid 671 through 679 removed outlier: 3.921A pdb=" N LEU A 675 " --> pdb=" O ASP A 671 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N THR A 679 " --> pdb=" O LEU A 675 " (cutoff:3.500A) Processing helix chain 'A' and resid 683 through 705 Processing helix chain 'A' and resid 732 through 742 removed outlier: 4.007A pdb=" N PHE A 736 " --> pdb=" O ARG A 732 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N PHE A 742 " --> pdb=" O GLU A 738 " (cutoff:3.500A) Processing helix chain 'A' and resid 748 through 763 Processing helix chain 'B' and resid 202 through 206 Processing helix chain 'B' and resid 211 through 226 removed outlier: 5.169A pdb=" N LEU B 222 " --> pdb=" O GLU B 218 " (cutoff:3.500A) Proline residue: B 223 - end of helix Processing helix chain 'B' and resid 226 through 233 removed outlier: 3.565A pdb=" N PHE B 230 " --> pdb=" O HIS B 226 " (cutoff:3.500A) Processing helix chain 'B' and resid 250 through 263 Processing helix chain 'B' and resid 270 through 277 removed outlier: 3.527A pdb=" N LYS B 277 " --> pdb=" O GLU B 273 " (cutoff:3.500A) Processing helix chain 'B' and resid 281 through 296 removed outlier: 3.583A pdb=" N PHE B 290 " --> pdb=" O LEU B 286 " (cutoff:3.500A) Processing helix chain 'B' and resid 305 through 310 removed outlier: 3.726A pdb=" N ILE B 309 " --> pdb=" O GLU B 305 " (cutoff:3.500A) Processing helix chain 'B' and resid 318 through 326 Processing helix chain 'B' and resid 328 through 334 Processing helix chain 'B' and resid 349 through 353 removed outlier: 4.017A pdb=" N ILE B 353 " --> pdb=" O PRO B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 354 through 359 removed outlier: 3.587A pdb=" N ARG B 359 " --> pdb=" O ALA B 356 " (cutoff:3.500A) Processing helix chain 'B' and resid 373 through 385 Processing helix chain 'B' and resid 398 through 403 Processing helix chain 'B' and resid 407 through 426 Processing helix chain 'B' and resid 439 through 445 removed outlier: 3.943A pdb=" N ASN B 443 " --> pdb=" O ALA B 439 " (cutoff:3.500A) Processing helix chain 'B' and resid 448 through 458 Processing helix chain 'B' and resid 475 through 479 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 Processing helix chain 'B' and resid 523 through 536 Processing helix chain 'B' and resid 543 through 554 Processing helix chain 'B' and resid 557 through 569 removed outlier: 3.908A pdb=" N GLU B 561 " --> pdb=" O ALA B 557 " (cutoff:3.500A) Processing helix chain 'B' and resid 580 through 586 Processing helix chain 'B' and resid 598 through 610 Processing helix chain 'B' and resid 625 through 629 Processing helix chain 'B' and resid 630 through 634 Processing helix chain 'B' and resid 649 through 661 removed outlier: 3.571A pdb=" N ALA B 655 " --> pdb=" O LYS B 651 " (cutoff:3.500A) Processing helix chain 'B' and resid 662 through 664 No H-bonds generated for 'chain 'B' and resid 662 through 664' Processing helix chain 'B' and resid 671 through 679 removed outlier: 3.875A pdb=" N LEU B 675 " --> pdb=" O ASP B 671 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N THR B 679 " --> pdb=" O LEU B 675 " (cutoff:3.500A) Processing helix chain 'B' and resid 683 through 705 Processing helix chain 'B' and resid 732 through 742 removed outlier: 4.010A pdb=" N PHE B 736 " --> pdb=" O ARG B 732 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N PHE B 742 " --> pdb=" O GLU B 738 " (cutoff:3.500A) Processing helix chain 'B' and resid 748 through 763 Processing helix chain 'C' and resid 202 through 206 Processing helix chain 'C' and resid 211 through 226 removed outlier: 5.126A pdb=" N LEU C 222 " --> pdb=" O GLU C 218 " (cutoff:3.500A) Proline residue: C 223 - end of helix Processing helix chain 'C' and resid 226 through 233 Processing helix chain 'C' and resid 250 through 263 Processing helix chain 'C' and resid 270 through 277 removed outlier: 3.759A pdb=" N LYS C 277 " --> pdb=" O GLU C 273 " (cutoff:3.500A) Processing helix chain 'C' and resid 280 through 296 removed outlier: 3.510A pdb=" N LYS C 295 " --> pdb=" O GLU C 291 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ASN C 296 " --> pdb=" O GLU C 292 " (cutoff:3.500A) Processing helix chain 'C' and resid 305 through 310 removed outlier: 3.834A pdb=" N ILE C 309 " --> pdb=" O GLU C 305 " (cutoff:3.500A) Processing helix chain 'C' and resid 318 through 326 Processing helix chain 'C' and resid 328 through 334 Processing helix chain 'C' and resid 349 through 353 removed outlier: 4.051A pdb=" N ILE C 353 " --> pdb=" O PRO C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 354 through 359 removed outlier: 3.574A pdb=" N ARG C 359 " --> pdb=" O ALA C 356 " (cutoff:3.500A) Processing helix chain 'C' and resid 373 through 385 Processing helix chain 'C' and resid 398 through 403 Processing helix chain 'C' and resid 407 through 426 Processing helix chain 'C' and resid 439 through 445 removed outlier: 3.715A pdb=" N ASN C 443 " --> pdb=" O ALA C 439 " (cutoff:3.500A) Processing helix chain 'C' and resid 448 through 458 Processing helix chain 'C' and resid 475 through 479 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 Processing helix chain 'C' and resid 523 through 535 Processing helix chain 'C' and resid 543 through 553 Processing helix chain 'C' and resid 557 through 569 removed outlier: 3.852A pdb=" N GLU C 561 " --> pdb=" O ALA C 557 " (cutoff:3.500A) Processing helix chain 'C' and resid 580 through 586 Processing helix chain 'C' and resid 598 through 610 removed outlier: 3.520A pdb=" N GLN C 603 " --> pdb=" O ARG C 599 " (cutoff:3.500A) Processing helix chain 'C' and resid 625 through 629 Processing helix chain 'C' and resid 630 through 634 removed outlier: 3.516A pdb=" N ILE C 633 " --> pdb=" O ASP C 630 " (cutoff:3.500A) Processing helix chain 'C' and resid 649 through 661 removed outlier: 3.619A pdb=" N ALA C 655 " --> pdb=" O LYS C 651 " (cutoff:3.500A) Processing helix chain 'C' and resid 662 through 664 No H-bonds generated for 'chain 'C' and resid 662 through 664' Processing helix chain 'C' and resid 671 through 679 removed outlier: 3.849A pdb=" N LEU C 675 " --> pdb=" O ASP C 671 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N THR C 679 " --> pdb=" O LEU C 675 " (cutoff:3.500A) Processing helix chain 'C' and resid 683 through 705 Processing helix chain 'C' and resid 732 through 742 removed outlier: 3.994A pdb=" N PHE C 736 " --> pdb=" O ARG C 732 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N PHE C 742 " --> pdb=" O GLU C 738 " (cutoff:3.500A) Processing helix chain 'C' and resid 748 through 763 Processing helix chain 'D' and resid 202 through 206 Processing helix chain 'D' and resid 211 through 226 removed outlier: 5.304A pdb=" N LEU D 222 " --> pdb=" O GLU D 218 " (cutoff:3.500A) Proline residue: D 223 - end of helix Processing helix chain 'D' and resid 226 through 233 removed outlier: 3.510A pdb=" N PHE D 230 " --> pdb=" O HIS D 226 " (cutoff:3.500A) Processing helix chain 'D' and resid 250 through 263 Processing helix chain 'D' and resid 270 through 277 removed outlier: 3.834A pdb=" N LYS D 277 " --> pdb=" O GLU D 273 " (cutoff:3.500A) Processing helix chain 'D' and resid 280 through 296 removed outlier: 3.527A pdb=" N LYS D 295 " --> pdb=" O GLU D 291 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ASN D 296 " --> pdb=" O GLU D 292 " (cutoff:3.500A) Processing helix chain 'D' and resid 305 through 310 removed outlier: 3.901A pdb=" N ILE D 309 " --> pdb=" O GLU D 305 " (cutoff:3.500A) Processing helix chain 'D' and resid 318 through 326 Processing helix chain 'D' and resid 328 through 334 Processing helix chain 'D' and resid 349 through 353 removed outlier: 3.775A pdb=" N ILE D 353 " --> pdb=" O PRO D 350 " (cutoff:3.500A) Processing helix chain 'D' and resid 354 through 359 removed outlier: 3.584A pdb=" N ARG D 359 " --> pdb=" O ALA D 356 " (cutoff:3.500A) Processing helix chain 'D' and resid 373 through 385 Processing helix chain 'D' and resid 398 through 403 Processing helix chain 'D' and resid 407 through 426 Processing helix chain 'D' and resid 439 through 445 removed outlier: 3.588A pdb=" N ASN D 443 " --> pdb=" O ALA D 439 " (cutoff:3.500A) Processing helix chain 'D' and resid 448 through 458 Processing helix chain 'D' and resid 475 through 479 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: 3.555A pdb=" N PHE D 506 " --> pdb=" O LYS D 502 " (cutoff:3.500A) Processing helix chain 'D' and resid 523 through 536 Processing helix chain 'D' and resid 543 through 553 Processing helix chain 'D' and resid 557 through 569 removed outlier: 3.864A pdb=" N GLU D 561 " --> pdb=" O ALA D 557 " (cutoff:3.500A) Processing helix chain 'D' and resid 580 through 586 Processing helix chain 'D' and resid 598 through 610 Processing helix chain 'D' and resid 625 through 629 Processing helix chain 'D' and resid 630 through 634 Processing helix chain 'D' and resid 649 through 661 removed outlier: 3.582A pdb=" N ALA D 655 " --> pdb=" O LYS D 651 " (cutoff:3.500A) Processing helix chain 'D' and resid 662 through 664 No H-bonds generated for 'chain 'D' and resid 662 through 664' Processing helix chain 'D' and resid 671 through 679 removed outlier: 3.921A pdb=" N LEU D 675 " --> pdb=" O ASP D 671 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N THR D 679 " --> pdb=" O LEU D 675 " (cutoff:3.500A) Processing helix chain 'D' and resid 683 through 705 Processing helix chain 'D' and resid 732 through 742 removed outlier: 4.011A pdb=" N PHE D 736 " --> pdb=" O ARG D 732 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N PHE D 742 " --> pdb=" O GLU D 738 " (cutoff:3.500A) Processing helix chain 'D' and resid 748 through 763 Processing helix chain 'E' and resid 202 through 206 Processing helix chain 'E' and resid 211 through 226 removed outlier: 5.178A pdb=" N LEU E 222 " --> pdb=" O GLU E 218 " (cutoff:3.500A) Proline residue: E 223 - end of helix Processing helix chain 'E' and resid 226 through 233 removed outlier: 3.574A pdb=" N PHE E 230 " --> pdb=" O HIS E 226 " (cutoff:3.500A) Processing helix chain 'E' and resid 250 through 263 Processing helix chain 'E' and resid 270 through 277 removed outlier: 3.535A pdb=" N LYS E 277 " --> pdb=" O GLU E 273 " (cutoff:3.500A) Processing helix chain 'E' and resid 280 through 296 removed outlier: 3.596A pdb=" N PHE E 290 " --> pdb=" O LEU E 286 " (cutoff:3.500A) Processing helix chain 'E' and resid 305 through 310 removed outlier: 3.780A pdb=" N ILE E 309 " --> pdb=" O GLU E 305 " (cutoff:3.500A) Processing helix chain 'E' and resid 318 through 326 Processing helix chain 'E' and resid 328 through 334 Processing helix chain 'E' and resid 349 through 353 removed outlier: 4.024A pdb=" N ILE E 353 " --> pdb=" O PRO E 350 " (cutoff:3.500A) Processing helix chain 'E' and resid 354 through 359 removed outlier: 3.594A pdb=" N ARG E 359 " --> pdb=" O ALA E 356 " (cutoff:3.500A) Processing helix chain 'E' and resid 373 through 385 Processing helix chain 'E' and resid 398 through 403 Processing helix chain 'E' and resid 407 through 426 Processing helix chain 'E' and resid 439 through 445 removed outlier: 3.936A pdb=" N ASN E 443 " --> pdb=" O ALA E 439 " (cutoff:3.500A) Processing helix chain 'E' and resid 448 through 457 Processing helix chain 'E' and resid 475 through 479 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: 3.617A pdb=" N PHE E 506 " --> pdb=" O LYS E 502 " (cutoff:3.500A) Processing helix chain 'E' and resid 523 through 536 Processing helix chain 'E' and resid 543 through 554 Processing helix chain 'E' and resid 557 through 569 removed outlier: 3.838A pdb=" N GLU E 561 " --> pdb=" O ALA E 557 " (cutoff:3.500A) Processing helix chain 'E' and resid 580 through 586 Processing helix chain 'E' and resid 598 through 610 Processing helix chain 'E' and resid 625 through 629 Processing helix chain 'E' and resid 630 through 634 Processing helix chain 'E' and resid 649 through 661 removed outlier: 3.572A pdb=" N ALA E 655 " --> pdb=" O LYS E 651 " (cutoff:3.500A) Processing helix chain 'E' and resid 662 through 664 No H-bonds generated for 'chain 'E' and resid 662 through 664' Processing helix chain 'E' and resid 671 through 679 removed outlier: 3.883A pdb=" N LEU E 675 " --> pdb=" O ASP E 671 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N THR E 679 " --> pdb=" O LEU E 675 " (cutoff:3.500A) Processing helix chain 'E' and resid 683 through 705 Processing helix chain 'E' and resid 732 through 742 removed outlier: 3.975A pdb=" N PHE E 736 " --> pdb=" O ARG E 732 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N PHE E 742 " --> pdb=" O GLU E 738 " (cutoff:3.500A) Processing helix chain 'E' and resid 748 through 763 Processing helix chain 'F' and resid 202 through 206 Processing helix chain 'F' and resid 211 through 226 removed outlier: 5.196A pdb=" N LEU F 222 " --> pdb=" O GLU F 218 " (cutoff:3.500A) Proline residue: F 223 - end of helix Processing helix chain 'F' and resid 226 through 233 removed outlier: 3.528A pdb=" N PHE F 230 " --> pdb=" O HIS F 226 " (cutoff:3.500A) Processing helix chain 'F' and resid 250 through 263 Processing helix chain 'F' and resid 270 through 277 removed outlier: 3.770A pdb=" N LYS F 277 " --> pdb=" O GLU F 273 " (cutoff:3.500A) Processing helix chain 'F' and resid 280 through 296 removed outlier: 3.591A pdb=" N PHE F 290 " --> pdb=" O LEU F 286 " (cutoff:3.500A) Processing helix chain 'F' and resid 305 through 310 removed outlier: 3.828A pdb=" N ILE F 309 " --> pdb=" O GLU F 305 " (cutoff:3.500A) Processing helix chain 'F' and resid 318 through 326 Processing helix chain 'F' and resid 328 through 334 Processing helix chain 'F' and resid 349 through 353 removed outlier: 4.052A pdb=" N ILE F 353 " --> pdb=" O PRO F 350 " (cutoff:3.500A) Processing helix chain 'F' and resid 354 through 359 removed outlier: 3.571A pdb=" N ARG F 359 " --> pdb=" O ALA F 356 " (cutoff:3.500A) Processing helix chain 'F' and resid 373 through 385 Processing helix chain 'F' and resid 398 through 403 Processing helix chain 'F' and resid 407 through 426 Processing helix chain 'F' and resid 439 through 445 removed outlier: 3.909A pdb=" N ASN F 443 " --> pdb=" O ALA F 439 " (cutoff:3.500A) Processing helix chain 'F' and resid 448 through 458 Processing helix chain 'F' and resid 475 through 479 Processing helix chain 'F' and resid 482 through 499 Proline residue: F 496 - end of helix Processing helix chain 'F' and resid 499 through 507 Processing helix chain 'F' and resid 523 through 536 Processing helix chain 'F' and resid 543 through 553 Processing helix chain 'F' and resid 557 through 569 removed outlier: 3.899A pdb=" N GLU F 561 " --> pdb=" O ALA F 557 " (cutoff:3.500A) Processing helix chain 'F' and resid 580 through 586 Processing helix chain 'F' and resid 598 through 610 Processing helix chain 'F' and resid 625 through 629 Processing helix chain 'F' and resid 630 through 634 removed outlier: 3.522A pdb=" N ILE F 633 " --> pdb=" O ASP F 630 " (cutoff:3.500A) Processing helix chain 'F' and resid 649 through 661 removed outlier: 3.587A pdb=" N ALA F 655 " --> pdb=" O LYS F 651 " (cutoff:3.500A) Processing helix chain 'F' and resid 662 through 664 No H-bonds generated for 'chain 'F' and resid 662 through 664' Processing helix chain 'F' and resid 671 through 679 removed outlier: 3.847A pdb=" N LEU F 675 " --> pdb=" O ASP F 671 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N THR F 679 " --> pdb=" O LEU F 675 " (cutoff:3.500A) Processing helix chain 'F' and resid 683 through 705 Processing helix chain 'F' and resid 732 through 742 removed outlier: 3.983A pdb=" N PHE F 736 " --> pdb=" O ARG F 732 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N PHE F 742 " --> pdb=" O GLU F 738 " (cutoff:3.500A) Processing helix chain 'F' and resid 748 through 763 Processing sheet with id=AA1, first strand: chain 'A' and resid 265 through 268 removed outlier: 6.225A pdb=" N PHE A 265 " --> pdb=" O ILE A 300 " (cutoff:3.500A) removed outlier: 7.368A pdb=" N PHE A 302 " --> pdb=" O PHE A 265 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N PHE A 267 " --> pdb=" O PHE A 302 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N ALA A 299 " --> pdb=" O ILE A 342 " (cutoff:3.500A) removed outlier: 7.450A pdb=" N MET A 344 " --> pdb=" O ALA A 299 " (cutoff:3.500A) removed outlier: 5.820A pdb=" N ILE A 301 " --> pdb=" O MET A 344 " (cutoff:3.500A) removed outlier: 7.602A pdb=" N ALA A 346 " --> pdb=" O ILE A 301 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 538 through 542 removed outlier: 6.772A pdb=" N CYS A 572 " --> pdb=" O PHE A 618 " (cutoff:3.500A) removed outlier: 7.840A pdb=" N ILE A 620 " --> pdb=" O CYS A 572 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N LEU A 574 " --> pdb=" O ILE A 620 " (cutoff:3.500A) removed outlier: 7.727A pdb=" N ALA A 622 " --> pdb=" O LEU A 574 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N PHE A 576 " --> pdb=" O ALA A 622 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLN A 641 " --> pdb=" O GLY A 513 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 265 through 268 removed outlier: 6.241A pdb=" N PHE B 265 " --> pdb=" O ILE B 300 " (cutoff:3.500A) removed outlier: 7.340A pdb=" N PHE B 302 " --> pdb=" O PHE B 265 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N PHE B 267 " --> pdb=" O PHE B 302 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N ALA B 299 " --> pdb=" O ILE B 342 " (cutoff:3.500A) removed outlier: 7.450A pdb=" N MET B 344 " --> pdb=" O ALA B 299 " (cutoff:3.500A) removed outlier: 5.819A pdb=" N ILE B 301 " --> pdb=" O MET B 344 " (cutoff:3.500A) removed outlier: 7.629A pdb=" N ALA B 346 " --> pdb=" O ILE B 301 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 538 through 542 removed outlier: 6.776A pdb=" N CYS B 572 " --> pdb=" O PHE B 618 " (cutoff:3.500A) removed outlier: 7.861A pdb=" N ILE B 620 " --> pdb=" O CYS B 572 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N LEU B 574 " --> pdb=" O ILE B 620 " (cutoff:3.500A) removed outlier: 7.751A pdb=" N ALA B 622 " --> pdb=" O LEU B 574 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N PHE B 576 " --> pdb=" O ALA B 622 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N GLN B 641 " --> pdb=" O GLY B 513 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 265 through 268 removed outlier: 6.248A pdb=" N PHE C 265 " --> pdb=" O ILE C 300 " (cutoff:3.500A) removed outlier: 7.371A pdb=" N PHE C 302 " --> pdb=" O PHE C 265 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N PHE C 267 " --> pdb=" O PHE C 302 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N ALA C 299 " --> pdb=" O ILE C 342 " (cutoff:3.500A) removed outlier: 7.431A pdb=" N MET C 344 " --> pdb=" O ALA C 299 " (cutoff:3.500A) removed outlier: 5.808A pdb=" N ILE C 301 " --> pdb=" O MET C 344 " (cutoff:3.500A) removed outlier: 7.547A pdb=" N ALA C 346 " --> pdb=" O ILE C 301 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 538 through 542 removed outlier: 6.751A pdb=" N CYS C 572 " --> pdb=" O PHE C 618 " (cutoff:3.500A) removed outlier: 7.848A pdb=" N ILE C 620 " --> pdb=" O CYS C 572 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N LEU C 574 " --> pdb=" O ILE C 620 " (cutoff:3.500A) removed outlier: 7.771A pdb=" N ALA C 622 " --> pdb=" O LEU C 574 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N PHE C 576 " --> pdb=" O ALA C 622 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N GLN C 641 " --> pdb=" O GLY C 513 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 265 through 268 removed outlier: 6.238A pdb=" N PHE D 265 " --> pdb=" O ILE D 300 " (cutoff:3.500A) removed outlier: 7.367A pdb=" N PHE D 302 " --> pdb=" O PHE D 265 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N PHE D 267 " --> pdb=" O PHE D 302 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N ALA D 299 " --> pdb=" O ILE D 342 " (cutoff:3.500A) removed outlier: 7.450A pdb=" N MET D 344 " --> pdb=" O ALA D 299 " (cutoff:3.500A) removed outlier: 5.826A pdb=" N ILE D 301 " --> pdb=" O MET D 344 " (cutoff:3.500A) removed outlier: 7.598A pdb=" N ALA D 346 " --> pdb=" O ILE D 301 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 538 through 542 removed outlier: 6.782A pdb=" N CYS D 572 " --> pdb=" O PHE D 618 " (cutoff:3.500A) removed outlier: 7.849A pdb=" N ILE D 620 " --> pdb=" O CYS D 572 " (cutoff:3.500A) removed outlier: 6.196A pdb=" N LEU D 574 " --> pdb=" O ILE D 620 " (cutoff:3.500A) removed outlier: 7.717A pdb=" N ALA D 622 " --> pdb=" O LEU D 574 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N PHE D 576 " --> pdb=" O ALA D 622 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N GLN D 641 " --> pdb=" O GLY D 513 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 265 through 268 removed outlier: 6.219A pdb=" N PHE E 265 " --> pdb=" O ILE E 300 " (cutoff:3.500A) removed outlier: 7.338A pdb=" N PHE E 302 " --> pdb=" O PHE E 265 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N PHE E 267 " --> pdb=" O PHE E 302 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N ALA E 299 " --> pdb=" O ILE E 342 " (cutoff:3.500A) removed outlier: 7.476A pdb=" N MET E 344 " --> pdb=" O ALA E 299 " (cutoff:3.500A) removed outlier: 5.843A pdb=" N ILE E 301 " --> pdb=" O MET E 344 " (cutoff:3.500A) removed outlier: 7.683A pdb=" N ALA E 346 " --> pdb=" O ILE E 301 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 538 through 542 removed outlier: 6.810A pdb=" N CYS E 572 " --> pdb=" O PHE E 618 " (cutoff:3.500A) removed outlier: 7.888A pdb=" N ILE E 620 " --> pdb=" O CYS E 572 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N LEU E 574 " --> pdb=" O ILE E 620 " (cutoff:3.500A) removed outlier: 7.756A pdb=" N ALA E 622 " --> pdb=" O LEU E 574 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N PHE E 576 " --> pdb=" O ALA E 622 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N GLN E 641 " --> pdb=" O GLY E 513 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 265 through 268 removed outlier: 6.243A pdb=" N PHE F 265 " --> pdb=" O ILE F 300 " (cutoff:3.500A) removed outlier: 7.364A pdb=" N PHE F 302 " --> pdb=" O PHE F 265 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N PHE F 267 " --> pdb=" O PHE F 302 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N ALA F 299 " --> pdb=" O ILE F 342 " (cutoff:3.500A) removed outlier: 7.427A pdb=" N MET F 344 " --> pdb=" O ALA F 299 " (cutoff:3.500A) removed outlier: 5.812A pdb=" N ILE F 301 " --> pdb=" O MET F 344 " (cutoff:3.500A) removed outlier: 7.545A pdb=" N ALA F 346 " --> pdb=" O ILE F 301 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 538 through 542 removed outlier: 6.750A pdb=" N CYS F 572 " --> pdb=" O PHE F 618 " (cutoff:3.500A) removed outlier: 7.847A pdb=" N ILE F 620 " --> pdb=" O CYS F 572 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N LEU F 574 " --> pdb=" O ILE F 620 " (cutoff:3.500A) removed outlier: 7.781A pdb=" N ALA F 622 " --> pdb=" O LEU F 574 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N PHE F 576 " --> pdb=" O ALA F 622 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N GLN F 641 " --> pdb=" O GLY F 513 " (cutoff:3.500A) 1256 hydrogen bonds defined for protein. 3558 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: 4.74 Time building geometry restraints manager: 3.02 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: 8690 1.34 - 1.46: 2863 1.46 - 1.57: 14319 1.57 - 1.69: 36 1.69 - 1.81: 222 Bond restraints: 26130 Sorted by residual: bond pdb=" C ASN A 460 " pdb=" N PRO A 461 " ideal model delta sigma weight residual 1.334 1.409 -0.075 2.34e-02 1.83e+03 1.04e+01 bond pdb=" C ASN D 460 " pdb=" N PRO D 461 " ideal model delta sigma weight residual 1.334 1.405 -0.071 2.34e-02 1.83e+03 9.29e+00 bond pdb=" C ASN F 460 " pdb=" N PRO F 461 " ideal model delta sigma weight residual 1.334 1.402 -0.068 2.34e-02 1.83e+03 8.40e+00 bond pdb=" C ASN C 460 " pdb=" N PRO C 461 " ideal model delta sigma weight residual 1.334 1.399 -0.065 2.34e-02 1.83e+03 7.67e+00 bond pdb=" C ASN B 460 " pdb=" N PRO B 461 " ideal model delta sigma weight residual 1.334 1.393 -0.059 2.34e-02 1.83e+03 6.37e+00 ... (remaining 26125 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.85: 34590 1.85 - 3.70: 527 3.70 - 5.56: 179 5.56 - 7.41: 36 7.41 - 9.26: 8 Bond angle restraints: 35340 Sorted by residual: angle pdb=" CA PRO E 461 " pdb=" N PRO E 461 " pdb=" CD PRO E 461 " ideal model delta sigma weight residual 112.00 106.23 5.77 1.40e+00 5.10e-01 1.70e+01 angle pdb=" CA PRO B 461 " pdb=" N PRO B 461 " pdb=" CD PRO B 461 " ideal model delta sigma weight residual 112.00 106.37 5.63 1.40e+00 5.10e-01 1.62e+01 angle pdb=" N LYS A 211 " pdb=" CA LYS A 211 " pdb=" C LYS A 211 " ideal model delta sigma weight residual 112.72 108.02 4.70 1.28e+00 6.10e-01 1.35e+01 angle pdb=" CA PRO F 461 " pdb=" N PRO F 461 " pdb=" CD PRO F 461 " ideal model delta sigma weight residual 112.00 106.92 5.08 1.40e+00 5.10e-01 1.32e+01 angle pdb=" CA PRO C 461 " pdb=" N PRO C 461 " pdb=" CD PRO C 461 " ideal model delta sigma weight residual 112.00 106.94 5.06 1.40e+00 5.10e-01 1.30e+01 ... (remaining 35335 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.88: 15133 20.88 - 41.75: 817 41.75 - 62.63: 120 62.63 - 83.51: 16 83.51 - 104.39: 12 Dihedral angle restraints: 16098 sinusoidal: 6738 harmonic: 9360 Sorted by residual: dihedral pdb=" C5' ADP D 901 " pdb=" O5' ADP D 901 " pdb=" PA ADP D 901 " pdb=" O2A ADP D 901 " ideal model delta sinusoidal sigma weight residual -60.00 -164.38 104.39 1 2.00e+01 2.50e-03 3.00e+01 dihedral pdb=" C5' ADP A 901 " pdb=" O5' ADP A 901 " pdb=" PA ADP A 901 " pdb=" O2A ADP A 901 " ideal model delta sinusoidal sigma weight residual -60.00 -164.13 104.13 1 2.00e+01 2.50e-03 2.99e+01 dihedral pdb=" C5' ADP B 901 " pdb=" O5' ADP B 901 " pdb=" PA ADP B 901 " pdb=" O2A ADP B 901 " ideal model delta sinusoidal sigma weight residual -60.00 -163.17 103.17 1 2.00e+01 2.50e-03 2.95e+01 ... (remaining 16095 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 2916 0.042 - 0.083: 748 0.083 - 0.125: 283 0.125 - 0.167: 14 0.167 - 0.208: 11 Chirality restraints: 3972 Sorted by residual: chirality pdb=" CB ILE B 303 " pdb=" CA ILE B 303 " pdb=" CG1 ILE B 303 " pdb=" CG2 ILE B 303 " both_signs ideal model delta sigma weight residual False 2.64 2.85 -0.21 2.00e-01 2.50e+01 1.09e+00 chirality pdb=" CB ILE C 303 " pdb=" CA ILE C 303 " pdb=" CG1 ILE C 303 " pdb=" CG2 ILE C 303 " both_signs ideal model delta sigma weight residual False 2.64 2.85 -0.21 2.00e-01 2.50e+01 1.08e+00 chirality pdb=" CB ILE D 303 " pdb=" CA ILE D 303 " pdb=" CG1 ILE D 303 " pdb=" CG2 ILE D 303 " both_signs ideal model delta sigma weight residual False 2.64 2.85 -0.20 2.00e-01 2.50e+01 1.03e+00 ... (remaining 3969 not shown) Planarity restraints: 4620 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN E 460 " 0.046 5.00e-02 4.00e+02 6.87e-02 7.55e+00 pdb=" N PRO E 461 " -0.119 5.00e-02 4.00e+02 pdb=" CA PRO E 461 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO E 461 " 0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN B 460 " -0.044 5.00e-02 4.00e+02 6.62e-02 7.00e+00 pdb=" N PRO B 461 " 0.114 5.00e-02 4.00e+02 pdb=" CA PRO B 461 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO B 461 " -0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN C 460 " 0.041 5.00e-02 4.00e+02 6.12e-02 5.99e+00 pdb=" N PRO C 461 " -0.106 5.00e-02 4.00e+02 pdb=" CA PRO C 461 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO C 461 " 0.035 5.00e-02 4.00e+02 ... (remaining 4617 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 1617 2.73 - 3.28: 27111 3.28 - 3.82: 42458 3.82 - 4.36: 54227 4.36 - 4.90: 88372 Nonbonded interactions: 213785 Sorted by model distance: nonbonded pdb=" NZ LYS A 663 " pdb=" O GLY B 507 " model vdw 2.193 3.120 nonbonded pdb=" NZ LYS D 663 " pdb=" O GLY E 507 " model vdw 2.195 3.120 nonbonded pdb=" OD1 ASP F 478 " pdb=" NH2 ARG F 662 " model vdw 2.207 3.120 nonbonded pdb=" O ASN D 624 " pdb=" OH TYR D 755 " model vdw 2.207 3.040 nonbonded pdb=" O ASN A 624 " pdb=" OH TYR A 755 " model vdw 2.207 3.040 ... (remaining 213780 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.280 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.340 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 24.130 Find NCS groups from input model: 0.550 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.500 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.990 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8199 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 : 0.003 0.075 26130 Z= 0.134 Angle : 0.647 9.262 35340 Z= 0.314 Chirality : 0.043 0.208 3972 Planarity : 0.004 0.069 4620 Dihedral : 12.942 104.385 10026 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 0.00 % Allowed : 0.04 % Favored : 99.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.19 % 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: 0.59 (0.15), residues: 3240 helix: 0.80 (0.13), residues: 1632 sheet: 0.80 (0.24), residues: 402 loop : -0.16 (0.19), residues: 1206 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 599 TYR 0.016 0.001 TYR C 244 PHE 0.010 0.001 PHE E 552 TRP 0.009 0.001 TRP F 454 HIS 0.003 0.001 HIS A 499 Details of bonding type rmsd/Z covalent geometry : bond 0.00314 / 0.13 (26130) covalent geometry : angle 0.64658 / 0.31 (35340) hydrogen bonds : bond 0.21146 / 14.39 ( 1256) hydrogen bonds : angle 6.58363 / 4.75 ( 3558) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6480 Ramachandran restraints generated. 3240 Oldfield, 0 Emsley, 3240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6480 Ramachandran restraints generated. 3240 Oldfield, 0 Emsley, 3240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 511 residues out of total 2706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 511 time to evaluate : 1.027 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 350 PRO cc_start: 0.8274 (Cg_exo) cc_final: 0.7940 (Cg_endo) REVERT: A 450 ASP cc_start: 0.9043 (m-30) cc_final: 0.8706 (m-30) REVERT: A 478 ASP cc_start: 0.8957 (m-30) cc_final: 0.8741 (m-30) REVERT: A 560 ARG cc_start: 0.8811 (ttt180) cc_final: 0.8570 (ttt-90) REVERT: A 663 LYS cc_start: 0.8859 (pttp) cc_final: 0.8473 (tptp) REVERT: B 288 LYS cc_start: 0.9196 (mttt) cc_final: 0.8908 (mtmp) REVERT: B 423 ILE cc_start: 0.8549 (mt) cc_final: 0.8346 (tt) REVERT: B 560 ARG cc_start: 0.8872 (ttt180) cc_final: 0.8220 (ttt180) REVERT: B 663 LYS cc_start: 0.9081 (pttt) cc_final: 0.8556 (tptp) REVERT: C 222 LEU cc_start: 0.8899 (tp) cc_final: 0.8449 (tp) REVERT: C 288 LYS cc_start: 0.9099 (mttt) cc_final: 0.8812 (mtmp) REVERT: C 350 PRO cc_start: 0.8262 (Cg_exo) cc_final: 0.8045 (Cg_endo) REVERT: C 449 MET cc_start: 0.8515 (tpt) cc_final: 0.8288 (tpt) REVERT: C 470 GLU cc_start: 0.8874 (pt0) cc_final: 0.8563 (pt0) REVERT: C 560 ARG cc_start: 0.8790 (ttt180) cc_final: 0.8320 (ttt180) REVERT: D 478 ASP cc_start: 0.8955 (m-30) cc_final: 0.8735 (m-30) REVERT: D 560 ARG cc_start: 0.8788 (ttt180) cc_final: 0.8553 (ttt-90) REVERT: D 663 LYS cc_start: 0.8875 (pttp) cc_final: 0.8483 (tptp) REVERT: E 288 LYS cc_start: 0.9172 (mttt) cc_final: 0.8937 (mtmp) REVERT: E 420 LEU cc_start: 0.8428 (mt) cc_final: 0.8227 (mm) REVERT: E 423 ILE cc_start: 0.8543 (mt) cc_final: 0.8329 (tt) REVERT: E 560 ARG cc_start: 0.8843 (ttt180) cc_final: 0.8223 (ttt180) REVERT: F 288 LYS cc_start: 0.9153 (mttt) cc_final: 0.8939 (mtmp) REVERT: F 449 MET cc_start: 0.8541 (tpt) cc_final: 0.8278 (tpt) REVERT: F 470 GLU cc_start: 0.8870 (pt0) cc_final: 0.8550 (pt0) REVERT: F 560 ARG cc_start: 0.8759 (ttt180) cc_final: 0.8284 (ttt180) outliers start: 0 outliers final: 4 residues processed: 511 average time/residue: 0.9199 time to fit residues: 521.1676 Evaluate side-chains 308 residues out of total 2706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 304 time to evaluate : 1.006 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 307 ASP Chi-restraints excluded: chain C residue 307 ASP Chi-restraints excluded: chain D residue 307 ASP Chi-restraints excluded: chain F residue 307 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 197 optimal weight: 0.5980 chunk 215 optimal weight: 0.9990 chunk 20 optimal weight: 0.8980 chunk 132 optimal weight: 7.9990 chunk 261 optimal weight: 2.9990 chunk 248 optimal weight: 0.8980 chunk 207 optimal weight: 0.6980 chunk 155 optimal weight: 0.9990 chunk 244 optimal weight: 0.0270 chunk 183 optimal weight: 0.7980 chunk 298 optimal weight: 0.9980 overall best weight: 0.6038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 226 HIS ** A 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 327 GLN ** B 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 443 ASN E 327 GLN ** E 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 327 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.117601 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.085193 restraints weight = 40761.211| |-----------------------------------------------------------------------------| r_work (start): 0.3125 rms_B_bonded: 3.17 r_work: 0.2961 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.2961 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8235 moved from start: 0.1994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 26130 Z= 0.149 Angle : 0.714 8.984 35340 Z= 0.340 Chirality : 0.045 0.193 3972 Planarity : 0.005 0.049 4620 Dihedral : 7.799 101.390 3644 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.80 % Favored : 94.20 % Rotamer: Outliers : 1.70 % Allowed : 9.42 % Favored : 88.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.19 % 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: 0.63 (0.15), residues: 3240 helix: 0.76 (0.12), residues: 1734 sheet: 0.56 (0.24), residues: 402 loop : 0.02 (0.20), residues: 1104 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 453 TYR 0.019 0.002 TYR A 244 PHE 0.022 0.001 PHE B 267 TRP 0.011 0.001 TRP E 454 HIS 0.008 0.002 HIS B 499 Details of bonding type rmsd/Z covalent geometry : bond 0.00341 / 0.15 (26130) covalent geometry : angle 0.71414 / 0.34 (35340) hydrogen bonds : bond 0.04569 / 3.04 ( 1256) hydrogen bonds : angle 4.79047 / 3.48 ( 3558) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6480 Ramachandran restraints generated. 3240 Oldfield, 0 Emsley, 3240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6480 Ramachandran restraints generated. 3240 Oldfield, 0 Emsley, 3240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 400 residues out of total 2706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 354 time to evaluate : 1.006 Fit side-chains REVERT: A 288 LYS cc_start: 0.9197 (mttt) cc_final: 0.8962 (mtmp) REVERT: A 397 GLU cc_start: 0.8505 (mm-30) cc_final: 0.8271 (tm-30) REVERT: A 402 GLU cc_start: 0.8844 (mp0) cc_final: 0.8512 (mp0) REVERT: A 417 GLU cc_start: 0.8606 (tp30) cc_final: 0.8373 (tt0) REVERT: A 450 ASP cc_start: 0.9095 (m-30) cc_final: 0.8758 (m-30) REVERT: A 478 ASP cc_start: 0.8976 (m-30) cc_final: 0.8689 (m-30) REVERT: A 560 ARG cc_start: 0.8923 (ttt180) cc_final: 0.8538 (ttt-90) REVERT: A 663 LYS cc_start: 0.9059 (pttp) cc_final: 0.8589 (tptp) REVERT: B 288 LYS cc_start: 0.9020 (mttt) cc_final: 0.8725 (mttp) REVERT: B 319 GLU cc_start: 0.6045 (tp30) cc_final: 0.5270 (tp30) REVERT: B 402 GLU cc_start: 0.8842 (mp0) cc_final: 0.8570 (mp0) REVERT: B 420 LEU cc_start: 0.8352 (OUTLIER) cc_final: 0.8041 (mm) REVERT: B 560 ARG cc_start: 0.8926 (ttt180) cc_final: 0.8253 (ttt180) REVERT: B 616 ASN cc_start: 0.8479 (t0) cc_final: 0.8252 (t0) REVERT: B 630 ASP cc_start: 0.8287 (p0) cc_final: 0.8073 (p0) REVERT: B 663 LYS cc_start: 0.9107 (pttt) cc_final: 0.8620 (tptp) REVERT: B 741 ARG cc_start: 0.7277 (OUTLIER) cc_final: 0.6763 (tpm170) REVERT: C 402 GLU cc_start: 0.8860 (mp0) cc_final: 0.8529 (mp0) REVERT: C 450 ASP cc_start: 0.9231 (m-30) cc_final: 0.8845 (m-30) REVERT: C 470 GLU cc_start: 0.8851 (pt0) cc_final: 0.8554 (pt0) REVERT: C 560 ARG cc_start: 0.8965 (ttt180) cc_final: 0.8430 (ttt180) REVERT: D 288 LYS cc_start: 0.9239 (mttt) cc_final: 0.9004 (mtmp) REVERT: D 402 GLU cc_start: 0.8819 (mp0) cc_final: 0.8503 (mp0) REVERT: D 450 ASP cc_start: 0.9217 (m-30) cc_final: 0.8689 (m-30) REVERT: D 478 ASP cc_start: 0.8973 (m-30) cc_final: 0.8651 (m-30) REVERT: D 560 ARG cc_start: 0.8941 (ttt180) cc_final: 0.8496 (ttt-90) REVERT: E 288 LYS cc_start: 0.9029 (mttt) cc_final: 0.8736 (mttp) REVERT: E 319 GLU cc_start: 0.5707 (tp30) cc_final: 0.4899 (tp30) REVERT: E 402 GLU cc_start: 0.8619 (mp0) cc_final: 0.8305 (pm20) REVERT: E 449 MET cc_start: 0.8519 (tpt) cc_final: 0.8043 (tpp) REVERT: E 560 ARG cc_start: 0.8918 (ttt180) cc_final: 0.8237 (ttt180) REVERT: E 616 ASN cc_start: 0.8427 (t0) cc_final: 0.8173 (t0) REVERT: E 630 ASP cc_start: 0.8191 (p0) cc_final: 0.7966 (p0) REVERT: F 222 LEU cc_start: 0.8724 (tp) cc_final: 0.8495 (tp) REVERT: F 288 LYS cc_start: 0.9137 (mttt) cc_final: 0.8903 (mtmp) REVERT: F 402 GLU cc_start: 0.8831 (mp0) cc_final: 0.8534 (mp0) REVERT: F 450 ASP cc_start: 0.9253 (m-30) cc_final: 0.8838 (m-30) REVERT: F 470 GLU cc_start: 0.8862 (pt0) cc_final: 0.8560 (pt0) REVERT: F 560 ARG cc_start: 0.8958 (ttt180) cc_final: 0.8438 (ttt180) outliers start: 46 outliers final: 15 residues processed: 383 average time/residue: 0.7621 time to fit residues: 330.3664 Evaluate side-chains 325 residues out of total 2706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 308 time to evaluate : 1.050 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 218 GLU Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 567 ARG Chi-restraints excluded: chain A residue 629 ILE Chi-restraints excluded: chain B residue 327 GLN Chi-restraints excluded: chain B residue 420 LEU Chi-restraints excluded: chain B residue 504 LEU Chi-restraints excluded: chain B residue 741 ARG Chi-restraints excluded: chain C residue 378 LEU Chi-restraints excluded: chain C residue 484 ASP Chi-restraints excluded: chain D residue 218 GLU Chi-restraints excluded: chain D residue 378 LEU Chi-restraints excluded: chain D residue 567 ARG Chi-restraints excluded: chain D residue 629 ILE Chi-restraints excluded: chain E residue 327 GLN Chi-restraints excluded: chain F residue 378 LEU Chi-restraints excluded: chain F residue 484 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 272 optimal weight: 3.9990 chunk 223 optimal weight: 1.9990 chunk 176 optimal weight: 0.8980 chunk 153 optimal weight: 1.9990 chunk 268 optimal weight: 4.9990 chunk 237 optimal weight: 1.9990 chunk 280 optimal weight: 3.9990 chunk 164 optimal weight: 4.9990 chunk 203 optimal weight: 3.9990 chunk 235 optimal weight: 0.3980 chunk 145 optimal weight: 1.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 499 HIS A 616 ASN A 763 GLN ** B 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 327 GLN ** B 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 499 HIS B 763 GLN ** C 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 499 HIS C 763 GLN D 327 GLN ** D 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 616 ASN D 763 GLN ** E 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 443 ASN E 499 HIS E 763 GLN ** F 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 499 HIS F 763 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.114445 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.081799 restraints weight = 40719.428| |-----------------------------------------------------------------------------| r_work (start): 0.3045 rms_B_bonded: 3.16 r_work: 0.2879 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.2879 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8209 moved from start: 0.2368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 26130 Z= 0.226 Angle : 0.714 9.065 35340 Z= 0.341 Chirality : 0.045 0.187 3972 Planarity : 0.005 0.051 4620 Dihedral : 7.669 104.751 3636 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.43 % Favored : 94.57 % Rotamer: Outliers : 2.14 % Allowed : 11.86 % Favored : 85.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.19 % 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: 0.64 (0.15), residues: 3240 helix: 0.82 (0.13), residues: 1716 sheet: 0.53 (0.24), residues: 402 loop : -0.03 (0.20), residues: 1122 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 365 TYR 0.023 0.002 TYR A 244 PHE 0.016 0.001 PHE B 267 TRP 0.011 0.002 TRP C 454 HIS 0.019 0.002 HIS E 317 Details of bonding type rmsd/Z covalent geometry : bond 0.00534 / 0.23 (26130) covalent geometry : angle 0.71410 / 0.34 (35340) hydrogen bonds : bond 0.04489 / 2.98 ( 1256) hydrogen bonds : angle 4.57388 / 3.30 ( 3558) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6480 Ramachandran restraints generated. 3240 Oldfield, 0 Emsley, 3240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6480 Ramachandran restraints generated. 3240 Oldfield, 0 Emsley, 3240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 373 residues out of total 2706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 315 time to evaluate : 0.980 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 239 ARG cc_start: 0.7576 (mmm160) cc_final: 0.7326 (mmm160) REVERT: A 288 LYS cc_start: 0.9196 (mttt) cc_final: 0.8957 (mtmp) REVERT: A 321 GLU cc_start: 0.8325 (OUTLIER) cc_final: 0.8098 (mp0) REVERT: A 359 ARG cc_start: 0.8399 (OUTLIER) cc_final: 0.8124 (mmt90) REVERT: A 397 GLU cc_start: 0.8587 (mm-30) cc_final: 0.8340 (mm-30) REVERT: A 450 ASP cc_start: 0.9128 (m-30) cc_final: 0.8800 (m-30) REVERT: A 478 ASP cc_start: 0.9004 (m-30) cc_final: 0.8711 (m-30) REVERT: A 560 ARG cc_start: 0.8886 (ttt180) cc_final: 0.8426 (ttt-90) REVERT: A 567 ARG cc_start: 0.8621 (OUTLIER) cc_final: 0.8100 (ttp80) REVERT: A 614 LYS cc_start: 0.8320 (tppt) cc_final: 0.8078 (mmtm) REVERT: A 616 ASN cc_start: 0.8260 (t0) cc_final: 0.8000 (t0) REVERT: B 288 LYS cc_start: 0.9025 (mttt) cc_final: 0.8738 (mtmp) REVERT: B 327 GLN cc_start: 0.8738 (OUTLIER) cc_final: 0.8338 (tp-100) REVERT: B 397 GLU cc_start: 0.8682 (mm-30) cc_final: 0.8434 (mm-30) REVERT: B 449 MET cc_start: 0.8616 (tpt) cc_final: 0.8063 (tpp) REVERT: B 560 ARG cc_start: 0.8944 (ttt180) cc_final: 0.8265 (ttt180) REVERT: B 741 ARG cc_start: 0.7332 (OUTLIER) cc_final: 0.6854 (tpm170) REVERT: C 222 LEU cc_start: 0.8860 (OUTLIER) cc_final: 0.8364 (tp) REVERT: C 273 GLU cc_start: 0.8375 (tm-30) cc_final: 0.8088 (tm-30) REVERT: C 319 GLU cc_start: 0.5513 (tp30) cc_final: 0.5247 (tp30) REVERT: C 397 GLU cc_start: 0.8545 (mm-30) cc_final: 0.8343 (mm-30) REVERT: C 449 MET cc_start: 0.8526 (tpt) cc_final: 0.8010 (tpp) REVERT: C 450 ASP cc_start: 0.9290 (m-30) cc_final: 0.8893 (m-30) REVERT: C 470 GLU cc_start: 0.8881 (pt0) cc_final: 0.8521 (pt0) REVERT: C 560 ARG cc_start: 0.8927 (ttt180) cc_final: 0.8340 (ttt180) REVERT: D 239 ARG cc_start: 0.7587 (mmm160) cc_final: 0.7340 (mmm160) REVERT: D 288 LYS cc_start: 0.9193 (mttt) cc_final: 0.8965 (mtmp) REVERT: D 397 GLU cc_start: 0.8547 (mm-30) cc_final: 0.8288 (tm-30) REVERT: D 478 ASP cc_start: 0.8989 (m-30) cc_final: 0.8690 (m-30) REVERT: D 560 ARG cc_start: 0.8889 (ttt180) cc_final: 0.8425 (ttt-90) REVERT: D 567 ARG cc_start: 0.8610 (OUTLIER) cc_final: 0.8069 (ttp80) REVERT: D 616 ASN cc_start: 0.8429 (t0) cc_final: 0.8068 (t0) REVERT: E 288 LYS cc_start: 0.9032 (mttt) cc_final: 0.8725 (mtmp) REVERT: E 397 GLU cc_start: 0.8692 (mm-30) cc_final: 0.8440 (mm-30) REVERT: E 449 MET cc_start: 0.8500 (tpt) cc_final: 0.7913 (tpp) REVERT: E 560 ARG cc_start: 0.8929 (ttt180) cc_final: 0.8259 (ttt180) REVERT: E 578 GLU cc_start: 0.8680 (OUTLIER) cc_final: 0.8429 (mt-10) REVERT: E 630 ASP cc_start: 0.8302 (p0) cc_final: 0.8094 (p0) REVERT: F 319 GLU cc_start: 0.5570 (tp30) cc_final: 0.5240 (tp30) REVERT: F 449 MET cc_start: 0.8538 (tpt) cc_final: 0.7999 (tpp) REVERT: F 450 ASP cc_start: 0.9314 (m-30) cc_final: 0.8902 (m-30) REVERT: F 470 GLU cc_start: 0.8884 (pt0) cc_final: 0.8491 (pt0) REVERT: F 560 ARG cc_start: 0.8938 (ttt180) cc_final: 0.8356 (ttt180) outliers start: 58 outliers final: 18 residues processed: 357 average time/residue: 0.7784 time to fit residues: 313.7616 Evaluate side-chains 309 residues out of total 2706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 283 time to evaluate : 1.091 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 307 ASP Chi-restraints excluded: chain A residue 321 GLU Chi-restraints excluded: chain A residue 359 ARG Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 475 THR Chi-restraints excluded: chain A residue 567 ARG Chi-restraints excluded: chain B residue 268 LEU Chi-restraints excluded: chain B residue 327 GLN Chi-restraints excluded: chain B residue 378 LEU Chi-restraints excluded: chain B residue 683 SER Chi-restraints excluded: chain B residue 741 ARG Chi-restraints excluded: chain C residue 222 LEU Chi-restraints excluded: chain C residue 378 LEU Chi-restraints excluded: chain C residue 484 ASP Chi-restraints excluded: chain D residue 218 GLU Chi-restraints excluded: chain D residue 307 ASP Chi-restraints excluded: chain D residue 378 LEU Chi-restraints excluded: chain D residue 475 THR Chi-restraints excluded: chain D residue 567 ARG Chi-restraints excluded: chain E residue 222 LEU Chi-restraints excluded: chain E residue 268 LEU Chi-restraints excluded: chain E residue 378 LEU Chi-restraints excluded: chain E residue 578 GLU Chi-restraints excluded: chain E residue 683 SER Chi-restraints excluded: chain F residue 378 LEU Chi-restraints excluded: chain F residue 484 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 204 optimal weight: 0.9990 chunk 241 optimal weight: 1.9990 chunk 53 optimal weight: 0.6980 chunk 315 optimal weight: 0.6980 chunk 120 optimal weight: 2.9990 chunk 243 optimal weight: 1.9990 chunk 10 optimal weight: 3.9990 chunk 195 optimal weight: 0.6980 chunk 139 optimal weight: 0.9990 chunk 37 optimal weight: 0.2980 chunk 1 optimal weight: 0.7980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 327 GLN D 348 ASN ** D 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 327 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 = 0.3591 r_free = 0.3591 target = 0.115855 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.083364 restraints weight = 40418.693| |-----------------------------------------------------------------------------| r_work (start): 0.3072 rms_B_bonded: 3.16 r_work: 0.2905 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.2905 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8181 moved from start: 0.2570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 26130 Z= 0.146 Angle : 0.682 10.035 35340 Z= 0.323 Chirality : 0.043 0.171 3972 Planarity : 0.004 0.050 4620 Dihedral : 7.491 100.947 3636 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Rotamer: Outliers : 2.22 % Allowed : 14.38 % Favored : 83.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.19 % 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: 0.72 (0.15), residues: 3240 helix: 0.90 (0.13), residues: 1716 sheet: 0.37 (0.24), residues: 402 loop : 0.04 (0.20), residues: 1122 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 349 TYR 0.022 0.002 TYR D 244 PHE 0.011 0.001 PHE E 267 TRP 0.013 0.001 TRP C 454 HIS 0.006 0.001 HIS B 317 Details of bonding type rmsd/Z covalent geometry : bond 0.00339 / 0.15 (26130) covalent geometry : angle 0.68237 / 0.32 (35340) hydrogen bonds : bond 0.03841 / 2.53 ( 1256) hydrogen bonds : angle 4.35729 / 3.15 ( 3558) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6480 Ramachandran restraints generated. 3240 Oldfield, 0 Emsley, 3240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6480 Ramachandran restraints generated. 3240 Oldfield, 0 Emsley, 3240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 374 residues out of total 2706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 314 time to evaluate : 1.055 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: A 288 LYS cc_start: 0.9179 (mttt) cc_final: 0.8949 (mtmp) REVERT: A 359 ARG cc_start: 0.8320 (OUTLIER) cc_final: 0.8049 (mmt90) REVERT: A 365 ARG cc_start: 0.8653 (mmt-90) cc_final: 0.8438 (mmm-85) REVERT: A 397 GLU cc_start: 0.8594 (mm-30) cc_final: 0.8323 (mm-30) REVERT: A 417 GLU cc_start: 0.8641 (tp30) cc_final: 0.8268 (tt0) REVERT: A 450 ASP cc_start: 0.9122 (m-30) cc_final: 0.8810 (m-30) REVERT: A 478 ASP cc_start: 0.8974 (m-30) cc_final: 0.8681 (m-30) REVERT: A 560 ARG cc_start: 0.8873 (ttt180) cc_final: 0.8403 (ttt-90) REVERT: A 567 ARG cc_start: 0.8675 (OUTLIER) cc_final: 0.8040 (ttp80) REVERT: A 614 LYS cc_start: 0.8356 (tppt) cc_final: 0.8101 (mmtm) REVERT: B 273 GLU cc_start: 0.8813 (tt0) cc_final: 0.8254 (tm-30) REVERT: B 288 LYS cc_start: 0.9071 (mttt) cc_final: 0.8727 (mtmp) REVERT: B 397 GLU cc_start: 0.8673 (mm-30) cc_final: 0.8398 (mm-30) REVERT: B 449 MET cc_start: 0.8599 (tpt) cc_final: 0.7987 (tpp) REVERT: B 560 ARG cc_start: 0.8920 (ttt180) cc_final: 0.8266 (ttt180) REVERT: B 578 GLU cc_start: 0.8576 (OUTLIER) cc_final: 0.8337 (mt-10) REVERT: B 663 LYS cc_start: 0.8948 (pttm) cc_final: 0.8415 (tptp) REVERT: B 741 ARG cc_start: 0.7317 (OUTLIER) cc_final: 0.6847 (tpm170) REVERT: C 222 LEU cc_start: 0.8835 (OUTLIER) cc_final: 0.8244 (tp) REVERT: C 273 GLU cc_start: 0.8385 (tm-30) cc_final: 0.8068 (tm-30) REVERT: C 449 MET cc_start: 0.8520 (tpt) cc_final: 0.8282 (tpt) REVERT: C 450 ASP cc_start: 0.9279 (m-30) cc_final: 0.8877 (m-30) REVERT: C 470 GLU cc_start: 0.8877 (pt0) cc_final: 0.8480 (pt0) REVERT: C 560 ARG cc_start: 0.8855 (ttt180) cc_final: 0.8296 (ttt180) REVERT: D 288 LYS cc_start: 0.9178 (mttt) cc_final: 0.8977 (mtmp) REVERT: D 327 GLN cc_start: 0.8587 (OUTLIER) cc_final: 0.7969 (tp-100) REVERT: D 365 ARG cc_start: 0.8608 (mmt-90) cc_final: 0.8401 (mmm-85) REVERT: D 397 GLU cc_start: 0.8563 (mm-30) cc_final: 0.8324 (mm-30) REVERT: D 478 ASP cc_start: 0.8985 (m-30) cc_final: 0.8664 (m-30) REVERT: D 560 ARG cc_start: 0.8888 (ttt180) cc_final: 0.8393 (ttt-90) REVERT: D 567 ARG cc_start: 0.8668 (OUTLIER) cc_final: 0.8024 (ttp80) REVERT: D 614 LYS cc_start: 0.8372 (tppt) cc_final: 0.8108 (mmtt) REVERT: E 288 LYS cc_start: 0.9040 (mttt) cc_final: 0.8764 (mtmp) REVERT: E 292 GLU cc_start: 0.8575 (pp20) cc_final: 0.8192 (pp20) REVERT: E 402 GLU cc_start: 0.8767 (OUTLIER) cc_final: 0.8507 (pm20) REVERT: E 449 MET cc_start: 0.8465 (tpt) cc_final: 0.7975 (tpp) REVERT: E 466 GLU cc_start: 0.8118 (pm20) cc_final: 0.7913 (pm20) REVERT: E 560 ARG cc_start: 0.8919 (ttt180) cc_final: 0.8261 (ttt180) REVERT: E 578 GLU cc_start: 0.8615 (OUTLIER) cc_final: 0.8372 (mt-10) REVERT: F 450 ASP cc_start: 0.9308 (m-30) cc_final: 0.8891 (m-30) REVERT: F 470 GLU cc_start: 0.8861 (pt0) cc_final: 0.8478 (pt0) REVERT: F 508 MET cc_start: 0.8945 (ttt) cc_final: 0.8705 (tmm) REVERT: F 560 ARG cc_start: 0.8861 (ttt180) cc_final: 0.8306 (ttt180) outliers start: 60 outliers final: 22 residues processed: 355 average time/residue: 0.7449 time to fit residues: 300.2233 Evaluate side-chains 322 residues out of total 2706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 291 time to evaluate : 0.971 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 218 GLU Chi-restraints excluded: chain A residue 359 ARG Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 402 GLU Chi-restraints excluded: chain A residue 475 THR Chi-restraints excluded: chain A residue 567 ARG Chi-restraints excluded: chain A residue 763 GLN Chi-restraints excluded: chain B residue 222 LEU Chi-restraints excluded: chain B residue 378 LEU Chi-restraints excluded: chain B residue 578 GLU Chi-restraints excluded: chain B residue 683 SER Chi-restraints excluded: chain B residue 741 ARG Chi-restraints excluded: chain C residue 222 LEU Chi-restraints excluded: chain C residue 378 LEU Chi-restraints excluded: chain C residue 484 ASP Chi-restraints excluded: chain C residue 763 GLN Chi-restraints excluded: chain D residue 327 GLN Chi-restraints excluded: chain D residue 378 LEU Chi-restraints excluded: chain D residue 475 THR Chi-restraints excluded: chain D residue 567 ARG Chi-restraints excluded: chain D residue 763 GLN Chi-restraints excluded: chain E residue 222 LEU Chi-restraints excluded: chain E residue 268 LEU Chi-restraints excluded: chain E residue 378 LEU Chi-restraints excluded: chain E residue 402 GLU Chi-restraints excluded: chain E residue 504 LEU Chi-restraints excluded: chain E residue 578 GLU Chi-restraints excluded: chain E residue 683 SER Chi-restraints excluded: chain F residue 378 LEU Chi-restraints excluded: chain F residue 484 ASP Chi-restraints excluded: chain F residue 763 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 118 optimal weight: 4.9990 chunk 54 optimal weight: 4.9990 chunk 296 optimal weight: 0.0870 chunk 218 optimal weight: 1.9990 chunk 13 optimal weight: 0.8980 chunk 179 optimal weight: 0.5980 chunk 290 optimal weight: 2.9990 chunk 294 optimal weight: 5.9990 chunk 191 optimal weight: 0.8980 chunk 153 optimal weight: 3.9990 chunk 272 optimal weight: 0.6980 overall best weight: 0.6358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 348 ASN ** A 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 616 ASN ** B 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 337 GLN ** B 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 616 ASN ** E 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 337 GLN ** E 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 327 GLN ** F 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.114742 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.081935 restraints weight = 40399.914| |-----------------------------------------------------------------------------| r_work (start): 0.3076 rms_B_bonded: 3.16 r_work: 0.2904 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.2904 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8186 moved from start: 0.2687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 26130 Z= 0.142 Angle : 0.672 9.091 35340 Z= 0.317 Chirality : 0.043 0.173 3972 Planarity : 0.004 0.050 4620 Dihedral : 7.372 97.707 3636 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.37 % Favored : 94.63 % Rotamer: Outliers : 2.29 % Allowed : 15.11 % Favored : 82.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.19 % 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: 0.81 (0.15), residues: 3240 helix: 0.95 (0.13), residues: 1746 sheet: 0.26 (0.24), residues: 402 loop : 0.19 (0.21), residues: 1092 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 349 TYR 0.018 0.002 TYR B 244 PHE 0.014 0.001 PHE C 267 TRP 0.014 0.001 TRP C 454 HIS 0.005 0.001 HIS B 317 Details of bonding type rmsd/Z covalent geometry : bond 0.00332 / 0.14 (26130) covalent geometry : angle 0.67246 / 0.32 (35340) hydrogen bonds : bond 0.03675 / 2.42 ( 1256) hydrogen bonds : angle 4.25007 / 3.07 ( 3558) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6480 Ramachandran restraints generated. 3240 Oldfield, 0 Emsley, 3240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6480 Ramachandran restraints generated. 3240 Oldfield, 0 Emsley, 3240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 378 residues out of total 2706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 316 time to evaluate : 1.134 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: A 288 LYS cc_start: 0.9157 (mttt) cc_final: 0.8909 (mtmp) REVERT: A 359 ARG cc_start: 0.8305 (mpt180) cc_final: 0.8044 (mmt90) REVERT: A 397 GLU cc_start: 0.8622 (mm-30) cc_final: 0.8344 (mm-30) REVERT: A 417 GLU cc_start: 0.8662 (tp30) cc_final: 0.8310 (tt0) REVERT: A 450 ASP cc_start: 0.9134 (m-30) cc_final: 0.8841 (m-30) REVERT: A 478 ASP cc_start: 0.8951 (m-30) cc_final: 0.8662 (m-30) REVERT: A 560 ARG cc_start: 0.8901 (ttt180) cc_final: 0.8416 (ttt-90) REVERT: A 567 ARG cc_start: 0.8692 (OUTLIER) cc_final: 0.8042 (ttp80) REVERT: B 273 GLU cc_start: 0.8818 (tt0) cc_final: 0.8304 (tm-30) REVERT: B 288 LYS cc_start: 0.9071 (mttt) cc_final: 0.8794 (mtmp) REVERT: B 397 GLU cc_start: 0.8673 (mm-30) cc_final: 0.8412 (mm-30) REVERT: B 449 MET cc_start: 0.8596 (tpt) cc_final: 0.7978 (tpp) REVERT: B 560 ARG cc_start: 0.8940 (ttt180) cc_final: 0.8291 (ttt180) REVERT: B 578 GLU cc_start: 0.8582 (OUTLIER) cc_final: 0.8340 (mt-10) REVERT: B 663 LYS cc_start: 0.8971 (pttm) cc_final: 0.8417 (tptp) REVERT: B 741 ARG cc_start: 0.7387 (OUTLIER) cc_final: 0.6880 (tpm170) REVERT: B 763 GLN cc_start: 0.5852 (OUTLIER) cc_final: 0.5161 (tp-100) REVERT: C 273 GLU cc_start: 0.8444 (tm-30) cc_final: 0.8105 (tm-30) REVERT: C 449 MET cc_start: 0.8471 (tpt) cc_final: 0.8231 (tpt) REVERT: C 450 ASP cc_start: 0.9289 (m-30) cc_final: 0.8873 (m-30) REVERT: C 470 GLU cc_start: 0.8856 (pt0) cc_final: 0.8490 (pt0) REVERT: C 560 ARG cc_start: 0.8863 (ttt180) cc_final: 0.8287 (ttt180) REVERT: D 288 LYS cc_start: 0.9171 (mttt) cc_final: 0.8940 (mtmp) REVERT: D 397 GLU cc_start: 0.8570 (mm-30) cc_final: 0.8335 (mm-30) REVERT: D 417 GLU cc_start: 0.8643 (tp30) cc_final: 0.8273 (tt0) REVERT: D 478 ASP cc_start: 0.8963 (m-30) cc_final: 0.8671 (m-30) REVERT: D 560 ARG cc_start: 0.8890 (ttt180) cc_final: 0.8390 (ttt-90) REVERT: D 567 ARG cc_start: 0.8696 (OUTLIER) cc_final: 0.8037 (ttp80) REVERT: E 288 LYS cc_start: 0.9040 (mttt) cc_final: 0.8775 (mtmp) REVERT: E 397 GLU cc_start: 0.8669 (mm-30) cc_final: 0.8422 (mm-30) REVERT: E 402 GLU cc_start: 0.8781 (OUTLIER) cc_final: 0.8540 (pm20) REVERT: E 449 MET cc_start: 0.8457 (tpt) cc_final: 0.7957 (tpp) REVERT: E 466 GLU cc_start: 0.8121 (pm20) cc_final: 0.7897 (pm20) REVERT: E 560 ARG cc_start: 0.8935 (ttt180) cc_final: 0.8291 (ttt180) REVERT: E 578 GLU cc_start: 0.8646 (OUTLIER) cc_final: 0.8397 (mt-10) REVERT: E 763 GLN cc_start: 0.5872 (OUTLIER) cc_final: 0.5183 (tp-100) REVERT: F 449 MET cc_start: 0.8467 (tpt) cc_final: 0.8230 (tpt) REVERT: F 450 ASP cc_start: 0.9309 (m-30) cc_final: 0.8876 (m-30) REVERT: F 470 GLU cc_start: 0.8859 (pt0) cc_final: 0.8496 (pt0) REVERT: F 560 ARG cc_start: 0.8859 (ttt180) cc_final: 0.8289 (ttt180) outliers start: 62 outliers final: 34 residues processed: 359 average time/residue: 0.7518 time to fit residues: 306.0775 Evaluate side-chains 332 residues out of total 2706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 290 time to evaluate : 0.960 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 218 GLU Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 402 GLU Chi-restraints excluded: chain A residue 475 THR Chi-restraints excluded: chain A residue 504 LEU Chi-restraints excluded: chain A residue 567 ARG Chi-restraints excluded: chain A residue 629 ILE Chi-restraints excluded: chain A residue 763 GLN Chi-restraints excluded: chain B residue 222 LEU Chi-restraints excluded: chain B residue 268 LEU Chi-restraints excluded: chain B residue 378 LEU Chi-restraints excluded: chain B residue 402 GLU Chi-restraints excluded: chain B residue 578 GLU Chi-restraints excluded: chain B residue 629 ILE Chi-restraints excluded: chain B residue 683 SER Chi-restraints excluded: chain B residue 741 ARG Chi-restraints excluded: chain B residue 763 GLN Chi-restraints excluded: chain C residue 222 LEU Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 378 LEU Chi-restraints excluded: chain C residue 402 GLU Chi-restraints excluded: chain C residue 763 GLN Chi-restraints excluded: chain D residue 367 VAL Chi-restraints excluded: chain D residue 378 LEU Chi-restraints excluded: chain D residue 402 GLU Chi-restraints excluded: chain D residue 475 THR Chi-restraints excluded: chain D residue 504 LEU Chi-restraints excluded: chain D residue 567 ARG Chi-restraints excluded: chain D residue 629 ILE Chi-restraints excluded: chain D residue 763 GLN Chi-restraints excluded: chain E residue 222 LEU Chi-restraints excluded: chain E residue 268 LEU Chi-restraints excluded: chain E residue 378 LEU Chi-restraints excluded: chain E residue 402 GLU Chi-restraints excluded: chain E residue 578 GLU Chi-restraints excluded: chain E residue 683 SER Chi-restraints excluded: chain E residue 763 GLN Chi-restraints excluded: chain F residue 367 VAL Chi-restraints excluded: chain F residue 378 LEU Chi-restraints excluded: chain F residue 402 GLU Chi-restraints excluded: chain F residue 763 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 234 optimal weight: 2.9990 chunk 173 optimal weight: 0.2980 chunk 260 optimal weight: 0.9980 chunk 310 optimal weight: 0.8980 chunk 133 optimal weight: 0.9990 chunk 63 optimal weight: 0.9990 chunk 279 optimal weight: 0.8980 chunk 19 optimal weight: 0.1980 chunk 84 optimal weight: 0.9990 chunk 137 optimal weight: 0.9990 chunk 147 optimal weight: 10.0000 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 337 GLN ** B 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 348 ASN ** D 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 327 GLN E 337 GLN ** E 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.116142 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.083880 restraints weight = 40603.163| |-----------------------------------------------------------------------------| r_work (start): 0.3077 rms_B_bonded: 3.16 r_work: 0.2913 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.2913 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8183 moved from start: 0.2828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 26130 Z= 0.143 Angle : 0.672 9.106 35340 Z= 0.316 Chirality : 0.043 0.176 3972 Planarity : 0.004 0.050 4620 Dihedral : 7.305 96.499 3636 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.37 % Favored : 94.63 % Rotamer: Outliers : 2.51 % Allowed : 15.96 % Favored : 81.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.19 % 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: 0.88 (0.15), residues: 3240 helix: 1.09 (0.13), residues: 1710 sheet: 0.20 (0.24), residues: 402 loop : 0.14 (0.20), residues: 1128 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 349 TYR 0.017 0.002 TYR D 244 PHE 0.034 0.001 PHE C 267 TRP 0.016 0.001 TRP C 454 HIS 0.005 0.001 HIS D 317 Details of bonding type rmsd/Z covalent geometry : bond 0.00335 / 0.14 (26130) covalent geometry : angle 0.67206 / 0.32 (35340) hydrogen bonds : bond 0.03566 / 2.35 ( 1256) hydrogen bonds : angle 4.18877 / 3.02 ( 3558) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6480 Ramachandran restraints generated. 3240 Oldfield, 0 Emsley, 3240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6480 Ramachandran restraints generated. 3240 Oldfield, 0 Emsley, 3240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 377 residues out of total 2706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 309 time to evaluate : 0.957 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: A 288 LYS cc_start: 0.9121 (mttt) cc_final: 0.8893 (mtmp) REVERT: A 359 ARG cc_start: 0.8257 (OUTLIER) cc_final: 0.8043 (mmt90) REVERT: A 397 GLU cc_start: 0.8592 (mm-30) cc_final: 0.8314 (mm-30) REVERT: A 417 GLU cc_start: 0.8667 (tp30) cc_final: 0.8302 (tt0) REVERT: A 450 ASP cc_start: 0.9111 (m-30) cc_final: 0.8808 (m-30) REVERT: A 478 ASP cc_start: 0.8955 (m-30) cc_final: 0.8663 (m-30) REVERT: A 560 ARG cc_start: 0.8913 (ttt180) cc_final: 0.8395 (ttt-90) REVERT: A 567 ARG cc_start: 0.8713 (OUTLIER) cc_final: 0.8061 (ttp80) REVERT: B 273 GLU cc_start: 0.8791 (tt0) cc_final: 0.8301 (tm-30) REVERT: B 288 LYS cc_start: 0.9079 (mttt) cc_final: 0.8795 (mtmp) REVERT: B 397 GLU cc_start: 0.8660 (mm-30) cc_final: 0.8399 (mm-30) REVERT: B 449 MET cc_start: 0.8613 (tpt) cc_final: 0.7976 (tpp) REVERT: B 560 ARG cc_start: 0.8923 (ttt180) cc_final: 0.8272 (ttt180) REVERT: B 578 GLU cc_start: 0.8589 (OUTLIER) cc_final: 0.8346 (mt-10) REVERT: B 616 ASN cc_start: 0.8664 (t0) cc_final: 0.8412 (t0) REVERT: B 741 ARG cc_start: 0.7378 (OUTLIER) cc_final: 0.6871 (tpm170) REVERT: B 763 GLN cc_start: 0.5871 (OUTLIER) cc_final: 0.5179 (tp-100) REVERT: C 273 GLU cc_start: 0.8463 (tm-30) cc_final: 0.8102 (tm-30) REVERT: C 344 MET cc_start: 0.9159 (OUTLIER) cc_final: 0.8666 (mtm) REVERT: C 449 MET cc_start: 0.8507 (tpt) cc_final: 0.8254 (tpt) REVERT: C 450 ASP cc_start: 0.9285 (m-30) cc_final: 0.8859 (m-30) REVERT: C 470 GLU cc_start: 0.8858 (pt0) cc_final: 0.8488 (pt0) REVERT: C 560 ARG cc_start: 0.8872 (ttt180) cc_final: 0.8273 (ttt180) REVERT: D 288 LYS cc_start: 0.9116 (mttt) cc_final: 0.8905 (mtmp) REVERT: D 321 GLU cc_start: 0.8005 (mp0) cc_final: 0.7359 (mp0) REVERT: D 397 GLU cc_start: 0.8562 (mm-30) cc_final: 0.8333 (mm-30) REVERT: D 417 GLU cc_start: 0.8662 (tp30) cc_final: 0.8286 (tt0) REVERT: D 478 ASP cc_start: 0.8969 (m-30) cc_final: 0.8675 (m-30) REVERT: D 560 ARG cc_start: 0.8911 (ttt180) cc_final: 0.8382 (ttt-90) REVERT: D 567 ARG cc_start: 0.8715 (OUTLIER) cc_final: 0.8047 (ttp80) REVERT: E 288 LYS cc_start: 0.9053 (mttt) cc_final: 0.8784 (mtmp) REVERT: E 397 GLU cc_start: 0.8666 (mm-30) cc_final: 0.8414 (mm-30) REVERT: E 402 GLU cc_start: 0.8800 (OUTLIER) cc_final: 0.8568 (pm20) REVERT: E 449 MET cc_start: 0.8468 (tpt) cc_final: 0.7961 (tpp) REVERT: E 466 GLU cc_start: 0.8123 (pm20) cc_final: 0.7918 (pm20) REVERT: E 560 ARG cc_start: 0.8939 (ttt180) cc_final: 0.8287 (ttt180) REVERT: E 578 GLU cc_start: 0.8632 (OUTLIER) cc_final: 0.8379 (mt-10) REVERT: E 763 GLN cc_start: 0.5893 (OUTLIER) cc_final: 0.5200 (tp-100) REVERT: F 449 MET cc_start: 0.8497 (tpt) cc_final: 0.8216 (tpt) REVERT: F 450 ASP cc_start: 0.9292 (m-30) cc_final: 0.8867 (m-30) REVERT: F 470 GLU cc_start: 0.8870 (pt0) cc_final: 0.8491 (pt0) REVERT: F 560 ARG cc_start: 0.8865 (ttt180) cc_final: 0.8278 (ttt180) REVERT: F 616 ASN cc_start: 0.8323 (t0) cc_final: 0.8057 (t0) outliers start: 68 outliers final: 34 residues processed: 358 average time/residue: 0.7317 time to fit residues: 297.7427 Evaluate side-chains 342 residues out of total 2706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 298 time to evaluate : 1.043 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 218 GLU Chi-restraints excluded: chain A residue 359 ARG Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 402 GLU Chi-restraints excluded: chain A residue 475 THR Chi-restraints excluded: chain A residue 504 LEU Chi-restraints excluded: chain A residue 567 ARG Chi-restraints excluded: chain A residue 763 GLN Chi-restraints excluded: chain B residue 222 LEU Chi-restraints excluded: chain B residue 268 LEU Chi-restraints excluded: chain B residue 378 LEU Chi-restraints excluded: chain B residue 402 GLU Chi-restraints excluded: chain B residue 578 GLU Chi-restraints excluded: chain B residue 683 SER Chi-restraints excluded: chain B residue 741 ARG Chi-restraints excluded: chain B residue 763 GLN Chi-restraints excluded: chain C residue 222 LEU Chi-restraints excluded: chain C residue 344 MET Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 378 LEU Chi-restraints excluded: chain C residue 402 GLU Chi-restraints excluded: chain C residue 484 ASP Chi-restraints excluded: chain C residue 763 GLN Chi-restraints excluded: chain D residue 367 VAL Chi-restraints excluded: chain D residue 378 LEU Chi-restraints excluded: chain D residue 402 GLU Chi-restraints excluded: chain D residue 475 THR Chi-restraints excluded: chain D residue 504 LEU Chi-restraints excluded: chain D residue 567 ARG Chi-restraints excluded: chain D residue 629 ILE Chi-restraints excluded: chain D residue 763 GLN Chi-restraints excluded: chain E residue 222 LEU Chi-restraints excluded: chain E residue 378 LEU Chi-restraints excluded: chain E residue 402 GLU Chi-restraints excluded: chain E residue 578 GLU Chi-restraints excluded: chain E residue 629 ILE Chi-restraints excluded: chain E residue 683 SER Chi-restraints excluded: chain E residue 763 GLN Chi-restraints excluded: chain F residue 367 VAL Chi-restraints excluded: chain F residue 378 LEU Chi-restraints excluded: chain F residue 402 GLU Chi-restraints excluded: chain F residue 484 ASP Chi-restraints excluded: chain F residue 763 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 238 optimal weight: 2.9990 chunk 268 optimal weight: 4.9990 chunk 254 optimal weight: 0.8980 chunk 285 optimal weight: 0.0470 chunk 246 optimal weight: 3.9990 chunk 273 optimal weight: 0.9980 chunk 93 optimal weight: 0.3980 chunk 215 optimal weight: 0.7980 chunk 118 optimal weight: 4.9990 chunk 167 optimal weight: 0.4980 chunk 170 optimal weight: 4.9990 overall best weight: 0.5278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 327 GLN ** B 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 499 HIS E 327 GLN E 398 GLN ** E 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.116681 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.084462 restraints weight = 40604.958| |-----------------------------------------------------------------------------| r_work (start): 0.3057 rms_B_bonded: 3.15 r_work: 0.2891 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.2891 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8154 moved from start: 0.2922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 26130 Z= 0.131 Angle : 0.670 9.115 35340 Z= 0.313 Chirality : 0.043 0.215 3972 Planarity : 0.004 0.054 4620 Dihedral : 7.191 93.678 3636 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.37 % Favored : 94.63 % Rotamer: Outliers : 2.48 % Allowed : 16.70 % Favored : 80.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.19 % 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: 0.86 (0.15), residues: 3240 helix: 1.07 (0.13), residues: 1728 sheet: 0.16 (0.24), residues: 402 loop : 0.12 (0.21), residues: 1110 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG D 349 TYR 0.015 0.002 TYR D 244 PHE 0.026 0.001 PHE C 267 TRP 0.018 0.001 TRP F 454 HIS 0.005 0.001 HIS D 317 Details of bonding type rmsd/Z covalent geometry : bond 0.00307 / 0.13 (26130) covalent geometry : angle 0.66983 / 0.31 (35340) hydrogen bonds : bond 0.03437 / 2.26 ( 1256) hydrogen bonds : angle 4.12719 / 2.98 ( 3558) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6480 Ramachandran restraints generated. 3240 Oldfield, 0 Emsley, 3240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6480 Ramachandran restraints generated. 3240 Oldfield, 0 Emsley, 3240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 379 residues out of total 2706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 312 time to evaluate : 0.935 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: A 288 LYS cc_start: 0.9073 (mttt) cc_final: 0.8839 (mtmp) REVERT: A 359 ARG cc_start: 0.8175 (OUTLIER) cc_final: 0.7952 (mmt90) REVERT: A 397 GLU cc_start: 0.8528 (mm-30) cc_final: 0.8267 (mm-30) REVERT: A 417 GLU cc_start: 0.8672 (tp30) cc_final: 0.8295 (tt0) REVERT: A 450 ASP cc_start: 0.9108 (m-30) cc_final: 0.8807 (m-30) REVERT: A 478 ASP cc_start: 0.8941 (m-30) cc_final: 0.8644 (m-30) REVERT: A 560 ARG cc_start: 0.8900 (ttt180) cc_final: 0.8367 (ttt-90) REVERT: A 567 ARG cc_start: 0.8714 (OUTLIER) cc_final: 0.8072 (ttp80) REVERT: B 273 GLU cc_start: 0.8754 (tt0) cc_final: 0.8292 (tm-30) REVERT: B 288 LYS cc_start: 0.9064 (mttt) cc_final: 0.8778 (mtmp) REVERT: B 397 GLU cc_start: 0.8628 (mm-30) cc_final: 0.8372 (mm-30) REVERT: B 423 ILE cc_start: 0.8441 (mt) cc_final: 0.8205 (tt) REVERT: B 449 MET cc_start: 0.8613 (tpt) cc_final: 0.7982 (tpp) REVERT: B 560 ARG cc_start: 0.8928 (ttt180) cc_final: 0.8272 (ttt180) REVERT: B 578 GLU cc_start: 0.8594 (OUTLIER) cc_final: 0.8357 (mt-10) REVERT: B 741 ARG cc_start: 0.7361 (OUTLIER) cc_final: 0.6860 (tpm170) REVERT: B 763 GLN cc_start: 0.5792 (OUTLIER) cc_final: 0.5165 (tp-100) REVERT: C 273 GLU cc_start: 0.8466 (tm-30) cc_final: 0.8089 (tm-30) REVERT: C 344 MET cc_start: 0.9118 (OUTLIER) cc_final: 0.8618 (mtm) REVERT: C 397 GLU cc_start: 0.8398 (OUTLIER) cc_final: 0.8182 (tm-30) REVERT: C 449 MET cc_start: 0.8500 (tpt) cc_final: 0.8256 (tpt) REVERT: C 450 ASP cc_start: 0.9302 (m-30) cc_final: 0.8879 (m-30) REVERT: C 470 GLU cc_start: 0.8873 (pt0) cc_final: 0.8481 (pt0) REVERT: C 560 ARG cc_start: 0.8841 (ttt180) cc_final: 0.8018 (tpp-160) REVERT: D 288 LYS cc_start: 0.9103 (mttt) cc_final: 0.8896 (mtmp) REVERT: D 321 GLU cc_start: 0.7975 (mp0) cc_final: 0.7423 (mp0) REVERT: D 397 GLU cc_start: 0.8558 (mm-30) cc_final: 0.8313 (mm-30) REVERT: D 417 GLU cc_start: 0.8655 (tp30) cc_final: 0.8284 (tt0) REVERT: D 478 ASP cc_start: 0.8945 (m-30) cc_final: 0.8640 (m-30) REVERT: D 560 ARG cc_start: 0.8887 (ttt180) cc_final: 0.8353 (ttt-90) REVERT: D 567 ARG cc_start: 0.8716 (OUTLIER) cc_final: 0.8063 (ttp80) REVERT: E 288 LYS cc_start: 0.9022 (mttt) cc_final: 0.8764 (mtmp) REVERT: E 397 GLU cc_start: 0.8678 (mm-30) cc_final: 0.8447 (mm-30) REVERT: E 402 GLU cc_start: 0.8803 (OUTLIER) cc_final: 0.8589 (pm20) REVERT: E 449 MET cc_start: 0.8452 (tpt) cc_final: 0.7913 (tpp) REVERT: E 466 GLU cc_start: 0.8113 (pm20) cc_final: 0.7901 (pm20) REVERT: E 560 ARG cc_start: 0.8920 (ttt180) cc_final: 0.8259 (ttt180) REVERT: E 578 GLU cc_start: 0.8650 (OUTLIER) cc_final: 0.8387 (mt-10) REVERT: E 763 GLN cc_start: 0.5756 (OUTLIER) cc_final: 0.5120 (tp-100) REVERT: F 222 LEU cc_start: 0.8757 (tt) cc_final: 0.8516 (tm) REVERT: F 449 MET cc_start: 0.8461 (tpt) cc_final: 0.8234 (tpt) REVERT: F 450 ASP cc_start: 0.9295 (m-30) cc_final: 0.8863 (m-30) REVERT: F 470 GLU cc_start: 0.8873 (pt0) cc_final: 0.8485 (pt0) REVERT: F 508 MET cc_start: 0.8987 (ttt) cc_final: 0.8768 (tmm) REVERT: F 560 ARG cc_start: 0.8852 (ttt180) cc_final: 0.8031 (tpp-160) outliers start: 67 outliers final: 32 residues processed: 356 average time/residue: 0.7295 time to fit residues: 295.3693 Evaluate side-chains 340 residues out of total 2706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 297 time to evaluate : 1.033 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 359 ARG Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 394 VAL Chi-restraints excluded: chain A residue 402 GLU Chi-restraints excluded: chain A residue 475 THR Chi-restraints excluded: chain A residue 504 LEU Chi-restraints excluded: chain A residue 567 ARG Chi-restraints excluded: chain A residue 763 GLN Chi-restraints excluded: chain B residue 378 LEU Chi-restraints excluded: chain B residue 402 GLU Chi-restraints excluded: chain B residue 578 GLU Chi-restraints excluded: chain B residue 683 SER Chi-restraints excluded: chain B residue 741 ARG Chi-restraints excluded: chain B residue 763 GLN Chi-restraints excluded: chain C residue 222 LEU Chi-restraints excluded: chain C residue 344 MET Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 378 LEU Chi-restraints excluded: chain C residue 397 GLU Chi-restraints excluded: chain C residue 402 GLU Chi-restraints excluded: chain C residue 484 ASP Chi-restraints excluded: chain C residue 763 GLN Chi-restraints excluded: chain D residue 378 LEU Chi-restraints excluded: chain D residue 402 GLU Chi-restraints excluded: chain D residue 475 THR Chi-restraints excluded: chain D residue 504 LEU Chi-restraints excluded: chain D residue 567 ARG Chi-restraints excluded: chain D residue 763 GLN Chi-restraints excluded: chain E residue 292 GLU Chi-restraints excluded: chain E residue 327 GLN Chi-restraints excluded: chain E residue 378 LEU Chi-restraints excluded: chain E residue 402 GLU Chi-restraints excluded: chain E residue 460 ASN Chi-restraints excluded: chain E residue 578 GLU Chi-restraints excluded: chain E residue 608 MET Chi-restraints excluded: chain E residue 629 ILE Chi-restraints excluded: chain E residue 683 SER Chi-restraints excluded: chain E residue 763 GLN Chi-restraints excluded: chain F residue 367 VAL Chi-restraints excluded: chain F residue 378 LEU Chi-restraints excluded: chain F residue 402 GLU Chi-restraints excluded: chain F residue 763 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 88 optimal weight: 0.3980 chunk 254 optimal weight: 0.2980 chunk 154 optimal weight: 1.9990 chunk 65 optimal weight: 0.0050 chunk 105 optimal weight: 0.6980 chunk 36 optimal weight: 2.9990 chunk 306 optimal weight: 0.6980 chunk 40 optimal weight: 0.7980 chunk 232 optimal weight: 0.7980 chunk 48 optimal weight: 0.8980 chunk 100 optimal weight: 0.5980 overall best weight: 0.3994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 327 GLN B 398 GLN ** C 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 327 GLN ** E 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 616 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.117197 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.085110 restraints weight = 40636.331| |-----------------------------------------------------------------------------| r_work (start): 0.3070 rms_B_bonded: 3.15 r_work: 0.2900 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.2900 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8146 moved from start: 0.2994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 26130 Z= 0.125 Angle : 0.675 9.134 35340 Z= 0.314 Chirality : 0.043 0.206 3972 Planarity : 0.004 0.049 4620 Dihedral : 7.068 90.179 3636 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.37 % Favored : 94.63 % Rotamer: Outliers : 2.40 % Allowed : 17.33 % Favored : 80.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.19 % 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: 0.91 (0.15), residues: 3240 helix: 1.13 (0.13), residues: 1728 sheet: 0.14 (0.24), residues: 402 loop : 0.14 (0.21), residues: 1110 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 365 TYR 0.015 0.002 TYR D 244 PHE 0.025 0.001 PHE C 267 TRP 0.019 0.001 TRP F 454 HIS 0.005 0.001 HIS D 317 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.12 (26130) covalent geometry : angle 0.67531 / 0.31 (35340) hydrogen bonds : bond 0.03332 / 2.19 ( 1256) hydrogen bonds : angle 4.06523 / 2.93 ( 3558) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6480 Ramachandran restraints generated. 3240 Oldfield, 0 Emsley, 3240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6480 Ramachandran restraints generated. 3240 Oldfield, 0 Emsley, 3240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 382 residues out of total 2706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 317 time to evaluate : 0.977 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 288 LYS cc_start: 0.9054 (mttt) cc_final: 0.8842 (mtmp) REVERT: A 359 ARG cc_start: 0.8114 (OUTLIER) cc_final: 0.7912 (mmt90) REVERT: A 379 GLU cc_start: 0.8736 (mt-10) cc_final: 0.8343 (tt0) REVERT: A 388 MET cc_start: 0.8627 (mtm) cc_final: 0.8395 (mtp) REVERT: A 397 GLU cc_start: 0.8536 (mm-30) cc_final: 0.8276 (mm-30) REVERT: A 417 GLU cc_start: 0.8658 (tp30) cc_final: 0.8277 (tt0) REVERT: A 450 ASP cc_start: 0.9113 (m-30) cc_final: 0.8825 (m-30) REVERT: A 478 ASP cc_start: 0.8932 (m-30) cc_final: 0.8656 (m-30) REVERT: A 560 ARG cc_start: 0.8893 (ttt180) cc_final: 0.8363 (ttt-90) REVERT: A 567 ARG cc_start: 0.8710 (OUTLIER) cc_final: 0.8056 (ttp80) REVERT: A 763 GLN cc_start: 0.5946 (OUTLIER) cc_final: 0.5285 (tt0) REVERT: B 273 GLU cc_start: 0.8746 (tt0) cc_final: 0.8297 (tm-30) REVERT: B 288 LYS cc_start: 0.9075 (mttt) cc_final: 0.8782 (mtmp) REVERT: B 397 GLU cc_start: 0.8632 (mm-30) cc_final: 0.8415 (mm-30) REVERT: B 449 MET cc_start: 0.8593 (tpt) cc_final: 0.7991 (tpp) REVERT: B 560 ARG cc_start: 0.8917 (ttt180) cc_final: 0.8266 (ttt180) REVERT: B 578 GLU cc_start: 0.8583 (OUTLIER) cc_final: 0.8347 (mt-10) REVERT: B 741 ARG cc_start: 0.7346 (OUTLIER) cc_final: 0.6828 (tpm170) REVERT: B 763 GLN cc_start: 0.5765 (OUTLIER) cc_final: 0.5144 (tp-100) REVERT: C 273 GLU cc_start: 0.8472 (tm-30) cc_final: 0.8090 (tm-30) REVERT: C 344 MET cc_start: 0.9118 (OUTLIER) cc_final: 0.8613 (mtm) REVERT: C 389 LYS cc_start: 0.8968 (tptp) cc_final: 0.8726 (tptp) REVERT: C 397 GLU cc_start: 0.8425 (mm-30) cc_final: 0.8221 (tm-30) REVERT: C 449 MET cc_start: 0.8502 (tpt) cc_final: 0.8263 (tpt) REVERT: C 450 ASP cc_start: 0.9299 (m-30) cc_final: 0.8879 (m-30) REVERT: C 470 GLU cc_start: 0.8878 (pt0) cc_final: 0.8480 (pt0) REVERT: C 560 ARG cc_start: 0.8844 (ttt180) cc_final: 0.8201 (ttt180) REVERT: D 288 LYS cc_start: 0.9062 (mttt) cc_final: 0.8862 (mtmp) REVERT: D 321 GLU cc_start: 0.7947 (mp0) cc_final: 0.7411 (mp0) REVERT: D 397 GLU cc_start: 0.8579 (mm-30) cc_final: 0.8265 (tm-30) REVERT: D 417 GLU cc_start: 0.8648 (tp30) cc_final: 0.8278 (tt0) REVERT: D 478 ASP cc_start: 0.8940 (m-30) cc_final: 0.8631 (m-30) REVERT: D 560 ARG cc_start: 0.8886 (ttt180) cc_final: 0.8348 (ttt-90) REVERT: D 567 ARG cc_start: 0.8720 (OUTLIER) cc_final: 0.8066 (ttp80) REVERT: D 763 GLN cc_start: 0.5723 (OUTLIER) cc_final: 0.5078 (tt0) REVERT: E 288 LYS cc_start: 0.9018 (mttt) cc_final: 0.8724 (mtmp) REVERT: E 379 GLU cc_start: 0.8762 (mt-10) cc_final: 0.8494 (tt0) REVERT: E 397 GLU cc_start: 0.8703 (mm-30) cc_final: 0.8464 (mm-30) REVERT: E 402 GLU cc_start: 0.8806 (OUTLIER) cc_final: 0.8557 (pm20) REVERT: E 449 MET cc_start: 0.8464 (tpt) cc_final: 0.7914 (tpp) REVERT: E 466 GLU cc_start: 0.8110 (pm20) cc_final: 0.7900 (pm20) REVERT: E 560 ARG cc_start: 0.8899 (ttt180) cc_final: 0.8247 (ttt180) REVERT: E 578 GLU cc_start: 0.8618 (OUTLIER) cc_final: 0.8364 (mt-10) REVERT: E 763 GLN cc_start: 0.5793 (OUTLIER) cc_final: 0.5171 (tp-100) REVERT: F 222 LEU cc_start: 0.8722 (tt) cc_final: 0.8488 (tm) REVERT: F 449 MET cc_start: 0.8452 (tpt) cc_final: 0.8209 (tpt) REVERT: F 450 ASP cc_start: 0.9298 (m-30) cc_final: 0.8863 (m-30) REVERT: F 470 GLU cc_start: 0.8877 (pt0) cc_final: 0.8485 (pt0) REVERT: F 560 ARG cc_start: 0.8832 (ttt180) cc_final: 0.8016 (tpp-160) outliers start: 65 outliers final: 31 residues processed: 363 average time/residue: 0.7250 time to fit residues: 299.7202 Evaluate side-chains 338 residues out of total 2706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 295 time to evaluate : 0.994 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 359 ARG Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 394 VAL Chi-restraints excluded: chain A residue 402 GLU Chi-restraints excluded: chain A residue 460 ASN Chi-restraints excluded: chain A residue 475 THR Chi-restraints excluded: chain A residue 504 LEU Chi-restraints excluded: chain A residue 567 ARG Chi-restraints excluded: chain A residue 763 GLN Chi-restraints excluded: chain B residue 378 LEU Chi-restraints excluded: chain B residue 402 GLU Chi-restraints excluded: chain B residue 578 GLU Chi-restraints excluded: chain B residue 683 SER Chi-restraints excluded: chain B residue 741 ARG Chi-restraints excluded: chain B residue 763 GLN Chi-restraints excluded: chain C residue 222 LEU Chi-restraints excluded: chain C residue 344 MET Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 378 LEU Chi-restraints excluded: chain C residue 402 GLU Chi-restraints excluded: chain C residue 484 ASP Chi-restraints excluded: chain C residue 763 GLN Chi-restraints excluded: chain D residue 367 VAL Chi-restraints excluded: chain D residue 378 LEU Chi-restraints excluded: chain D residue 402 GLU Chi-restraints excluded: chain D residue 475 THR Chi-restraints excluded: chain D residue 504 LEU Chi-restraints excluded: chain D residue 567 ARG Chi-restraints excluded: chain D residue 763 GLN Chi-restraints excluded: chain E residue 327 GLN Chi-restraints excluded: chain E residue 378 LEU Chi-restraints excluded: chain E residue 402 GLU Chi-restraints excluded: chain E residue 460 ASN Chi-restraints excluded: chain E residue 578 GLU Chi-restraints excluded: chain E residue 629 ILE Chi-restraints excluded: chain E residue 683 SER Chi-restraints excluded: chain E residue 763 GLN Chi-restraints excluded: chain F residue 367 VAL Chi-restraints excluded: chain F residue 378 LEU Chi-restraints excluded: chain F residue 402 GLU Chi-restraints excluded: chain F residue 484 ASP Chi-restraints excluded: chain F residue 763 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 227 optimal weight: 0.3980 chunk 249 optimal weight: 0.9990 chunk 311 optimal weight: 0.5980 chunk 56 optimal weight: 2.9990 chunk 10 optimal weight: 3.9990 chunk 244 optimal weight: 0.4980 chunk 134 optimal weight: 0.8980 chunk 41 optimal weight: 0.5980 chunk 300 optimal weight: 1.9990 chunk 269 optimal weight: 0.9990 chunk 223 optimal weight: 1.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 348 ASN ** A 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 327 GLN ** C 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 327 GLN ** D 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 327 GLN ** E 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.116858 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.084692 restraints weight = 40676.382| |-----------------------------------------------------------------------------| r_work (start): 0.3060 rms_B_bonded: 3.15 r_work: 0.2895 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.2895 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8156 moved from start: 0.3031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 26130 Z= 0.137 Angle : 0.688 9.149 35340 Z= 0.320 Chirality : 0.043 0.192 3972 Planarity : 0.004 0.049 4620 Dihedral : 7.041 88.985 3636 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.52 % Favored : 94.48 % Rotamer: Outliers : 2.33 % Allowed : 17.41 % Favored : 80.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.19 % 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: 0.94 (0.15), residues: 3240 helix: 1.17 (0.13), residues: 1728 sheet: 0.15 (0.24), residues: 402 loop : 0.13 (0.21), residues: 1110 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 349 TYR 0.014 0.002 TYR B 244 PHE 0.025 0.001 PHE C 267 TRP 0.022 0.002 TRP C 454 HIS 0.004 0.001 HIS D 317 Details of bonding type rmsd/Z covalent geometry : bond 0.00325 / 0.14 (26130) covalent geometry : angle 0.68824 / 0.32 (35340) hydrogen bonds : bond 0.03371 / 2.22 ( 1256) hydrogen bonds : angle 4.06592 / 2.93 ( 3558) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6480 Ramachandran restraints generated. 3240 Oldfield, 0 Emsley, 3240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6480 Ramachandran restraints generated. 3240 Oldfield, 0 Emsley, 3240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 365 residues out of total 2706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 302 time to evaluate : 1.098 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 288 LYS cc_start: 0.9061 (mttt) cc_final: 0.8849 (mtmp) REVERT: A 359 ARG cc_start: 0.8191 (OUTLIER) cc_final: 0.7977 (mmt90) REVERT: A 379 GLU cc_start: 0.8732 (mt-10) cc_final: 0.8336 (tt0) REVERT: A 397 GLU cc_start: 0.8523 (mm-30) cc_final: 0.8282 (mm-30) REVERT: A 417 GLU cc_start: 0.8641 (tp30) cc_final: 0.8244 (tt0) REVERT: A 450 ASP cc_start: 0.9100 (m-30) cc_final: 0.8807 (m-30) REVERT: A 478 ASP cc_start: 0.8943 (m-30) cc_final: 0.8643 (m-30) REVERT: A 560 ARG cc_start: 0.8896 (ttt180) cc_final: 0.8356 (ttt-90) REVERT: A 567 ARG cc_start: 0.8723 (OUTLIER) cc_final: 0.8073 (ttp80) REVERT: A 763 GLN cc_start: 0.5945 (OUTLIER) cc_final: 0.5286 (tt0) REVERT: B 273 GLU cc_start: 0.8741 (tt0) cc_final: 0.8302 (tm-30) REVERT: B 288 LYS cc_start: 0.9080 (mttt) cc_final: 0.8794 (mtmp) REVERT: B 292 GLU cc_start: 0.8561 (OUTLIER) cc_final: 0.8347 (pp20) REVERT: B 379 GLU cc_start: 0.8798 (mt-10) cc_final: 0.8527 (tt0) REVERT: B 397 GLU cc_start: 0.8695 (mm-30) cc_final: 0.8463 (mm-30) REVERT: B 449 MET cc_start: 0.8611 (tpt) cc_final: 0.8028 (tpp) REVERT: B 560 ARG cc_start: 0.8941 (ttt180) cc_final: 0.8287 (ttt180) REVERT: B 578 GLU cc_start: 0.8611 (OUTLIER) cc_final: 0.8372 (mt-10) REVERT: B 741 ARG cc_start: 0.7364 (OUTLIER) cc_final: 0.6839 (tpm170) REVERT: B 763 GLN cc_start: 0.5807 (OUTLIER) cc_final: 0.5187 (tp-100) REVERT: C 273 GLU cc_start: 0.8499 (tm-30) cc_final: 0.8102 (tm-30) REVERT: C 344 MET cc_start: 0.9108 (OUTLIER) cc_final: 0.8607 (mtm) REVERT: C 389 LYS cc_start: 0.8964 (tptp) cc_final: 0.8722 (tptp) REVERT: C 397 GLU cc_start: 0.8432 (mm-30) cc_final: 0.8171 (tm-30) REVERT: C 449 MET cc_start: 0.8508 (tpt) cc_final: 0.8263 (tpt) REVERT: C 450 ASP cc_start: 0.9299 (m-30) cc_final: 0.8875 (m-30) REVERT: C 470 GLU cc_start: 0.8883 (pt0) cc_final: 0.8482 (pt0) REVERT: C 560 ARG cc_start: 0.8845 (ttt180) cc_final: 0.8213 (ttt180) REVERT: D 288 LYS cc_start: 0.9065 (mttt) cc_final: 0.8860 (mtmp) REVERT: D 321 GLU cc_start: 0.8000 (mp0) cc_final: 0.7436 (mp0) REVERT: D 397 GLU cc_start: 0.8577 (mm-30) cc_final: 0.8281 (tm-30) REVERT: D 417 GLU cc_start: 0.8651 (tp30) cc_final: 0.8248 (tt0) REVERT: D 478 ASP cc_start: 0.8946 (m-30) cc_final: 0.8661 (m-30) REVERT: D 560 ARG cc_start: 0.8899 (ttt180) cc_final: 0.8358 (ttt-90) REVERT: D 567 ARG cc_start: 0.8729 (OUTLIER) cc_final: 0.8087 (ttp80) REVERT: D 763 GLN cc_start: 0.5886 (OUTLIER) cc_final: 0.5232 (tt0) REVERT: E 288 LYS cc_start: 0.8951 (mttt) cc_final: 0.8696 (mtmp) REVERT: E 379 GLU cc_start: 0.8761 (mt-10) cc_final: 0.8493 (tt0) REVERT: E 397 GLU cc_start: 0.8723 (mm-30) cc_final: 0.8472 (mm-30) REVERT: E 449 MET cc_start: 0.8488 (tpt) cc_final: 0.7924 (tpp) REVERT: E 466 GLU cc_start: 0.8137 (pm20) cc_final: 0.7904 (pm20) REVERT: E 560 ARG cc_start: 0.8909 (ttt180) cc_final: 0.8256 (ttt180) REVERT: E 578 GLU cc_start: 0.8677 (OUTLIER) cc_final: 0.8436 (mt-10) REVERT: E 763 GLN cc_start: 0.5844 (OUTLIER) cc_final: 0.5224 (tp-100) REVERT: F 449 MET cc_start: 0.8471 (tpt) cc_final: 0.8161 (tpt) REVERT: F 450 ASP cc_start: 0.9299 (m-30) cc_final: 0.8858 (m-30) REVERT: F 470 GLU cc_start: 0.8878 (pt0) cc_final: 0.8483 (pt0) REVERT: F 560 ARG cc_start: 0.8848 (ttt180) cc_final: 0.8035 (tpp-160) outliers start: 63 outliers final: 33 residues processed: 348 average time/residue: 0.7167 time to fit residues: 284.4202 Evaluate side-chains 340 residues out of total 2706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 295 time to evaluate : 1.011 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 359 ARG Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 394 VAL Chi-restraints excluded: chain A residue 402 GLU Chi-restraints excluded: chain A residue 460 ASN Chi-restraints excluded: chain A residue 475 THR Chi-restraints excluded: chain A residue 504 LEU Chi-restraints excluded: chain A residue 567 ARG Chi-restraints excluded: chain A residue 763 GLN Chi-restraints excluded: chain B residue 268 LEU Chi-restraints excluded: chain B residue 292 GLU Chi-restraints excluded: chain B residue 378 LEU Chi-restraints excluded: chain B residue 402 GLU Chi-restraints excluded: chain B residue 578 GLU Chi-restraints excluded: chain B residue 683 SER Chi-restraints excluded: chain B residue 741 ARG Chi-restraints excluded: chain B residue 763 GLN Chi-restraints excluded: chain C residue 344 MET Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 378 LEU Chi-restraints excluded: chain C residue 402 GLU Chi-restraints excluded: chain C residue 484 ASP Chi-restraints excluded: chain C residue 763 GLN Chi-restraints excluded: chain D residue 268 LEU Chi-restraints excluded: chain D residue 367 VAL Chi-restraints excluded: chain D residue 378 LEU Chi-restraints excluded: chain D residue 402 GLU Chi-restraints excluded: chain D residue 475 THR Chi-restraints excluded: chain D residue 504 LEU Chi-restraints excluded: chain D residue 567 ARG Chi-restraints excluded: chain D residue 763 GLN Chi-restraints excluded: chain E residue 327 GLN Chi-restraints excluded: chain E residue 378 LEU Chi-restraints excluded: chain E residue 402 GLU Chi-restraints excluded: chain E residue 460 ASN Chi-restraints excluded: chain E residue 578 GLU Chi-restraints excluded: chain E residue 683 SER Chi-restraints excluded: chain E residue 763 GLN Chi-restraints excluded: chain F residue 367 VAL Chi-restraints excluded: chain F residue 378 LEU Chi-restraints excluded: chain F residue 390 LEU Chi-restraints excluded: chain F residue 402 GLU Chi-restraints excluded: chain F residue 484 ASP Chi-restraints excluded: chain F residue 763 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 9 optimal weight: 0.4980 chunk 83 optimal weight: 0.8980 chunk 5 optimal weight: 0.7980 chunk 174 optimal weight: 2.9990 chunk 175 optimal weight: 0.6980 chunk 187 optimal weight: 0.7980 chunk 79 optimal weight: 1.9990 chunk 322 optimal weight: 4.9990 chunk 66 optimal weight: 2.9990 chunk 271 optimal weight: 0.9980 chunk 80 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 327 GLN ** C 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 327 GLN ** D 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 327 GLN ** E 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 327 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 = 0.3597 r_free = 0.3597 target = 0.114998 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.082518 restraints weight = 40530.474| |-----------------------------------------------------------------------------| r_work (start): 0.3079 rms_B_bonded: 3.15 r_work: 0.2916 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.2916 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8187 moved from start: 0.3070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 26130 Z= 0.149 Angle : 0.711 10.369 35340 Z= 0.331 Chirality : 0.043 0.203 3972 Planarity : 0.004 0.049 4620 Dihedral : 7.082 89.830 3636 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer: Outliers : 1.77 % Allowed : 17.96 % Favored : 80.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.19 % 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: 0.94 (0.15), residues: 3240 helix: 1.17 (0.13), residues: 1728 sheet: 0.16 (0.24), residues: 402 loop : 0.12 (0.21), residues: 1110 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 349 TYR 0.015 0.002 TYR B 244 PHE 0.027 0.001 PHE C 267 TRP 0.029 0.002 TRP F 454 HIS 0.004 0.001 HIS B 317 Details of bonding type rmsd/Z covalent geometry : bond 0.00356 / 0.15 (26130) covalent geometry : angle 0.71085 / 0.33 (35340) hydrogen bonds : bond 0.03436 / 2.26 ( 1256) hydrogen bonds : angle 4.08883 / 2.94 ( 3558) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6480 Ramachandran restraints generated. 3240 Oldfield, 0 Emsley, 3240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6480 Ramachandran restraints generated. 3240 Oldfield, 0 Emsley, 3240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 349 residues out of total 2706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 301 time to evaluate : 1.006 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 288 LYS cc_start: 0.9086 (mttt) cc_final: 0.8858 (mtmp) REVERT: A 359 ARG cc_start: 0.8257 (OUTLIER) cc_final: 0.8031 (mmt90) REVERT: A 397 GLU cc_start: 0.8521 (mm-30) cc_final: 0.8296 (mm-30) REVERT: A 450 ASP cc_start: 0.9086 (m-30) cc_final: 0.8762 (m-30) REVERT: A 478 ASP cc_start: 0.8954 (m-30) cc_final: 0.8658 (m-30) REVERT: A 560 ARG cc_start: 0.8919 (ttt180) cc_final: 0.8370 (ttt-90) REVERT: A 567 ARG cc_start: 0.8731 (OUTLIER) cc_final: 0.8084 (ttp80) REVERT: B 273 GLU cc_start: 0.8751 (tt0) cc_final: 0.8317 (tm-30) REVERT: B 288 LYS cc_start: 0.9070 (mttt) cc_final: 0.8782 (mtmp) REVERT: B 292 GLU cc_start: 0.8572 (OUTLIER) cc_final: 0.8340 (pp20) REVERT: B 327 GLN cc_start: 0.8668 (OUTLIER) cc_final: 0.8219 (tp-100) REVERT: B 379 GLU cc_start: 0.8791 (mt-10) cc_final: 0.8530 (tt0) REVERT: B 397 GLU cc_start: 0.8638 (mm-30) cc_final: 0.8398 (mm-30) REVERT: B 449 MET cc_start: 0.8590 (tpt) cc_final: 0.8003 (tpp) REVERT: B 560 ARG cc_start: 0.8950 (ttt180) cc_final: 0.8310 (ttt180) REVERT: B 578 GLU cc_start: 0.8662 (OUTLIER) cc_final: 0.8419 (mt-10) REVERT: B 741 ARG cc_start: 0.7397 (OUTLIER) cc_final: 0.6869 (tpm170) REVERT: B 763 GLN cc_start: 0.5782 (OUTLIER) cc_final: 0.5141 (tp-100) REVERT: C 273 GLU cc_start: 0.8536 (tm-30) cc_final: 0.8205 (tm-30) REVERT: C 389 LYS cc_start: 0.8977 (tptp) cc_final: 0.8755 (tptp) REVERT: C 397 GLU cc_start: 0.8450 (OUTLIER) cc_final: 0.8200 (tm-30) REVERT: C 449 MET cc_start: 0.8539 (tpt) cc_final: 0.8283 (tpt) REVERT: C 450 ASP cc_start: 0.9300 (m-30) cc_final: 0.8863 (m-30) REVERT: C 470 GLU cc_start: 0.8877 (pt0) cc_final: 0.8473 (pt0) REVERT: C 560 ARG cc_start: 0.8879 (ttt180) cc_final: 0.8235 (ttt180) REVERT: D 288 LYS cc_start: 0.9078 (mttt) cc_final: 0.8870 (mtmp) REVERT: D 321 GLU cc_start: 0.8031 (mp0) cc_final: 0.7505 (mp0) REVERT: D 327 GLN cc_start: 0.8625 (OUTLIER) cc_final: 0.7927 (tp-100) REVERT: D 397 GLU cc_start: 0.8570 (mm-30) cc_final: 0.8284 (tm-30) REVERT: D 417 GLU cc_start: 0.8674 (tp30) cc_final: 0.8367 (tp30) REVERT: D 478 ASP cc_start: 0.8969 (m-30) cc_final: 0.8667 (m-30) REVERT: D 560 ARG cc_start: 0.8924 (ttt180) cc_final: 0.8384 (ttt-90) REVERT: D 567 ARG cc_start: 0.8734 (OUTLIER) cc_final: 0.8088 (ttp80) REVERT: E 288 LYS cc_start: 0.8981 (mttt) cc_final: 0.8633 (mttp) REVERT: E 379 GLU cc_start: 0.8768 (mt-10) cc_final: 0.8508 (tt0) REVERT: E 397 GLU cc_start: 0.8692 (mm-30) cc_final: 0.8446 (mm-30) REVERT: E 449 MET cc_start: 0.8516 (tpt) cc_final: 0.7958 (tpp) REVERT: E 466 GLU cc_start: 0.8158 (pm20) cc_final: 0.7923 (pm20) REVERT: E 560 ARG cc_start: 0.8920 (ttt180) cc_final: 0.8286 (ttt180) REVERT: E 578 GLU cc_start: 0.8697 (OUTLIER) cc_final: 0.8458 (mt-10) REVERT: E 763 GLN cc_start: 0.5872 (OUTLIER) cc_final: 0.5264 (tp-100) REVERT: F 449 MET cc_start: 0.8485 (tpt) cc_final: 0.8167 (tpt) REVERT: F 450 ASP cc_start: 0.9294 (m-30) cc_final: 0.8848 (m-30) REVERT: F 470 GLU cc_start: 0.8879 (pt0) cc_final: 0.8483 (pt0) REVERT: F 560 ARG cc_start: 0.8880 (ttt180) cc_final: 0.8062 (tpp-160) outliers start: 48 outliers final: 35 residues processed: 336 average time/residue: 0.7527 time to fit residues: 287.2542 Evaluate side-chains 341 residues out of total 2706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 294 time to evaluate : 0.698 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 359 ARG Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 394 VAL Chi-restraints excluded: chain A residue 402 GLU Chi-restraints excluded: chain A residue 460 ASN Chi-restraints excluded: chain A residue 475 THR Chi-restraints excluded: chain A residue 504 LEU Chi-restraints excluded: chain A residue 567 ARG Chi-restraints excluded: chain A residue 763 GLN Chi-restraints excluded: chain B residue 268 LEU Chi-restraints excluded: chain B residue 292 GLU Chi-restraints excluded: chain B residue 327 GLN Chi-restraints excluded: chain B residue 378 LEU Chi-restraints excluded: chain B residue 402 GLU Chi-restraints excluded: chain B residue 578 GLU Chi-restraints excluded: chain B residue 683 SER Chi-restraints excluded: chain B residue 741 ARG Chi-restraints excluded: chain B residue 763 GLN Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 378 LEU Chi-restraints excluded: chain C residue 397 GLU Chi-restraints excluded: chain C residue 402 GLU Chi-restraints excluded: chain C residue 484 ASP Chi-restraints excluded: chain C residue 763 GLN Chi-restraints excluded: chain D residue 268 LEU Chi-restraints excluded: chain D residue 327 GLN Chi-restraints excluded: chain D residue 367 VAL Chi-restraints excluded: chain D residue 378 LEU Chi-restraints excluded: chain D residue 402 GLU Chi-restraints excluded: chain D residue 475 THR Chi-restraints excluded: chain D residue 567 ARG Chi-restraints excluded: chain D residue 763 GLN Chi-restraints excluded: chain E residue 327 GLN Chi-restraints excluded: chain E residue 378 LEU Chi-restraints excluded: chain E residue 402 GLU Chi-restraints excluded: chain E residue 460 ASN Chi-restraints excluded: chain E residue 578 GLU Chi-restraints excluded: chain E residue 683 SER Chi-restraints excluded: chain E residue 763 GLN Chi-restraints excluded: chain F residue 367 VAL Chi-restraints excluded: chain F residue 378 LEU Chi-restraints excluded: chain F residue 390 LEU Chi-restraints excluded: chain F residue 402 GLU Chi-restraints excluded: chain F residue 467 THR Chi-restraints excluded: chain F residue 484 ASP Chi-restraints excluded: chain F residue 763 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 271 optimal weight: 0.9980 chunk 252 optimal weight: 0.5980 chunk 79 optimal weight: 0.7980 chunk 180 optimal weight: 1.9990 chunk 18 optimal weight: 3.9990 chunk 109 optimal weight: 0.9990 chunk 262 optimal weight: 2.9990 chunk 191 optimal weight: 1.9990 chunk 283 optimal weight: 0.6980 chunk 317 optimal weight: 2.9990 chunk 44 optimal weight: 0.0030 overall best weight: 0.6190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 327 GLN ** C 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 327 GLN ** D 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 327 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 = 0.3599 r_free = 0.3599 target = 0.115129 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.082710 restraints weight = 40505.237| |-----------------------------------------------------------------------------| r_work (start): 0.3082 rms_B_bonded: 3.15 r_work: 0.2913 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.2913 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8218 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 : 0.006 0.384 26130 Z= 0.277 Angle : 0.919 59.132 35340 Z= 0.510 Chirality : 0.046 0.761 3972 Planarity : 0.005 0.143 4620 Dihedral : 7.080 89.832 3636 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 9.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer: Outliers : 1.92 % Allowed : 18.00 % Favored : 80.08 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.19 % 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: 0.94 (0.15), residues: 3240 helix: 1.17 (0.13), residues: 1728 sheet: 0.16 (0.24), residues: 402 loop : 0.12 (0.21), residues: 1110 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 349 TYR 0.015 0.002 TYR B 244 PHE 0.026 0.001 PHE C 267 TRP 0.026 0.002 TRP F 454 HIS 0.004 0.001 HIS B 317 Details of bonding type rmsd/Z covalent geometry : bond 0.00589 / 0.28 (26130) covalent geometry : angle 0.91888 / 0.51 (35340) hydrogen bonds : bond 0.03432 / 2.26 ( 1256) hydrogen bonds : angle 4.08940 / 2.94 ( 3558) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8872.47 seconds wall clock time: 151 minutes 46.90 seconds (9106.90 seconds total)