Starting phenix.real_space_refine on Wed Apr 8 06:55:36 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/10qr_75392/04_2026/10qr_75392.cif Found real_map, /net/cci-nas-00/data/ceres_data/10qr_75392/04_2026/10qr_75392.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/10qr_75392/04_2026/10qr_75392.map" default_real_map = "/net/cci-nas-00/data/ceres_data/10qr_75392/04_2026/10qr_75392.map" model { file = "/net/cci-nas-00/data/ceres_data/10qr_75392/04_2026/10qr_75392.cif" } default_model = "/net/cci-nas-00/data/ceres_data/10qr_75392/04_2026/10qr_75392.cif" } resolution = 2.3 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= 0.009 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 24 5.49 5 Mg 12 5.21 5 S 180 5.16 5 C 21756 2.51 5 N 6132 2.21 5 O 6654 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 222 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 34758 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 5732 Number of conformers: 1 Conformer: "" Number of residues, atoms: 732, 5732 Classifications: {'peptide': 732} Link IDs: {'CIS': 1, 'PCIS': 3, 'PTRANS': 36, 'TRANS': 691} Chain breaks: 1 Chain: "B" Number of atoms: 5732 Number of conformers: 1 Conformer: "" Number of residues, atoms: 732, 5732 Classifications: {'peptide': 732} Link IDs: {'CIS': 1, 'PCIS': 3, 'PTRANS': 36, 'TRANS': 691} Chain breaks: 1 Chain: "A" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {' MG': 2, 'ADP': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {' MG': 2, 'ADP': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "A" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Chain: "B" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Chain: "C" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Chain: "D" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Chain: "E" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Chain: "F" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Restraints were copied for chains: C, D, E, F Time building chain proxies: 8.33, per 1000 atoms: 0.24 Number of scatterers: 34758 At special positions: 0 Unit cell: (177.487, 173.105, 97.8736, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 180 16.00 P 24 15.00 Mg 12 11.99 O 6654 8.00 N 6132 7.00 C 21756 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: 2.93 Conformation dependent library (CDL) restraints added in 1.5 seconds 8736 Ramachandran restraints generated. 4368 Oldfield, 0 Emsley, 4368 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8184 Finding SS restraints... Secondary structure from input PDB file: 204 helices and 36 sheets defined 48.8% alpha, 10.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.26 Creating SS restraints... Processing helix chain 'A' and resid 61 through 65 removed outlier: 4.158A pdb=" N ARG A 64 " --> pdb=" O GLY A 61 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 93 removed outlier: 3.988A pdb=" N ASN A 91 " --> pdb=" O VAL A 87 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N LEU A 92 " --> pdb=" O VAL A 88 " (cutoff:3.500A) Processing helix chain 'A' and resid 130 through 135 Processing helix chain 'A' and resid 135 through 140 Processing helix chain 'A' and resid 202 through 206 Processing helix chain 'A' and resid 211 through 226 removed outlier: 5.116A 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: 3.807A 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 277 removed outlier: 3.847A pdb=" N LYS A 277 " --> pdb=" O GLU A 273 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 296 removed outlier: 3.760A pdb=" N PHE A 290 " --> pdb=" O LEU A 286 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N LYS A 295 " --> pdb=" O GLU A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 305 through 310 removed outlier: 3.736A pdb=" N ILE A 309 " --> pdb=" O GLU A 305 " (cutoff:3.500A) Processing helix chain 'A' and resid 318 through 326 removed outlier: 4.005A pdb=" N ARG A 322 " --> pdb=" O GLY A 318 " (cutoff:3.500A) Processing helix chain 'A' and resid 327 through 335 removed outlier: 3.774A pdb=" N LEU A 335 " --> pdb=" O LEU A 331 " (cutoff:3.500A) Processing helix chain 'A' and resid 349 through 353 removed outlier: 3.931A pdb=" N ILE A 353 " --> pdb=" O PRO A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 354 through 359 Processing helix chain 'A' and resid 373 through 385 Processing helix chain 'A' and resid 397 through 402 Processing helix chain 'A' and resid 407 through 425 Processing helix chain 'A' and resid 438 through 445 removed outlier: 3.661A pdb=" N MET A 442 " --> pdb=" O ASP A 438 " (cutoff:3.500A) Processing helix chain 'A' and resid 448 through 458 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 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: 3.955A 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 611 Processing helix chain 'A' and resid 625 through 629 Processing helix chain 'A' and resid 630 through 635 removed outlier: 3.691A pdb=" N ARG A 635 " --> pdb=" O ALA A 632 " (cutoff:3.500A) Processing helix chain 'A' and resid 649 through 662 Processing helix chain 'A' and resid 671 through 679 Processing helix chain 'A' and resid 683 through 705 Processing helix chain 'A' and resid 732 through 741 Processing helix chain 'A' and resid 748 through 765 removed outlier: 3.573A pdb=" N LEU A 762 " --> pdb=" O PHE A 758 " (cutoff:3.500A) Processing helix chain 'B' and resid 61 through 65 removed outlier: 4.158A pdb=" N ARG B 64 " --> pdb=" O GLY B 61 " (cutoff:3.500A) Processing helix chain 'B' and resid 85 through 93 removed outlier: 3.988A pdb=" N ASN B 91 " --> pdb=" O VAL B 87 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N LEU B 92 " --> pdb=" O VAL B 88 " (cutoff:3.500A) Processing helix chain 'B' and resid 130 through 135 Processing helix chain 'B' and resid 135 through 140 Processing helix chain 'B' and resid 202 through 206 Processing helix chain 'B' and resid 211 through 226 removed outlier: 5.117A 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: 3.808A 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: 3.847A pdb=" N LYS B 277 " --> pdb=" O GLU B 273 " (cutoff:3.500A) Processing helix chain 'B' and resid 280 through 296 removed outlier: 3.761A pdb=" N PHE B 290 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N LYS B 295 " --> pdb=" O GLU B 291 " (cutoff:3.500A) Processing helix chain 'B' and resid 305 through 310 removed outlier: 3.736A pdb=" N ILE B 309 " --> pdb=" O GLU B 305 " (cutoff:3.500A) Processing helix chain 'B' and resid 318 through 326 removed outlier: 4.005A pdb=" N ARG B 322 " --> pdb=" O GLY B 318 " (cutoff:3.500A) Processing helix chain 'B' and resid 327 through 335 removed outlier: 3.773A pdb=" N LEU B 335 " --> pdb=" O LEU B 331 " (cutoff:3.500A) Processing helix chain 'B' and resid 349 through 353 removed outlier: 3.931A pdb=" N ILE B 353 " --> pdb=" O PRO B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 354 through 359 Processing helix chain 'B' and resid 373 through 385 Processing helix chain 'B' and resid 397 through 402 Processing helix chain 'B' and resid 407 through 425 Processing helix chain 'B' and resid 438 through 445 removed outlier: 3.661A pdb=" N MET B 442 " --> pdb=" O ASP B 438 " (cutoff:3.500A) Processing helix chain 'B' and resid 448 through 458 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 553 Processing helix chain 'B' and resid 557 through 569 removed outlier: 3.956A 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 611 Processing helix chain 'B' and resid 625 through 629 Processing helix chain 'B' and resid 630 through 635 removed outlier: 3.691A pdb=" N ARG B 635 " --> pdb=" O ALA B 632 " (cutoff:3.500A) Processing helix chain 'B' and resid 649 through 662 Processing helix chain 'B' and resid 671 through 679 Processing helix chain 'B' and resid 683 through 705 Processing helix chain 'B' and resid 732 through 741 Processing helix chain 'B' and resid 748 through 765 removed outlier: 3.574A pdb=" N LEU B 762 " --> pdb=" O PHE B 758 " (cutoff:3.500A) Processing helix chain 'C' and resid 61 through 65 removed outlier: 4.157A pdb=" N ARG C 64 " --> pdb=" O GLY C 61 " (cutoff:3.500A) Processing helix chain 'C' and resid 85 through 93 removed outlier: 3.988A pdb=" N ASN C 91 " --> pdb=" O VAL C 87 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N LEU C 92 " --> pdb=" O VAL C 88 " (cutoff:3.500A) Processing helix chain 'C' and resid 130 through 135 Processing helix chain 'C' and resid 135 through 140 Processing helix chain 'C' and resid 202 through 206 Processing helix chain 'C' and resid 211 through 226 removed outlier: 5.116A pdb=" N LEU C 222 " --> pdb=" O GLU C 218 " (cutoff:3.500A) Proline residue: C 223 - end of helix Processing helix chain 'C' and resid 226 through 233 removed outlier: 3.808A pdb=" N PHE C 230 " --> pdb=" O HIS C 226 " (cutoff:3.500A) Processing helix chain 'C' and resid 250 through 263 Processing helix chain 'C' and resid 270 through 277 removed outlier: 3.847A pdb=" N LYS C 277 " --> pdb=" O GLU C 273 " (cutoff:3.500A) Processing helix chain 'C' and resid 280 through 296 removed outlier: 3.760A pdb=" N PHE C 290 " --> pdb=" O LEU C 286 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N LYS C 295 " --> pdb=" O GLU C 291 " (cutoff:3.500A) Processing helix chain 'C' and resid 305 through 310 removed outlier: 3.735A pdb=" N ILE C 309 " --> pdb=" O GLU C 305 " (cutoff:3.500A) Processing helix chain 'C' and resid 318 through 326 removed outlier: 4.005A pdb=" N ARG C 322 " --> pdb=" O GLY C 318 " (cutoff:3.500A) Processing helix chain 'C' and resid 327 through 335 removed outlier: 3.774A pdb=" N LEU C 335 " --> pdb=" O LEU C 331 " (cutoff:3.500A) Processing helix chain 'C' and resid 349 through 353 removed outlier: 3.931A pdb=" N ILE C 353 " --> pdb=" O PRO C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 354 through 359 Processing helix chain 'C' and resid 373 through 385 Processing helix chain 'C' and resid 397 through 402 Processing helix chain 'C' and resid 407 through 425 Processing helix chain 'C' and resid 438 through 445 removed outlier: 3.661A pdb=" N MET C 442 " --> pdb=" O ASP C 438 " (cutoff:3.500A) Processing helix chain 'C' and resid 448 through 458 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 536 Processing helix chain 'C' and resid 543 through 553 Processing helix chain 'C' and resid 557 through 569 removed outlier: 3.956A 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 611 Processing helix chain 'C' and resid 625 through 629 Processing helix chain 'C' and resid 630 through 635 removed outlier: 3.690A pdb=" N ARG C 635 " --> pdb=" O ALA C 632 " (cutoff:3.500A) Processing helix chain 'C' and resid 649 through 662 Processing helix chain 'C' and resid 671 through 679 Processing helix chain 'C' and resid 683 through 705 Processing helix chain 'C' and resid 732 through 741 Processing helix chain 'C' and resid 748 through 765 removed outlier: 3.573A pdb=" N LEU C 762 " --> pdb=" O PHE C 758 " (cutoff:3.500A) Processing helix chain 'D' and resid 61 through 65 removed outlier: 4.158A pdb=" N ARG D 64 " --> pdb=" O GLY D 61 " (cutoff:3.500A) Processing helix chain 'D' and resid 85 through 93 removed outlier: 3.988A pdb=" N ASN D 91 " --> pdb=" O VAL D 87 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N LEU D 92 " --> pdb=" O VAL D 88 " (cutoff:3.500A) Processing helix chain 'D' and resid 130 through 135 Processing helix chain 'D' and resid 135 through 140 Processing helix chain 'D' and resid 202 through 206 Processing helix chain 'D' and resid 211 through 226 removed outlier: 5.116A 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: 3.807A 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: 3.847A pdb=" N LYS D 277 " --> pdb=" O GLU D 273 " (cutoff:3.500A) Processing helix chain 'D' and resid 280 through 296 removed outlier: 3.760A pdb=" N PHE D 290 " --> pdb=" O LEU D 286 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N LYS D 295 " --> pdb=" O GLU D 291 " (cutoff:3.500A) Processing helix chain 'D' and resid 305 through 310 removed outlier: 3.736A pdb=" N ILE D 309 " --> pdb=" O GLU D 305 " (cutoff:3.500A) Processing helix chain 'D' and resid 318 through 326 removed outlier: 4.005A pdb=" N ARG D 322 " --> pdb=" O GLY D 318 " (cutoff:3.500A) Processing helix chain 'D' and resid 327 through 335 removed outlier: 3.774A pdb=" N LEU D 335 " --> pdb=" O LEU D 331 " (cutoff:3.500A) Processing helix chain 'D' and resid 349 through 353 removed outlier: 3.931A pdb=" N ILE D 353 " --> pdb=" O PRO D 350 " (cutoff:3.500A) Processing helix chain 'D' and resid 354 through 359 Processing helix chain 'D' and resid 373 through 385 Processing helix chain 'D' and resid 397 through 402 Processing helix chain 'D' and resid 407 through 425 Processing helix chain 'D' and resid 438 through 445 removed outlier: 3.661A pdb=" N MET D 442 " --> pdb=" O ASP D 438 " (cutoff:3.500A) Processing helix chain 'D' and resid 448 through 458 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 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: 3.955A 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 611 Processing helix chain 'D' and resid 625 through 629 Processing helix chain 'D' and resid 630 through 635 removed outlier: 3.691A pdb=" N ARG D 635 " --> pdb=" O ALA D 632 " (cutoff:3.500A) Processing helix chain 'D' and resid 649 through 662 Processing helix chain 'D' and resid 671 through 679 Processing helix chain 'D' and resid 683 through 705 Processing helix chain 'D' and resid 732 through 741 Processing helix chain 'D' and resid 748 through 765 removed outlier: 3.573A pdb=" N LEU D 762 " --> pdb=" O PHE D 758 " (cutoff:3.500A) Processing helix chain 'E' and resid 61 through 65 removed outlier: 4.157A pdb=" N ARG E 64 " --> pdb=" O GLY E 61 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 93 removed outlier: 3.988A pdb=" N ASN E 91 " --> pdb=" O VAL E 87 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N LEU E 92 " --> pdb=" O VAL E 88 " (cutoff:3.500A) Processing helix chain 'E' and resid 130 through 135 Processing helix chain 'E' and resid 135 through 140 Processing helix chain 'E' and resid 202 through 206 Processing helix chain 'E' and resid 211 through 226 removed outlier: 5.117A 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: 3.806A 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: 3.847A pdb=" N LYS E 277 " --> pdb=" O GLU E 273 " (cutoff:3.500A) Processing helix chain 'E' and resid 280 through 296 removed outlier: 3.759A pdb=" N PHE E 290 " --> pdb=" O LEU E 286 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N LYS E 295 " --> pdb=" O GLU E 291 " (cutoff:3.500A) Processing helix chain 'E' and resid 305 through 310 removed outlier: 3.735A pdb=" N ILE E 309 " --> pdb=" O GLU E 305 " (cutoff:3.500A) Processing helix chain 'E' and resid 318 through 326 removed outlier: 4.004A pdb=" N ARG E 322 " --> pdb=" O GLY E 318 " (cutoff:3.500A) Processing helix chain 'E' and resid 327 through 335 removed outlier: 3.774A pdb=" N LEU E 335 " --> pdb=" O LEU E 331 " (cutoff:3.500A) Processing helix chain 'E' and resid 349 through 353 removed outlier: 3.931A pdb=" N ILE E 353 " --> pdb=" O PRO E 350 " (cutoff:3.500A) Processing helix chain 'E' and resid 354 through 359 Processing helix chain 'E' and resid 373 through 385 Processing helix chain 'E' and resid 397 through 402 Processing helix chain 'E' and resid 407 through 425 Processing helix chain 'E' and resid 438 through 445 removed outlier: 3.661A pdb=" N MET E 442 " --> pdb=" O ASP E 438 " (cutoff:3.500A) Processing helix chain 'E' and resid 448 through 458 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 Processing helix chain 'E' and resid 523 through 536 Processing helix chain 'E' and resid 543 through 553 Processing helix chain 'E' and resid 557 through 569 removed outlier: 3.956A 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 611 Processing helix chain 'E' and resid 625 through 629 Processing helix chain 'E' and resid 630 through 635 removed outlier: 3.691A pdb=" N ARG E 635 " --> pdb=" O ALA E 632 " (cutoff:3.500A) Processing helix chain 'E' and resid 649 through 662 Processing helix chain 'E' and resid 671 through 679 Processing helix chain 'E' and resid 683 through 705 Processing helix chain 'E' and resid 732 through 741 Processing helix chain 'E' and resid 748 through 765 removed outlier: 3.573A pdb=" N LEU E 762 " --> pdb=" O PHE E 758 " (cutoff:3.500A) Processing helix chain 'F' and resid 61 through 65 removed outlier: 4.158A pdb=" N ARG F 64 " --> pdb=" O GLY F 61 " (cutoff:3.500A) Processing helix chain 'F' and resid 85 through 93 removed outlier: 3.988A pdb=" N ASN F 91 " --> pdb=" O VAL F 87 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N LEU F 92 " --> pdb=" O VAL F 88 " (cutoff:3.500A) Processing helix chain 'F' and resid 130 through 135 Processing helix chain 'F' and resid 135 through 140 Processing helix chain 'F' and resid 202 through 206 Processing helix chain 'F' and resid 211 through 226 removed outlier: 5.117A 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: 3.806A 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: 3.848A pdb=" N LYS F 277 " --> pdb=" O GLU F 273 " (cutoff:3.500A) Processing helix chain 'F' and resid 280 through 296 removed outlier: 3.760A pdb=" N PHE F 290 " --> pdb=" O LEU F 286 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N LYS F 295 " --> pdb=" O GLU F 291 " (cutoff:3.500A) Processing helix chain 'F' and resid 305 through 310 removed outlier: 3.736A pdb=" N ILE F 309 " --> pdb=" O GLU F 305 " (cutoff:3.500A) Processing helix chain 'F' and resid 318 through 326 removed outlier: 4.004A pdb=" N ARG F 322 " --> pdb=" O GLY F 318 " (cutoff:3.500A) Processing helix chain 'F' and resid 327 through 335 removed outlier: 3.774A pdb=" N LEU F 335 " --> pdb=" O LEU F 331 " (cutoff:3.500A) Processing helix chain 'F' and resid 349 through 353 removed outlier: 3.931A pdb=" N ILE F 353 " --> pdb=" O PRO F 350 " (cutoff:3.500A) Processing helix chain 'F' and resid 354 through 359 Processing helix chain 'F' and resid 373 through 385 Processing helix chain 'F' and resid 397 through 402 Processing helix chain 'F' and resid 407 through 425 Processing helix chain 'F' and resid 438 through 445 removed outlier: 3.661A pdb=" N MET F 442 " --> pdb=" O ASP F 438 " (cutoff:3.500A) Processing helix chain 'F' and resid 448 through 458 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: 3.955A 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 611 Processing helix chain 'F' and resid 625 through 629 Processing helix chain 'F' and resid 630 through 635 removed outlier: 3.691A pdb=" N ARG F 635 " --> pdb=" O ALA F 632 " (cutoff:3.500A) Processing helix chain 'F' and resid 649 through 662 Processing helix chain 'F' and resid 671 through 679 Processing helix chain 'F' and resid 683 through 705 Processing helix chain 'F' and resid 732 through 741 Processing helix chain 'F' and resid 748 through 765 removed outlier: 3.573A pdb=" N LEU F 762 " --> pdb=" O PHE F 758 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 29 removed outlier: 6.561A pdb=" N ILE A 27 " --> pdb=" O ILE A 82 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 38 through 41 removed outlier: 6.011A pdb=" N VAL A 39 " --> pdb=" O LEU A 72 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N CYS A 69 " --> pdb=" O VAL A 57 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N VAL A 57 " --> pdb=" O CYS A 69 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N LEU A 58 " --> pdb=" O GLN A 103 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N GLN A 103 " --> pdb=" O LEU A 58 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 115 through 118 removed outlier: 8.246A pdb=" N HIS A 115 " --> pdb=" O VAL A 166 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N VAL A 166 " --> pdb=" O HIS A 115 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 145 through 147 removed outlier: 3.552A pdb=" N ILE A 146 " --> pdb=" O CYS A 174 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 265 through 268 removed outlier: 6.261A pdb=" N PHE A 265 " --> pdb=" O ILE A 300 " (cutoff:3.500A) removed outlier: 7.449A pdb=" N PHE A 302 " --> pdb=" O PHE A 265 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N PHE A 267 " --> pdb=" O PHE A 302 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N ALA A 299 " --> pdb=" O ILE A 342 " (cutoff:3.500A) removed outlier: 7.484A pdb=" N MET A 344 " --> pdb=" O ALA A 299 " (cutoff:3.500A) removed outlier: 5.838A pdb=" N ILE A 301 " --> pdb=" O MET A 344 " (cutoff:3.500A) removed outlier: 7.568A pdb=" N ALA A 346 " --> pdb=" O ILE A 301 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 538 through 542 removed outlier: 7.559A pdb=" N GLY A 513 " --> pdb=" O GLN A 641 " (cutoff:3.500A) removed outlier: 8.321A pdb=" N ILE A 643 " --> pdb=" O GLY A 513 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N LEU A 515 " --> pdb=" O ILE A 643 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 27 through 29 removed outlier: 6.561A pdb=" N ILE B 27 " --> pdb=" O ILE B 82 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'B' and resid 38 through 41 removed outlier: 6.012A pdb=" N VAL B 39 " --> pdb=" O LEU B 72 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N CYS B 69 " --> pdb=" O VAL B 57 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N VAL B 57 " --> pdb=" O CYS B 69 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N LEU B 58 " --> pdb=" O GLN B 103 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N GLN B 103 " --> pdb=" O LEU B 58 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 115 through 118 removed outlier: 8.245A pdb=" N HIS B 115 " --> pdb=" O VAL B 166 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N VAL B 166 " --> pdb=" O HIS B 115 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 145 through 147 removed outlier: 3.552A pdb=" N ILE B 146 " --> pdb=" O CYS B 174 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 265 through 268 removed outlier: 6.261A pdb=" N PHE B 265 " --> pdb=" O ILE B 300 " (cutoff:3.500A) removed outlier: 7.449A pdb=" N PHE B 302 " --> pdb=" O PHE B 265 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N PHE B 267 " --> pdb=" O PHE B 302 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N ALA B 299 " --> pdb=" O ILE B 342 " (cutoff:3.500A) removed outlier: 7.484A pdb=" N MET B 344 " --> pdb=" O ALA B 299 " (cutoff:3.500A) removed outlier: 5.839A pdb=" N ILE B 301 " --> pdb=" O MET B 344 " (cutoff:3.500A) removed outlier: 7.568A pdb=" N ALA B 346 " --> pdb=" O ILE B 301 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 538 through 542 removed outlier: 7.559A pdb=" N GLY B 513 " --> pdb=" O GLN B 641 " (cutoff:3.500A) removed outlier: 8.321A pdb=" N ILE B 643 " --> pdb=" O GLY B 513 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N LEU B 515 " --> pdb=" O ILE B 643 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 27 through 29 removed outlier: 6.561A pdb=" N ILE C 27 " --> pdb=" O ILE C 82 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'C' and resid 38 through 41 removed outlier: 6.012A pdb=" N VAL C 39 " --> pdb=" O LEU C 72 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N CYS C 69 " --> pdb=" O VAL C 57 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N VAL C 57 " --> pdb=" O CYS C 69 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N LEU C 58 " --> pdb=" O GLN C 103 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N GLN C 103 " --> pdb=" O LEU C 58 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 115 through 118 removed outlier: 8.245A pdb=" N HIS C 115 " --> pdb=" O VAL C 166 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N VAL C 166 " --> pdb=" O HIS C 115 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 145 through 147 removed outlier: 3.552A pdb=" N ILE C 146 " --> pdb=" O CYS C 174 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 265 through 268 removed outlier: 6.261A pdb=" N PHE C 265 " --> pdb=" O ILE C 300 " (cutoff:3.500A) removed outlier: 7.449A pdb=" N PHE C 302 " --> pdb=" O PHE C 265 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N PHE C 267 " --> pdb=" O PHE C 302 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N ALA C 299 " --> pdb=" O ILE C 342 " (cutoff:3.500A) removed outlier: 7.485A pdb=" N MET C 344 " --> pdb=" O ALA C 299 " (cutoff:3.500A) removed outlier: 5.838A pdb=" N ILE C 301 " --> pdb=" O MET C 344 " (cutoff:3.500A) removed outlier: 7.568A pdb=" N ALA C 346 " --> pdb=" O ILE C 301 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 538 through 542 removed outlier: 7.559A pdb=" N GLY C 513 " --> pdb=" O GLN C 641 " (cutoff:3.500A) removed outlier: 8.321A pdb=" N ILE C 643 " --> pdb=" O GLY C 513 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N LEU C 515 " --> pdb=" O ILE C 643 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 27 through 29 removed outlier: 6.561A pdb=" N ILE D 27 " --> pdb=" O ILE D 82 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC1 Processing sheet with id=AC2, first strand: chain 'D' and resid 38 through 41 removed outlier: 6.011A pdb=" N VAL D 39 " --> pdb=" O LEU D 72 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N CYS D 69 " --> pdb=" O VAL D 57 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N VAL D 57 " --> pdb=" O CYS D 69 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N LEU D 58 " --> pdb=" O GLN D 103 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N GLN D 103 " --> pdb=" O LEU D 58 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 115 through 118 removed outlier: 8.246A pdb=" N HIS D 115 " --> pdb=" O VAL D 166 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N VAL D 166 " --> pdb=" O HIS D 115 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 145 through 147 removed outlier: 3.552A pdb=" N ILE D 146 " --> pdb=" O CYS D 174 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 265 through 268 removed outlier: 6.261A pdb=" N PHE D 265 " --> pdb=" O ILE D 300 " (cutoff:3.500A) removed outlier: 7.449A pdb=" N PHE D 302 " --> pdb=" O PHE D 265 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N PHE D 267 " --> pdb=" O PHE D 302 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N ALA D 299 " --> pdb=" O ILE D 342 " (cutoff:3.500A) removed outlier: 7.484A pdb=" N MET D 344 " --> pdb=" O ALA D 299 " (cutoff:3.500A) removed outlier: 5.838A pdb=" N ILE D 301 " --> pdb=" O MET D 344 " (cutoff:3.500A) removed outlier: 7.568A pdb=" N ALA D 346 " --> pdb=" O ILE D 301 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 538 through 542 removed outlier: 7.559A pdb=" N GLY D 513 " --> pdb=" O GLN D 641 " (cutoff:3.500A) removed outlier: 8.321A pdb=" N ILE D 643 " --> pdb=" O GLY D 513 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N LEU D 515 " --> pdb=" O ILE D 643 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 27 through 29 removed outlier: 6.562A pdb=" N ILE E 27 " --> pdb=" O ILE E 82 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, first strand: chain 'E' and resid 38 through 41 removed outlier: 6.011A pdb=" N VAL E 39 " --> pdb=" O LEU E 72 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N CYS E 69 " --> pdb=" O VAL E 57 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N VAL E 57 " --> pdb=" O CYS E 69 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N LEU E 58 " --> pdb=" O GLN E 103 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N GLN E 103 " --> pdb=" O LEU E 58 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'E' and resid 115 through 118 removed outlier: 8.246A pdb=" N HIS E 115 " --> pdb=" O VAL E 166 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N VAL E 166 " --> pdb=" O HIS E 115 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'E' and resid 145 through 147 removed outlier: 3.552A pdb=" N ILE E 146 " --> pdb=" O CYS E 174 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'E' and resid 265 through 268 removed outlier: 6.260A pdb=" N PHE E 265 " --> pdb=" O ILE E 300 " (cutoff:3.500A) removed outlier: 7.449A pdb=" N PHE E 302 " --> pdb=" O PHE E 265 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N PHE E 267 " --> pdb=" O PHE E 302 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N ALA E 299 " --> pdb=" O ILE E 342 " (cutoff:3.500A) removed outlier: 7.484A pdb=" N MET E 344 " --> pdb=" O ALA E 299 " (cutoff:3.500A) removed outlier: 5.838A pdb=" N ILE E 301 " --> pdb=" O MET E 344 " (cutoff:3.500A) removed outlier: 7.568A pdb=" N ALA E 346 " --> pdb=" O ILE E 301 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'E' and resid 538 through 542 removed outlier: 7.559A pdb=" N GLY E 513 " --> pdb=" O GLN E 641 " (cutoff:3.500A) removed outlier: 8.321A pdb=" N ILE E 643 " --> pdb=" O GLY E 513 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N LEU E 515 " --> pdb=" O ILE E 643 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'F' and resid 27 through 29 removed outlier: 6.561A pdb=" N ILE F 27 " --> pdb=" O ILE F 82 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD4 Processing sheet with id=AD5, first strand: chain 'F' and resid 38 through 41 removed outlier: 6.012A pdb=" N VAL F 39 " --> pdb=" O LEU F 72 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N CYS F 69 " --> pdb=" O VAL F 57 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N VAL F 57 " --> pdb=" O CYS F 69 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N LEU F 58 " --> pdb=" O GLN F 103 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N GLN F 103 " --> pdb=" O LEU F 58 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'F' and resid 115 through 118 removed outlier: 8.246A pdb=" N HIS F 115 " --> pdb=" O VAL F 166 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N VAL F 166 " --> pdb=" O HIS F 115 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'F' and resid 145 through 147 removed outlier: 3.551A pdb=" N ILE F 146 " --> pdb=" O CYS F 174 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'F' and resid 265 through 268 removed outlier: 6.261A pdb=" N PHE F 265 " --> pdb=" O ILE F 300 " (cutoff:3.500A) removed outlier: 7.449A pdb=" N PHE F 302 " --> pdb=" O PHE F 265 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N PHE F 267 " --> pdb=" O PHE F 302 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N ALA F 299 " --> pdb=" O ILE F 342 " (cutoff:3.500A) removed outlier: 7.484A pdb=" N MET F 344 " --> pdb=" O ALA F 299 " (cutoff:3.500A) removed outlier: 5.838A pdb=" N ILE F 301 " --> pdb=" O MET F 344 " (cutoff:3.500A) removed outlier: 7.568A pdb=" N ALA F 346 " --> pdb=" O ILE F 301 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'F' and resid 538 through 542 removed outlier: 7.559A pdb=" N GLY F 513 " --> pdb=" O GLN F 641 " (cutoff:3.500A) removed outlier: 8.321A pdb=" N ILE F 643 " --> pdb=" O GLY F 513 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N LEU F 515 " --> pdb=" O ILE F 643 " (cutoff:3.500A) 1410 hydrogen bonds defined for protein. 3978 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 7.18 Time building geometry restraints manager: 3.84 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: 11270 1.34 - 1.45: 3751 1.45 - 1.57: 19959 1.57 - 1.69: 36 1.69 - 1.81: 288 Bond restraints: 35304 Sorted by residual: bond pdb=" C4 ADP E 902 " pdb=" C5 ADP E 902 " ideal model delta sigma weight residual 1.490 1.380 0.110 2.00e-02 2.50e+03 3.02e+01 bond pdb=" C4 ADP C 902 " pdb=" C5 ADP C 902 " ideal model delta sigma weight residual 1.490 1.380 0.110 2.00e-02 2.50e+03 3.00e+01 bond pdb=" C4 ADP C 903 " pdb=" C5 ADP C 903 " ideal model delta sigma weight residual 1.490 1.380 0.110 2.00e-02 2.50e+03 3.00e+01 bond pdb=" C4 ADP A 901 " pdb=" C5 ADP A 901 " ideal model delta sigma weight residual 1.490 1.381 0.109 2.00e-02 2.50e+03 2.99e+01 bond pdb=" C4 ADP D 902 " pdb=" C5 ADP D 902 " ideal model delta sigma weight residual 1.490 1.381 0.109 2.00e-02 2.50e+03 2.99e+01 ... (remaining 35299 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.53: 46733 2.53 - 5.07: 797 5.07 - 7.60: 128 7.60 - 10.13: 48 10.13 - 12.66: 24 Bond angle restraints: 47730 Sorted by residual: angle pdb=" N LYS E 425 " pdb=" CA LYS E 425 " pdb=" C LYS E 425 " ideal model delta sigma weight residual 113.20 107.66 5.54 1.21e+00 6.83e-01 2.10e+01 angle pdb=" N LYS B 425 " pdb=" CA LYS B 425 " pdb=" C LYS B 425 " ideal model delta sigma weight residual 113.20 107.67 5.53 1.21e+00 6.83e-01 2.09e+01 angle pdb=" N LYS D 425 " pdb=" CA LYS D 425 " pdb=" C LYS D 425 " ideal model delta sigma weight residual 113.20 107.67 5.53 1.21e+00 6.83e-01 2.09e+01 angle pdb=" N LYS A 425 " pdb=" CA LYS A 425 " pdb=" C LYS A 425 " ideal model delta sigma weight residual 113.20 107.67 5.53 1.21e+00 6.83e-01 2.09e+01 angle pdb=" N LYS C 425 " pdb=" CA LYS C 425 " pdb=" C LYS C 425 " ideal model delta sigma weight residual 113.20 107.68 5.52 1.21e+00 6.83e-01 2.08e+01 ... (remaining 47725 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.38: 20514 26.38 - 52.75: 1136 52.75 - 79.13: 148 79.13 - 105.50: 30 105.50 - 131.88: 6 Dihedral angle restraints: 21834 sinusoidal: 9204 harmonic: 12630 Sorted by residual: dihedral pdb=" O2A ADP C 902 " pdb=" O3A ADP C 902 " pdb=" PA ADP C 902 " pdb=" PB ADP C 902 " ideal model delta sinusoidal sigma weight residual -60.00 71.88 -131.88 1 2.00e+01 2.50e-03 4.00e+01 dihedral pdb=" O2A ADP B 902 " pdb=" O3A ADP B 902 " pdb=" PA ADP B 902 " pdb=" PB ADP B 902 " ideal model delta sinusoidal sigma weight residual -60.00 71.86 -131.86 1 2.00e+01 2.50e-03 4.00e+01 dihedral pdb=" O2A ADP D 902 " pdb=" O3A ADP D 902 " pdb=" PA ADP D 902 " pdb=" PB ADP D 902 " ideal model delta sinusoidal sigma weight residual -60.00 71.84 -131.84 1 2.00e+01 2.50e-03 4.00e+01 ... (remaining 21831 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 3862 0.046 - 0.092: 1059 0.092 - 0.139: 355 0.139 - 0.185: 70 0.185 - 0.231: 12 Chirality restraints: 5358 Sorted by residual: chirality pdb=" CA LYS C 211 " pdb=" N LYS C 211 " pdb=" C LYS C 211 " pdb=" CB LYS C 211 " both_signs ideal model delta sigma weight residual False 2.51 2.74 -0.23 2.00e-01 2.50e+01 1.34e+00 chirality pdb=" CA LYS D 211 " pdb=" N LYS D 211 " pdb=" C LYS D 211 " pdb=" CB LYS D 211 " both_signs ideal model delta sigma weight residual False 2.51 2.74 -0.23 2.00e-01 2.50e+01 1.33e+00 chirality pdb=" CA LYS A 211 " pdb=" N LYS A 211 " pdb=" C LYS A 211 " pdb=" CB LYS A 211 " both_signs ideal model delta sigma weight residual False 2.51 2.74 -0.23 2.00e-01 2.50e+01 1.33e+00 ... (remaining 5355 not shown) Planarity restraints: 6270 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLN E 327 " 0.018 2.00e-02 2.50e+03 3.70e-02 1.37e+01 pdb=" C GLN E 327 " -0.064 2.00e-02 2.50e+03 pdb=" O GLN E 327 " 0.024 2.00e-02 2.50e+03 pdb=" N LEU E 328 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN F 327 " -0.018 2.00e-02 2.50e+03 3.70e-02 1.37e+01 pdb=" C GLN F 327 " 0.064 2.00e-02 2.50e+03 pdb=" O GLN F 327 " -0.024 2.00e-02 2.50e+03 pdb=" N LEU F 328 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN A 327 " -0.018 2.00e-02 2.50e+03 3.70e-02 1.37e+01 pdb=" C GLN A 327 " 0.064 2.00e-02 2.50e+03 pdb=" O GLN A 327 " -0.024 2.00e-02 2.50e+03 pdb=" N LEU A 328 " -0.022 2.00e-02 2.50e+03 ... (remaining 6267 not shown) Histogram of nonbonded interaction distances: 0.29 - 1.21: 30 1.21 - 2.13: 126 2.13 - 3.06: 22758 3.06 - 3.98: 91247 3.98 - 4.90: 161510 Warning: very small nonbonded interaction distances. Nonbonded interactions: 275671 Sorted by model distance: nonbonded pdb=" C SER B 276 " pdb=" CZ ARG C 323 " model vdw 0.288 3.500 nonbonded pdb=" C SER D 276 " pdb=" CZ ARG E 323 " model vdw 0.288 3.500 nonbonded pdb=" C SER A 276 " pdb=" CZ ARG B 323 " model vdw 0.288 3.500 nonbonded pdb=" CZ ARG A 323 " pdb=" C SER F 276 " model vdw 0.288 3.500 nonbonded pdb=" C SER C 276 " pdb=" CZ ARG D 323 " model vdw 0.288 3.500 ... (remaining 275666 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' and (resid 21 through 772 or resid 902 or resid 904)) selection = (chain 'B' and (resid 21 through 772 or resid 902 or resid 904)) selection = (chain 'C' and (resid 21 through 772 or resid 902 or resid 904)) selection = (chain 'D' and (resid 21 through 772 or resid 902 or resid 904)) selection = (chain 'E' and (resid 21 through 772 or resid 902 or resid 904)) selection = (chain 'F' and (resid 21 through 772 or resid 902 or resid 904)) } 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: 7.120 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: 0.040 Extract box with map and model: 0.630 Check model and map are aligned: 0.110 Set scattering table: 0.100 Process input model: 32.150 Find NCS groups from input model: 0.990 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:6.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.900 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6106 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.110 35304 Z= 0.306 Angle : 0.892 12.664 47730 Z= 0.492 Chirality : 0.050 0.231 5358 Planarity : 0.005 0.049 6270 Dihedral : 15.570 131.879 13650 Min Nonbonded Distance : 0.288 Molprobity Statistics. All-atom Clashscore : 16.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.05 % Favored : 92.95 % Rotamer: Outliers : 0.11 % Allowed : 15.97 % Favored : 83.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.14 % 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: -0.25 (0.12), residues: 4368 helix: 0.53 (0.12), residues: 1806 sheet: 0.89 (0.23), residues: 540 loop : -1.09 (0.13), residues: 2022 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 599 TYR 0.024 0.002 TYR B 244 PHE 0.012 0.001 PHE C 552 TRP 0.007 0.001 TRP F 551 HIS 0.003 0.001 HIS C 406 Details of bonding type rmsd covalent geometry : bond 0.00506 (35304) covalent geometry : angle 0.89222 (47730) hydrogen bonds : bond 0.18064 ( 1410) hydrogen bonds : angle 6.19221 ( 3978) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8736 Ramachandran restraints generated. 4368 Oldfield, 0 Emsley, 4368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8736 Ramachandran restraints generated. 4368 Oldfield, 0 Emsley, 4368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 602 residues out of total 3732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 598 time to evaluate : 1.272 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 2 residues processed: 598 average time/residue: 0.8425 time to fit residues: 584.8171 Evaluate side-chains 231 residues out of total 3732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 229 time to evaluate : 1.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 450 ASP Chi-restraints excluded: chain D residue 450 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 432 optimal weight: 3.9990 chunk 197 optimal weight: 3.9990 chunk 388 optimal weight: 0.8980 chunk 215 optimal weight: 1.9990 chunk 20 optimal weight: 3.9990 chunk 132 optimal weight: 3.9990 chunk 261 optimal weight: 10.0000 chunk 248 optimal weight: 9.9990 chunk 207 optimal weight: 0.0870 chunk 401 optimal weight: 0.8980 chunk 424 optimal weight: 0.9980 overall best weight: 0.9760 ------------------------------------------------------------------------------- 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 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 460 ASN ** D 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4318 r_free = 0.4318 target = 0.157464 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.107803 restraints weight = 59247.653| |-----------------------------------------------------------------------------| r_work (start): 0.3538 rms_B_bonded: 3.22 r_work: 0.3392 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.3392 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8169 moved from start: 0.2414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 35304 Z= 0.159 Angle : 0.747 11.275 47730 Z= 0.365 Chirality : 0.046 0.142 5358 Planarity : 0.005 0.049 6270 Dihedral : 8.481 128.207 4906 Min Nonbonded Distance : 1.882 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.41 % Favored : 93.59 % Rotamer: Outliers : 2.17 % Allowed : 17.82 % Favored : 80.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.14 % 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: 0.18 (0.13), residues: 4368 helix: 0.91 (0.12), residues: 1842 sheet: 0.81 (0.22), residues: 546 loop : -0.81 (0.14), residues: 1980 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 225 TYR 0.012 0.001 TYR E 244 PHE 0.010 0.001 PHE C 290 TRP 0.005 0.001 TRP F 551 HIS 0.017 0.001 HIS B 317 Details of bonding type rmsd covalent geometry : bond 0.00359 (35304) covalent geometry : angle 0.74663 (47730) hydrogen bonds : bond 0.04890 ( 1410) hydrogen bonds : angle 5.30018 ( 3978) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8736 Ramachandran restraints generated. 4368 Oldfield, 0 Emsley, 4368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8736 Ramachandran restraints generated. 4368 Oldfield, 0 Emsley, 4368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 390 residues out of total 3732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 309 time to evaluate : 1.247 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 273 GLU cc_start: 0.8582 (OUTLIER) cc_final: 0.8087 (tm-30) REVERT: A 612 SER cc_start: 0.6986 (p) cc_final: 0.6784 (m) REVERT: B 221 GLU cc_start: 0.8668 (OUTLIER) cc_final: 0.8396 (pm20) REVERT: B 317 HIS cc_start: 0.4992 (t70) cc_final: 0.4734 (t70) REVERT: B 742 PHE cc_start: 0.8493 (m-80) cc_final: 0.8289 (m-80) REVERT: B 754 LYS cc_start: 0.8297 (OUTLIER) cc_final: 0.7855 (tmtm) REVERT: B 756 GLU cc_start: 0.8622 (OUTLIER) cc_final: 0.8420 (mt-10) REVERT: C 221 GLU cc_start: 0.8795 (OUTLIER) cc_final: 0.8466 (pm20) REVERT: C 442 MET cc_start: 0.8524 (mmp) cc_final: 0.8317 (mmm) REVERT: C 445 LEU cc_start: 0.8621 (tt) cc_final: 0.8400 (mp) REVERT: D 273 GLU cc_start: 0.8582 (OUTLIER) cc_final: 0.8089 (tm-30) REVERT: D 612 SER cc_start: 0.6965 (p) cc_final: 0.6762 (m) REVERT: E 221 GLU cc_start: 0.8687 (OUTLIER) cc_final: 0.8406 (pm20) REVERT: E 742 PHE cc_start: 0.8485 (m-80) cc_final: 0.8281 (m-80) REVERT: E 754 LYS cc_start: 0.8302 (OUTLIER) cc_final: 0.7861 (tmtm) REVERT: E 756 GLU cc_start: 0.8616 (OUTLIER) cc_final: 0.8414 (mt-10) REVERT: F 221 GLU cc_start: 0.8801 (OUTLIER) cc_final: 0.8468 (pm20) REVERT: F 442 MET cc_start: 0.8509 (mmp) cc_final: 0.8308 (mmm) REVERT: F 445 LEU cc_start: 0.8619 (tt) cc_final: 0.8398 (mp) outliers start: 81 outliers final: 8 residues processed: 365 average time/residue: 0.8677 time to fit residues: 367.3679 Evaluate side-chains 233 residues out of total 3732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 215 time to evaluate : 1.274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 273 GLU Chi-restraints excluded: chain A residue 658 LYS Chi-restraints excluded: chain B residue 218 GLU Chi-restraints excluded: chain B residue 221 GLU Chi-restraints excluded: chain B residue 615 LYS Chi-restraints excluded: chain B residue 754 LYS Chi-restraints excluded: chain B residue 756 GLU Chi-restraints excluded: chain C residue 221 GLU Chi-restraints excluded: chain C residue 615 LYS Chi-restraints excluded: chain D residue 273 GLU Chi-restraints excluded: chain D residue 658 LYS Chi-restraints excluded: chain E residue 218 GLU Chi-restraints excluded: chain E residue 221 GLU Chi-restraints excluded: chain E residue 615 LYS Chi-restraints excluded: chain E residue 754 LYS Chi-restraints excluded: chain E residue 756 GLU Chi-restraints excluded: chain F residue 221 GLU Chi-restraints excluded: chain F residue 615 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 434 optimal weight: 0.9980 chunk 111 optimal weight: 0.7980 chunk 308 optimal weight: 10.0000 chunk 158 optimal weight: 3.9990 chunk 286 optimal weight: 2.9990 chunk 321 optimal weight: 0.9990 chunk 126 optimal weight: 3.9990 chunk 305 optimal weight: 30.0000 chunk 259 optimal weight: 9.9990 chunk 382 optimal weight: 9.9990 chunk 277 optimal weight: 2.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 103 GLN ** A 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 103 GLN B 327 GLN B 443 ASN C 103 GLN C 327 GLN D 103 GLN ** D 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 327 GLN E 443 ASN F 103 GLN F 327 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4235 r_free = 0.4235 target = 0.150853 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.099169 restraints weight = 59202.779| |-----------------------------------------------------------------------------| r_work (start): 0.3381 rms_B_bonded: 3.26 r_work: 0.3219 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.3219 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8304 moved from start: 0.3700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 35304 Z= 0.185 Angle : 0.695 7.674 47730 Z= 0.340 Chirality : 0.046 0.143 5358 Planarity : 0.005 0.047 6270 Dihedral : 7.747 117.060 4902 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.07 % Favored : 93.93 % Rotamer: Outliers : 3.22 % Allowed : 16.48 % Favored : 80.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.14 % 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: 0.22 (0.13), residues: 4368 helix: 0.95 (0.12), residues: 1842 sheet: 0.81 (0.21), residues: 546 loop : -0.79 (0.14), residues: 1980 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG F 349 TYR 0.012 0.001 TYR B 244 PHE 0.015 0.002 PHE D 503 TRP 0.007 0.001 TRP F 454 HIS 0.019 0.001 HIS D 317 Details of bonding type rmsd covalent geometry : bond 0.00434 (35304) covalent geometry : angle 0.69547 (47730) hydrogen bonds : bond 0.04831 ( 1410) hydrogen bonds : angle 5.05278 ( 3978) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8736 Ramachandran restraints generated. 4368 Oldfield, 0 Emsley, 4368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8736 Ramachandran restraints generated. 4368 Oldfield, 0 Emsley, 4368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 381 residues out of total 3732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 261 time to evaluate : 1.314 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 84 MET cc_start: 0.8248 (ptt) cc_final: 0.8020 (ptt) REVERT: A 470 GLU cc_start: 0.8342 (pm20) cc_final: 0.8028 (mt-10) REVERT: A 742 PHE cc_start: 0.8403 (m-80) cc_final: 0.8104 (m-80) REVERT: B 221 GLU cc_start: 0.8529 (OUTLIER) cc_final: 0.8295 (pm20) REVERT: B 273 GLU cc_start: 0.8798 (OUTLIER) cc_final: 0.8414 (tm-30) REVERT: B 327 GLN cc_start: 0.8148 (OUTLIER) cc_final: 0.7832 (tp40) REVERT: B 470 GLU cc_start: 0.8378 (pm20) cc_final: 0.8044 (mt-10) REVERT: B 742 PHE cc_start: 0.8709 (m-80) cc_final: 0.8426 (m-80) REVERT: B 754 LYS cc_start: 0.8255 (OUTLIER) cc_final: 0.8011 (tmtm) REVERT: C 153 LEU cc_start: 0.5986 (OUTLIER) cc_final: 0.5628 (tp) REVERT: C 221 GLU cc_start: 0.8679 (OUTLIER) cc_final: 0.8284 (pm20) REVERT: C 442 MET cc_start: 0.8718 (mmp) cc_final: 0.8464 (mmm) REVERT: C 445 LEU cc_start: 0.8866 (tt) cc_final: 0.8612 (mp) REVERT: C 742 PHE cc_start: 0.8509 (m-80) cc_final: 0.8132 (m-80) REVERT: D 84 MET cc_start: 0.8258 (ptt) cc_final: 0.8032 (ptt) REVERT: D 470 GLU cc_start: 0.8349 (pm20) cc_final: 0.8028 (mt-10) REVERT: D 742 PHE cc_start: 0.8405 (m-80) cc_final: 0.8106 (m-80) REVERT: E 221 GLU cc_start: 0.8521 (OUTLIER) cc_final: 0.8285 (pm20) REVERT: E 273 GLU cc_start: 0.8798 (OUTLIER) cc_final: 0.8418 (tm-30) REVERT: E 327 GLN cc_start: 0.8140 (OUTLIER) cc_final: 0.7820 (tp40) REVERT: E 470 GLU cc_start: 0.8371 (pm20) cc_final: 0.8036 (mt-10) REVERT: E 678 MET cc_start: 0.8148 (mmm) cc_final: 0.7946 (mmm) REVERT: E 742 PHE cc_start: 0.8707 (m-80) cc_final: 0.8429 (m-80) REVERT: F 153 LEU cc_start: 0.6063 (OUTLIER) cc_final: 0.5703 (tp) REVERT: F 221 GLU cc_start: 0.8657 (OUTLIER) cc_final: 0.8250 (pm20) REVERT: F 442 MET cc_start: 0.8683 (mmp) cc_final: 0.8442 (mmm) REVERT: F 445 LEU cc_start: 0.8866 (tt) cc_final: 0.8611 (mp) REVERT: F 742 PHE cc_start: 0.8509 (m-80) cc_final: 0.8132 (m-80) outliers start: 120 outliers final: 21 residues processed: 361 average time/residue: 0.7225 time to fit residues: 310.6452 Evaluate side-chains 234 residues out of total 3732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 202 time to evaluate : 1.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 399 VAL Chi-restraints excluded: chain B residue 94 VAL Chi-restraints excluded: chain B residue 221 GLU Chi-restraints excluded: chain B residue 273 GLU Chi-restraints excluded: chain B residue 282 SER Chi-restraints excluded: chain B residue 327 GLN Chi-restraints excluded: chain B residue 399 VAL Chi-restraints excluded: chain B residue 754 LYS Chi-restraints excluded: chain C residue 94 VAL Chi-restraints excluded: chain C residue 153 LEU Chi-restraints excluded: chain C residue 221 GLU Chi-restraints excluded: chain C residue 282 SER Chi-restraints excluded: chain C residue 364 ASP Chi-restraints excluded: chain C residue 399 VAL Chi-restraints excluded: chain C residue 615 LYS Chi-restraints excluded: chain D residue 94 VAL Chi-restraints excluded: chain D residue 399 VAL Chi-restraints excluded: chain D residue 658 LYS Chi-restraints excluded: chain E residue 94 VAL Chi-restraints excluded: chain E residue 221 GLU Chi-restraints excluded: chain E residue 273 GLU Chi-restraints excluded: chain E residue 282 SER Chi-restraints excluded: chain E residue 327 GLN Chi-restraints excluded: chain E residue 399 VAL Chi-restraints excluded: chain F residue 94 VAL Chi-restraints excluded: chain F residue 153 LEU Chi-restraints excluded: chain F residue 221 GLU Chi-restraints excluded: chain F residue 282 SER Chi-restraints excluded: chain F residue 364 ASP Chi-restraints excluded: chain F residue 399 VAL Chi-restraints excluded: chain F residue 615 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 379 optimal weight: 2.9990 chunk 148 optimal weight: 0.6980 chunk 69 optimal weight: 0.6980 chunk 52 optimal weight: 2.9990 chunk 208 optimal weight: 0.8980 chunk 250 optimal weight: 7.9990 chunk 27 optimal weight: 8.9990 chunk 91 optimal weight: 3.9990 chunk 170 optimal weight: 5.9990 chunk 150 optimal weight: 8.9990 chunk 354 optimal weight: 0.7980 overall best weight: 1.2182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 443 ASN B 327 GLN C 327 GLN ** C 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 443 ASN E 103 GLN ** E 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 327 GLN ** F 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 327 GLN ** F 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4228 r_free = 0.4228 target = 0.150495 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.099576 restraints weight = 58995.694| |-----------------------------------------------------------------------------| r_work (start): 0.3393 rms_B_bonded: 3.20 r_work: 0.3232 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.3232 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8296 moved from start: 0.4057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 35304 Z= 0.143 Angle : 0.654 11.029 47730 Z= 0.314 Chirality : 0.045 0.146 5358 Planarity : 0.004 0.046 6270 Dihedral : 7.554 116.271 4902 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.98 % Favored : 94.02 % Rotamer: Outliers : 2.09 % Allowed : 18.54 % Favored : 79.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.14 % 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: 0.38 (0.13), residues: 4368 helix: 1.11 (0.12), residues: 1842 sheet: 0.85 (0.21), residues: 546 loop : -0.71 (0.14), residues: 1980 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 349 TYR 0.013 0.001 TYR C 244 PHE 0.009 0.001 PHE C 506 TRP 0.003 0.001 TRP F 551 HIS 0.014 0.001 HIS B 317 Details of bonding type rmsd covalent geometry : bond 0.00338 (35304) covalent geometry : angle 0.65367 (47730) hydrogen bonds : bond 0.04159 ( 1410) hydrogen bonds : angle 4.84365 ( 3978) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8736 Ramachandran restraints generated. 4368 Oldfield, 0 Emsley, 4368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8736 Ramachandran restraints generated. 4368 Oldfield, 0 Emsley, 4368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 308 residues out of total 3732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 230 time to evaluate : 1.317 Fit side-chains REVERT: A 36 ASN cc_start: 0.7957 (m-40) cc_final: 0.7407 (t0) REVERT: A 742 PHE cc_start: 0.8456 (m-80) cc_final: 0.8061 (m-80) REVERT: B 36 ASN cc_start: 0.8141 (m-40) cc_final: 0.7521 (t0) REVERT: B 221 GLU cc_start: 0.8521 (OUTLIER) cc_final: 0.8315 (pm20) REVERT: B 327 GLN cc_start: 0.8180 (OUTLIER) cc_final: 0.7744 (tp40) REVERT: B 427 MET cc_start: 0.7753 (tpp) cc_final: 0.7401 (tpp) REVERT: B 430 ILE cc_start: 0.5337 (OUTLIER) cc_final: 0.5081 (pp) REVERT: B 442 MET cc_start: 0.8685 (OUTLIER) cc_final: 0.8473 (mmt) REVERT: B 742 PHE cc_start: 0.8749 (m-80) cc_final: 0.8455 (m-80) REVERT: C 153 LEU cc_start: 0.5629 (OUTLIER) cc_final: 0.5325 (tp) REVERT: C 221 GLU cc_start: 0.8661 (OUTLIER) cc_final: 0.8408 (pm20) REVERT: C 327 GLN cc_start: 0.8166 (OUTLIER) cc_final: 0.7960 (tp40) REVERT: C 427 MET cc_start: 0.7501 (tpt) cc_final: 0.7268 (tpp) REVERT: C 442 MET cc_start: 0.8697 (mmp) cc_final: 0.8411 (mmm) REVERT: C 445 LEU cc_start: 0.8881 (tt) cc_final: 0.8579 (mp) REVERT: C 742 PHE cc_start: 0.8532 (m-80) cc_final: 0.8212 (m-80) REVERT: D 36 ASN cc_start: 0.7961 (m-40) cc_final: 0.7408 (t0) REVERT: D 658 LYS cc_start: 0.9088 (OUTLIER) cc_final: 0.8865 (mttt) REVERT: D 742 PHE cc_start: 0.8455 (m-80) cc_final: 0.8057 (m-80) REVERT: E 36 ASN cc_start: 0.8145 (m-40) cc_final: 0.7524 (t0) REVERT: E 221 GLU cc_start: 0.8531 (OUTLIER) cc_final: 0.8326 (pm20) REVERT: E 327 GLN cc_start: 0.8176 (OUTLIER) cc_final: 0.7729 (tp40) REVERT: E 427 MET cc_start: 0.7762 (tpp) cc_final: 0.7414 (tpp) REVERT: E 430 ILE cc_start: 0.5327 (OUTLIER) cc_final: 0.5071 (pp) REVERT: E 442 MET cc_start: 0.8679 (OUTLIER) cc_final: 0.8469 (mmt) REVERT: E 742 PHE cc_start: 0.8759 (m-80) cc_final: 0.8466 (m-80) REVERT: F 153 LEU cc_start: 0.5754 (OUTLIER) cc_final: 0.5452 (tp) REVERT: F 221 GLU cc_start: 0.8650 (OUTLIER) cc_final: 0.8293 (pm20) REVERT: F 327 GLN cc_start: 0.8156 (OUTLIER) cc_final: 0.7945 (tp40) REVERT: F 427 MET cc_start: 0.7460 (tpp) cc_final: 0.7188 (tpp) REVERT: F 430 ILE cc_start: 0.5137 (OUTLIER) cc_final: 0.4752 (pp) REVERT: F 442 MET cc_start: 0.8694 (mmp) cc_final: 0.8419 (mmm) REVERT: F 445 LEU cc_start: 0.8886 (tt) cc_final: 0.8592 (mp) REVERT: F 742 PHE cc_start: 0.8533 (m-80) cc_final: 0.8211 (m-80) outliers start: 78 outliers final: 17 residues processed: 285 average time/residue: 0.6906 time to fit residues: 236.5012 Evaluate side-chains 232 residues out of total 3732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 199 time to evaluate : 1.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 307 ASP Chi-restraints excluded: chain A residue 399 VAL Chi-restraints excluded: chain B residue 94 VAL Chi-restraints excluded: chain B residue 221 GLU Chi-restraints excluded: chain B residue 282 SER Chi-restraints excluded: chain B residue 327 GLN Chi-restraints excluded: chain B residue 430 ILE Chi-restraints excluded: chain B residue 442 MET Chi-restraints excluded: chain C residue 94 VAL Chi-restraints excluded: chain C residue 153 LEU Chi-restraints excluded: chain C residue 221 GLU Chi-restraints excluded: chain C residue 282 SER Chi-restraints excluded: chain C residue 327 GLN Chi-restraints excluded: chain C residue 615 LYS Chi-restraints excluded: chain D residue 94 VAL Chi-restraints excluded: chain D residue 307 ASP Chi-restraints excluded: chain D residue 399 VAL Chi-restraints excluded: chain D residue 658 LYS Chi-restraints excluded: chain E residue 94 VAL Chi-restraints excluded: chain E residue 221 GLU Chi-restraints excluded: chain E residue 282 SER Chi-restraints excluded: chain E residue 327 GLN Chi-restraints excluded: chain E residue 430 ILE Chi-restraints excluded: chain E residue 442 MET Chi-restraints excluded: chain F residue 94 VAL Chi-restraints excluded: chain F residue 153 LEU Chi-restraints excluded: chain F residue 221 GLU Chi-restraints excluded: chain F residue 282 SER Chi-restraints excluded: chain F residue 327 GLN Chi-restraints excluded: chain F residue 399 VAL Chi-restraints excluded: chain F residue 430 ILE Chi-restraints excluded: chain F residue 615 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 213 optimal weight: 5.9990 chunk 370 optimal weight: 2.9990 chunk 183 optimal weight: 4.9990 chunk 101 optimal weight: 0.9980 chunk 262 optimal weight: 7.9990 chunk 284 optimal weight: 4.9990 chunk 384 optimal weight: 2.9990 chunk 63 optimal weight: 6.9990 chunk 65 optimal weight: 1.9990 chunk 221 optimal weight: 6.9990 chunk 22 optimal weight: 0.0060 overall best weight: 1.8002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 458 GLN B 327 GLN C 327 GLN C 568 GLN D 458 GLN E 327 GLN F 327 GLN ** F 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 568 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4208 r_free = 0.4208 target = 0.148958 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.097923 restraints weight = 58729.448| |-----------------------------------------------------------------------------| r_work (start): 0.3364 rms_B_bonded: 3.22 r_work: 0.3201 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.3201 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8329 moved from start: 0.4430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 35304 Z= 0.176 Angle : 0.681 13.932 47730 Z= 0.326 Chirality : 0.046 0.160 5358 Planarity : 0.004 0.047 6270 Dihedral : 7.542 115.225 4902 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.11 % Favored : 93.89 % Rotamer: Outliers : 2.25 % Allowed : 18.92 % Favored : 78.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.14 % 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: 0.41 (0.13), residues: 4368 helix: 1.14 (0.12), residues: 1848 sheet: 0.83 (0.21), residues: 546 loop : -0.69 (0.14), residues: 1974 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 349 TYR 0.014 0.001 TYR F 244 PHE 0.009 0.001 PHE E 736 TRP 0.005 0.001 TRP B 454 HIS 0.007 0.001 HIS B 317 Details of bonding type rmsd covalent geometry : bond 0.00424 (35304) covalent geometry : angle 0.68150 (47730) hydrogen bonds : bond 0.04363 ( 1410) hydrogen bonds : angle 4.85559 ( 3978) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8736 Ramachandran restraints generated. 4368 Oldfield, 0 Emsley, 4368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8736 Ramachandran restraints generated. 4368 Oldfield, 0 Emsley, 4368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 3732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 205 time to evaluate : 1.295 Fit side-chains REVERT: A 319 GLU cc_start: 0.7929 (OUTLIER) cc_final: 0.7555 (tm-30) REVERT: A 742 PHE cc_start: 0.8522 (m-80) cc_final: 0.8275 (m-80) REVERT: B 36 ASN cc_start: 0.8196 (m-40) cc_final: 0.7586 (t0) REVERT: B 221 GLU cc_start: 0.8534 (OUTLIER) cc_final: 0.8312 (pm20) REVERT: B 317 HIS cc_start: 0.4910 (t-170) cc_final: 0.4485 (t-170) REVERT: B 327 GLN cc_start: 0.8314 (OUTLIER) cc_final: 0.7960 (tp40) REVERT: B 427 MET cc_start: 0.7753 (tpp) cc_final: 0.7341 (tpp) REVERT: B 742 PHE cc_start: 0.8771 (m-80) cc_final: 0.8532 (m-80) REVERT: C 153 LEU cc_start: 0.5811 (OUTLIER) cc_final: 0.5521 (tp) REVERT: C 221 GLU cc_start: 0.8663 (OUTLIER) cc_final: 0.8308 (pm20) REVERT: C 327 GLN cc_start: 0.8520 (OUTLIER) cc_final: 0.8068 (tp40) REVERT: C 442 MET cc_start: 0.8777 (mmp) cc_final: 0.8430 (mmm) REVERT: C 445 LEU cc_start: 0.8929 (tt) cc_final: 0.8607 (mp) REVERT: D 658 LYS cc_start: 0.9109 (OUTLIER) cc_final: 0.8902 (mttt) REVERT: D 663 LYS cc_start: 0.8477 (tptp) cc_final: 0.8236 (tptt) REVERT: D 742 PHE cc_start: 0.8525 (m-80) cc_final: 0.8277 (m-80) REVERT: E 36 ASN cc_start: 0.8188 (m-40) cc_final: 0.7578 (t0) REVERT: E 221 GLU cc_start: 0.8537 (OUTLIER) cc_final: 0.8330 (pm20) REVERT: E 327 GLN cc_start: 0.8304 (OUTLIER) cc_final: 0.8069 (tp40) REVERT: E 427 MET cc_start: 0.7750 (tpp) cc_final: 0.7336 (tpp) REVERT: E 678 MET cc_start: 0.8090 (mmm) cc_final: 0.7865 (mmm) REVERT: E 742 PHE cc_start: 0.8771 (m-80) cc_final: 0.8533 (m-80) REVERT: F 153 LEU cc_start: 0.5884 (OUTLIER) cc_final: 0.5603 (tp) REVERT: F 221 GLU cc_start: 0.8649 (OUTLIER) cc_final: 0.8296 (pm20) REVERT: F 327 GLN cc_start: 0.8499 (OUTLIER) cc_final: 0.8060 (tp40) REVERT: F 427 MET cc_start: 0.7599 (tpp) cc_final: 0.7391 (tpp) REVERT: F 442 MET cc_start: 0.8757 (mmp) cc_final: 0.8417 (mmm) REVERT: F 445 LEU cc_start: 0.8935 (tt) cc_final: 0.8617 (mp) outliers start: 84 outliers final: 25 residues processed: 271 average time/residue: 0.6451 time to fit residues: 213.5538 Evaluate side-chains 230 residues out of total 3732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 193 time to evaluate : 1.479 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 319 GLU Chi-restraints excluded: chain A residue 364 ASP Chi-restraints excluded: chain B residue 94 VAL Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain B residue 221 GLU Chi-restraints excluded: chain B residue 282 SER Chi-restraints excluded: chain B residue 327 GLN Chi-restraints excluded: chain B residue 364 ASP Chi-restraints excluded: chain B residue 399 VAL Chi-restraints excluded: chain C residue 94 VAL Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain C residue 153 LEU Chi-restraints excluded: chain C residue 221 GLU Chi-restraints excluded: chain C residue 282 SER Chi-restraints excluded: chain C residue 327 GLN Chi-restraints excluded: chain C residue 399 VAL Chi-restraints excluded: chain C residue 615 LYS Chi-restraints excluded: chain D residue 94 VAL Chi-restraints excluded: chain D residue 123 VAL Chi-restraints excluded: chain D residue 364 ASP Chi-restraints excluded: chain D residue 658 LYS Chi-restraints excluded: chain E residue 94 VAL Chi-restraints excluded: chain E residue 123 VAL Chi-restraints excluded: chain E residue 221 GLU Chi-restraints excluded: chain E residue 282 SER Chi-restraints excluded: chain E residue 327 GLN Chi-restraints excluded: chain E residue 399 VAL Chi-restraints excluded: chain F residue 94 VAL Chi-restraints excluded: chain F residue 123 VAL Chi-restraints excluded: chain F residue 153 LEU Chi-restraints excluded: chain F residue 221 GLU Chi-restraints excluded: chain F residue 282 SER Chi-restraints excluded: chain F residue 327 GLN Chi-restraints excluded: chain F residue 399 VAL Chi-restraints excluded: chain F residue 615 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 16 optimal weight: 2.9990 chunk 42 optimal weight: 5.9990 chunk 377 optimal weight: 0.4980 chunk 409 optimal weight: 7.9990 chunk 165 optimal weight: 0.9990 chunk 332 optimal weight: 0.0470 chunk 214 optimal weight: 0.7980 chunk 232 optimal weight: 10.0000 chunk 139 optimal weight: 4.9990 chunk 228 optimal weight: 3.9990 chunk 187 optimal weight: 8.9990 overall best weight: 1.0682 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 327 GLN E 327 GLN ** F 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4215 r_free = 0.4215 target = 0.149555 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.098661 restraints weight = 58678.430| |-----------------------------------------------------------------------------| r_work (start): 0.3383 rms_B_bonded: 3.17 r_work: 0.3220 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.3220 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8315 moved from start: 0.4608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 35304 Z= 0.139 Angle : 0.667 15.216 47730 Z= 0.315 Chirality : 0.045 0.217 5358 Planarity : 0.004 0.047 6270 Dihedral : 7.465 115.528 4902 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.86 % Favored : 94.14 % Rotamer: Outliers : 1.96 % Allowed : 19.83 % Favored : 78.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.14 % 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: 0.48 (0.13), residues: 4368 helix: 1.20 (0.12), residues: 1848 sheet: 0.86 (0.21), residues: 546 loop : -0.66 (0.14), residues: 1974 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG F 349 TYR 0.012 0.001 TYR D 244 PHE 0.006 0.001 PHE B 506 TRP 0.003 0.001 TRP A 476 HIS 0.004 0.001 HIS D 317 Details of bonding type rmsd covalent geometry : bond 0.00327 (35304) covalent geometry : angle 0.66685 (47730) hydrogen bonds : bond 0.03953 ( 1410) hydrogen bonds : angle 4.71975 ( 3978) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8736 Ramachandran restraints generated. 4368 Oldfield, 0 Emsley, 4368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8736 Ramachandran restraints generated. 4368 Oldfield, 0 Emsley, 4368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 3732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 210 time to evaluate : 1.317 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 153 LEU cc_start: 0.6313 (OUTLIER) cc_final: 0.6003 (tt) REVERT: A 663 LYS cc_start: 0.8472 (tptp) cc_final: 0.8262 (tptt) REVERT: A 674 PHE cc_start: 0.8495 (t80) cc_final: 0.8216 (t80) REVERT: A 742 PHE cc_start: 0.8521 (m-80) cc_final: 0.8271 (m-80) REVERT: B 221 GLU cc_start: 0.8538 (OUTLIER) cc_final: 0.8312 (pm20) REVERT: B 317 HIS cc_start: 0.4786 (t-170) cc_final: 0.4380 (t-170) REVERT: B 327 GLN cc_start: 0.8216 (OUTLIER) cc_final: 0.7912 (tp40) REVERT: B 427 MET cc_start: 0.7732 (tpp) cc_final: 0.7296 (tpp) REVERT: B 742 PHE cc_start: 0.8767 (m-80) cc_final: 0.8522 (m-80) REVERT: C 153 LEU cc_start: 0.5796 (OUTLIER) cc_final: 0.5484 (tp) REVERT: C 221 GLU cc_start: 0.8679 (OUTLIER) cc_final: 0.8318 (pm20) REVERT: C 427 MET cc_start: 0.7415 (tpp) cc_final: 0.7197 (tpp) REVERT: C 442 MET cc_start: 0.8773 (mmp) cc_final: 0.8415 (mmm) REVERT: C 445 LEU cc_start: 0.8923 (tt) cc_final: 0.8615 (mp) REVERT: D 153 LEU cc_start: 0.6315 (OUTLIER) cc_final: 0.6004 (tt) REVERT: D 663 LYS cc_start: 0.8472 (tptp) cc_final: 0.8262 (tptt) REVERT: D 674 PHE cc_start: 0.8491 (t80) cc_final: 0.8210 (t80) REVERT: D 742 PHE cc_start: 0.8519 (m-80) cc_final: 0.8266 (m-80) REVERT: E 221 GLU cc_start: 0.8540 (OUTLIER) cc_final: 0.8328 (pm20) REVERT: E 319 GLU cc_start: 0.7967 (OUTLIER) cc_final: 0.7669 (tm-30) REVERT: E 327 GLN cc_start: 0.8171 (OUTLIER) cc_final: 0.7827 (tp40) REVERT: E 427 MET cc_start: 0.7741 (tpp) cc_final: 0.7308 (tpp) REVERT: E 678 MET cc_start: 0.8121 (mmm) cc_final: 0.7871 (mmm) REVERT: E 742 PHE cc_start: 0.8768 (m-80) cc_final: 0.8524 (m-80) REVERT: F 153 LEU cc_start: 0.5869 (OUTLIER) cc_final: 0.5551 (tp) REVERT: F 221 GLU cc_start: 0.8651 (OUTLIER) cc_final: 0.8299 (pm20) REVERT: F 442 MET cc_start: 0.8753 (mmp) cc_final: 0.8386 (mmm) REVERT: F 445 LEU cc_start: 0.8933 (tt) cc_final: 0.8626 (mp) outliers start: 73 outliers final: 27 residues processed: 267 average time/residue: 0.6922 time to fit residues: 222.7183 Evaluate side-chains 234 residues out of total 3732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 196 time to evaluate : 1.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 282 SER Chi-restraints excluded: chain A residue 399 VAL Chi-restraints excluded: chain B residue 94 VAL Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain B residue 221 GLU Chi-restraints excluded: chain B residue 282 SER Chi-restraints excluded: chain B residue 327 GLN Chi-restraints excluded: chain B residue 399 VAL Chi-restraints excluded: chain C residue 94 VAL Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain C residue 153 LEU Chi-restraints excluded: chain C residue 221 GLU Chi-restraints excluded: chain C residue 282 SER Chi-restraints excluded: chain C residue 399 VAL Chi-restraints excluded: chain C residue 615 LYS Chi-restraints excluded: chain D residue 94 VAL Chi-restraints excluded: chain D residue 123 VAL Chi-restraints excluded: chain D residue 153 LEU Chi-restraints excluded: chain D residue 282 SER Chi-restraints excluded: chain D residue 399 VAL Chi-restraints excluded: chain E residue 94 VAL Chi-restraints excluded: chain E residue 123 VAL Chi-restraints excluded: chain E residue 221 GLU Chi-restraints excluded: chain E residue 282 SER Chi-restraints excluded: chain E residue 319 GLU Chi-restraints excluded: chain E residue 327 GLN Chi-restraints excluded: chain E residue 399 VAL Chi-restraints excluded: chain F residue 94 VAL Chi-restraints excluded: chain F residue 123 VAL Chi-restraints excluded: chain F residue 153 LEU Chi-restraints excluded: chain F residue 221 GLU Chi-restraints excluded: chain F residue 282 SER Chi-restraints excluded: chain F residue 317 HIS Chi-restraints excluded: chain F residue 399 VAL Chi-restraints excluded: chain F residue 615 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 50 optimal weight: 3.9990 chunk 165 optimal weight: 2.9990 chunk 435 optimal weight: 0.8980 chunk 254 optimal weight: 0.8980 chunk 80 optimal weight: 4.9990 chunk 280 optimal weight: 0.9980 chunk 172 optimal weight: 3.9990 chunk 12 optimal weight: 5.9990 chunk 313 optimal weight: 0.0970 chunk 46 optimal weight: 3.9990 chunk 141 optimal weight: 0.1980 overall best weight: 0.6178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 327 GLN C 327 GLN E 327 GLN F 327 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4221 r_free = 0.4221 target = 0.149964 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.099583 restraints weight = 59310.300| |-----------------------------------------------------------------------------| r_work (start): 0.3404 rms_B_bonded: 3.08 r_work: 0.3245 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.3245 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8289 moved from start: 0.4742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 35304 Z= 0.122 Angle : 0.668 14.673 47730 Z= 0.313 Chirality : 0.044 0.137 5358 Planarity : 0.004 0.046 6270 Dihedral : 7.323 116.208 4902 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.72 % Favored : 94.28 % Rotamer: Outliers : 1.85 % Allowed : 20.20 % Favored : 77.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.14 % 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: 0.57 (0.13), residues: 4368 helix: 1.28 (0.13), residues: 1848 sheet: 0.88 (0.21), residues: 546 loop : -0.60 (0.14), residues: 1974 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG F 349 TYR 0.012 0.001 TYR F 244 PHE 0.005 0.001 PHE E 506 TRP 0.003 0.001 TRP A 476 HIS 0.004 0.001 HIS D 317 Details of bonding type rmsd covalent geometry : bond 0.00282 (35304) covalent geometry : angle 0.66803 (47730) hydrogen bonds : bond 0.03614 ( 1410) hydrogen bonds : angle 4.56824 ( 3978) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8736 Ramachandran restraints generated. 4368 Oldfield, 0 Emsley, 4368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8736 Ramachandran restraints generated. 4368 Oldfield, 0 Emsley, 4368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 3732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 215 time to evaluate : 1.338 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 153 LEU cc_start: 0.6313 (OUTLIER) cc_final: 0.6006 (tt) REVERT: A 239 ARG cc_start: 0.7843 (ttm-80) cc_final: 0.7541 (mtp85) REVERT: A 319 GLU cc_start: 0.7978 (OUTLIER) cc_final: 0.7656 (tm-30) REVERT: A 663 LYS cc_start: 0.8460 (tptp) cc_final: 0.8258 (tptt) REVERT: A 674 PHE cc_start: 0.8482 (t80) cc_final: 0.8192 (t80) REVERT: A 742 PHE cc_start: 0.8522 (m-80) cc_final: 0.8273 (m-80) REVERT: B 28 VAL cc_start: 0.7917 (t) cc_final: 0.7536 (p) REVERT: B 221 GLU cc_start: 0.8496 (OUTLIER) cc_final: 0.8295 (pm20) REVERT: B 317 HIS cc_start: 0.4768 (t-90) cc_final: 0.4383 (t-170) REVERT: B 327 GLN cc_start: 0.8146 (OUTLIER) cc_final: 0.7782 (tp40) REVERT: B 427 MET cc_start: 0.7753 (tpp) cc_final: 0.7356 (tpp) REVERT: B 674 PHE cc_start: 0.8518 (t80) cc_final: 0.8282 (t80) REVERT: B 742 PHE cc_start: 0.8797 (m-80) cc_final: 0.8580 (m-80) REVERT: C 153 LEU cc_start: 0.5756 (OUTLIER) cc_final: 0.5453 (tp) REVERT: C 221 GLU cc_start: 0.8665 (OUTLIER) cc_final: 0.8293 (pm20) REVERT: C 327 GLN cc_start: 0.8006 (OUTLIER) cc_final: 0.6582 (tp-100) REVERT: C 427 MET cc_start: 0.7512 (tpp) cc_final: 0.7240 (tpp) REVERT: C 442 MET cc_start: 0.8748 (mmp) cc_final: 0.8374 (mmm) REVERT: C 445 LEU cc_start: 0.8927 (tt) cc_final: 0.8599 (mp) REVERT: C 584 LYS cc_start: 0.8419 (OUTLIER) cc_final: 0.8168 (mttp) REVERT: C 674 PHE cc_start: 0.8495 (t80) cc_final: 0.8281 (t80) REVERT: D 153 LEU cc_start: 0.6324 (OUTLIER) cc_final: 0.6012 (tt) REVERT: D 239 ARG cc_start: 0.7841 (ttm-80) cc_final: 0.7537 (mtp85) REVERT: D 663 LYS cc_start: 0.8445 (tptp) cc_final: 0.8244 (tptt) REVERT: D 674 PHE cc_start: 0.8481 (t80) cc_final: 0.8188 (t80) REVERT: D 742 PHE cc_start: 0.8529 (m-80) cc_final: 0.8283 (m-80) REVERT: E 28 VAL cc_start: 0.7930 (t) cc_final: 0.7551 (p) REVERT: E 317 HIS cc_start: 0.5932 (p90) cc_final: 0.5627 (p90) REVERT: E 319 GLU cc_start: 0.7913 (OUTLIER) cc_final: 0.7593 (tm-30) REVERT: E 327 GLN cc_start: 0.8107 (OUTLIER) cc_final: 0.7692 (tp40) REVERT: E 427 MET cc_start: 0.7753 (tpp) cc_final: 0.7358 (tpp) REVERT: E 678 MET cc_start: 0.8144 (mmm) cc_final: 0.7883 (mmm) REVERT: E 742 PHE cc_start: 0.8794 (m-80) cc_final: 0.8579 (m-80) REVERT: E 754 LYS cc_start: 0.9031 (OUTLIER) cc_final: 0.8696 (tmmt) REVERT: F 153 LEU cc_start: 0.5825 (OUTLIER) cc_final: 0.5526 (tp) REVERT: F 221 GLU cc_start: 0.8649 (OUTLIER) cc_final: 0.8288 (pm20) REVERT: F 327 GLN cc_start: 0.8137 (OUTLIER) cc_final: 0.7903 (tp40) REVERT: F 427 MET cc_start: 0.7534 (tpp) cc_final: 0.7050 (tpp) REVERT: F 442 MET cc_start: 0.8724 (mmp) cc_final: 0.8355 (mmm) REVERT: F 445 LEU cc_start: 0.8923 (tt) cc_final: 0.8596 (mp) REVERT: F 584 LYS cc_start: 0.8435 (OUTLIER) cc_final: 0.8183 (mttp) outliers start: 69 outliers final: 27 residues processed: 278 average time/residue: 0.7459 time to fit residues: 247.2633 Evaluate side-chains 248 residues out of total 3732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 205 time to evaluate : 1.148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 319 GLU Chi-restraints excluded: chain A residue 399 VAL Chi-restraints excluded: chain B residue 94 VAL Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain B residue 221 GLU Chi-restraints excluded: chain B residue 282 SER Chi-restraints excluded: chain B residue 307 ASP Chi-restraints excluded: chain B residue 327 GLN Chi-restraints excluded: chain B residue 399 VAL Chi-restraints excluded: chain C residue 94 VAL Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain C residue 153 LEU Chi-restraints excluded: chain C residue 221 GLU Chi-restraints excluded: chain C residue 282 SER Chi-restraints excluded: chain C residue 327 GLN Chi-restraints excluded: chain C residue 514 VAL Chi-restraints excluded: chain C residue 584 LYS Chi-restraints excluded: chain C residue 615 LYS Chi-restraints excluded: chain D residue 94 VAL Chi-restraints excluded: chain D residue 123 VAL Chi-restraints excluded: chain D residue 153 LEU Chi-restraints excluded: chain D residue 399 VAL Chi-restraints excluded: chain E residue 94 VAL Chi-restraints excluded: chain E residue 123 VAL Chi-restraints excluded: chain E residue 282 SER Chi-restraints excluded: chain E residue 307 ASP Chi-restraints excluded: chain E residue 319 GLU Chi-restraints excluded: chain E residue 327 GLN Chi-restraints excluded: chain E residue 399 VAL Chi-restraints excluded: chain E residue 754 LYS Chi-restraints excluded: chain F residue 94 VAL Chi-restraints excluded: chain F residue 123 VAL Chi-restraints excluded: chain F residue 153 LEU Chi-restraints excluded: chain F residue 221 GLU Chi-restraints excluded: chain F residue 282 SER Chi-restraints excluded: chain F residue 327 GLN Chi-restraints excluded: chain F residue 399 VAL Chi-restraints excluded: chain F residue 514 VAL Chi-restraints excluded: chain F residue 584 LYS Chi-restraints excluded: chain F residue 615 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 166 optimal weight: 1.9990 chunk 202 optimal weight: 4.9990 chunk 100 optimal weight: 2.9990 chunk 36 optimal weight: 0.4980 chunk 162 optimal weight: 50.0000 chunk 127 optimal weight: 0.9990 chunk 384 optimal weight: 0.7980 chunk 414 optimal weight: 0.0970 chunk 208 optimal weight: 4.9990 chunk 230 optimal weight: 5.9990 chunk 4 optimal weight: 10.0000 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 226 HIS B 327 GLN ** C 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 327 GLN ** F 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 327 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4218 r_free = 0.4218 target = 0.149817 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.099467 restraints weight = 58452.323| |-----------------------------------------------------------------------------| r_work (start): 0.3403 rms_B_bonded: 3.10 r_work: 0.3244 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.3244 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8299 moved from start: 0.4879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 35304 Z= 0.129 Angle : 0.681 16.723 47730 Z= 0.320 Chirality : 0.044 0.206 5358 Planarity : 0.004 0.046 6270 Dihedral : 7.295 115.840 4902 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.00 % Favored : 94.00 % Rotamer: Outliers : 2.20 % Allowed : 20.34 % Favored : 77.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.14 % 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: 0.61 (0.13), residues: 4368 helix: 1.31 (0.13), residues: 1848 sheet: 0.88 (0.21), residues: 546 loop : -0.56 (0.14), residues: 1974 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG F 349 TYR 0.013 0.001 TYR F 244 PHE 0.012 0.001 PHE F 674 TRP 0.003 0.001 TRP B 454 HIS 0.004 0.001 HIS D 317 Details of bonding type rmsd covalent geometry : bond 0.00306 (35304) covalent geometry : angle 0.68112 (47730) hydrogen bonds : bond 0.03653 ( 1410) hydrogen bonds : angle 4.55007 ( 3978) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8736 Ramachandran restraints generated. 4368 Oldfield, 0 Emsley, 4368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8736 Ramachandran restraints generated. 4368 Oldfield, 0 Emsley, 4368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 3732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 219 time to evaluate : 1.435 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 153 LEU cc_start: 0.6240 (OUTLIER) cc_final: 0.5916 (tt) REVERT: A 239 ARG cc_start: 0.7840 (ttm-80) cc_final: 0.7542 (mtp85) REVERT: A 319 GLU cc_start: 0.7974 (OUTLIER) cc_final: 0.7644 (tm-30) REVERT: A 742 PHE cc_start: 0.8558 (m-80) cc_final: 0.8310 (m-80) REVERT: B 28 VAL cc_start: 0.8032 (t) cc_final: 0.7644 (p) REVERT: B 153 LEU cc_start: 0.6198 (OUTLIER) cc_final: 0.5876 (tt) REVERT: B 221 GLU cc_start: 0.8477 (OUTLIER) cc_final: 0.8265 (pm20) REVERT: B 327 GLN cc_start: 0.8099 (OUTLIER) cc_final: 0.7786 (tp40) REVERT: B 427 MET cc_start: 0.7729 (tpp) cc_final: 0.7288 (tpp) REVERT: B 674 PHE cc_start: 0.8531 (t80) cc_final: 0.8292 (t80) REVERT: B 742 PHE cc_start: 0.8796 (m-80) cc_final: 0.8593 (m-80) REVERT: C 153 LEU cc_start: 0.5763 (OUTLIER) cc_final: 0.5454 (tp) REVERT: C 221 GLU cc_start: 0.8619 (OUTLIER) cc_final: 0.8326 (pm20) REVERT: C 442 MET cc_start: 0.8715 (mmp) cc_final: 0.8281 (mmm) REVERT: C 445 LEU cc_start: 0.8927 (tt) cc_final: 0.8605 (mp) REVERT: C 674 PHE cc_start: 0.8485 (t80) cc_final: 0.8254 (t80) REVERT: D 153 LEU cc_start: 0.6226 (OUTLIER) cc_final: 0.5903 (tt) REVERT: D 239 ARG cc_start: 0.7840 (ttm-80) cc_final: 0.7541 (mtp85) REVERT: D 663 LYS cc_start: 0.8434 (tptp) cc_final: 0.8233 (tptt) REVERT: D 742 PHE cc_start: 0.8555 (m-80) cc_final: 0.8310 (m-80) REVERT: E 28 VAL cc_start: 0.8027 (t) cc_final: 0.7642 (p) REVERT: E 153 LEU cc_start: 0.6205 (OUTLIER) cc_final: 0.5880 (tt) REVERT: E 317 HIS cc_start: 0.6015 (p90) cc_final: 0.5745 (p90) REVERT: E 319 GLU cc_start: 0.7910 (OUTLIER) cc_final: 0.7613 (tm-30) REVERT: E 327 GLN cc_start: 0.8037 (OUTLIER) cc_final: 0.7685 (tp40) REVERT: E 427 MET cc_start: 0.7731 (tpp) cc_final: 0.7286 (tpp) REVERT: E 678 MET cc_start: 0.8162 (mmm) cc_final: 0.7879 (mmm) REVERT: E 742 PHE cc_start: 0.8789 (m-80) cc_final: 0.8587 (m-80) REVERT: E 754 LYS cc_start: 0.9010 (OUTLIER) cc_final: 0.8708 (tmmt) REVERT: F 153 LEU cc_start: 0.5817 (OUTLIER) cc_final: 0.5514 (tp) REVERT: F 221 GLU cc_start: 0.8606 (OUTLIER) cc_final: 0.8272 (pm20) REVERT: F 319 GLU cc_start: 0.8160 (OUTLIER) cc_final: 0.7661 (tm-30) REVERT: F 327 GLN cc_start: 0.7936 (OUTLIER) cc_final: 0.6786 (tp-100) REVERT: F 427 MET cc_start: 0.7528 (tpp) cc_final: 0.7185 (tpp) REVERT: F 442 MET cc_start: 0.8694 (mmp) cc_final: 0.8264 (mmm) REVERT: F 445 LEU cc_start: 0.8928 (tt) cc_final: 0.8611 (mp) outliers start: 82 outliers final: 32 residues processed: 290 average time/residue: 0.7304 time to fit residues: 253.0529 Evaluate side-chains 251 residues out of total 3732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 203 time to evaluate : 1.638 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 282 SER Chi-restraints excluded: chain A residue 319 GLU Chi-restraints excluded: chain A residue 399 VAL Chi-restraints excluded: chain B residue 94 VAL Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain B residue 153 LEU Chi-restraints excluded: chain B residue 221 GLU Chi-restraints excluded: chain B residue 282 SER Chi-restraints excluded: chain B residue 307 ASP Chi-restraints excluded: chain B residue 327 GLN Chi-restraints excluded: chain B residue 399 VAL Chi-restraints excluded: chain B residue 514 VAL Chi-restraints excluded: chain C residue 94 VAL Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain C residue 153 LEU Chi-restraints excluded: chain C residue 221 GLU Chi-restraints excluded: chain C residue 282 SER Chi-restraints excluded: chain C residue 399 VAL Chi-restraints excluded: chain C residue 514 VAL Chi-restraints excluded: chain C residue 615 LYS Chi-restraints excluded: chain D residue 94 VAL Chi-restraints excluded: chain D residue 123 VAL Chi-restraints excluded: chain D residue 153 LEU Chi-restraints excluded: chain D residue 282 SER Chi-restraints excluded: chain D residue 399 VAL Chi-restraints excluded: chain E residue 94 VAL Chi-restraints excluded: chain E residue 123 VAL Chi-restraints excluded: chain E residue 153 LEU Chi-restraints excluded: chain E residue 282 SER Chi-restraints excluded: chain E residue 307 ASP Chi-restraints excluded: chain E residue 319 GLU Chi-restraints excluded: chain E residue 327 GLN Chi-restraints excluded: chain E residue 399 VAL Chi-restraints excluded: chain E residue 514 VAL Chi-restraints excluded: chain E residue 754 LYS Chi-restraints excluded: chain F residue 94 VAL Chi-restraints excluded: chain F residue 123 VAL Chi-restraints excluded: chain F residue 153 LEU Chi-restraints excluded: chain F residue 221 GLU Chi-restraints excluded: chain F residue 282 SER Chi-restraints excluded: chain F residue 319 GLU Chi-restraints excluded: chain F residue 327 GLN Chi-restraints excluded: chain F residue 399 VAL Chi-restraints excluded: chain F residue 514 VAL Chi-restraints excluded: chain F residue 615 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 105 optimal weight: 7.9990 chunk 146 optimal weight: 10.0000 chunk 193 optimal weight: 2.9990 chunk 366 optimal weight: 7.9990 chunk 59 optimal weight: 0.0670 chunk 241 optimal weight: 3.9990 chunk 72 optimal weight: 9.9990 chunk 5 optimal weight: 9.9990 chunk 211 optimal weight: 0.9980 chunk 296 optimal weight: 20.0000 chunk 301 optimal weight: 20.0000 overall best weight: 3.2124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 327 GLN C 327 GLN E 327 GLN ** F 317 HIS ** 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 = 0.4164 r_free = 0.4164 target = 0.145813 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.094322 restraints weight = 58788.866| |-----------------------------------------------------------------------------| r_work (start): 0.3308 rms_B_bonded: 3.07 r_work: 0.3143 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.3143 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8364 moved from start: 0.5333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.076 35304 Z= 0.264 Angle : 0.781 10.638 47730 Z= 0.377 Chirality : 0.049 0.235 5358 Planarity : 0.005 0.049 6270 Dihedral : 7.540 110.648 4902 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.43 % Favored : 93.57 % Rotamer: Outliers : 1.74 % Allowed : 20.98 % Favored : 77.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.14 % 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: 0.40 (0.13), residues: 4368 helix: 1.06 (0.12), residues: 1854 sheet: 0.74 (0.21), residues: 546 loop : -0.59 (0.14), residues: 1968 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG D 745 TYR 0.017 0.002 TYR C 244 PHE 0.017 0.002 PHE C 736 TRP 0.007 0.001 TRP F 454 HIS 0.010 0.001 HIS B 317 Details of bonding type rmsd covalent geometry : bond 0.00628 (35304) covalent geometry : angle 0.78119 (47730) hydrogen bonds : bond 0.05052 ( 1410) hydrogen bonds : angle 4.91786 ( 3978) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8736 Ramachandran restraints generated. 4368 Oldfield, 0 Emsley, 4368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8736 Ramachandran restraints generated. 4368 Oldfield, 0 Emsley, 4368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 3732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 209 time to evaluate : 1.309 Fit side-chains REVERT: A 153 LEU cc_start: 0.6324 (OUTLIER) cc_final: 0.5977 (tt) REVERT: A 319 GLU cc_start: 0.7933 (OUTLIER) cc_final: 0.7585 (tm-30) REVERT: B 36 ASN cc_start: 0.8192 (m-40) cc_final: 0.7586 (t0) REVERT: B 221 GLU cc_start: 0.8535 (OUTLIER) cc_final: 0.8272 (pm20) REVERT: B 327 GLN cc_start: 0.8340 (OUTLIER) cc_final: 0.7605 (tp-100) REVERT: B 427 MET cc_start: 0.7847 (tpp) cc_final: 0.7370 (tpp) REVERT: C 153 LEU cc_start: 0.5998 (OUTLIER) cc_final: 0.5652 (tt) REVERT: C 221 GLU cc_start: 0.8647 (OUTLIER) cc_final: 0.8321 (pm20) REVERT: C 427 MET cc_start: 0.7525 (tpt) cc_final: 0.7131 (tpp) REVERT: C 442 MET cc_start: 0.8812 (mmp) cc_final: 0.8355 (mmm) REVERT: C 445 LEU cc_start: 0.8995 (tt) cc_final: 0.8666 (mp) REVERT: D 153 LEU cc_start: 0.6301 (OUTLIER) cc_final: 0.5956 (tt) REVERT: E 36 ASN cc_start: 0.8187 (m-40) cc_final: 0.7581 (t0) REVERT: E 317 HIS cc_start: 0.6550 (p90) cc_final: 0.6248 (p90) REVERT: E 319 GLU cc_start: 0.7922 (OUTLIER) cc_final: 0.7633 (tm-30) REVERT: E 327 GLN cc_start: 0.8370 (OUTLIER) cc_final: 0.7613 (tp-100) REVERT: E 427 MET cc_start: 0.7848 (tpp) cc_final: 0.7372 (tpp) REVERT: F 153 LEU cc_start: 0.5999 (OUTLIER) cc_final: 0.5650 (tp) REVERT: F 221 GLU cc_start: 0.8629 (OUTLIER) cc_final: 0.8312 (pm20) REVERT: F 327 GLN cc_start: 0.8129 (OUTLIER) cc_final: 0.7819 (tp40) REVERT: F 442 MET cc_start: 0.8782 (mmp) cc_final: 0.8407 (mmm) outliers start: 65 outliers final: 29 residues processed: 272 average time/residue: 0.7604 time to fit residues: 245.1938 Evaluate side-chains 221 residues out of total 3732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 180 time to evaluate : 1.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 319 GLU Chi-restraints excluded: chain B residue 94 VAL Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain B residue 221 GLU Chi-restraints excluded: chain B residue 282 SER Chi-restraints excluded: chain B residue 327 GLN Chi-restraints excluded: chain B residue 399 VAL Chi-restraints excluded: chain B residue 514 VAL Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 94 VAL Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain C residue 153 LEU Chi-restraints excluded: chain C residue 221 GLU Chi-restraints excluded: chain C residue 282 SER Chi-restraints excluded: chain C residue 330 THR Chi-restraints excluded: chain C residue 364 ASP Chi-restraints excluded: chain C residue 399 VAL Chi-restraints excluded: chain C residue 514 VAL Chi-restraints excluded: chain D residue 94 VAL Chi-restraints excluded: chain D residue 123 VAL Chi-restraints excluded: chain D residue 153 LEU Chi-restraints excluded: chain E residue 94 VAL Chi-restraints excluded: chain E residue 123 VAL Chi-restraints excluded: chain E residue 282 SER Chi-restraints excluded: chain E residue 319 GLU Chi-restraints excluded: chain E residue 327 GLN Chi-restraints excluded: chain E residue 399 VAL Chi-restraints excluded: chain E residue 514 VAL Chi-restraints excluded: chain F residue 51 LEU Chi-restraints excluded: chain F residue 94 VAL Chi-restraints excluded: chain F residue 123 VAL Chi-restraints excluded: chain F residue 153 LEU Chi-restraints excluded: chain F residue 221 GLU Chi-restraints excluded: chain F residue 282 SER Chi-restraints excluded: chain F residue 327 GLN Chi-restraints excluded: chain F residue 364 ASP Chi-restraints excluded: chain F residue 399 VAL Chi-restraints excluded: chain F residue 514 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 221 optimal weight: 1.9990 chunk 34 optimal weight: 0.9990 chunk 264 optimal weight: 1.9990 chunk 170 optimal weight: 4.9990 chunk 329 optimal weight: 4.9990 chunk 298 optimal weight: 9.9990 chunk 87 optimal weight: 10.0000 chunk 262 optimal weight: 2.9990 chunk 426 optimal weight: 1.9990 chunk 6 optimal weight: 10.0000 chunk 366 optimal weight: 8.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 327 GLN B 460 ASN ** C 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 327 GLN E 460 ASN ** F 317 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 = 0.4165 r_free = 0.4165 target = 0.145925 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.094754 restraints weight = 59396.048| |-----------------------------------------------------------------------------| r_work (start): 0.3336 rms_B_bonded: 3.05 r_work: 0.3173 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3173 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8335 moved from start: 0.5495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 35304 Z= 0.190 Angle : 0.738 11.653 47730 Z= 0.353 Chirality : 0.046 0.210 5358 Planarity : 0.004 0.052 6270 Dihedral : 7.439 112.775 4902 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.88 % Favored : 94.12 % Rotamer: Outliers : 1.34 % Allowed : 21.41 % Favored : 77.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.14 % 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: 0.39 (0.13), residues: 4368 helix: 1.09 (0.12), residues: 1854 sheet: 0.65 (0.21), residues: 546 loop : -0.61 (0.14), residues: 1968 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 745 TYR 0.018 0.001 TYR E 244 PHE 0.010 0.001 PHE F 736 TRP 0.004 0.001 TRP F 454 HIS 0.009 0.001 HIS B 317 Details of bonding type rmsd covalent geometry : bond 0.00458 (35304) covalent geometry : angle 0.73790 (47730) hydrogen bonds : bond 0.04357 ( 1410) hydrogen bonds : angle 4.78848 ( 3978) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8736 Ramachandran restraints generated. 4368 Oldfield, 0 Emsley, 4368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8736 Ramachandran restraints generated. 4368 Oldfield, 0 Emsley, 4368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 3732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 199 time to evaluate : 1.380 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 153 LEU cc_start: 0.6163 (OUTLIER) cc_final: 0.5814 (tt) REVERT: A 319 GLU cc_start: 0.7877 (OUTLIER) cc_final: 0.6869 (tp30) REVERT: B 36 ASN cc_start: 0.8275 (m-40) cc_final: 0.7626 (t0) REVERT: B 153 LEU cc_start: 0.6188 (OUTLIER) cc_final: 0.5698 (tt) REVERT: B 221 GLU cc_start: 0.8542 (OUTLIER) cc_final: 0.8286 (pm20) REVERT: B 327 GLN cc_start: 0.8300 (OUTLIER) cc_final: 0.7884 (tp40) REVERT: B 427 MET cc_start: 0.7815 (tpp) cc_final: 0.7334 (tpp) REVERT: C 153 LEU cc_start: 0.5938 (OUTLIER) cc_final: 0.5570 (tt) REVERT: C 221 GLU cc_start: 0.8658 (OUTLIER) cc_final: 0.8344 (pm20) REVERT: C 427 MET cc_start: 0.7497 (tpt) cc_final: 0.7019 (tpp) REVERT: C 442 MET cc_start: 0.8764 (mmp) cc_final: 0.8382 (mmm) REVERT: C 445 LEU cc_start: 0.9006 (tt) cc_final: 0.8679 (mp) REVERT: D 153 LEU cc_start: 0.6151 (OUTLIER) cc_final: 0.5802 (tt) REVERT: E 36 ASN cc_start: 0.8282 (m-40) cc_final: 0.7650 (t0) REVERT: E 153 LEU cc_start: 0.6181 (OUTLIER) cc_final: 0.5689 (tt) REVERT: E 317 HIS cc_start: 0.6305 (p90) cc_final: 0.5897 (p90) REVERT: E 319 GLU cc_start: 0.7916 (OUTLIER) cc_final: 0.7631 (tm-30) REVERT: E 327 GLN cc_start: 0.8294 (OUTLIER) cc_final: 0.7858 (tp40) REVERT: E 427 MET cc_start: 0.7810 (tpp) cc_final: 0.7332 (tpp) REVERT: F 153 LEU cc_start: 0.5913 (OUTLIER) cc_final: 0.5552 (tt) REVERT: F 221 GLU cc_start: 0.8664 (OUTLIER) cc_final: 0.8358 (pm20) REVERT: F 327 GLN cc_start: 0.8265 (OUTLIER) cc_final: 0.7958 (tp40) REVERT: F 442 MET cc_start: 0.8761 (mmp) cc_final: 0.8451 (mmm) outliers start: 50 outliers final: 27 residues processed: 247 average time/residue: 0.7577 time to fit residues: 222.1685 Evaluate side-chains 225 residues out of total 3732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 184 time to evaluate : 1.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 319 GLU Chi-restraints excluded: chain B residue 94 VAL Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain B residue 153 LEU Chi-restraints excluded: chain B residue 221 GLU Chi-restraints excluded: chain B residue 282 SER Chi-restraints excluded: chain B residue 327 GLN Chi-restraints excluded: chain B residue 399 VAL Chi-restraints excluded: chain B residue 514 VAL Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 94 VAL Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain C residue 153 LEU Chi-restraints excluded: chain C residue 221 GLU Chi-restraints excluded: chain C residue 282 SER Chi-restraints excluded: chain C residue 364 ASP Chi-restraints excluded: chain C residue 399 VAL Chi-restraints excluded: chain C residue 514 VAL Chi-restraints excluded: chain D residue 94 VAL Chi-restraints excluded: chain D residue 123 VAL Chi-restraints excluded: chain D residue 153 LEU Chi-restraints excluded: chain E residue 94 VAL Chi-restraints excluded: chain E residue 123 VAL Chi-restraints excluded: chain E residue 153 LEU Chi-restraints excluded: chain E residue 282 SER Chi-restraints excluded: chain E residue 319 GLU Chi-restraints excluded: chain E residue 327 GLN Chi-restraints excluded: chain E residue 399 VAL Chi-restraints excluded: chain E residue 514 VAL Chi-restraints excluded: chain F residue 51 LEU Chi-restraints excluded: chain F residue 94 VAL Chi-restraints excluded: chain F residue 123 VAL Chi-restraints excluded: chain F residue 153 LEU Chi-restraints excluded: chain F residue 221 GLU Chi-restraints excluded: chain F residue 282 SER Chi-restraints excluded: chain F residue 327 GLN Chi-restraints excluded: chain F residue 364 ASP Chi-restraints excluded: chain F residue 514 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 55 optimal weight: 0.6980 chunk 103 optimal weight: 0.9990 chunk 379 optimal weight: 0.9980 chunk 383 optimal weight: 0.8980 chunk 19 optimal weight: 0.7980 chunk 403 optimal weight: 5.9990 chunk 357 optimal weight: 2.9990 chunk 306 optimal weight: 3.9990 chunk 322 optimal weight: 0.9990 chunk 287 optimal weight: 0.7980 chunk 177 optimal weight: 2.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 327 GLN ** C 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 327 GLN ** F 317 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 = 0.4181 r_free = 0.4181 target = 0.147138 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.096608 restraints weight = 58931.710| |-----------------------------------------------------------------------------| r_work (start): 0.3369 rms_B_bonded: 3.05 r_work: 0.3209 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3209 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8307 moved from start: 0.5564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 35304 Z= 0.137 Angle : 0.722 11.389 47730 Z= 0.343 Chirality : 0.045 0.199 5358 Planarity : 0.004 0.049 6270 Dihedral : 7.289 112.737 4902 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.98 % Favored : 94.02 % Rotamer: Outliers : 1.34 % Allowed : 21.62 % Favored : 77.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.14 % 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: 0.45 (0.13), residues: 4368 helix: 1.17 (0.13), residues: 1848 sheet: 0.64 (0.21), residues: 558 loop : -0.60 (0.14), residues: 1962 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 745 TYR 0.018 0.001 TYR B 244 PHE 0.013 0.001 PHE D 363 TRP 0.003 0.001 TRP F 476 HIS 0.009 0.001 HIS B 317 Details of bonding type rmsd covalent geometry : bond 0.00327 (35304) covalent geometry : angle 0.72186 (47730) hydrogen bonds : bond 0.03815 ( 1410) hydrogen bonds : angle 4.64106 ( 3978) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 15913.57 seconds wall clock time: 270 minutes 29.71 seconds (16229.71 seconds total)