Starting phenix.real_space_refine on Thu Jul 2 16:57:00 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7ekl_31169/07_2026/7ekl_31169.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ekl_31169/07_2026/7ekl_31169.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7ekl_31169/07_2026/7ekl_31169.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ekl_31169/07_2026/7ekl_31169.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7ekl_31169/07_2026/7ekl_31169.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7ekl_31169/07_2026/7ekl_31169.cif" model { file = "/net/cci-nas-00/data/ceres_data/7ekl_31169/07_2026/7ekl_31169.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ekl_31169/07_2026/7ekl_31169.cif" } resolution = 3.5 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= 0.004 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 6 5.49 5 Mg 2 5.21 5 S 34 5.16 5 C 6022 2.51 5 N 1624 2.21 5 O 1706 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 24 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 9394 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 4665 Number of conformers: 1 Conformer: "" Number of residues, atoms: 590, 4665 Classifications: {'peptide': 590} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 13, 'TRANS': 576} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'ARG:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 8 Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Restraints were copied for chains: B Time building chain proxies: 3.22, per 1000 atoms: 0.34 Number of scatterers: 9394 At special positions: 0 Unit cell: (88.27, 74.69, 138.71, 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 34 16.00 P 6 15.00 Mg 2 11.99 O 1706 8.00 N 1624 7.00 C 6022 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: 0.82 Conformation dependent library (CDL) restraints added in 209.5 milliseconds 2352 Ramachandran restraints generated. 1176 Oldfield, 0 Emsley, 1176 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2168 Finding SS restraints... Secondary structure from input PDB file: 70 helices and 4 sheets defined 60.8% alpha, 7.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.21 Creating SS restraints... Processing helix chain 'A' and resid 241 through 246 Processing helix chain 'A' and resid 248 through 253 removed outlier: 3.566A pdb=" N LEU A 253 " --> pdb=" O SER A 250 " (cutoff:3.500A) Processing helix chain 'A' and resid 258 through 263 removed outlier: 3.666A pdb=" N LEU A 263 " --> pdb=" O PRO A 259 " (cutoff:3.500A) Processing helix chain 'A' and resid 264 through 295 removed outlier: 3.560A pdb=" N GLY A 270 " --> pdb=" O LEU A 266 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ARG A 276 " --> pdb=" O MET A 272 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ALA A 277 " --> pdb=" O GLY A 273 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N VAL A 280 " --> pdb=" O ARG A 276 " (cutoff:3.500A) Proline residue: A 283 - end of helix removed outlier: 3.716A pdb=" N ILE A 289 " --> pdb=" O PHE A 285 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N VAL A 290 " --> pdb=" O TYR A 286 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N LEU A 293 " --> pdb=" O ILE A 289 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 317 removed outlier: 4.578A pdb=" N TRP A 304 " --> pdb=" O ASN A 300 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N THR A 305 " --> pdb=" O SER A 301 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N SER A 308 " --> pdb=" O TRP A 304 " (cutoff:3.500A) Processing helix chain 'A' and resid 328 through 335 removed outlier: 3.557A pdb=" N ILE A 335 " --> pdb=" O THR A 331 " (cutoff:3.500A) Processing helix chain 'A' and resid 337 through 347 removed outlier: 3.888A pdb=" N ARG A 343 " --> pdb=" O GLN A 339 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N GLU A 346 " --> pdb=" O SER A 342 " (cutoff:3.500A) Processing helix chain 'A' and resid 357 through 364 removed outlier: 3.759A pdb=" N HIS A 361 " --> pdb=" O SER A 357 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LEU A 362 " --> pdb=" O LEU A 358 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N GLY A 363 " --> pdb=" O ARG A 359 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 373 removed outlier: 3.537A pdb=" N ARG A 371 " --> pdb=" O GLY A 367 " (cutoff:3.500A) Processing helix chain 'A' and resid 376 through 385 removed outlier: 3.853A pdb=" N VAL A 380 " --> pdb=" O GLY A 376 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N THR A 381 " --> pdb=" O THR A 377 " (cutoff:3.500A) Processing helix chain 'A' and resid 391 through 404 Processing helix chain 'A' and resid 412 through 427 removed outlier: 3.662A pdb=" N VAL A 417 " --> pdb=" O PHE A 413 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N PHE A 418 " --> pdb=" O GLY A 414 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N MET A 421 " --> pdb=" O VAL A 417 " (cutoff:3.500A) Processing helix chain 'A' and resid 431 through 447 removed outlier: 5.053A pdb=" N LYS A 437 " --> pdb=" O GLU A 433 " (cutoff:3.500A) removed outlier: 5.110A pdb=" N PHE A 438 " --> pdb=" O TRP A 434 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ARG A 439 " --> pdb=" O ARG A 435 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ARG A 440 " --> pdb=" O THR A 436 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N ALA A 441 " --> pdb=" O LYS A 437 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N MET A 442 " --> pdb=" O PHE A 438 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ASN A 443 " --> pdb=" O ARG A 439 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N THR A 444 " --> pdb=" O ARG A 440 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N GLN A 445 " --> pdb=" O ALA A 441 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ASN A 447 " --> pdb=" O ASN A 443 " (cutoff:3.500A) Processing helix chain 'A' and resid 450 through 456 removed outlier: 3.738A pdb=" N ASP A 455 " --> pdb=" O ALA A 451 " (cutoff:3.500A) Processing helix chain 'A' and resid 459 through 466 removed outlier: 3.967A pdb=" N VAL A 463 " --> pdb=" O ASN A 459 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N TYR A 466 " --> pdb=" O THR A 462 " (cutoff:3.500A) Processing helix chain 'A' and resid 470 through 478 removed outlier: 3.879A pdb=" N TYR A 476 " --> pdb=" O GLU A 472 " (cutoff:3.500A) Processing helix chain 'A' and resid 480 through 485 Processing helix chain 'A' and resid 487 through 492 Processing helix chain 'A' and resid 493 through 499 Processing helix chain 'A' and resid 501 through 522 removed outlier: 3.564A pdb=" N LEU A 510 " --> pdb=" O GLY A 506 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N LEU A 515 " --> pdb=" O ALA A 511 " (cutoff:3.500A) Processing helix chain 'A' and resid 526 through 535 Processing helix chain 'A' and resid 536 through 541 Processing helix chain 'A' and resid 542 through 547 Processing helix chain 'A' and resid 550 through 569 removed outlier: 3.969A pdb=" N THR A 556 " --> pdb=" O ARG A 552 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ASN A 557 " --> pdb=" O MET A 553 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N MET A 561 " --> pdb=" O ASN A 557 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N MET A 564 " --> pdb=" O ASP A 560 " (cutoff:3.500A) Processing helix chain 'A' and resid 628 through 636 removed outlier: 3.628A pdb=" N ILE A 632 " --> pdb=" O GLY A 628 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N LEU A 633 " --> pdb=" O LYS A 629 " (cutoff:3.500A) Processing helix chain 'A' and resid 658 through 663 removed outlier: 3.554A pdb=" N ARG A 663 " --> pdb=" O GLN A 659 " (cutoff:3.500A) Processing helix chain 'A' and resid 679 through 685 removed outlier: 3.546A pdb=" N ARG A 685 " --> pdb=" O ALA A 681 " (cutoff:3.500A) Processing helix chain 'A' and resid 692 through 700 removed outlier: 3.515A pdb=" N ALA A 698 " --> pdb=" O ASP A 694 " (cutoff:3.500A) Processing helix chain 'A' and resid 705 through 710 removed outlier: 3.945A pdb=" N MET A 710 " --> pdb=" O HIS A 706 " (cutoff:3.500A) Processing helix chain 'A' and resid 714 through 718 removed outlier: 3.784A pdb=" N ARG A 717 " --> pdb=" O GLU A 714 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N THR A 718 " --> pdb=" O GLY A 715 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 714 through 718' Processing helix chain 'A' and resid 721 through 725 removed outlier: 3.722A pdb=" N GLY A 724 " --> pdb=" O GLY A 721 " (cutoff:3.500A) Processing helix chain 'A' and resid 730 through 744 removed outlier: 3.708A pdb=" N VAL A 735 " --> pdb=" O GLU A 731 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N ALA A 736 " --> pdb=" O LYS A 732 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N THR A 740 " --> pdb=" O ALA A 736 " (cutoff:3.500A) Processing helix chain 'A' and resid 762 through 770 removed outlier: 3.854A pdb=" N SER A 768 " --> pdb=" O ALA A 764 " (cutoff:3.500A) Processing helix chain 'A' and resid 808 through 813 removed outlier: 3.513A pdb=" N SER A 813 " --> pdb=" O GLU A 809 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 827 removed outlier: 3.761A pdb=" N GLN A 825 " --> pdb=" O MET A 821 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N GLY A 827 " --> pdb=" O GLN A 823 " (cutoff:3.500A) Processing helix chain 'B' and resid 241 through 246 Processing helix chain 'B' and resid 248 through 253 removed outlier: 3.565A pdb=" N LEU B 253 " --> pdb=" O SER B 250 " (cutoff:3.500A) Processing helix chain 'B' and resid 258 through 263 removed outlier: 3.667A pdb=" N LEU B 263 " --> pdb=" O PRO B 259 " (cutoff:3.500A) Processing helix chain 'B' and resid 264 through 295 removed outlier: 3.560A pdb=" N GLY B 270 " --> pdb=" O LEU B 266 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ARG B 276 " --> pdb=" O MET B 272 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ALA B 277 " --> pdb=" O GLY B 273 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N VAL B 280 " --> pdb=" O ARG B 276 " (cutoff:3.500A) Proline residue: B 283 - end of helix removed outlier: 3.716A pdb=" N ILE B 289 " --> pdb=" O PHE B 285 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N VAL B 290 " --> pdb=" O TYR B 286 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N LEU B 293 " --> pdb=" O ILE B 289 " (cutoff:3.500A) Processing helix chain 'B' and resid 298 through 317 removed outlier: 4.578A pdb=" N TRP B 304 " --> pdb=" O ASN B 300 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N THR B 305 " --> pdb=" O SER B 301 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N SER B 308 " --> pdb=" O TRP B 304 " (cutoff:3.500A) Processing helix chain 'B' and resid 328 through 335 removed outlier: 3.557A pdb=" N ILE B 335 " --> pdb=" O THR B 331 " (cutoff:3.500A) Processing helix chain 'B' and resid 337 through 347 removed outlier: 3.888A pdb=" N ARG B 343 " --> pdb=" O GLN B 339 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N GLU B 346 " --> pdb=" O SER B 342 " (cutoff:3.500A) Processing helix chain 'B' and resid 357 through 364 removed outlier: 3.759A pdb=" N HIS B 361 " --> pdb=" O SER B 357 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LEU B 362 " --> pdb=" O LEU B 358 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N GLY B 363 " --> pdb=" O ARG B 359 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 373 removed outlier: 3.537A pdb=" N ARG B 371 " --> pdb=" O GLY B 367 " (cutoff:3.500A) Processing helix chain 'B' and resid 376 through 385 removed outlier: 3.853A pdb=" N VAL B 380 " --> pdb=" O GLY B 376 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N THR B 381 " --> pdb=" O THR B 377 " (cutoff:3.500A) Processing helix chain 'B' and resid 391 through 404 Processing helix chain 'B' and resid 412 through 427 removed outlier: 3.662A pdb=" N VAL B 417 " --> pdb=" O PHE B 413 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N PHE B 418 " --> pdb=" O GLY B 414 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N MET B 421 " --> pdb=" O VAL B 417 " (cutoff:3.500A) Processing helix chain 'B' and resid 431 through 447 removed outlier: 5.053A pdb=" N LYS B 437 " --> pdb=" O GLU B 433 " (cutoff:3.500A) removed outlier: 5.110A pdb=" N PHE B 438 " --> pdb=" O TRP B 434 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ARG B 439 " --> pdb=" O ARG B 435 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ARG B 440 " --> pdb=" O THR B 436 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N ALA B 441 " --> pdb=" O LYS B 437 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N MET B 442 " --> pdb=" O PHE B 438 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ASN B 443 " --> pdb=" O ARG B 439 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N THR B 444 " --> pdb=" O ARG B 440 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N GLN B 445 " --> pdb=" O ALA B 441 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ASN B 447 " --> pdb=" O ASN B 443 " (cutoff:3.500A) Processing helix chain 'B' and resid 450 through 456 removed outlier: 3.738A pdb=" N ASP B 455 " --> pdb=" O ALA B 451 " (cutoff:3.500A) Processing helix chain 'B' and resid 459 through 466 removed outlier: 3.966A pdb=" N VAL B 463 " --> pdb=" O ASN B 459 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N TYR B 466 " --> pdb=" O THR B 462 " (cutoff:3.500A) Processing helix chain 'B' and resid 470 through 478 removed outlier: 3.879A pdb=" N TYR B 476 " --> pdb=" O GLU B 472 " (cutoff:3.500A) Processing helix chain 'B' and resid 480 through 485 Processing helix chain 'B' and resid 487 through 492 Processing helix chain 'B' and resid 493 through 499 Processing helix chain 'B' and resid 501 through 522 removed outlier: 3.563A pdb=" N LEU B 510 " --> pdb=" O GLY B 506 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N LEU B 515 " --> pdb=" O ALA B 511 " (cutoff:3.500A) Processing helix chain 'B' and resid 526 through 535 Processing helix chain 'B' and resid 536 through 541 Processing helix chain 'B' and resid 542 through 547 Processing helix chain 'B' and resid 550 through 569 removed outlier: 3.969A pdb=" N THR B 556 " --> pdb=" O ARG B 552 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ASN B 557 " --> pdb=" O MET B 553 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N MET B 561 " --> pdb=" O ASN B 557 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N MET B 564 " --> pdb=" O ASP B 560 " (cutoff:3.500A) Processing helix chain 'B' and resid 628 through 636 removed outlier: 3.627A pdb=" N ILE B 632 " --> pdb=" O GLY B 628 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N LEU B 633 " --> pdb=" O LYS B 629 " (cutoff:3.500A) Processing helix chain 'B' and resid 658 through 663 removed outlier: 3.554A pdb=" N ARG B 663 " --> pdb=" O GLN B 659 " (cutoff:3.500A) Processing helix chain 'B' and resid 679 through 685 removed outlier: 3.546A pdb=" N ARG B 685 " --> pdb=" O ALA B 681 " (cutoff:3.500A) Processing helix chain 'B' and resid 692 through 700 removed outlier: 3.514A pdb=" N ALA B 698 " --> pdb=" O ASP B 694 " (cutoff:3.500A) Processing helix chain 'B' and resid 705 through 710 removed outlier: 3.945A pdb=" N MET B 710 " --> pdb=" O HIS B 706 " (cutoff:3.500A) Processing helix chain 'B' and resid 714 through 718 removed outlier: 3.784A pdb=" N ARG B 717 " --> pdb=" O GLU B 714 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N THR B 718 " --> pdb=" O GLY B 715 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 714 through 718' Processing helix chain 'B' and resid 721 through 725 removed outlier: 3.722A pdb=" N GLY B 724 " --> pdb=" O GLY B 721 " (cutoff:3.500A) Processing helix chain 'B' and resid 730 through 744 removed outlier: 3.708A pdb=" N VAL B 735 " --> pdb=" O GLU B 731 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N ALA B 736 " --> pdb=" O LYS B 732 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N THR B 740 " --> pdb=" O ALA B 736 " (cutoff:3.500A) Processing helix chain 'B' and resid 762 through 770 removed outlier: 3.853A pdb=" N SER B 768 " --> pdb=" O ALA B 764 " (cutoff:3.500A) Processing helix chain 'B' and resid 808 through 813 removed outlier: 3.513A pdb=" N SER B 813 " --> pdb=" O GLU B 809 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 827 removed outlier: 3.760A pdb=" N GLN B 825 " --> pdb=" O MET B 821 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N GLY B 827 " --> pdb=" O GLN B 823 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 606 through 613 removed outlier: 7.088A pdb=" N GLN A 607 " --> pdb=" O HIS A 596 " (cutoff:3.500A) removed outlier: 7.064A pdb=" N HIS A 596 " --> pdb=" O GLN A 607 " (cutoff:3.500A) removed outlier: 5.615A pdb=" N VAL A 609 " --> pdb=" O ASN A 594 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N PHE A 611 " --> pdb=" O PHE A 592 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N VAL A 595 " --> pdb=" O SER A 644 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N SER A 644 " --> pdb=" O VAL A 595 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 666 through 669 removed outlier: 5.924A pdb=" N LEU A 619 " --> pdb=" O VAL A 780 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N THR A 618 " --> pdb=" O GLN A 793 " (cutoff:3.500A) removed outlier: 8.067A pdb=" N LEU A 795 " --> pdb=" O THR A 618 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N ALA A 620 " --> pdb=" O LEU A 795 " (cutoff:3.500A) removed outlier: 7.479A pdb=" N ILE A 797 " --> pdb=" O ALA A 620 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N VAL A 622 " --> pdb=" O ILE A 797 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N GLU A 804 " --> pdb=" O VAL A 796 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 606 through 613 removed outlier: 7.088A pdb=" N GLN B 607 " --> pdb=" O HIS B 596 " (cutoff:3.500A) removed outlier: 7.064A pdb=" N HIS B 596 " --> pdb=" O GLN B 607 " (cutoff:3.500A) removed outlier: 5.615A pdb=" N VAL B 609 " --> pdb=" O ASN B 594 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N PHE B 611 " --> pdb=" O PHE B 592 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N VAL B 595 " --> pdb=" O SER B 644 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N SER B 644 " --> pdb=" O VAL B 595 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 666 through 669 removed outlier: 5.924A pdb=" N LEU B 619 " --> pdb=" O VAL B 780 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N THR B 618 " --> pdb=" O GLN B 793 " (cutoff:3.500A) removed outlier: 8.067A pdb=" N LEU B 795 " --> pdb=" O THR B 618 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N ALA B 620 " --> pdb=" O LEU B 795 " (cutoff:3.500A) removed outlier: 7.479A pdb=" N ILE B 797 " --> pdb=" O ALA B 620 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N VAL B 622 " --> pdb=" O ILE B 797 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N GLU B 804 " --> pdb=" O VAL B 796 " (cutoff:3.500A) 358 hydrogen bonds defined for protein. 1044 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: 1.50 Time building geometry restraints manager: 1.03 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1985 1.33 - 1.45: 2196 1.45 - 1.57: 5335 1.57 - 1.69: 10 1.69 - 1.81: 56 Bond restraints: 9582 Sorted by residual: bond pdb=" C4 ATP B 901 " pdb=" C5 ATP B 901 " ideal model delta sigma weight residual 1.388 1.468 -0.080 1.00e-02 1.00e+04 6.42e+01 bond pdb=" C4 ATP A 901 " pdb=" C5 ATP A 901 " ideal model delta sigma weight residual 1.388 1.467 -0.079 1.00e-02 1.00e+04 6.30e+01 bond pdb=" C5 ATP B 901 " pdb=" C6 ATP B 901 " ideal model delta sigma weight residual 1.409 1.478 -0.069 1.00e-02 1.00e+04 4.77e+01 bond pdb=" C5 ATP A 901 " pdb=" C6 ATP A 901 " ideal model delta sigma weight residual 1.409 1.478 -0.069 1.00e-02 1.00e+04 4.77e+01 bond pdb=" C8 ATP B 901 " pdb=" N7 ATP B 901 " ideal model delta sigma weight residual 1.310 1.354 -0.044 1.00e-02 1.00e+04 1.98e+01 ... (remaining 9577 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.58: 12848 3.58 - 7.15: 140 7.15 - 10.73: 20 10.73 - 14.31: 0 14.31 - 17.88: 4 Bond angle restraints: 13012 Sorted by residual: angle pdb=" PA ATP B 901 " pdb=" O3A ATP B 901 " pdb=" PB ATP B 901 " ideal model delta sigma weight residual 136.83 118.95 17.88 1.00e+00 1.00e+00 3.20e+02 angle pdb=" PA ATP A 901 " pdb=" O3A ATP A 901 " pdb=" PB ATP A 901 " ideal model delta sigma weight residual 136.83 118.96 17.87 1.00e+00 1.00e+00 3.19e+02 angle pdb=" PB ATP A 901 " pdb=" O3B ATP A 901 " pdb=" PG ATP A 901 " ideal model delta sigma weight residual 139.87 123.78 16.09 1.00e+00 1.00e+00 2.59e+02 angle pdb=" PB ATP B 901 " pdb=" O3B ATP B 901 " pdb=" PG ATP B 901 " ideal model delta sigma weight residual 139.87 123.79 16.08 1.00e+00 1.00e+00 2.59e+02 angle pdb=" C5 ATP A 901 " pdb=" C4 ATP A 901 " pdb=" N3 ATP A 901 " ideal model delta sigma weight residual 126.80 118.75 8.05 1.00e+00 1.00e+00 6.49e+01 ... (remaining 13007 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.91: 5260 14.91 - 29.82: 254 29.82 - 44.73: 78 44.73 - 59.65: 4 59.65 - 74.56: 8 Dihedral angle restraints: 5604 sinusoidal: 2214 harmonic: 3390 Sorted by residual: dihedral pdb=" CA MET A 553 " pdb=" C MET A 553 " pdb=" N ILE A 554 " pdb=" CA ILE A 554 " ideal model delta harmonic sigma weight residual 180.00 155.99 24.01 0 5.00e+00 4.00e-02 2.31e+01 dihedral pdb=" CA MET B 553 " pdb=" C MET B 553 " pdb=" N ILE B 554 " pdb=" CA ILE B 554 " ideal model delta harmonic sigma weight residual 180.00 156.02 23.98 0 5.00e+00 4.00e-02 2.30e+01 dihedral pdb=" CA ILE A 267 " pdb=" C ILE A 267 " pdb=" N CYS A 268 " pdb=" CA CYS A 268 " ideal model delta harmonic sigma weight residual 180.00 157.02 22.98 0 5.00e+00 4.00e-02 2.11e+01 ... (remaining 5601 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 1061 0.044 - 0.087: 311 0.087 - 0.131: 99 0.131 - 0.175: 20 0.175 - 0.219: 5 Chirality restraints: 1496 Sorted by residual: chirality pdb=" CA GLU A 469 " pdb=" N GLU A 469 " pdb=" C GLU A 469 " pdb=" CB GLU A 469 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.20e+00 chirality pdb=" CA GLU B 469 " pdb=" N GLU B 469 " pdb=" C GLU B 469 " pdb=" CB GLU B 469 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.19e+00 chirality pdb=" CA LYS B 464 " pdb=" N LYS B 464 " pdb=" C LYS B 464 " pdb=" CB LYS B 464 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.15e+00 ... (remaining 1493 not shown) Planarity restraints: 1632 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU A 727 " -0.009 2.00e-02 2.50e+03 1.84e-02 3.40e+00 pdb=" C LEU A 727 " 0.032 2.00e-02 2.50e+03 pdb=" O LEU A 727 " -0.012 2.00e-02 2.50e+03 pdb=" N SER A 728 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU B 727 " -0.009 2.00e-02 2.50e+03 1.84e-02 3.38e+00 pdb=" C LEU B 727 " 0.032 2.00e-02 2.50e+03 pdb=" O LEU B 727 " -0.012 2.00e-02 2.50e+03 pdb=" N SER B 728 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER A 258 " -0.030 5.00e-02 4.00e+02 4.59e-02 3.37e+00 pdb=" N PRO A 259 " 0.079 5.00e-02 4.00e+02 pdb=" CA PRO A 259 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO A 259 " -0.026 5.00e-02 4.00e+02 ... (remaining 1629 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 345 2.69 - 3.24: 8586 3.24 - 3.80: 14100 3.80 - 4.35: 19732 4.35 - 4.90: 31676 Nonbonded interactions: 74439 Sorted by model distance: nonbonded pdb=" OE1 GLN A 671 " pdb="MG MG A 902 " model vdw 2.141 2.170 nonbonded pdb=" OE1 GLN B 671 " pdb="MG MG B 902 " model vdw 2.141 2.170 nonbonded pdb=" O1G ATP A 901 " pdb="MG MG A 902 " model vdw 2.160 2.170 nonbonded pdb=" O1G ATP B 901 " pdb="MG MG B 902 " model vdw 2.161 2.170 nonbonded pdb=" OG SER A 630 " pdb="MG MG A 902 " model vdw 2.216 2.170 ... (remaining 74434 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } 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 group one per residue 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: 0.620 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.120 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 9.950 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.010 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:0.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8348 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 0.080 9582 Z= 0.308 Angle : 1.133 17.881 13012 Z= 0.754 Chirality : 0.048 0.219 1496 Planarity : 0.005 0.046 1632 Dihedral : 10.534 74.557 3436 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.17 % Allowed : 2.89 % Favored : 96.94 % Rotamer: Outliers : 0.81 % Allowed : 5.24 % Favored : 93.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -5.70 (0.17), residues: 1176 helix: -4.63 (0.08), residues: 716 sheet: -0.16 (0.61), residues: 82 loop : -2.26 (0.25), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 365 TYR 0.031 0.002 TYR B 551 PHE 0.022 0.003 PHE B 639 TRP 0.023 0.002 TRP B 488 HIS 0.007 0.002 HIS A 354 Details of bonding type rmsd/Z covalent geometry : bond 0.00508 / 0.31 ( 9582) covalent geometry : angle 1.13341 / 0.75 (13012) hydrogen bonds : bond 0.32485 / 20.81 ( 358) hydrogen bonds : angle 10.21563 / 7.02 ( 1044) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2352 Ramachandran restraints generated. 1176 Oldfield, 0 Emsley, 1176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2352 Ramachandran restraints generated. 1176 Oldfield, 0 Emsley, 1176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 213 time to evaluate : 0.234 Fit side-chains REVERT: A 455 ASP cc_start: 0.7905 (t70) cc_final: 0.7619 (t0) REVERT: A 491 SER cc_start: 0.9230 (t) cc_final: 0.8850 (m) REVERT: A 518 TYR cc_start: 0.8572 (t80) cc_final: 0.8133 (t80) REVERT: A 759 THR cc_start: 0.8355 (t) cc_final: 0.8120 (p) REVERT: B 455 ASP cc_start: 0.7960 (t70) cc_final: 0.7648 (t0) REVERT: B 491 SER cc_start: 0.9181 (t) cc_final: 0.8792 (m) REVERT: B 518 TYR cc_start: 0.8492 (t80) cc_final: 0.8064 (t80) REVERT: B 563 ASN cc_start: 0.8150 (m110) cc_final: 0.7897 (m110) REVERT: B 759 THR cc_start: 0.8406 (t) cc_final: 0.8082 (p) outliers start: 8 outliers final: 2 residues processed: 217 average time/residue: 0.1072 time to fit residues: 30.3591 Evaluate side-chains 99 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 97 time to evaluate : 0.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 781 VAL Chi-restraints excluded: chain B residue 781 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 108 optimal weight: 0.0570 chunk 49 optimal weight: 4.9990 chunk 97 optimal weight: 2.9990 chunk 113 optimal weight: 3.9990 chunk 53 optimal weight: 0.9990 chunk 5 optimal weight: 0.9990 chunk 33 optimal weight: 6.9990 chunk 65 optimal weight: 7.9990 chunk 62 optimal weight: 0.8980 chunk 51 optimal weight: 0.9990 chunk 117 optimal weight: 9.9990 overall best weight: 0.7904 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 279 ASN A 316 GLN A 498 ASN A 563 ASN A 596 HIS A 607 GLN A 752 GLN A 766 GLN B 279 ASN B 316 GLN B 498 ASN B 596 HIS B 607 GLN B 752 GLN B 766 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.130477 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.111447 restraints weight = 12625.836| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.114427 restraints weight = 6917.247| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.116334 restraints weight = 4673.346| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.117664 restraints weight = 3617.744| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.118506 restraints weight = 3039.153| |-----------------------------------------------------------------------------| r_work (final): 0.3260 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8355 moved from start: 0.2393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 9582 Z= 0.117 Angle : 0.572 7.417 13012 Z= 0.311 Chirality : 0.040 0.134 1496 Planarity : 0.004 0.034 1632 Dihedral : 6.428 76.226 1312 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 2.72 % Allowed : 8.57 % Favored : 88.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.89 (0.19), residues: 1176 helix: -3.10 (0.14), residues: 706 sheet: 0.01 (0.56), residues: 82 loop : -1.65 (0.26), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 648 TYR 0.013 0.002 TYR A 465 PHE 0.012 0.002 PHE B 592 TRP 0.012 0.001 TRP A 822 HIS 0.004 0.001 HIS A 808 Details of bonding type rmsd/Z covalent geometry : bond 0.00260 / 0.12 ( 9582) covalent geometry : angle 0.57250 / 0.31 (13012) hydrogen bonds : bond 0.04422 / 2.87 ( 358) hydrogen bonds : angle 5.19039 / 3.50 ( 1044) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2352 Ramachandran restraints generated. 1176 Oldfield, 0 Emsley, 1176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2352 Ramachandran restraints generated. 1176 Oldfield, 0 Emsley, 1176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 116 time to evaluate : 0.242 Fit side-chains REVERT: A 346 GLU cc_start: 0.7851 (tp30) cc_final: 0.7363 (tp30) REVERT: A 455 ASP cc_start: 0.7976 (t70) cc_final: 0.7719 (t0) REVERT: A 503 LEU cc_start: 0.8479 (OUTLIER) cc_final: 0.8040 (tp) REVERT: A 553 MET cc_start: 0.7247 (ptm) cc_final: 0.7027 (ptm) REVERT: A 759 THR cc_start: 0.8401 (t) cc_final: 0.8139 (p) REVERT: B 346 GLU cc_start: 0.7858 (tp30) cc_final: 0.7438 (tp30) REVERT: B 455 ASP cc_start: 0.7920 (t70) cc_final: 0.7508 (t0) REVERT: B 503 LEU cc_start: 0.8395 (OUTLIER) cc_final: 0.8066 (tp) REVERT: B 553 MET cc_start: 0.7173 (ptm) cc_final: 0.6965 (ptm) REVERT: B 614 MET cc_start: 0.8206 (mmm) cc_final: 0.7938 (mmm) outliers start: 27 outliers final: 9 residues processed: 137 average time/residue: 0.0772 time to fit residues: 15.2208 Evaluate side-chains 101 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 90 time to evaluate : 0.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 496 LEU Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 669 VAL Chi-restraints excluded: chain A residue 680 ILE Chi-restraints excluded: chain A residue 781 VAL Chi-restraints excluded: chain B residue 496 LEU Chi-restraints excluded: chain B residue 503 LEU Chi-restraints excluded: chain B residue 669 VAL Chi-restraints excluded: chain B residue 680 ILE Chi-restraints excluded: chain B residue 781 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 105 optimal weight: 5.9990 chunk 86 optimal weight: 4.9990 chunk 61 optimal weight: 2.9990 chunk 67 optimal weight: 5.9990 chunk 78 optimal weight: 7.9990 chunk 104 optimal weight: 4.9990 chunk 18 optimal weight: 3.9990 chunk 91 optimal weight: 4.9990 chunk 2 optimal weight: 0.6980 chunk 76 optimal weight: 4.9990 chunk 5 optimal weight: 4.9990 overall best weight: 3.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 498 ASN A 607 GLN A 683 ASN A 752 GLN B 498 ASN B 607 GLN B 683 ASN B 752 GLN B 766 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.109581 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2890 r_free = 0.2890 target = 0.088413 restraints weight = 13306.822| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2927 r_free = 0.2927 target = 0.091078 restraints weight = 7819.018| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.2952 r_free = 0.2952 target = 0.092867 restraints weight = 5549.238| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2968 r_free = 0.2968 target = 0.093991 restraints weight = 4438.050| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.2979 r_free = 0.2979 target = 0.094766 restraints weight = 3843.688| |-----------------------------------------------------------------------------| r_work (final): 0.2989 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8536 moved from start: 0.3146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.064 9582 Z= 0.299 Angle : 0.673 7.188 13012 Z= 0.357 Chirality : 0.046 0.148 1496 Planarity : 0.004 0.036 1632 Dihedral : 6.256 58.005 1312 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 3.83 % Allowed : 9.48 % Favored : 86.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.87 (0.22), residues: 1176 helix: -2.26 (0.17), residues: 722 sheet: 1.35 (0.68), residues: 50 loop : -1.24 (0.28), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 739 TYR 0.020 0.002 TYR A 476 PHE 0.018 0.002 PHE A 676 TRP 0.010 0.001 TRP B 488 HIS 0.004 0.002 HIS B 354 Details of bonding type rmsd/Z covalent geometry : bond 0.00724 / 0.30 ( 9582) covalent geometry : angle 0.67253 / 0.36 (13012) hydrogen bonds : bond 0.04583 / 2.93 ( 358) hydrogen bonds : angle 4.94511 / 3.31 ( 1044) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2352 Ramachandran restraints generated. 1176 Oldfield, 0 Emsley, 1176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2352 Ramachandran restraints generated. 1176 Oldfield, 0 Emsley, 1176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 92 time to evaluate : 0.354 Fit side-chains REVERT: A 346 GLU cc_start: 0.7928 (tp30) cc_final: 0.7384 (tp30) REVERT: A 486 LEU cc_start: 0.8834 (OUTLIER) cc_final: 0.8634 (tt) REVERT: A 503 LEU cc_start: 0.8639 (OUTLIER) cc_final: 0.8220 (tp) REVERT: A 759 THR cc_start: 0.8692 (t) cc_final: 0.8408 (p) REVERT: A 804 GLU cc_start: 0.7743 (OUTLIER) cc_final: 0.7498 (pm20) REVERT: B 322 SER cc_start: 0.8785 (t) cc_final: 0.8321 (p) REVERT: B 346 GLU cc_start: 0.7860 (tp30) cc_final: 0.7374 (tp30) REVERT: B 486 LEU cc_start: 0.8784 (OUTLIER) cc_final: 0.8544 (tt) REVERT: B 503 LEU cc_start: 0.8574 (OUTLIER) cc_final: 0.8200 (tp) REVERT: B 614 MET cc_start: 0.8227 (mmm) cc_final: 0.7957 (mmm) REVERT: B 804 GLU cc_start: 0.7731 (OUTLIER) cc_final: 0.7505 (pm20) REVERT: B 822 TRP cc_start: 0.9094 (t-100) cc_final: 0.8873 (t-100) outliers start: 38 outliers final: 20 residues processed: 127 average time/residue: 0.0711 time to fit residues: 13.2436 Evaluate side-chains 105 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 79 time to evaluate : 0.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 263 LEU Chi-restraints excluded: chain A residue 267 ILE Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain A residue 426 THR Chi-restraints excluded: chain A residue 469 GLU Chi-restraints excluded: chain A residue 486 LEU Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 668 VAL Chi-restraints excluded: chain A residue 669 VAL Chi-restraints excluded: chain A residue 680 ILE Chi-restraints excluded: chain A residue 781 VAL Chi-restraints excluded: chain A residue 804 GLU Chi-restraints excluded: chain B residue 263 LEU Chi-restraints excluded: chain B residue 267 ILE Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 425 LEU Chi-restraints excluded: chain B residue 426 THR Chi-restraints excluded: chain B residue 486 LEU Chi-restraints excluded: chain B residue 503 LEU Chi-restraints excluded: chain B residue 668 VAL Chi-restraints excluded: chain B residue 669 VAL Chi-restraints excluded: chain B residue 680 ILE Chi-restraints excluded: chain B residue 781 VAL Chi-restraints excluded: chain B residue 804 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 60 optimal weight: 3.9990 chunk 8 optimal weight: 0.8980 chunk 55 optimal weight: 10.0000 chunk 117 optimal weight: 0.9980 chunk 108 optimal weight: 0.8980 chunk 63 optimal weight: 0.7980 chunk 102 optimal weight: 0.9990 chunk 57 optimal weight: 8.9990 chunk 114 optimal weight: 1.9990 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 2.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 498 ASN A 752 GLN B 498 ASN B 752 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.115726 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2986 r_free = 0.2986 target = 0.094556 restraints weight = 13075.408| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.097401 restraints weight = 7477.481| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.099321 restraints weight = 5223.688| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.100569 restraints weight = 4125.371| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.101361 restraints weight = 3527.007| |-----------------------------------------------------------------------------| r_work (final): 0.3082 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8450 moved from start: 0.3344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 9582 Z= 0.100 Angle : 0.516 10.389 13012 Z= 0.264 Chirality : 0.040 0.127 1496 Planarity : 0.003 0.024 1632 Dihedral : 5.313 36.808 1312 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 3.43 % Allowed : 11.49 % Favored : 85.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.16 (0.23), residues: 1176 helix: -1.53 (0.19), residues: 724 sheet: 0.29 (0.55), residues: 82 loop : -1.20 (0.29), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 648 TYR 0.009 0.001 TYR B 530 PHE 0.007 0.001 PHE A 676 TRP 0.006 0.001 TRP A 822 HIS 0.004 0.001 HIS B 808 Details of bonding type rmsd/Z covalent geometry : bond 0.00229 / 0.10 ( 9582) covalent geometry : angle 0.51642 / 0.26 (13012) hydrogen bonds : bond 0.02982 / 1.93 ( 358) hydrogen bonds : angle 4.36274 / 2.90 ( 1044) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2352 Ramachandran restraints generated. 1176 Oldfield, 0 Emsley, 1176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2352 Ramachandran restraints generated. 1176 Oldfield, 0 Emsley, 1176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 107 time to evaluate : 0.295 Fit side-chains REVERT: A 346 GLU cc_start: 0.7940 (tp30) cc_final: 0.7515 (tp30) REVERT: A 455 ASP cc_start: 0.8206 (t70) cc_final: 0.7449 (t0) REVERT: A 503 LEU cc_start: 0.8484 (OUTLIER) cc_final: 0.8101 (tp) REVERT: A 603 ARG cc_start: 0.6831 (ptm160) cc_final: 0.6506 (ttp-170) REVERT: A 804 GLU cc_start: 0.7680 (OUTLIER) cc_final: 0.7465 (pm20) REVERT: B 322 SER cc_start: 0.8653 (t) cc_final: 0.8113 (p) REVERT: B 346 GLU cc_start: 0.7852 (tp30) cc_final: 0.7497 (tp30) REVERT: B 455 ASP cc_start: 0.8190 (t70) cc_final: 0.7446 (t0) REVERT: B 486 LEU cc_start: 0.8734 (OUTLIER) cc_final: 0.8492 (tt) REVERT: B 503 LEU cc_start: 0.8425 (OUTLIER) cc_final: 0.8105 (tp) REVERT: B 603 ARG cc_start: 0.6810 (ptm160) cc_final: 0.6508 (ttp-170) REVERT: B 614 MET cc_start: 0.8152 (mmm) cc_final: 0.7949 (mmm) REVERT: B 804 GLU cc_start: 0.7646 (OUTLIER) cc_final: 0.7439 (pm20) outliers start: 34 outliers final: 19 residues processed: 136 average time/residue: 0.0683 time to fit residues: 14.2778 Evaluate side-chains 111 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 87 time to evaluate : 0.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 267 ILE Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 668 VAL Chi-restraints excluded: chain A residue 669 VAL Chi-restraints excluded: chain A residue 680 ILE Chi-restraints excluded: chain A residue 710 MET Chi-restraints excluded: chain A residue 781 VAL Chi-restraints excluded: chain A residue 804 GLU Chi-restraints excluded: chain B residue 267 ILE Chi-restraints excluded: chain B residue 425 LEU Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain B residue 486 LEU Chi-restraints excluded: chain B residue 503 LEU Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 668 VAL Chi-restraints excluded: chain B residue 669 VAL Chi-restraints excluded: chain B residue 680 ILE Chi-restraints excluded: chain B residue 710 MET Chi-restraints excluded: chain B residue 781 VAL Chi-restraints excluded: chain B residue 804 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 58 optimal weight: 0.9980 chunk 114 optimal weight: 0.3980 chunk 89 optimal weight: 0.7980 chunk 68 optimal weight: 0.8980 chunk 22 optimal weight: 0.0970 chunk 8 optimal weight: 4.9990 chunk 53 optimal weight: 2.9990 chunk 32 optimal weight: 3.9990 chunk 48 optimal weight: 3.9990 chunk 9 optimal weight: 0.8980 chunk 91 optimal weight: 2.9990 overall best weight: 0.6178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 766 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.118865 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.097841 restraints weight = 12789.178| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.100536 restraints weight = 7525.281| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.102365 restraints weight = 5344.875| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.103486 restraints weight = 4281.572| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.104257 restraints weight = 3712.860| |-----------------------------------------------------------------------------| r_work (final): 0.3104 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8459 moved from start: 0.3558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 9582 Z= 0.087 Angle : 0.488 8.591 13012 Z= 0.247 Chirality : 0.039 0.128 1496 Planarity : 0.002 0.023 1632 Dihedral : 4.866 33.515 1312 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 3.02 % Allowed : 13.21 % Favored : 83.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.60 (0.24), residues: 1176 helix: -1.07 (0.20), residues: 732 sheet: 0.53 (0.55), residues: 82 loop : -1.02 (0.30), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 648 TYR 0.008 0.001 TYR B 530 PHE 0.007 0.001 PHE A 676 TRP 0.009 0.001 TRP B 822 HIS 0.005 0.001 HIS B 808 Details of bonding type rmsd/Z covalent geometry : bond 0.00197 / 0.09 ( 9582) covalent geometry : angle 0.48808 / 0.25 (13012) hydrogen bonds : bond 0.02682 / 1.74 ( 358) hydrogen bonds : angle 4.08431 / 2.71 ( 1044) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2352 Ramachandran restraints generated. 1176 Oldfield, 0 Emsley, 1176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2352 Ramachandran restraints generated. 1176 Oldfield, 0 Emsley, 1176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 101 time to evaluate : 0.324 Fit side-chains REVERT: A 455 ASP cc_start: 0.8269 (t70) cc_final: 0.7544 (t0) REVERT: A 503 LEU cc_start: 0.8462 (OUTLIER) cc_final: 0.8081 (tp) REVERT: A 603 ARG cc_start: 0.6691 (ptm160) cc_final: 0.6449 (ttp-170) REVERT: B 322 SER cc_start: 0.8458 (t) cc_final: 0.8088 (p) REVERT: B 455 ASP cc_start: 0.8257 (t70) cc_final: 0.7573 (t0) REVERT: B 486 LEU cc_start: 0.8764 (OUTLIER) cc_final: 0.8551 (tt) REVERT: B 503 LEU cc_start: 0.8393 (OUTLIER) cc_final: 0.8075 (tp) REVERT: B 603 ARG cc_start: 0.6689 (ptm160) cc_final: 0.6442 (ttp-170) outliers start: 30 outliers final: 17 residues processed: 126 average time/residue: 0.0647 time to fit residues: 12.2654 Evaluate side-chains 104 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 84 time to evaluate : 0.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 267 ILE Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 668 VAL Chi-restraints excluded: chain A residue 669 VAL Chi-restraints excluded: chain A residue 680 ILE Chi-restraints excluded: chain A residue 710 MET Chi-restraints excluded: chain A residue 781 VAL Chi-restraints excluded: chain A residue 785 LEU Chi-restraints excluded: chain B residue 267 ILE Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain B residue 486 LEU Chi-restraints excluded: chain B residue 503 LEU Chi-restraints excluded: chain B residue 668 VAL Chi-restraints excluded: chain B residue 669 VAL Chi-restraints excluded: chain B residue 680 ILE Chi-restraints excluded: chain B residue 710 MET Chi-restraints excluded: chain B residue 781 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 37 optimal weight: 8.9990 chunk 101 optimal weight: 5.9990 chunk 111 optimal weight: 0.9980 chunk 64 optimal weight: 3.9990 chunk 67 optimal weight: 6.9990 chunk 4 optimal weight: 0.7980 chunk 29 optimal weight: 0.9990 chunk 71 optimal weight: 1.9990 chunk 9 optimal weight: 0.9980 chunk 110 optimal weight: 6.9990 chunk 80 optimal weight: 5.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.115565 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2975 r_free = 0.2975 target = 0.093779 restraints weight = 12954.443| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.096621 restraints weight = 7504.960| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.098380 restraints weight = 5278.494| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.099693 restraints weight = 4227.143| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.100416 restraints weight = 3634.409| |-----------------------------------------------------------------------------| r_work (final): 0.3088 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8449 moved from start: 0.3671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9582 Z= 0.113 Angle : 0.499 7.805 13012 Z= 0.253 Chirality : 0.040 0.137 1496 Planarity : 0.003 0.022 1632 Dihedral : 4.832 35.147 1312 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 3.43 % Allowed : 13.61 % Favored : 82.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.28 (0.25), residues: 1176 helix: -0.84 (0.20), residues: 732 sheet: 0.66 (0.57), residues: 84 loop : -0.87 (0.30), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 330 TYR 0.009 0.001 TYR B 530 PHE 0.008 0.001 PHE A 676 TRP 0.004 0.001 TRP A 822 HIS 0.003 0.001 HIS B 808 Details of bonding type rmsd/Z covalent geometry : bond 0.00268 / 0.11 ( 9582) covalent geometry : angle 0.49909 / 0.25 (13012) hydrogen bonds : bond 0.02780 / 1.79 ( 358) hydrogen bonds : angle 4.05415 / 2.70 ( 1044) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2352 Ramachandran restraints generated. 1176 Oldfield, 0 Emsley, 1176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2352 Ramachandran restraints generated. 1176 Oldfield, 0 Emsley, 1176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 92 time to evaluate : 0.225 Fit side-chains REVERT: A 272 MET cc_start: 0.7874 (ttm) cc_final: 0.7640 (mtp) REVERT: A 455 ASP cc_start: 0.8306 (t70) cc_final: 0.7583 (t0) REVERT: A 503 LEU cc_start: 0.8473 (OUTLIER) cc_final: 0.8108 (tp) REVERT: A 603 ARG cc_start: 0.6807 (ptm160) cc_final: 0.6562 (ttp-170) REVERT: B 322 SER cc_start: 0.8577 (t) cc_final: 0.8008 (p) REVERT: B 346 GLU cc_start: 0.7849 (tp30) cc_final: 0.7494 (tp30) REVERT: B 455 ASP cc_start: 0.8289 (t70) cc_final: 0.7564 (t0) REVERT: B 486 LEU cc_start: 0.8780 (OUTLIER) cc_final: 0.8548 (tt) REVERT: B 503 LEU cc_start: 0.8425 (OUTLIER) cc_final: 0.8132 (tp) REVERT: B 603 ARG cc_start: 0.6765 (ptm160) cc_final: 0.6509 (ttp-170) outliers start: 34 outliers final: 24 residues processed: 120 average time/residue: 0.0702 time to fit residues: 12.8158 Evaluate side-chains 111 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 84 time to evaluate : 0.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 263 LEU Chi-restraints excluded: chain A residue 267 ILE Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 491 SER Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 668 VAL Chi-restraints excluded: chain A residue 669 VAL Chi-restraints excluded: chain A residue 680 ILE Chi-restraints excluded: chain A residue 710 MET Chi-restraints excluded: chain A residue 781 VAL Chi-restraints excluded: chain A residue 785 LEU Chi-restraints excluded: chain B residue 263 LEU Chi-restraints excluded: chain B residue 267 ILE Chi-restraints excluded: chain B residue 289 ILE Chi-restraints excluded: chain B residue 351 SER Chi-restraints excluded: chain B residue 425 LEU Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain B residue 486 LEU Chi-restraints excluded: chain B residue 491 SER Chi-restraints excluded: chain B residue 503 LEU Chi-restraints excluded: chain B residue 668 VAL Chi-restraints excluded: chain B residue 669 VAL Chi-restraints excluded: chain B residue 680 ILE Chi-restraints excluded: chain B residue 710 MET Chi-restraints excluded: chain B residue 781 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 85 optimal weight: 0.4980 chunk 3 optimal weight: 0.7980 chunk 80 optimal weight: 4.9990 chunk 15 optimal weight: 0.9990 chunk 104 optimal weight: 4.9990 chunk 107 optimal weight: 0.9980 chunk 55 optimal weight: 5.9990 chunk 95 optimal weight: 4.9990 chunk 13 optimal weight: 0.1980 chunk 22 optimal weight: 1.9990 chunk 33 optimal weight: 5.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 733 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.118204 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.096548 restraints weight = 12791.896| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.099422 restraints weight = 7352.264| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.101375 restraints weight = 5147.721| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.102486 restraints weight = 4071.409| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.103411 restraints weight = 3530.556| |-----------------------------------------------------------------------------| r_work (final): 0.3115 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8428 moved from start: 0.3799 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 9582 Z= 0.086 Angle : 0.477 9.482 13012 Z= 0.240 Chirality : 0.039 0.130 1496 Planarity : 0.002 0.023 1632 Dihedral : 4.600 31.579 1312 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 3.02 % Allowed : 14.21 % Favored : 82.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.04 (0.25), residues: 1176 helix: -0.58 (0.20), residues: 748 sheet: 0.79 (0.57), residues: 84 loop : -0.95 (0.31), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 784 TYR 0.020 0.001 TYR B 818 PHE 0.007 0.001 PHE A 611 TRP 0.004 0.000 TRP A 334 HIS 0.003 0.001 HIS A 808 Details of bonding type rmsd/Z covalent geometry : bond 0.00195 / 0.09 ( 9582) covalent geometry : angle 0.47667 / 0.24 (13012) hydrogen bonds : bond 0.02501 / 1.62 ( 358) hydrogen bonds : angle 3.89343 / 2.59 ( 1044) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2352 Ramachandran restraints generated. 1176 Oldfield, 0 Emsley, 1176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2352 Ramachandran restraints generated. 1176 Oldfield, 0 Emsley, 1176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 97 time to evaluate : 0.298 Fit side-chains REVERT: A 293 LEU cc_start: 0.9047 (mt) cc_final: 0.8761 (mp) REVERT: A 455 ASP cc_start: 0.8335 (t70) cc_final: 0.7666 (t0) REVERT: A 503 LEU cc_start: 0.8445 (OUTLIER) cc_final: 0.8100 (tp) REVERT: A 603 ARG cc_start: 0.6788 (ptm160) cc_final: 0.6553 (ttp-170) REVERT: B 322 SER cc_start: 0.8419 (t) cc_final: 0.7955 (p) REVERT: B 455 ASP cc_start: 0.8345 (t70) cc_final: 0.7680 (t0) REVERT: B 486 LEU cc_start: 0.8745 (OUTLIER) cc_final: 0.8514 (tt) REVERT: B 498 ASN cc_start: 0.8267 (OUTLIER) cc_final: 0.7826 (m-40) REVERT: B 503 LEU cc_start: 0.8399 (OUTLIER) cc_final: 0.8143 (tp) REVERT: B 603 ARG cc_start: 0.6777 (ptm160) cc_final: 0.6535 (ttp-170) outliers start: 30 outliers final: 21 residues processed: 120 average time/residue: 0.0606 time to fit residues: 11.2182 Evaluate side-chains 117 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 92 time to evaluate : 0.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 263 LEU Chi-restraints excluded: chain A residue 267 ILE Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain A residue 458 LEU Chi-restraints excluded: chain A residue 491 SER Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 668 VAL Chi-restraints excluded: chain A residue 669 VAL Chi-restraints excluded: chain A residue 680 ILE Chi-restraints excluded: chain A residue 710 MET Chi-restraints excluded: chain A residue 781 VAL Chi-restraints excluded: chain B residue 267 ILE Chi-restraints excluded: chain B residue 289 ILE Chi-restraints excluded: chain B residue 425 LEU Chi-restraints excluded: chain B residue 458 LEU Chi-restraints excluded: chain B residue 486 LEU Chi-restraints excluded: chain B residue 498 ASN Chi-restraints excluded: chain B residue 503 LEU Chi-restraints excluded: chain B residue 668 VAL Chi-restraints excluded: chain B residue 669 VAL Chi-restraints excluded: chain B residue 680 ILE Chi-restraints excluded: chain B residue 697 GLU Chi-restraints excluded: chain B residue 710 MET Chi-restraints excluded: chain B residue 781 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 0 optimal weight: 10.0000 chunk 72 optimal weight: 4.9990 chunk 71 optimal weight: 1.9990 chunk 87 optimal weight: 0.7980 chunk 16 optimal weight: 4.9990 chunk 1 optimal weight: 3.9990 chunk 84 optimal weight: 0.7980 chunk 43 optimal weight: 5.9990 chunk 83 optimal weight: 0.0770 chunk 29 optimal weight: 0.9990 chunk 114 optimal weight: 0.8980 overall best weight: 0.7140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 338 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.119367 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.098144 restraints weight = 12716.447| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.100883 restraints weight = 7512.209| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.102705 restraints weight = 5352.129| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.103862 restraints weight = 4274.057| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.104736 restraints weight = 3706.191| |-----------------------------------------------------------------------------| r_work (final): 0.3146 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8442 moved from start: 0.3900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 9582 Z= 0.087 Angle : 0.484 10.531 13012 Z= 0.243 Chirality : 0.039 0.171 1496 Planarity : 0.002 0.023 1632 Dihedral : 4.498 30.726 1312 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 2.92 % Allowed : 15.02 % Favored : 82.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.75 (0.25), residues: 1176 helix: -0.35 (0.20), residues: 748 sheet: 1.02 (0.58), residues: 84 loop : -0.88 (0.31), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 589 TYR 0.007 0.001 TYR B 530 PHE 0.006 0.001 PHE A 676 TRP 0.004 0.000 TRP A 822 HIS 0.003 0.001 HIS A 808 Details of bonding type rmsd/Z covalent geometry : bond 0.00201 / 0.09 ( 9582) covalent geometry : angle 0.48385 / 0.24 (13012) hydrogen bonds : bond 0.02467 / 1.60 ( 358) hydrogen bonds : angle 3.82677 / 2.55 ( 1044) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2352 Ramachandran restraints generated. 1176 Oldfield, 0 Emsley, 1176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2352 Ramachandran restraints generated. 1176 Oldfield, 0 Emsley, 1176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 96 time to evaluate : 0.201 Fit side-chains REVERT: A 455 ASP cc_start: 0.8336 (t70) cc_final: 0.7687 (t0) REVERT: A 498 ASN cc_start: 0.8339 (OUTLIER) cc_final: 0.7910 (m-40) REVERT: A 503 LEU cc_start: 0.8443 (OUTLIER) cc_final: 0.8123 (tp) REVERT: A 603 ARG cc_start: 0.6842 (ptm160) cc_final: 0.6591 (ttp-170) REVERT: B 322 SER cc_start: 0.8326 (t) cc_final: 0.7905 (p) REVERT: B 455 ASP cc_start: 0.8338 (t70) cc_final: 0.7694 (t0) REVERT: B 486 LEU cc_start: 0.8732 (OUTLIER) cc_final: 0.8527 (tt) REVERT: B 503 LEU cc_start: 0.8423 (OUTLIER) cc_final: 0.8136 (tp) REVERT: B 603 ARG cc_start: 0.6834 (ptm160) cc_final: 0.6570 (ttp-170) outliers start: 29 outliers final: 24 residues processed: 120 average time/residue: 0.0591 time to fit residues: 11.0630 Evaluate side-chains 121 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 93 time to evaluate : 0.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 263 LEU Chi-restraints excluded: chain A residue 267 ILE Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain A residue 458 LEU Chi-restraints excluded: chain A residue 491 SER Chi-restraints excluded: chain A residue 498 ASN Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 668 VAL Chi-restraints excluded: chain A residue 669 VAL Chi-restraints excluded: chain A residue 680 ILE Chi-restraints excluded: chain A residue 710 MET Chi-restraints excluded: chain A residue 762 GLU Chi-restraints excluded: chain A residue 781 VAL Chi-restraints excluded: chain B residue 267 ILE Chi-restraints excluded: chain B residue 289 ILE Chi-restraints excluded: chain B residue 351 SER Chi-restraints excluded: chain B residue 425 LEU Chi-restraints excluded: chain B residue 458 LEU Chi-restraints excluded: chain B residue 486 LEU Chi-restraints excluded: chain B residue 491 SER Chi-restraints excluded: chain B residue 503 LEU Chi-restraints excluded: chain B residue 668 VAL Chi-restraints excluded: chain B residue 669 VAL Chi-restraints excluded: chain B residue 680 ILE Chi-restraints excluded: chain B residue 697 GLU Chi-restraints excluded: chain B residue 710 MET Chi-restraints excluded: chain B residue 781 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 67 optimal weight: 0.0020 chunk 73 optimal weight: 0.0970 chunk 58 optimal weight: 2.9990 chunk 3 optimal weight: 0.9990 chunk 4 optimal weight: 0.9990 chunk 45 optimal weight: 1.9990 chunk 92 optimal weight: 5.9990 chunk 30 optimal weight: 0.9990 chunk 70 optimal weight: 0.9990 chunk 33 optimal weight: 5.9990 chunk 11 optimal weight: 1.9990 overall best weight: 0.6192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 338 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.118989 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.097380 restraints weight = 12785.285| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.100273 restraints weight = 7334.256| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 61)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.102213 restraints weight = 5125.127| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.103365 restraints weight = 4052.475| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.104269 restraints weight = 3497.907| |-----------------------------------------------------------------------------| r_work (final): 0.3127 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8409 moved from start: 0.3990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 9582 Z= 0.082 Angle : 0.480 10.989 13012 Z= 0.240 Chirality : 0.039 0.176 1496 Planarity : 0.002 0.023 1632 Dihedral : 4.370 28.595 1312 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 3.23 % Allowed : 15.12 % Favored : 81.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.48 (0.25), residues: 1176 helix: -0.16 (0.20), residues: 756 sheet: 1.13 (0.59), residues: 84 loop : -0.75 (0.32), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 589 TYR 0.015 0.001 TYR A 818 PHE 0.007 0.001 PHE B 676 TRP 0.010 0.001 TRP B 546 HIS 0.003 0.001 HIS A 808 Details of bonding type rmsd/Z covalent geometry : bond 0.00185 / 0.08 ( 9582) covalent geometry : angle 0.47955 / 0.24 (13012) hydrogen bonds : bond 0.02398 / 1.55 ( 358) hydrogen bonds : angle 3.75560 / 2.50 ( 1044) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2352 Ramachandran restraints generated. 1176 Oldfield, 0 Emsley, 1176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2352 Ramachandran restraints generated. 1176 Oldfield, 0 Emsley, 1176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 99 time to evaluate : 0.312 Fit side-chains REVERT: A 455 ASP cc_start: 0.8338 (t70) cc_final: 0.7694 (t0) REVERT: A 498 ASN cc_start: 0.8288 (OUTLIER) cc_final: 0.7993 (m-40) REVERT: A 503 LEU cc_start: 0.8403 (OUTLIER) cc_final: 0.8107 (tp) REVERT: A 603 ARG cc_start: 0.6943 (ptm160) cc_final: 0.6685 (ttp-170) REVERT: B 322 SER cc_start: 0.8306 (t) cc_final: 0.7880 (p) REVERT: B 455 ASP cc_start: 0.8356 (t70) cc_final: 0.7698 (t0) REVERT: B 486 LEU cc_start: 0.8716 (OUTLIER) cc_final: 0.8509 (tt) REVERT: B 498 ASN cc_start: 0.8264 (OUTLIER) cc_final: 0.7921 (m-40) REVERT: B 503 LEU cc_start: 0.8367 (OUTLIER) cc_final: 0.8113 (tp) REVERT: B 603 ARG cc_start: 0.6927 (ptm160) cc_final: 0.6686 (ttp-170) outliers start: 32 outliers final: 22 residues processed: 125 average time/residue: 0.0629 time to fit residues: 12.2968 Evaluate side-chains 120 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 93 time to evaluate : 0.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 263 LEU Chi-restraints excluded: chain A residue 267 ILE Chi-restraints excluded: chain A residue 351 SER Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain A residue 491 SER Chi-restraints excluded: chain A residue 498 ASN Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 668 VAL Chi-restraints excluded: chain A residue 669 VAL Chi-restraints excluded: chain A residue 680 ILE Chi-restraints excluded: chain A residue 710 MET Chi-restraints excluded: chain A residue 762 GLU Chi-restraints excluded: chain A residue 781 VAL Chi-restraints excluded: chain B residue 267 ILE Chi-restraints excluded: chain B residue 289 ILE Chi-restraints excluded: chain B residue 351 SER Chi-restraints excluded: chain B residue 425 LEU Chi-restraints excluded: chain B residue 458 LEU Chi-restraints excluded: chain B residue 486 LEU Chi-restraints excluded: chain B residue 498 ASN Chi-restraints excluded: chain B residue 503 LEU Chi-restraints excluded: chain B residue 669 VAL Chi-restraints excluded: chain B residue 680 ILE Chi-restraints excluded: chain B residue 697 GLU Chi-restraints excluded: chain B residue 710 MET Chi-restraints excluded: chain B residue 781 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 51 optimal weight: 5.9990 chunk 55 optimal weight: 8.9990 chunk 14 optimal weight: 0.9980 chunk 33 optimal weight: 6.9990 chunk 64 optimal weight: 1.9990 chunk 85 optimal weight: 0.0370 chunk 84 optimal weight: 0.0040 chunk 39 optimal weight: 1.9990 chunk 62 optimal weight: 0.8980 chunk 71 optimal weight: 3.9990 chunk 60 optimal weight: 3.9990 overall best weight: 0.7872 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.118510 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.097238 restraints weight = 12732.273| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.099976 restraints weight = 7599.560| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.101794 restraints weight = 5450.995| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.102890 restraints weight = 4364.310| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.103767 restraints weight = 3805.519| |-----------------------------------------------------------------------------| r_work (final): 0.3133 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8440 moved from start: 0.4036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 9582 Z= 0.089 Angle : 0.484 11.187 13012 Z= 0.242 Chirality : 0.039 0.177 1496 Planarity : 0.002 0.023 1632 Dihedral : 4.357 29.707 1312 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 2.82 % Allowed : 16.23 % Favored : 80.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.33 (0.26), residues: 1176 helix: -0.05 (0.20), residues: 756 sheet: 1.14 (0.59), residues: 84 loop : -0.65 (0.32), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 589 TYR 0.009 0.001 TYR B 530 PHE 0.006 0.001 PHE A 611 TRP 0.008 0.001 TRP B 546 HIS 0.002 0.001 HIS A 808 Details of bonding type rmsd/Z covalent geometry : bond 0.00207 / 0.09 ( 9582) covalent geometry : angle 0.48383 / 0.24 (13012) hydrogen bonds : bond 0.02468 / 1.59 ( 358) hydrogen bonds : angle 3.75312 / 2.50 ( 1044) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2352 Ramachandran restraints generated. 1176 Oldfield, 0 Emsley, 1176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2352 Ramachandran restraints generated. 1176 Oldfield, 0 Emsley, 1176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 99 time to evaluate : 0.266 Fit side-chains REVERT: A 455 ASP cc_start: 0.8341 (t70) cc_final: 0.7735 (t0) REVERT: A 498 ASN cc_start: 0.8338 (OUTLIER) cc_final: 0.7962 (m-40) REVERT: A 503 LEU cc_start: 0.8427 (OUTLIER) cc_final: 0.8125 (tp) REVERT: A 523 GLN cc_start: 0.8939 (mp10) cc_final: 0.8519 (mp10) REVERT: A 603 ARG cc_start: 0.6957 (ptm160) cc_final: 0.6732 (ttp-170) REVERT: B 292 LEU cc_start: 0.8554 (mt) cc_final: 0.8151 (mp) REVERT: B 322 SER cc_start: 0.8260 (t) cc_final: 0.7870 (p) REVERT: B 455 ASP cc_start: 0.8330 (t70) cc_final: 0.7738 (t0) REVERT: B 486 LEU cc_start: 0.8733 (OUTLIER) cc_final: 0.8532 (tt) REVERT: B 498 ASN cc_start: 0.8343 (OUTLIER) cc_final: 0.7955 (m-40) REVERT: B 503 LEU cc_start: 0.8395 (OUTLIER) cc_final: 0.8150 (tp) REVERT: B 603 ARG cc_start: 0.6882 (ptm160) cc_final: 0.6670 (ttp-170) outliers start: 28 outliers final: 23 residues processed: 122 average time/residue: 0.0590 time to fit residues: 11.1596 Evaluate side-chains 125 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 97 time to evaluate : 0.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 263 LEU Chi-restraints excluded: chain A residue 267 ILE Chi-restraints excluded: chain A residue 351 SER Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain A residue 491 SER Chi-restraints excluded: chain A residue 498 ASN Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 668 VAL Chi-restraints excluded: chain A residue 669 VAL Chi-restraints excluded: chain A residue 680 ILE Chi-restraints excluded: chain A residue 710 MET Chi-restraints excluded: chain A residue 762 GLU Chi-restraints excluded: chain A residue 781 VAL Chi-restraints excluded: chain B residue 267 ILE Chi-restraints excluded: chain B residue 289 ILE Chi-restraints excluded: chain B residue 351 SER Chi-restraints excluded: chain B residue 425 LEU Chi-restraints excluded: chain B residue 458 LEU Chi-restraints excluded: chain B residue 486 LEU Chi-restraints excluded: chain B residue 491 SER Chi-restraints excluded: chain B residue 498 ASN Chi-restraints excluded: chain B residue 503 LEU Chi-restraints excluded: chain B residue 669 VAL Chi-restraints excluded: chain B residue 680 ILE Chi-restraints excluded: chain B residue 697 GLU Chi-restraints excluded: chain B residue 710 MET Chi-restraints excluded: chain B residue 781 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 78 optimal weight: 0.6980 chunk 104 optimal weight: 0.0270 chunk 90 optimal weight: 2.9990 chunk 28 optimal weight: 5.9990 chunk 29 optimal weight: 0.7980 chunk 79 optimal weight: 0.5980 chunk 16 optimal weight: 3.9990 chunk 77 optimal weight: 1.9990 chunk 91 optimal weight: 0.7980 chunk 6 optimal weight: 4.9990 chunk 34 optimal weight: 0.0000 overall best weight: 0.4242 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.121450 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.100483 restraints weight = 12548.109| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.103260 restraints weight = 7402.256| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.105080 restraints weight = 5239.311| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.106174 restraints weight = 4197.703| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.107011 restraints weight = 3640.651| |-----------------------------------------------------------------------------| r_work (final): 0.3170 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8405 moved from start: 0.4131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 9582 Z= 0.075 Angle : 0.475 11.275 13012 Z= 0.238 Chirality : 0.039 0.162 1496 Planarity : 0.002 0.023 1632 Dihedral : 4.208 27.856 1312 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 2.42 % Allowed : 16.83 % Favored : 80.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.10 (0.26), residues: 1176 helix: 0.14 (0.21), residues: 760 sheet: 1.17 (0.59), residues: 84 loop : -0.58 (0.33), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 589 TYR 0.008 0.001 TYR B 530 PHE 0.007 0.001 PHE A 413 TRP 0.007 0.001 TRP A 822 HIS 0.003 0.001 HIS B 808 Details of bonding type rmsd/Z covalent geometry : bond 0.00163 / 0.07 ( 9582) covalent geometry : angle 0.47527 / 0.24 (13012) hydrogen bonds : bond 0.02269 / 1.47 ( 358) hydrogen bonds : angle 3.66547 / 2.44 ( 1044) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1198.02 seconds wall clock time: 21 minutes 24.74 seconds (1284.74 seconds total)