Starting phenix.real_space_refine on Tue Mar 3 23:53:56 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ekl_31169/03_2026/7ekl_31169.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ekl_31169/03_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_31169/03_2026/7ekl_31169.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ekl_31169/03_2026/7ekl_31169.map" model { file = "/net/cci-nas-00/data/ceres_data/7ekl_31169/03_2026/7ekl_31169.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ekl_31169/03_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-5986/lib/python3.9/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: 3.42, per 1000 atoms: 0.36 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: 0.72 Conformation dependent library (CDL) restraints added in 345.3 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: 0.33 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: 1.45 Time building geometry restraints manager: 1.00 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: 5276 14.91 - 29.82: 280 29.82 - 44.73: 88 44.73 - 59.65: 10 59.65 - 74.56: 12 Dihedral angle restraints: 5666 sinusoidal: 2276 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 5663 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: 0.02 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: 0.600 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.150 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 10.810 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:1.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.860 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8085 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 : 11.151 74.557 3498 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 covalent geometry : bond 0.00508 ( 9582) covalent geometry : angle 1.13341 (13012) hydrogen bonds : bond 0.32485 ( 358) hydrogen bonds : angle 10.21563 ( 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 : 0.332 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: 0.1293 time to fit residues: 36.3196 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 : 0.351 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3461 r_free = 0.3461 target = 0.130679 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.111464 restraints weight = 12625.668| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.114500 restraints weight = 6828.412| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.116454 restraints weight = 4587.964| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.117819 restraints weight = 3535.312| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.118719 restraints weight = 2955.032| |-----------------------------------------------------------------------------| r_work (final): 0.3308 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8074 moved from start: 0.2445 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= 0.119 Angle : 0.572 7.440 13012 Z= 0.308 Chirality : 0.040 0.133 1496 Planarity : 0.004 0.034 1632 Dihedral : 8.252 85.720 1374 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 2.72 % Allowed : 8.67 % Favored : 88.61 % 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: -3.86 (0.20), residues: 1176 helix: -3.08 (0.14), residues: 706 sheet: 0.03 (0.56), residues: 82 loop : -1.64 (0.27), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 648 TYR 0.014 0.002 TYR A 465 PHE 0.013 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 covalent geometry : bond 0.00259 ( 9582) covalent geometry : angle 0.57190 (13012) hydrogen bonds : bond 0.04125 ( 358) hydrogen bonds : angle 5.15823 ( 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 145 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 118 time to evaluate : 0.275 Fit side-chains REVERT: A 346 GLU cc_start: 0.7880 (tp30) cc_final: 0.7383 (tp30) REVERT: A 455 ASP cc_start: 0.7977 (t70) cc_final: 0.7720 (t0) REVERT: A 503 LEU cc_start: 0.8446 (OUTLIER) cc_final: 0.8026 (tp) REVERT: A 553 MET cc_start: 0.7264 (ptm) cc_final: 0.7039 (ptm) REVERT: A 759 THR cc_start: 0.8413 (t) cc_final: 0.8128 (p) REVERT: B 346 GLU cc_start: 0.7888 (tp30) cc_final: 0.7450 (tp30) REVERT: B 455 ASP cc_start: 0.7970 (t70) cc_final: 0.7566 (t0) REVERT: B 503 LEU cc_start: 0.8360 (OUTLIER) cc_final: 0.8051 (tp) REVERT: B 553 MET cc_start: 0.7193 (ptm) cc_final: 0.6976 (ptm) REVERT: B 614 MET cc_start: 0.8242 (mmm) cc_final: 0.7970 (mmm) outliers start: 27 outliers final: 9 residues processed: 139 average time/residue: 0.0960 time to fit residues: 18.8898 Evaluate side-chains 99 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 88 time to evaluate : 0.341 ------------------------------------------------------------------------------- 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: 3.9990 chunk 61 optimal weight: 0.0970 chunk 67 optimal weight: 5.9990 chunk 78 optimal weight: 0.0970 chunk 104 optimal weight: 5.9990 chunk 18 optimal weight: 3.9990 chunk 91 optimal weight: 0.4980 chunk 2 optimal weight: 2.9990 chunk 76 optimal weight: 4.9990 chunk 5 optimal weight: 0.9990 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 498 ASN B 766 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.129103 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.109568 restraints weight = 12670.352| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.112600 restraints weight = 6938.299| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.114595 restraints weight = 4709.782| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.115824 restraints weight = 3652.517| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.116696 restraints weight = 3102.095| |-----------------------------------------------------------------------------| r_work (final): 0.3199 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8116 moved from start: 0.2914 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= 0.109 Angle : 0.503 6.080 13012 Z= 0.268 Chirality : 0.039 0.129 1496 Planarity : 0.003 0.029 1632 Dihedral : 7.795 89.954 1374 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 3.12 % Allowed : 9.88 % Favored : 87.00 % 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: -2.64 (0.22), residues: 1176 helix: -1.95 (0.18), residues: 712 sheet: 0.07 (0.54), residues: 82 loop : -1.35 (0.28), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 648 TYR 0.011 0.001 TYR A 465 PHE 0.010 0.001 PHE B 592 TRP 0.007 0.001 TRP B 488 HIS 0.005 0.001 HIS B 808 Details of bonding type rmsd covalent geometry : bond 0.00253 ( 9582) covalent geometry : angle 0.50273 (13012) hydrogen bonds : bond 0.03439 ( 358) hydrogen bonds : angle 4.50057 ( 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 148 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 117 time to evaluate : 0.344 Fit side-chains REVERT: A 346 GLU cc_start: 0.7929 (tp30) cc_final: 0.7495 (tp30) REVERT: A 421 MET cc_start: 0.8026 (tpp) cc_final: 0.7817 (mmp) REVERT: A 455 ASP cc_start: 0.8062 (t70) cc_final: 0.7809 (t0) REVERT: A 503 LEU cc_start: 0.8433 (OUTLIER) cc_final: 0.8027 (tp) REVERT: B 322 SER cc_start: 0.8551 (t) cc_final: 0.7963 (p) REVERT: B 346 GLU cc_start: 0.7836 (tp30) cc_final: 0.7490 (tp30) REVERT: B 455 ASP cc_start: 0.8011 (t70) cc_final: 0.7675 (t0) REVERT: B 503 LEU cc_start: 0.8283 (OUTLIER) cc_final: 0.7971 (tp) REVERT: B 603 ARG cc_start: 0.6695 (ptm160) cc_final: 0.6435 (ttp-170) outliers start: 31 outliers final: 17 residues processed: 144 average time/residue: 0.0759 time to fit residues: 16.0780 Evaluate side-chains 114 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 95 time to evaluate : 0.263 ------------------------------------------------------------------------------- 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 496 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 B residue 263 LEU Chi-restraints excluded: chain B residue 267 ILE Chi-restraints excluded: chain B residue 425 LEU Chi-restraints excluded: chain B residue 496 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 60 optimal weight: 0.0170 chunk 8 optimal weight: 6.9990 chunk 55 optimal weight: 10.0000 chunk 117 optimal weight: 9.9990 chunk 108 optimal weight: 0.6980 chunk 63 optimal weight: 0.6980 chunk 102 optimal weight: 0.9990 chunk 57 optimal weight: 10.0000 chunk 114 optimal weight: 7.9990 chunk 103 optimal weight: 0.0030 chunk 77 optimal weight: 0.8980 overall best weight: 0.4628 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 498 ASN A 683 ASN B 683 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.130726 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.110675 restraints weight = 12688.922| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.113763 restraints weight = 6977.052| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.115771 restraints weight = 4715.313| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.117061 restraints weight = 3678.307| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.117928 restraints weight = 3117.390| |-----------------------------------------------------------------------------| r_work (final): 0.3295 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8083 moved from start: 0.3302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 9582 Z= 0.082 Angle : 0.476 8.156 13012 Z= 0.246 Chirality : 0.038 0.127 1496 Planarity : 0.003 0.027 1632 Dihedral : 7.268 83.779 1374 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 2.82 % Allowed : 11.90 % Favored : 85.28 % 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: -1.82 (0.24), residues: 1176 helix: -1.23 (0.19), residues: 714 sheet: 0.28 (0.53), residues: 82 loop : -1.12 (0.29), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 648 TYR 0.008 0.001 TYR B 530 PHE 0.007 0.001 PHE A 592 TRP 0.005 0.000 TRP B 488 HIS 0.004 0.001 HIS A 808 Details of bonding type rmsd covalent geometry : bond 0.00177 ( 9582) covalent geometry : angle 0.47570 (13012) hydrogen bonds : bond 0.02671 ( 358) hydrogen bonds : angle 4.08268 ( 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: 28 poor density : 113 time to evaluate : 0.363 Fit side-chains REVERT: A 346 GLU cc_start: 0.7797 (tp30) cc_final: 0.7540 (mm-30) REVERT: A 455 ASP cc_start: 0.8222 (t70) cc_final: 0.7997 (t0) REVERT: A 503 LEU cc_start: 0.8307 (OUTLIER) cc_final: 0.7963 (tp) REVERT: A 595 VAL cc_start: 0.9005 (OUTLIER) cc_final: 0.8771 (p) REVERT: A 603 ARG cc_start: 0.6760 (ptm160) cc_final: 0.6546 (ttp-170) REVERT: B 322 SER cc_start: 0.8465 (t) cc_final: 0.7901 (p) REVERT: B 455 ASP cc_start: 0.8227 (t70) cc_final: 0.7915 (t0) REVERT: B 503 LEU cc_start: 0.8215 (OUTLIER) cc_final: 0.7963 (tp) REVERT: B 595 VAL cc_start: 0.8968 (OUTLIER) cc_final: 0.8724 (p) REVERT: B 603 ARG cc_start: 0.6642 (ptm160) cc_final: 0.6411 (ttp-170) outliers start: 28 outliers final: 15 residues processed: 136 average time/residue: 0.0757 time to fit residues: 15.5069 Evaluate side-chains 116 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 97 time to evaluate : 0.230 ------------------------------------------------------------------------------- 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 496 LEU 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 672 ASP 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 425 LEU Chi-restraints excluded: chain B residue 503 LEU Chi-restraints excluded: chain B residue 595 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 58 optimal weight: 1.9990 chunk 114 optimal weight: 3.9990 chunk 89 optimal weight: 0.9990 chunk 68 optimal weight: 2.9990 chunk 22 optimal weight: 1.9990 chunk 8 optimal weight: 0.0060 chunk 53 optimal weight: 9.9990 chunk 32 optimal weight: 3.9990 chunk 48 optimal weight: 0.6980 chunk 9 optimal weight: 0.9980 chunk 91 optimal weight: 2.9990 overall best weight: 0.9400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 733 GLN B 693 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.120821 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.099865 restraints weight = 12815.759| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.102582 restraints weight = 7495.431| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.104409 restraints weight = 5305.855| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.105543 restraints weight = 4240.807| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.106341 restraints weight = 3674.067| |-----------------------------------------------------------------------------| r_work (final): 0.3156 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8156 moved from start: 0.3469 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= 0.101 Angle : 0.486 7.567 13012 Z= 0.249 Chirality : 0.039 0.134 1496 Planarity : 0.002 0.023 1632 Dihedral : 6.925 83.520 1374 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 3.73 % Allowed : 11.29 % Favored : 84.98 % 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: -1.44 (0.24), residues: 1176 helix: -0.89 (0.20), residues: 728 sheet: 0.56 (0.55), residues: 82 loop : -1.07 (0.29), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 638 TYR 0.008 0.001 TYR B 476 PHE 0.007 0.001 PHE B 611 TRP 0.008 0.001 TRP B 822 HIS 0.003 0.001 HIS B 808 Details of bonding type rmsd covalent geometry : bond 0.00235 ( 9582) covalent geometry : angle 0.48638 (13012) hydrogen bonds : bond 0.02693 ( 358) hydrogen bonds : angle 3.96454 ( 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 135 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 98 time to evaluate : 0.326 Fit side-chains REVERT: A 346 GLU cc_start: 0.7791 (tp30) cc_final: 0.7568 (mm-30) REVERT: A 455 ASP cc_start: 0.8201 (t70) cc_final: 0.7894 (t0) REVERT: A 503 LEU cc_start: 0.8401 (OUTLIER) cc_final: 0.8031 (tp) REVERT: B 322 SER cc_start: 0.8423 (t) cc_final: 0.7949 (p) REVERT: B 455 ASP cc_start: 0.8282 (t70) cc_final: 0.7991 (t0) REVERT: B 503 LEU cc_start: 0.8357 (OUTLIER) cc_final: 0.8059 (tp) REVERT: B 603 ARG cc_start: 0.6611 (ptm160) cc_final: 0.6404 (ttp-170) outliers start: 37 outliers final: 21 residues processed: 127 average time/residue: 0.0856 time to fit residues: 15.9658 Evaluate side-chains 114 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 91 time to evaluate : 0.383 ------------------------------------------------------------------------------- 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 400 ILE Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 553 MET Chi-restraints excluded: chain A residue 668 VAL Chi-restraints excluded: chain A residue 669 VAL Chi-restraints excluded: chain A residue 672 ASP 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 425 LEU Chi-restraints excluded: chain B residue 487 GLU 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 781 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 37 optimal weight: 9.9990 chunk 101 optimal weight: 0.9980 chunk 111 optimal weight: 1.9990 chunk 64 optimal weight: 2.9990 chunk 67 optimal weight: 4.9990 chunk 4 optimal weight: 0.8980 chunk 29 optimal weight: 4.9990 chunk 71 optimal weight: 4.9990 chunk 9 optimal weight: 2.9990 chunk 110 optimal weight: 0.9980 chunk 80 optimal weight: 4.9990 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 607 GLN B 607 GLN B 766 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.117003 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.095553 restraints weight = 12932.116| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.098272 restraints weight = 7700.641| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.100051 restraints weight = 5492.705| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.101134 restraints weight = 4437.617| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.101916 restraints weight = 3870.246| |-----------------------------------------------------------------------------| r_work (final): 0.3114 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8215 moved from start: 0.3604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9582 Z= 0.144 Angle : 0.517 7.816 13012 Z= 0.265 Chirality : 0.041 0.135 1496 Planarity : 0.003 0.023 1632 Dihedral : 6.811 86.066 1374 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 3.63 % Allowed : 12.50 % Favored : 83.87 % 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: -1.18 (0.24), residues: 1176 helix: -0.72 (0.20), residues: 730 sheet: 0.77 (0.56), residues: 82 loop : -0.94 (0.30), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 330 TYR 0.011 0.001 TYR A 476 PHE 0.009 0.001 PHE A 676 TRP 0.004 0.001 TRP A 334 HIS 0.002 0.001 HIS B 808 Details of bonding type rmsd covalent geometry : bond 0.00345 ( 9582) covalent geometry : angle 0.51696 (13012) hydrogen bonds : bond 0.02934 ( 358) hydrogen bonds : angle 4.01289 ( 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 131 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 95 time to evaluate : 0.351 Fit side-chains REVERT: A 346 GLU cc_start: 0.7808 (tp30) cc_final: 0.7406 (tp30) REVERT: A 455 ASP cc_start: 0.8273 (t70) cc_final: 0.7575 (t0) REVERT: A 503 LEU cc_start: 0.8511 (OUTLIER) cc_final: 0.8134 (tp) REVERT: B 322 SER cc_start: 0.8486 (t) cc_final: 0.7993 (p) REVERT: B 455 ASP cc_start: 0.8343 (t70) cc_final: 0.7669 (t0) REVERT: B 503 LEU cc_start: 0.8478 (OUTLIER) cc_final: 0.8159 (tp) REVERT: B 603 ARG cc_start: 0.6752 (ptm160) cc_final: 0.6538 (ttp-170) outliers start: 36 outliers final: 23 residues processed: 122 average time/residue: 0.0693 time to fit residues: 13.1897 Evaluate side-chains 115 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 90 time to evaluate : 0.344 ------------------------------------------------------------------------------- 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 400 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 553 MET 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 263 LEU Chi-restraints excluded: chain B residue 267 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 487 GLU 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 781 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 85 optimal weight: 0.6980 chunk 3 optimal weight: 1.9990 chunk 80 optimal weight: 5.9990 chunk 15 optimal weight: 0.9980 chunk 104 optimal weight: 0.9980 chunk 107 optimal weight: 0.6980 chunk 55 optimal weight: 5.9990 chunk 95 optimal weight: 0.9980 chunk 13 optimal weight: 0.0970 chunk 22 optimal weight: 0.5980 chunk 33 optimal weight: 4.9990 overall best weight: 0.6178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 338 GLN A 607 GLN B 607 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.120430 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.098771 restraints weight = 12717.953| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.101642 restraints weight = 7280.012| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.103405 restraints weight = 5074.914| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.104746 restraints weight = 4052.440| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.105538 restraints weight = 3475.691| |-----------------------------------------------------------------------------| r_work (final): 0.3116 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8140 moved from start: 0.3771 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= 0.084 Angle : 0.479 9.373 13012 Z= 0.244 Chirality : 0.039 0.153 1496 Planarity : 0.002 0.023 1632 Dihedral : 6.480 79.630 1374 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 2.42 % Allowed : 14.11 % Favored : 83.47 % 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: -0.87 (0.25), residues: 1176 helix: -0.44 (0.20), residues: 742 sheet: 0.90 (0.58), residues: 84 loop : -0.92 (0.30), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 648 TYR 0.014 0.001 TYR A 818 PHE 0.007 0.001 PHE A 611 TRP 0.009 0.001 TRP B 822 HIS 0.003 0.001 HIS A 808 Details of bonding type rmsd covalent geometry : bond 0.00186 ( 9582) covalent geometry : angle 0.47880 (13012) hydrogen bonds : bond 0.02486 ( 358) hydrogen bonds : angle 3.84195 ( 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: 24 poor density : 103 time to evaluate : 0.350 Fit side-chains REVERT: A 293 LEU cc_start: 0.9103 (mt) cc_final: 0.8789 (mp) REVERT: A 346 GLU cc_start: 0.7747 (tp30) cc_final: 0.7530 (mm-30) REVERT: A 455 ASP cc_start: 0.8340 (t70) cc_final: 0.7638 (t0) REVERT: A 503 LEU cc_start: 0.8428 (OUTLIER) cc_final: 0.8075 (tp) REVERT: B 322 SER cc_start: 0.8384 (t) cc_final: 0.7937 (p) REVERT: B 455 ASP cc_start: 0.8324 (t70) cc_final: 0.7666 (t0) REVERT: B 503 LEU cc_start: 0.8351 (OUTLIER) cc_final: 0.8069 (tp) REVERT: B 603 ARG cc_start: 0.6876 (ptm160) cc_final: 0.6663 (ttp-170) outliers start: 24 outliers final: 16 residues processed: 124 average time/residue: 0.0758 time to fit residues: 14.4483 Evaluate side-chains 109 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 91 time to evaluate : 0.221 ------------------------------------------------------------------------------- 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 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 B residue 263 LEU Chi-restraints excluded: chain B residue 267 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 491 SER 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=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: 7.9990 chunk 87 optimal weight: 5.9990 chunk 16 optimal weight: 0.9980 chunk 1 optimal weight: 2.9990 chunk 84 optimal weight: 0.8980 chunk 43 optimal weight: 4.9990 chunk 83 optimal weight: 0.4980 chunk 29 optimal weight: 0.8980 chunk 114 optimal weight: 5.9990 overall best weight: 1.2582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 607 GLN B 607 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.118018 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.096471 restraints weight = 12750.137| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.099168 restraints weight = 7602.975| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.100966 restraints weight = 5469.637| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.102127 restraints weight = 4402.745| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.102963 restraints weight = 3811.649| |-----------------------------------------------------------------------------| r_work (final): 0.3117 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8197 moved from start: 0.3822 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= 0.121 Angle : 0.510 9.602 13012 Z= 0.258 Chirality : 0.040 0.171 1496 Planarity : 0.002 0.022 1632 Dihedral : 6.527 84.071 1374 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 2.72 % Allowed : 14.42 % Favored : 82.86 % 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: -0.63 (0.25), residues: 1176 helix: -0.28 (0.21), residues: 732 sheet: 1.04 (0.58), residues: 84 loop : -0.78 (0.30), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 589 TYR 0.010 0.001 TYR B 476 PHE 0.008 0.001 PHE B 676 TRP 0.006 0.001 TRP B 822 HIS 0.002 0.001 HIS B 808 Details of bonding type rmsd covalent geometry : bond 0.00288 ( 9582) covalent geometry : angle 0.51007 (13012) hydrogen bonds : bond 0.02738 ( 358) hydrogen bonds : angle 3.87494 ( 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 119 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 92 time to evaluate : 0.345 Fit side-chains REVERT: A 346 GLU cc_start: 0.7800 (tp30) cc_final: 0.7406 (tp30) REVERT: A 455 ASP cc_start: 0.8360 (t70) cc_final: 0.7699 (t0) REVERT: A 503 LEU cc_start: 0.8530 (OUTLIER) cc_final: 0.8163 (tp) REVERT: B 322 SER cc_start: 0.8380 (t) cc_final: 0.7914 (p) REVERT: B 455 ASP cc_start: 0.8346 (t70) cc_final: 0.7701 (t0) REVERT: B 503 LEU cc_start: 0.8464 (OUTLIER) cc_final: 0.8151 (tp) REVERT: B 603 ARG cc_start: 0.6858 (ptm160) cc_final: 0.6601 (ttp-170) outliers start: 27 outliers final: 23 residues processed: 114 average time/residue: 0.0652 time to fit residues: 11.8707 Evaluate side-chains 115 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 90 time to evaluate : 0.248 ------------------------------------------------------------------------------- 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 400 ILE Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain A residue 458 LEU Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 553 MET 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 B residue 263 LEU Chi-restraints excluded: chain B residue 267 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 487 GLU 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 781 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 67 optimal weight: 5.9990 chunk 73 optimal weight: 0.5980 chunk 58 optimal weight: 9.9990 chunk 3 optimal weight: 3.9990 chunk 4 optimal weight: 0.9980 chunk 45 optimal weight: 1.9990 chunk 92 optimal weight: 5.9990 chunk 30 optimal weight: 0.9990 chunk 70 optimal weight: 3.9990 chunk 33 optimal weight: 0.9990 chunk 11 optimal weight: 0.0970 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 607 GLN B 607 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.119193 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.097194 restraints weight = 12761.924| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.100067 restraints weight = 7365.163| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.102010 restraints weight = 5166.585| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.103274 restraints weight = 4078.397| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.104048 restraints weight = 3518.041| |-----------------------------------------------------------------------------| r_work (final): 0.3117 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8155 moved from start: 0.3930 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= 0.089 Angle : 0.492 11.477 13012 Z= 0.246 Chirality : 0.039 0.148 1496 Planarity : 0.002 0.022 1632 Dihedral : 6.371 82.092 1374 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 2.62 % Allowed : 14.92 % Favored : 82.46 % 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: -0.38 (0.25), residues: 1176 helix: -0.07 (0.21), residues: 734 sheet: 1.15 (0.59), residues: 84 loop : -0.71 (0.31), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 589 TYR 0.014 0.001 TYR B 818 PHE 0.007 0.001 PHE A 611 TRP 0.006 0.000 TRP B 822 HIS 0.003 0.001 HIS B 808 Details of bonding type rmsd covalent geometry : bond 0.00204 ( 9582) covalent geometry : angle 0.49193 (13012) hydrogen bonds : bond 0.02508 ( 358) hydrogen bonds : angle 3.78292 ( 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 126 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 100 time to evaluate : 0.289 Fit side-chains REVERT: A 293 LEU cc_start: 0.9071 (mt) cc_final: 0.8732 (mp) REVERT: A 346 GLU cc_start: 0.7789 (tp30) cc_final: 0.7402 (tp30) REVERT: A 455 ASP cc_start: 0.8337 (t70) cc_final: 0.7674 (t0) REVERT: A 503 LEU cc_start: 0.8439 (OUTLIER) cc_final: 0.8098 (tp) REVERT: B 322 SER cc_start: 0.8346 (t) cc_final: 0.7928 (p) REVERT: B 455 ASP cc_start: 0.8350 (t70) cc_final: 0.7696 (t0) REVERT: B 503 LEU cc_start: 0.8390 (OUTLIER) cc_final: 0.8103 (tp) outliers start: 26 outliers final: 21 residues processed: 122 average time/residue: 0.0700 time to fit residues: 13.0341 Evaluate side-chains 115 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 92 time to evaluate : 0.299 ------------------------------------------------------------------------------- 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 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 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 458 LEU Chi-restraints excluded: chain B residue 487 GLU 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 781 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 51 optimal weight: 4.9990 chunk 55 optimal weight: 10.0000 chunk 14 optimal weight: 0.3980 chunk 33 optimal weight: 5.9990 chunk 64 optimal weight: 1.9990 chunk 85 optimal weight: 2.9990 chunk 84 optimal weight: 6.9990 chunk 39 optimal weight: 1.9990 chunk 62 optimal weight: 0.7980 chunk 71 optimal weight: 3.9990 chunk 60 optimal weight: 3.9990 overall best weight: 1.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 354 HIS A 607 GLN B 607 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.115705 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2965 r_free = 0.2965 target = 0.093434 restraints weight = 12796.925| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.096219 restraints weight = 7516.276| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.098109 restraints weight = 5343.537| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.099219 restraints weight = 4269.564| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.100054 restraints weight = 3713.634| |-----------------------------------------------------------------------------| r_work (final): 0.3070 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8206 moved from start: 0.3937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 9582 Z= 0.146 Angle : 0.534 12.126 13012 Z= 0.268 Chirality : 0.042 0.154 1496 Planarity : 0.003 0.022 1632 Dihedral : 6.576 89.451 1374 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 2.72 % Allowed : 15.22 % 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: -0.28 (0.26), residues: 1176 helix: -0.04 (0.21), residues: 718 sheet: 1.07 (0.59), residues: 84 loop : -0.50 (0.32), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 589 TYR 0.012 0.001 TYR B 476 PHE 0.009 0.001 PHE A 611 TRP 0.007 0.001 TRP B 822 HIS 0.002 0.001 HIS A 808 Details of bonding type rmsd covalent geometry : bond 0.00351 ( 9582) covalent geometry : angle 0.53365 (13012) hydrogen bonds : bond 0.02932 ( 358) hydrogen bonds : angle 3.93872 ( 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 110 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 83 time to evaluate : 0.385 Fit side-chains REVERT: A 346 GLU cc_start: 0.7807 (tp30) cc_final: 0.7393 (tp30) REVERT: A 455 ASP cc_start: 0.8365 (t70) cc_final: 0.7719 (t0) REVERT: A 503 LEU cc_start: 0.8541 (OUTLIER) cc_final: 0.8174 (tp) REVERT: B 292 LEU cc_start: 0.8688 (mt) cc_final: 0.8296 (mp) REVERT: B 322 SER cc_start: 0.8515 (t) cc_final: 0.7976 (p) REVERT: B 455 ASP cc_start: 0.8395 (t70) cc_final: 0.7770 (t0) REVERT: B 503 LEU cc_start: 0.8516 (OUTLIER) cc_final: 0.8218 (tp) outliers start: 27 outliers final: 25 residues processed: 106 average time/residue: 0.0606 time to fit residues: 10.6769 Evaluate side-chains 109 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 82 time to evaluate : 0.363 ------------------------------------------------------------------------------- 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 503 LEU Chi-restraints excluded: chain A residue 553 MET 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 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 458 LEU Chi-restraints excluded: chain B residue 487 GLU Chi-restraints excluded: chain B residue 491 SER Chi-restraints excluded: chain B residue 503 LEU Chi-restraints excluded: chain B residue 553 MET 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 781 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 78 optimal weight: 0.7980 chunk 104 optimal weight: 1.9990 chunk 90 optimal weight: 2.9990 chunk 28 optimal weight: 4.9990 chunk 29 optimal weight: 0.9980 chunk 79 optimal weight: 0.9990 chunk 16 optimal weight: 0.0370 chunk 77 optimal weight: 2.9990 chunk 91 optimal weight: 0.9990 chunk 6 optimal weight: 3.9990 chunk 34 optimal weight: 1.9990 overall best weight: 0.7662 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.118473 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.096300 restraints weight = 12580.707| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.099160 restraints weight = 7307.329| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.101002 restraints weight = 5167.803| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.102304 restraints weight = 4134.356| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.103020 restraints weight = 3561.020| |-----------------------------------------------------------------------------| r_work (final): 0.3113 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8157 moved from start: 0.4037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 9582 Z= 0.091 Angle : 0.513 12.332 13012 Z= 0.251 Chirality : 0.039 0.138 1496 Planarity : 0.002 0.022 1632 Dihedral : 6.337 85.275 1374 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 2.42 % Allowed : 15.93 % 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: -0.16 (0.26), residues: 1176 helix: 0.05 (0.21), residues: 732 sheet: 1.14 (0.59), residues: 84 loop : -0.45 (0.33), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 589 TYR 0.011 0.001 TYR B 818 PHE 0.007 0.001 PHE A 676 TRP 0.007 0.001 TRP B 822 HIS 0.003 0.001 HIS B 808 Details of bonding type rmsd covalent geometry : bond 0.00209 ( 9582) covalent geometry : angle 0.51288 (13012) hydrogen bonds : bond 0.02532 ( 358) hydrogen bonds : angle 3.80023 ( 1044) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1320.46 seconds wall clock time: 23 minutes 28.66 seconds (1408.66 seconds total)