Starting phenix.real_space_refine on Fri Mar 14 00:31:32 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ekl_31169/03_2025/7ekl_31169.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ekl_31169/03_2025/7ekl_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_2025/7ekl_31169.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ekl_31169/03_2025/7ekl_31169.map" model { file = "/net/cci-nas-00/data/ceres_data/7ekl_31169/03_2025/7ekl_31169.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ekl_31169/03_2025/7ekl_31169.cif" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/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: 8.66, per 1000 atoms: 0.92 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: 2.31 Conformation dependent library (CDL) restraints added in 1.1 seconds 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: 1.04 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: 2.49 Time building geometry restraints manager: 2.73 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: 0.04 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: 0.540 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: 0.010 Extract box with map and model: 0.370 Check model and map are aligned: 0.050 Set scattering table: 0.100 Process input model: 26.280 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.020 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:2.500 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.000 ------------------------------------------------------------------------------- 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= 0.327 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.023 0.002 TRP B 488 HIS 0.007 0.002 HIS A 354 PHE 0.022 0.003 PHE B 639 TYR 0.031 0.002 TYR B 551 ARG 0.011 0.001 ARG A 365 *********************** 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 : 1.035 Fit side-chains REVERT: A 455 ASP cc_start: 0.7905 (t70) cc_final: 0.7618 (t0) REVERT: A 491 SER cc_start: 0.9230 (t) cc_final: 0.8851 (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: 0.8118 (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: 0.8793 (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: 0.8079 (p) outliers start: 8 outliers final: 2 residues processed: 217 average time/residue: 0.2769 time to fit residues: 78.1219 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 : 0.978 ------------------------------------------------------------------------------- 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 99 optimal weight: 0.0270 chunk 89 optimal weight: 0.6980 chunk 49 optimal weight: 4.9990 chunk 30 optimal weight: 0.9990 chunk 60 optimal weight: 0.0040 chunk 47 optimal weight: 0.0270 chunk 92 optimal weight: 4.9990 chunk 35 optimal weight: 5.9990 chunk 56 optimal weight: 0.4980 chunk 68 optimal weight: 2.9990 chunk 107 optimal weight: 0.6980 overall best weight: 0.2508 ------------------------------------------------------------------------------- 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 607 GLN B 752 GLN B 766 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.138651 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.119409 restraints weight = 12837.612| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.122541 restraints weight = 6899.538| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.124550 restraints weight = 4667.765| |-----------------------------------------------------------------------------| r_work (final): 0.3421 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8086 moved from start: 0.2408 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= 0.136 Angle : 0.562 7.174 13012 Z= 0.302 Chirality : 0.040 0.134 1496 Planarity : 0.004 0.035 1632 Dihedral : 8.281 86.879 1374 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 2.52 % Allowed : 8.67 % Favored : 88.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.85 (0.19), residues: 1176 helix: -3.07 (0.14), residues: 706 sheet: 0.06 (0.56), residues: 82 loop : -1.65 (0.26), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 822 HIS 0.004 0.001 HIS A 808 PHE 0.012 0.001 PHE B 592 TYR 0.013 0.001 TYR A 465 ARG 0.005 0.001 ARG A 648 *********************** 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 155 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 130 time to evaluate : 1.042 Fit side-chains REVERT: A 346 GLU cc_start: 0.7839 (tp30) cc_final: 0.7562 (mm-30) REVERT: A 455 ASP cc_start: 0.7897 (t70) cc_final: 0.7648 (t0) REVERT: A 503 LEU cc_start: 0.8347 (OUTLIER) cc_final: 0.7881 (tp) REVERT: A 553 MET cc_start: 0.7179 (ptm) cc_final: 0.6976 (ptm) REVERT: A 759 THR cc_start: 0.8262 (t) cc_final: 0.8031 (p) REVERT: B 346 GLU cc_start: 0.7818 (tp30) cc_final: 0.7437 (tp30) REVERT: B 455 ASP cc_start: 0.7868 (t70) cc_final: 0.7631 (t0) REVERT: B 503 LEU cc_start: 0.8234 (OUTLIER) cc_final: 0.7883 (tp) REVERT: B 614 MET cc_start: 0.8213 (mmm) cc_final: 0.7946 (mmm) outliers start: 25 outliers final: 8 residues processed: 149 average time/residue: 0.2242 time to fit residues: 46.3082 Evaluate side-chains 102 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 92 time to evaluate : 1.042 ------------------------------------------------------------------------------- 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 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 50 optimal weight: 6.9990 chunk 90 optimal weight: 0.8980 chunk 35 optimal weight: 7.9990 chunk 43 optimal weight: 0.3980 chunk 98 optimal weight: 5.9990 chunk 115 optimal weight: 7.9990 chunk 79 optimal weight: 0.8980 chunk 42 optimal weight: 0.4980 chunk 1 optimal weight: 0.5980 chunk 3 optimal weight: 0.9980 chunk 71 optimal weight: 4.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 596 HIS B 766 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.131565 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.112136 restraints weight = 12688.832| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.115208 restraints weight = 6907.685| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.117234 restraints weight = 4649.948| |-----------------------------------------------------------------------------| r_work (final): 0.3150 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8116 moved from start: 0.2926 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= 0.135 Angle : 0.493 5.843 13012 Z= 0.262 Chirality : 0.039 0.126 1496 Planarity : 0.003 0.029 1632 Dihedral : 7.875 89.487 1374 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 3.02 % Allowed : 10.79 % Favored : 86.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.50 (0.22), residues: 1176 helix: -1.86 (0.18), residues: 708 sheet: 0.23 (0.55), residues: 82 loop : -1.29 (0.28), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 822 HIS 0.005 0.001 HIS B 808 PHE 0.010 0.001 PHE B 592 TYR 0.011 0.001 TYR A 465 ARG 0.006 0.000 ARG B 648 *********************** 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 147 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 117 time to evaluate : 0.920 Fit side-chains REVERT: A 346 GLU cc_start: 0.7861 (tp30) cc_final: 0.7611 (mm-30) REVERT: A 421 MET cc_start: 0.8034 (tpp) cc_final: 0.7802 (mmp) REVERT: A 455 ASP cc_start: 0.8015 (t70) cc_final: 0.7778 (t0) REVERT: A 503 LEU cc_start: 0.8357 (OUTLIER) cc_final: 0.7951 (tp) REVERT: B 272 MET cc_start: 0.8022 (ttm) cc_final: 0.7691 (mtp) REVERT: B 322 SER cc_start: 0.8469 (t) cc_final: 0.7903 (p) REVERT: B 455 ASP cc_start: 0.7993 (t70) cc_final: 0.7769 (t0) REVERT: B 503 LEU cc_start: 0.8253 (OUTLIER) cc_final: 0.7937 (tp) REVERT: B 603 ARG cc_start: 0.6696 (ptm160) cc_final: 0.6471 (ttp-170) outliers start: 30 outliers final: 15 residues processed: 143 average time/residue: 0.1718 time to fit residues: 36.8330 Evaluate side-chains 118 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 101 time to evaluate : 0.986 ------------------------------------------------------------------------------- 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 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 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 0 optimal weight: 10.0000 chunk 107 optimal weight: 1.9990 chunk 109 optimal weight: 0.7980 chunk 75 optimal weight: 3.9990 chunk 87 optimal weight: 8.9990 chunk 62 optimal weight: 1.9990 chunk 58 optimal weight: 0.9980 chunk 84 optimal weight: 0.7980 chunk 43 optimal weight: 3.9990 chunk 2 optimal weight: 0.0770 chunk 93 optimal weight: 3.9990 overall best weight: 0.9340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 683 ASN B 683 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.129790 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.109811 restraints weight = 12602.958| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.112848 restraints weight = 6955.873| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.114860 restraints weight = 4740.694| |-----------------------------------------------------------------------------| r_work (final): 0.3123 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8141 moved from start: 0.3218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 9582 Z= 0.154 Angle : 0.493 8.203 13012 Z= 0.255 Chirality : 0.039 0.126 1496 Planarity : 0.003 0.028 1632 Dihedral : 7.559 89.565 1374 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 3.43 % Allowed : 12.50 % Favored : 84.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.79 (0.24), residues: 1176 helix: -1.20 (0.19), residues: 712 sheet: 0.30 (0.54), residues: 82 loop : -1.13 (0.29), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 488 HIS 0.004 0.001 HIS B 808 PHE 0.008 0.001 PHE A 611 TYR 0.008 0.001 TYR B 465 ARG 0.005 0.000 ARG B 648 *********************** 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 142 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 108 time to evaluate : 1.083 Fit side-chains REVERT: A 272 MET cc_start: 0.7844 (ttm) cc_final: 0.7608 (mtp) REVERT: A 346 GLU cc_start: 0.7842 (tp30) cc_final: 0.7611 (mm-30) REVERT: A 455 ASP cc_start: 0.8145 (t70) cc_final: 0.7896 (t0) REVERT: A 503 LEU cc_start: 0.8364 (OUTLIER) cc_final: 0.7998 (tp) REVERT: A 595 VAL cc_start: 0.9024 (OUTLIER) cc_final: 0.8796 (p) REVERT: A 603 ARG cc_start: 0.6808 (ptm160) cc_final: 0.6529 (ttp-170) REVERT: B 272 MET cc_start: 0.8038 (ttm) cc_final: 0.7748 (mtp) REVERT: B 322 SER cc_start: 0.8505 (t) cc_final: 0.8001 (p) REVERT: B 455 ASP cc_start: 0.8165 (t70) cc_final: 0.7843 (t0) REVERT: B 503 LEU cc_start: 0.8250 (OUTLIER) cc_final: 0.7969 (tp) REVERT: B 595 VAL cc_start: 0.8988 (OUTLIER) cc_final: 0.8755 (p) REVERT: B 603 ARG cc_start: 0.6774 (ptm160) cc_final: 0.6516 (ttp-170) outliers start: 34 outliers final: 17 residues processed: 138 average time/residue: 0.1932 time to fit residues: 38.6175 Evaluate side-chains 118 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 97 time to evaluate : 0.955 ------------------------------------------------------------------------------- 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 595 VAL Chi-restraints excluded: chain A residue 668 VAL Chi-restraints excluded: chain A residue 669 VAL Chi-restraints excluded: chain A residue 680 ILE Chi-restraints excluded: chain A residue 710 MET Chi-restraints excluded: chain A residue 781 VAL Chi-restraints excluded: chain 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 491 SER 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 27 optimal weight: 2.9990 chunk 89 optimal weight: 4.9990 chunk 76 optimal weight: 8.9990 chunk 82 optimal weight: 0.0270 chunk 67 optimal weight: 5.9990 chunk 11 optimal weight: 0.9980 chunk 54 optimal weight: 0.9980 chunk 15 optimal weight: 2.9990 chunk 46 optimal weight: 0.9990 chunk 39 optimal weight: 0.9990 chunk 38 optimal weight: 7.9990 overall best weight: 0.8042 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 733 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.120729 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.099696 restraints weight = 12796.444| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.102380 restraints weight = 7508.460| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.104282 restraints weight = 5306.392| |-----------------------------------------------------------------------------| r_work (final): 0.3128 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8170 moved from start: 0.3423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 9582 Z= 0.136 Angle : 0.480 8.086 13012 Z= 0.245 Chirality : 0.039 0.128 1496 Planarity : 0.002 0.023 1632 Dihedral : 7.221 88.718 1374 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 2.82 % Allowed : 13.00 % Favored : 84.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.26 (0.24), residues: 1176 helix: -0.74 (0.20), residues: 710 sheet: 0.53 (0.56), residues: 84 loop : -1.01 (0.29), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 822 HIS 0.004 0.001 HIS B 808 PHE 0.007 0.001 PHE A 611 TYR 0.008 0.001 TYR A 476 ARG 0.005 0.000 ARG B 648 *********************** 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 132 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 104 time to evaluate : 1.035 Fit side-chains REVERT: A 346 GLU cc_start: 0.7755 (tp30) cc_final: 0.7539 (mm-30) REVERT: A 455 ASP cc_start: 0.8233 (t70) cc_final: 0.7918 (t0) REVERT: A 503 LEU cc_start: 0.8392 (OUTLIER) cc_final: 0.8035 (tp) REVERT: B 272 MET cc_start: 0.7982 (ttm) cc_final: 0.7738 (mtp) REVERT: B 322 SER cc_start: 0.8443 (t) cc_final: 0.7973 (p) REVERT: B 455 ASP cc_start: 0.8237 (t70) cc_final: 0.7964 (t0) REVERT: B 503 LEU cc_start: 0.8321 (OUTLIER) cc_final: 0.8044 (tp) REVERT: B 595 VAL cc_start: 0.9049 (OUTLIER) cc_final: 0.8806 (p) REVERT: B 603 ARG cc_start: 0.6774 (ptm160) cc_final: 0.6546 (ttp-170) outliers start: 28 outliers final: 16 residues processed: 127 average time/residue: 0.1984 time to fit residues: 36.8053 Evaluate side-chains 113 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 94 time to evaluate : 0.963 ------------------------------------------------------------------------------- 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 503 LEU Chi-restraints excluded: chain A residue 668 VAL Chi-restraints excluded: chain A residue 669 VAL Chi-restraints excluded: chain A residue 680 ILE Chi-restraints excluded: chain A residue 710 MET Chi-restraints excluded: chain A residue 781 VAL Chi-restraints excluded: chain B residue 263 LEU Chi-restraints excluded: chain B residue 267 ILE Chi-restraints excluded: chain B residue 425 LEU Chi-restraints excluded: chain B residue 491 SER 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 105 optimal weight: 1.9990 chunk 74 optimal weight: 2.9990 chunk 52 optimal weight: 0.9980 chunk 20 optimal weight: 2.9990 chunk 2 optimal weight: 1.9990 chunk 47 optimal weight: 4.9990 chunk 21 optimal weight: 6.9990 chunk 65 optimal weight: 5.9990 chunk 89 optimal weight: 3.9990 chunk 54 optimal weight: 0.9980 chunk 35 optimal weight: 8.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 607 GLN ** A 733 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3251 r_free = 0.3251 target = 0.115120 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2967 r_free = 0.2967 target = 0.093301 restraints weight = 12901.523| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.096082 restraints weight = 7541.316| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.097854 restraints weight = 5352.402| |-----------------------------------------------------------------------------| r_work (final): 0.3039 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8235 moved from start: 0.3550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 9582 Z= 0.247 Angle : 0.531 6.920 13012 Z= 0.274 Chirality : 0.042 0.139 1496 Planarity : 0.003 0.023 1632 Dihedral : 7.079 89.522 1374 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 3.63 % Allowed : 13.41 % Favored : 82.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.12 (0.25), residues: 1176 helix: -0.68 (0.20), residues: 718 sheet: 0.60 (0.54), residues: 82 loop : -0.85 (0.31), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 488 HIS 0.002 0.001 HIS A 665 PHE 0.011 0.001 PHE A 676 TYR 0.013 0.001 TYR A 476 ARG 0.004 0.000 ARG B 648 *********************** 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 129 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 93 time to evaluate : 1.093 Fit side-chains REVERT: A 346 GLU cc_start: 0.7865 (tp30) cc_final: 0.7446 (tp30) REVERT: A 455 ASP cc_start: 0.8299 (t70) cc_final: 0.7593 (t0) REVERT: A 503 LEU cc_start: 0.8534 (OUTLIER) cc_final: 0.8134 (tp) REVERT: A 553 MET cc_start: 0.6997 (OUTLIER) cc_final: 0.6770 (ttp) REVERT: B 272 MET cc_start: 0.8108 (ttm) cc_final: 0.7791 (mtp) REVERT: B 322 SER cc_start: 0.8533 (t) cc_final: 0.8010 (p) REVERT: B 455 ASP cc_start: 0.8240 (t70) cc_final: 0.7520 (t0) REVERT: B 503 LEU cc_start: 0.8482 (OUTLIER) cc_final: 0.8153 (tp) REVERT: B 603 ARG cc_start: 0.6889 (ptm160) cc_final: 0.6655 (ttp-170) outliers start: 36 outliers final: 20 residues processed: 119 average time/residue: 0.1795 time to fit residues: 32.4677 Evaluate side-chains 113 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 90 time to evaluate : 1.104 ------------------------------------------------------------------------------- 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 289 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 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 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 781 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 76 optimal weight: 4.9990 chunk 24 optimal weight: 4.9990 chunk 21 optimal weight: 0.9990 chunk 26 optimal weight: 0.5980 chunk 32 optimal weight: 0.9980 chunk 14 optimal weight: 0.0020 chunk 69 optimal weight: 0.9980 chunk 90 optimal weight: 2.9990 chunk 112 optimal weight: 4.9990 chunk 17 optimal weight: 6.9990 chunk 87 optimal weight: 3.9990 overall best weight: 0.7190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 339 GLN A 607 GLN ** A 733 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 607 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.118196 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.096400 restraints weight = 12771.829| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.099266 restraints weight = 7361.460| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.101223 restraints weight = 5152.553| |-----------------------------------------------------------------------------| r_work (final): 0.3064 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8178 moved from start: 0.3720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 9582 Z= 0.130 Angle : 0.493 9.218 13012 Z= 0.250 Chirality : 0.039 0.164 1496 Planarity : 0.002 0.023 1632 Dihedral : 6.622 83.916 1374 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 3.12 % Allowed : 13.71 % Favored : 83.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.76 (0.25), residues: 1176 helix: -0.38 (0.21), residues: 716 sheet: 0.81 (0.57), residues: 84 loop : -0.75 (0.30), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 822 HIS 0.003 0.001 HIS B 808 PHE 0.007 0.001 PHE A 611 TYR 0.010 0.001 TYR B 818 ARG 0.008 0.000 ARG B 589 *********************** 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 128 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 97 time to evaluate : 1.055 Fit side-chains REVERT: A 346 GLU cc_start: 0.7771 (tp30) cc_final: 0.7550 (mm-30) REVERT: A 455 ASP cc_start: 0.8336 (t70) cc_final: 0.7642 (t0) REVERT: A 503 LEU cc_start: 0.8452 (OUTLIER) cc_final: 0.8097 (tp) REVERT: B 272 MET cc_start: 0.7992 (ttm) cc_final: 0.7745 (mtp) REVERT: B 322 SER cc_start: 0.8469 (t) cc_final: 0.7969 (p) REVERT: B 455 ASP cc_start: 0.8354 (t70) cc_final: 0.7680 (t0) REVERT: B 503 LEU cc_start: 0.8397 (OUTLIER) cc_final: 0.8098 (tp) REVERT: B 603 ARG cc_start: 0.6920 (ptm160) cc_final: 0.6677 (ttp-170) outliers start: 31 outliers final: 23 residues processed: 121 average time/residue: 0.1723 time to fit residues: 31.9231 Evaluate side-chains 120 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 95 time to evaluate : 1.048 ------------------------------------------------------------------------------- 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 289 ILE Chi-restraints excluded: chain A residue 351 SER Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 668 VAL Chi-restraints excluded: chain A residue 669 VAL Chi-restraints excluded: chain A residue 680 ILE Chi-restraints excluded: chain A residue 781 VAL Chi-restraints excluded: chain B residue 267 ILE Chi-restraints excluded: chain B residue 289 ILE Chi-restraints excluded: chain B residue 351 SER Chi-restraints excluded: chain B residue 425 LEU Chi-restraints excluded: chain B residue 430 VAL 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 99 optimal weight: 5.9990 chunk 104 optimal weight: 2.9990 chunk 30 optimal weight: 2.9990 chunk 12 optimal weight: 5.9990 chunk 9 optimal weight: 0.6980 chunk 73 optimal weight: 0.0070 chunk 105 optimal weight: 3.9990 chunk 29 optimal weight: 1.9990 chunk 96 optimal weight: 0.8980 chunk 62 optimal weight: 2.9990 chunk 82 optimal weight: 0.8980 overall best weight: 0.9000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 607 GLN ** A 733 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 338 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 = 0.3291 r_free = 0.3291 target = 0.118275 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.096324 restraints weight = 12897.297| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.099209 restraints weight = 7449.032| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.101128 restraints weight = 5210.678| |-----------------------------------------------------------------------------| r_work (final): 0.3071 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8191 moved from start: 0.3797 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= 0.148 Angle : 0.490 10.213 13012 Z= 0.249 Chirality : 0.040 0.169 1496 Planarity : 0.002 0.022 1632 Dihedral : 6.508 83.819 1374 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 2.72 % Allowed : 14.62 % Favored : 82.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.50 (0.25), residues: 1176 helix: -0.17 (0.21), residues: 716 sheet: 0.99 (0.58), residues: 84 loop : -0.67 (0.30), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 822 HIS 0.003 0.001 HIS A 808 PHE 0.007 0.001 PHE A 611 TYR 0.008 0.001 TYR B 530 ARG 0.006 0.000 ARG B 589 *********************** 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 124 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 97 time to evaluate : 0.995 Fit side-chains REVERT: A 293 LEU cc_start: 0.9020 (mt) cc_final: 0.8692 (mp) REVERT: A 346 GLU cc_start: 0.7794 (tp30) cc_final: 0.7582 (mm-30) REVERT: A 455 ASP cc_start: 0.8333 (t70) cc_final: 0.7660 (t0) REVERT: A 503 LEU cc_start: 0.8456 (OUTLIER) cc_final: 0.8105 (tp) REVERT: B 272 MET cc_start: 0.7997 (ttm) cc_final: 0.7755 (mtp) REVERT: B 322 SER cc_start: 0.8378 (t) cc_final: 0.7909 (p) REVERT: B 455 ASP cc_start: 0.8343 (t70) cc_final: 0.7704 (t0) REVERT: B 503 LEU cc_start: 0.8421 (OUTLIER) cc_final: 0.8124 (tp) REVERT: B 603 ARG cc_start: 0.6916 (ptm160) cc_final: 0.6671 (ttp-170) outliers start: 27 outliers final: 23 residues processed: 119 average time/residue: 0.1676 time to fit residues: 30.5401 Evaluate side-chains 117 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 92 time to evaluate : 0.936 ------------------------------------------------------------------------------- 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 289 ILE Chi-restraints excluded: chain A residue 351 SER 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 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 113 optimal weight: 5.9990 chunk 5 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 109 optimal weight: 0.8980 chunk 110 optimal weight: 7.9990 chunk 55 optimal weight: 5.9990 chunk 11 optimal weight: 3.9990 chunk 117 optimal weight: 9.9990 chunk 101 optimal weight: 5.9990 chunk 111 optimal weight: 0.8980 chunk 2 optimal weight: 0.8980 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 733 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 733 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.115539 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2968 r_free = 0.2968 target = 0.093451 restraints weight = 12858.965| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.096255 restraints weight = 7566.328| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.097956 restraints weight = 5361.370| |-----------------------------------------------------------------------------| r_work (final): 0.3041 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8236 moved from start: 0.3846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 9582 Z= 0.237 Angle : 0.534 10.666 13012 Z= 0.272 Chirality : 0.042 0.194 1496 Planarity : 0.003 0.024 1632 Dihedral : 6.682 89.966 1374 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 3.02 % Allowed : 14.82 % Favored : 82.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.47 (0.25), residues: 1176 helix: -0.21 (0.21), residues: 722 sheet: 1.01 (0.59), residues: 84 loop : -0.52 (0.31), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 334 HIS 0.003 0.001 HIS B 808 PHE 0.010 0.001 PHE A 676 TYR 0.015 0.001 TYR B 818 ARG 0.006 0.000 ARG B 589 *********************** 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 124 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 94 time to evaluate : 1.096 Fit side-chains REVERT: A 346 GLU cc_start: 0.7817 (tp30) cc_final: 0.7419 (tp30) REVERT: A 455 ASP cc_start: 0.8288 (t70) cc_final: 0.7617 (t0) REVERT: A 503 LEU cc_start: 0.8552 (OUTLIER) cc_final: 0.8179 (tp) REVERT: B 272 MET cc_start: 0.8071 (ttm) cc_final: 0.7757 (mtp) REVERT: B 322 SER cc_start: 0.8459 (t) cc_final: 0.7897 (p) REVERT: B 455 ASP cc_start: 0.8367 (t70) cc_final: 0.7742 (t0) REVERT: B 503 LEU cc_start: 0.8538 (OUTLIER) cc_final: 0.8232 (tp) REVERT: B 603 ARG cc_start: 0.7001 (ptm160) cc_final: 0.6744 (ttp-170) outliers start: 30 outliers final: 27 residues processed: 119 average time/residue: 0.1804 time to fit residues: 32.1212 Evaluate side-chains 120 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 91 time to evaluate : 1.040 ------------------------------------------------------------------------------- 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 289 ILE Chi-restraints excluded: chain A residue 351 SER 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 668 VAL Chi-restraints excluded: chain A residue 669 VAL Chi-restraints excluded: chain A residue 680 ILE Chi-restraints excluded: chain A residue 689 VAL Chi-restraints excluded: chain A residue 776 ARG 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 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 20 optimal weight: 0.8980 chunk 83 optimal weight: 1.9990 chunk 11 optimal weight: 0.1980 chunk 80 optimal weight: 4.9990 chunk 110 optimal weight: 2.9990 chunk 21 optimal weight: 1.9990 chunk 96 optimal weight: 0.9980 chunk 86 optimal weight: 3.9990 chunk 65 optimal weight: 0.4980 chunk 25 optimal weight: 0.9990 chunk 14 optimal weight: 0.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 733 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 733 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.117570 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.095396 restraints weight = 12868.904| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.098087 restraints weight = 7458.998| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.100095 restraints weight = 5274.252| |-----------------------------------------------------------------------------| r_work (final): 0.3088 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8178 moved from start: 0.3972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 9582 Z= 0.130 Angle : 0.491 11.372 13012 Z= 0.249 Chirality : 0.039 0.162 1496 Planarity : 0.002 0.022 1632 Dihedral : 6.348 84.246 1374 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 2.72 % Allowed : 15.62 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.22 (0.26), residues: 1176 helix: 0.04 (0.21), residues: 722 sheet: 1.04 (0.59), residues: 84 loop : -0.54 (0.32), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 822 HIS 0.003 0.001 HIS B 808 PHE 0.007 0.001 PHE A 611 TYR 0.008 0.001 TYR B 530 ARG 0.006 0.000 ARG B 589 ********************** 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 129 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 102 time to evaluate : 0.949 Fit side-chains REVERT: A 346 GLU cc_start: 0.7789 (tp30) cc_final: 0.7405 (tp30) REVERT: A 455 ASP cc_start: 0.8354 (t70) cc_final: 0.7683 (t0) REVERT: A 503 LEU cc_start: 0.8444 (OUTLIER) cc_final: 0.8108 (tp) REVERT: B 272 MET cc_start: 0.7984 (ttm) cc_final: 0.7739 (mtp) REVERT: B 322 SER cc_start: 0.8375 (t) cc_final: 0.7857 (p) REVERT: B 455 ASP cc_start: 0.8357 (t70) cc_final: 0.7707 (t0) REVERT: B 503 LEU cc_start: 0.8426 (OUTLIER) cc_final: 0.8144 (tp) REVERT: B 603 ARG cc_start: 0.6947 (ptm160) cc_final: 0.6725 (ttp-170) outliers start: 27 outliers final: 23 residues processed: 124 average time/residue: 0.1638 time to fit residues: 31.1228 Evaluate side-chains 120 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 95 time to evaluate : 1.093 ------------------------------------------------------------------------------- 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 289 ILE Chi-restraints excluded: chain A residue 351 SER 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 668 VAL Chi-restraints excluded: chain A residue 669 VAL Chi-restraints excluded: chain A residue 680 ILE Chi-restraints excluded: chain A residue 776 ARG 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 425 LEU 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 6 optimal weight: 2.9990 chunk 78 optimal weight: 0.9990 chunk 39 optimal weight: 0.9980 chunk 80 optimal weight: 0.4980 chunk 91 optimal weight: 3.9990 chunk 93 optimal weight: 0.0170 chunk 10 optimal weight: 3.9990 chunk 104 optimal weight: 0.9980 chunk 90 optimal weight: 0.9980 chunk 18 optimal weight: 0.9980 chunk 24 optimal weight: 5.9990 overall best weight: 0.7018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 338 GLN ** A 733 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.129245 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.109152 restraints weight = 12210.032| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.111871 restraints weight = 7368.582| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.113647 restraints weight = 5258.970| |-----------------------------------------------------------------------------| r_work (final): 0.3119 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8208 moved from start: 0.4033 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= 0.130 Angle : 0.491 11.185 13012 Z= 0.247 Chirality : 0.039 0.156 1496 Planarity : 0.002 0.022 1632 Dihedral : 6.278 85.736 1374 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 2.72 % Allowed : 15.93 % Favored : 81.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.19 (0.26), residues: 1176 helix: 0.07 (0.21), residues: 750 sheet: 1.05 (0.59), residues: 84 loop : -0.57 (0.33), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 822 HIS 0.003 0.001 HIS A 808 PHE 0.007 0.001 PHE A 611 TYR 0.008 0.001 TYR B 530 ARG 0.006 0.000 ARG B 589 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2565.37 seconds wall clock time: 45 minutes 32.82 seconds (2732.82 seconds total)