Starting phenix.real_space_refine on Sat Dec 28 23:48:30 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ekl_31169/12_2024/7ekl_31169.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ekl_31169/12_2024/7ekl_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_31169/12_2024/7ekl_31169.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ekl_31169/12_2024/7ekl_31169.map" model { file = "/net/cci-nas-00/data/ceres_data/7ekl_31169/12_2024/7ekl_31169.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ekl_31169/12_2024/7ekl_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-5532/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: 8.43, per 1000 atoms: 0.90 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: 2.50 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: 1.05 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: 2.41 Time building geometry restraints manager: 2.56 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: 0.00 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: 0.320 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: 0.350 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 25.990 Find NCS groups from input model: 0.260 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: 0.010 Load rotamer database and sin/cos tables:2.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.990 ------------------------------------------------------------------------------- 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 : 1.207 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: 0.2889 time to fit residues: 81.6688 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 : 1.024 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8098 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 : 0.944 Fit side-chains REVERT: A 346 GLU cc_start: 0.7818 (tp30) cc_final: 0.7546 (mm-30) REVERT: A 455 ASP cc_start: 0.7893 (t70) cc_final: 0.7641 (t0) REVERT: A 503 LEU cc_start: 0.8357 (OUTLIER) cc_final: 0.7881 (tp) REVERT: A 759 THR cc_start: 0.8247 (t) cc_final: 0.8001 (p) REVERT: B 346 GLU cc_start: 0.7794 (tp30) cc_final: 0.7427 (tp30) REVERT: B 455 ASP cc_start: 0.7869 (t70) cc_final: 0.7628 (t0) REVERT: B 503 LEU cc_start: 0.8254 (OUTLIER) cc_final: 0.7892 (tp) REVERT: B 614 MET cc_start: 0.8225 (mmm) cc_final: 0.7948 (mmm) outliers start: 25 outliers final: 8 residues processed: 149 average time/residue: 0.2359 time to fit residues: 48.5756 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 : 1.119 ------------------------------------------------------------------------------- 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 59 optimal weight: 10.0000 chunk 33 optimal weight: 5.9990 chunk 89 optimal weight: 3.9990 chunk 72 optimal weight: 3.9990 chunk 29 optimal weight: 5.9990 chunk 107 optimal weight: 4.9990 chunk 115 optimal weight: 10.0000 chunk 95 optimal weight: 5.9990 chunk 106 optimal weight: 0.0970 chunk 36 optimal weight: 1.9990 chunk 86 optimal weight: 3.9990 overall best weight: 2.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 498 ASN A 607 GLN A 683 ASN B 498 ASN B 596 HIS B 607 GLN B 683 ASN B 766 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8295 moved from start: 0.3053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 9582 Z= 0.380 Angle : 0.626 6.826 13012 Z= 0.330 Chirality : 0.044 0.139 1496 Planarity : 0.004 0.031 1632 Dihedral : 8.013 79.878 1374 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 3.73 % Allowed : 10.08 % 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: -2.86 (0.22), residues: 1176 helix: -2.18 (0.17), residues: 720 sheet: 0.23 (0.57), residues: 82 loop : -1.35 (0.29), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 488 HIS 0.003 0.002 HIS B 808 PHE 0.015 0.002 PHE B 409 TYR 0.018 0.002 TYR A 476 ARG 0.006 0.001 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 138 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 101 time to evaluate : 1.016 Fit side-chains REVERT: A 346 GLU cc_start: 0.7827 (tp30) cc_final: 0.7347 (tp30) REVERT: A 455 ASP cc_start: 0.8081 (t70) cc_final: 0.7721 (t0) REVERT: A 503 LEU cc_start: 0.8603 (OUTLIER) cc_final: 0.8164 (tp) REVERT: A 759 THR cc_start: 0.8570 (t) cc_final: 0.8297 (p) REVERT: B 272 MET cc_start: 0.8082 (ttm) cc_final: 0.7637 (mtp) REVERT: B 322 SER cc_start: 0.8687 (t) cc_final: 0.8089 (p) REVERT: B 346 GLU cc_start: 0.7795 (tp30) cc_final: 0.7354 (tp30) REVERT: B 503 LEU cc_start: 0.8570 (OUTLIER) cc_final: 0.8201 (tp) REVERT: B 614 MET cc_start: 0.8203 (mmm) cc_final: 0.7965 (mmm) REVERT: B 822 TRP cc_start: 0.9001 (t-100) cc_final: 0.8786 (t-100) outliers start: 37 outliers final: 23 residues processed: 135 average time/residue: 0.2054 time to fit residues: 39.9009 Evaluate side-chains 111 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 86 time to evaluate : 1.118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 263 LEU Chi-restraints excluded: chain A residue 267 ILE Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain A residue 426 THR Chi-restraints excluded: chain A residue 469 GLU Chi-restraints excluded: chain A residue 496 LEU Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 668 VAL Chi-restraints excluded: chain A residue 669 VAL Chi-restraints excluded: chain A residue 680 ILE Chi-restraints excluded: chain A residue 781 VAL Chi-restraints excluded: chain B residue 263 LEU Chi-restraints excluded: chain B residue 267 ILE Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 425 LEU Chi-restraints excluded: chain B residue 426 THR Chi-restraints excluded: chain B residue 491 SER Chi-restraints excluded: chain B residue 496 LEU Chi-restraints excluded: chain B residue 503 LEU Chi-restraints excluded: chain B residue 668 VAL Chi-restraints excluded: chain B residue 669 VAL Chi-restraints excluded: chain B residue 680 ILE Chi-restraints excluded: chain B residue 781 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 106 optimal weight: 1.9990 chunk 80 optimal weight: 5.9990 chunk 55 optimal weight: 10.0000 chunk 11 optimal weight: 0.8980 chunk 51 optimal weight: 3.9990 chunk 72 optimal weight: 3.9990 chunk 107 optimal weight: 0.4980 chunk 114 optimal weight: 6.9990 chunk 56 optimal weight: 0.9980 chunk 102 optimal weight: 2.9990 chunk 30 optimal weight: 0.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 498 ASN B 498 ASN B 607 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8238 moved from start: 0.3319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9582 Z= 0.165 Angle : 0.527 10.187 13012 Z= 0.269 Chirality : 0.040 0.128 1496 Planarity : 0.003 0.023 1632 Dihedral : 7.221 86.943 1374 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 3.43 % Allowed : 12.10 % Favored : 84.48 % 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: -2.03 (0.24), residues: 1176 helix: -1.45 (0.19), residues: 714 sheet: 0.33 (0.56), residues: 82 loop : -1.14 (0.29), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 822 HIS 0.005 0.001 HIS A 808 PHE 0.008 0.001 PHE A 676 TYR 0.009 0.001 TYR B 530 ARG 0.004 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 139 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 105 time to evaluate : 0.989 Fit side-chains REVERT: A 346 GLU cc_start: 0.7844 (tp30) cc_final: 0.7462 (tp30) REVERT: A 455 ASP cc_start: 0.8173 (t70) cc_final: 0.7455 (t0) REVERT: A 503 LEU cc_start: 0.8519 (OUTLIER) cc_final: 0.8089 (tp) REVERT: A 603 ARG cc_start: 0.6856 (ptm160) cc_final: 0.6582 (ttp-170) REVERT: A 759 THR cc_start: 0.8552 (t) cc_final: 0.8326 (p) REVERT: B 272 MET cc_start: 0.7988 (ttm) cc_final: 0.7673 (mtp) REVERT: B 322 SER cc_start: 0.8584 (t) cc_final: 0.8070 (p) REVERT: B 346 GLU cc_start: 0.7784 (tp30) cc_final: 0.7463 (tp30) REVERT: B 455 ASP cc_start: 0.8158 (t70) cc_final: 0.7441 (t0) REVERT: B 503 LEU cc_start: 0.8468 (OUTLIER) cc_final: 0.8124 (tp) REVERT: B 603 ARG cc_start: 0.6825 (ptm160) cc_final: 0.6561 (ttp-170) outliers start: 34 outliers final: 19 residues processed: 137 average time/residue: 0.1733 time to fit residues: 35.7977 Evaluate side-chains 114 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 93 time to evaluate : 1.036 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 263 LEU Chi-restraints excluded: chain A residue 267 ILE Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 668 VAL Chi-restraints excluded: chain A residue 669 VAL Chi-restraints excluded: chain A residue 680 ILE Chi-restraints excluded: chain A residue 710 MET Chi-restraints excluded: chain A residue 781 VAL Chi-restraints excluded: chain B residue 267 ILE Chi-restraints excluded: chain B residue 425 LEU Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain B residue 458 LEU Chi-restraints excluded: chain B residue 503 LEU Chi-restraints excluded: chain B residue 668 VAL Chi-restraints excluded: chain B residue 669 VAL Chi-restraints excluded: chain B residue 680 ILE Chi-restraints excluded: chain B residue 710 MET Chi-restraints excluded: chain B residue 781 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 94 optimal weight: 8.9990 chunk 64 optimal weight: 5.9990 chunk 1 optimal weight: 0.6980 chunk 84 optimal weight: 1.9990 chunk 47 optimal weight: 3.9990 chunk 97 optimal weight: 9.9990 chunk 78 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 58 optimal weight: 1.9990 chunk 102 optimal weight: 1.9990 chunk 28 optimal weight: 5.9990 overall best weight: 1.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 607 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8275 moved from start: 0.3525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 9582 Z= 0.240 Angle : 0.551 8.583 13012 Z= 0.280 Chirality : 0.041 0.132 1496 Planarity : 0.003 0.022 1632 Dihedral : 6.965 88.569 1374 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 3.23 % Allowed : 13.10 % Favored : 83.67 % 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: -1.70 (0.24), residues: 1176 helix: -1.17 (0.20), residues: 728 sheet: 0.49 (0.55), residues: 82 loop : -1.04 (0.30), residues: 366 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 0.011 0.001 PHE A 676 TYR 0.011 0.001 TYR A 476 ARG 0.004 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 123 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 91 time to evaluate : 1.070 Fit side-chains REVERT: A 346 GLU cc_start: 0.7860 (tp30) cc_final: 0.7503 (tp30) REVERT: A 455 ASP cc_start: 0.8221 (t70) cc_final: 0.7508 (t0) REVERT: A 503 LEU cc_start: 0.8570 (OUTLIER) cc_final: 0.8157 (tp) REVERT: A 603 ARG cc_start: 0.6827 (ptm160) cc_final: 0.6566 (ttp-170) REVERT: A 759 THR cc_start: 0.8600 (t) cc_final: 0.8367 (p) REVERT: B 272 MET cc_start: 0.8043 (ttm) cc_final: 0.7700 (mtp) REVERT: B 322 SER cc_start: 0.8582 (t) cc_final: 0.8135 (p) REVERT: B 346 GLU cc_start: 0.7788 (tp30) cc_final: 0.7466 (tp30) REVERT: B 455 ASP cc_start: 0.8232 (t70) cc_final: 0.7539 (t0) REVERT: B 503 LEU cc_start: 0.8506 (OUTLIER) cc_final: 0.8147 (tp) REVERT: B 603 ARG cc_start: 0.6803 (ptm160) cc_final: 0.6547 (ttp-170) outliers start: 32 outliers final: 25 residues processed: 119 average time/residue: 0.1887 time to fit residues: 33.8533 Evaluate side-chains 111 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 84 time to evaluate : 1.072 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 263 LEU Chi-restraints excluded: chain A residue 267 ILE Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 458 LEU Chi-restraints excluded: chain A residue 491 SER 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 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 668 VAL Chi-restraints excluded: chain B residue 669 VAL Chi-restraints excluded: chain B residue 673 THR Chi-restraints excluded: chain B residue 680 ILE Chi-restraints excluded: chain B residue 710 MET Chi-restraints excluded: chain B residue 781 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 38 optimal weight: 9.9990 chunk 102 optimal weight: 0.0770 chunk 22 optimal weight: 0.7980 chunk 66 optimal weight: 0.7980 chunk 28 optimal weight: 4.9990 chunk 114 optimal weight: 3.9990 chunk 94 optimal weight: 0.2980 chunk 52 optimal weight: 5.9990 chunk 9 optimal weight: 0.7980 chunk 37 optimal weight: 3.9990 chunk 59 optimal weight: 10.0000 overall best weight: 0.5538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 607 GLN B 766 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 moved from start: 0.3672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 9582 Z= 0.117 Angle : 0.490 8.465 13012 Z= 0.249 Chirality : 0.039 0.129 1496 Planarity : 0.002 0.023 1632 Dihedral : 6.509 81.764 1374 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 2.52 % Allowed : 14.01 % Favored : 83.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.21 (0.25), residues: 1176 helix: -0.76 (0.20), residues: 726 sheet: 0.68 (0.55), residues: 82 loop : -0.86 (0.30), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.000 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 B 471 ARG 0.003 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 125 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 100 time to evaluate : 1.139 Fit side-chains REVERT: A 455 ASP cc_start: 0.8311 (t70) cc_final: 0.7642 (t0) REVERT: A 498 ASN cc_start: 0.8355 (OUTLIER) cc_final: 0.7928 (m-40) REVERT: A 503 LEU cc_start: 0.8439 (OUTLIER) cc_final: 0.8093 (tp) REVERT: A 603 ARG cc_start: 0.6806 (ptm160) cc_final: 0.6593 (ttp-170) REVERT: B 272 MET cc_start: 0.7943 (ttm) cc_final: 0.7653 (mtp) REVERT: B 322 SER cc_start: 0.8439 (t) cc_final: 0.8079 (p) REVERT: B 455 ASP cc_start: 0.8332 (t70) cc_final: 0.7673 (t0) REVERT: B 503 LEU cc_start: 0.8397 (OUTLIER) cc_final: 0.8092 (tp) REVERT: B 603 ARG cc_start: 0.6742 (ptm160) cc_final: 0.6532 (ttp-170) outliers start: 25 outliers final: 19 residues processed: 121 average time/residue: 0.1914 time to fit residues: 34.6156 Evaluate side-chains 110 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 88 time to evaluate : 1.029 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 263 LEU Chi-restraints excluded: chain A residue 267 ILE Chi-restraints excluded: chain A residue 351 SER Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain A residue 498 ASN 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 710 MET Chi-restraints excluded: chain A residue 781 VAL Chi-restraints excluded: chain B residue 267 ILE Chi-restraints excluded: chain B residue 289 ILE Chi-restraints excluded: chain B residue 425 LEU Chi-restraints excluded: chain B residue 491 SER Chi-restraints excluded: chain B residue 503 LEU Chi-restraints excluded: chain B residue 668 VAL Chi-restraints excluded: chain B residue 669 VAL Chi-restraints excluded: chain B residue 680 ILE Chi-restraints excluded: chain B residue 697 GLU Chi-restraints excluded: chain B residue 710 MET Chi-restraints excluded: chain B residue 781 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 110 optimal weight: 6.9990 chunk 12 optimal weight: 4.9990 chunk 65 optimal weight: 5.9990 chunk 83 optimal weight: 3.9990 chunk 64 optimal weight: 0.9990 chunk 96 optimal weight: 9.9990 chunk 63 optimal weight: 1.9990 chunk 113 optimal weight: 0.2980 chunk 71 optimal weight: 7.9990 chunk 69 optimal weight: 0.8980 chunk 52 optimal weight: 2.9990 overall best weight: 1.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 607 GLN B 733 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8255 moved from start: 0.3762 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9582 Z= 0.207 Angle : 0.517 9.038 13012 Z= 0.265 Chirality : 0.041 0.164 1496 Planarity : 0.003 0.023 1632 Dihedral : 6.636 89.713 1374 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 3.53 % Allowed : 13.81 % 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: -1.10 (0.25), residues: 1176 helix: -0.65 (0.20), residues: 736 sheet: 0.69 (0.58), residues: 84 loop : -0.88 (0.30), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 334 HIS 0.003 0.001 HIS B 808 PHE 0.009 0.001 PHE A 676 TYR 0.010 0.001 TYR B 818 ARG 0.003 0.000 ARG B 648 *********************** 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 126 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 91 time to evaluate : 1.062 Fit side-chains REVERT: A 272 MET cc_start: 0.7799 (ttm) cc_final: 0.7562 (mtp) REVERT: A 455 ASP cc_start: 0.8287 (t70) cc_final: 0.7614 (t0) REVERT: A 503 LEU cc_start: 0.8541 (OUTLIER) cc_final: 0.8148 (tp) REVERT: A 603 ARG cc_start: 0.6934 (ptm160) cc_final: 0.6686 (ttp-170) REVERT: B 272 MET cc_start: 0.8003 (ttm) cc_final: 0.7668 (mtp) REVERT: B 322 SER cc_start: 0.8414 (t) cc_final: 0.7992 (p) REVERT: B 455 ASP cc_start: 0.8306 (t70) cc_final: 0.7629 (t0) REVERT: B 503 LEU cc_start: 0.8501 (OUTLIER) cc_final: 0.8174 (tp) REVERT: B 603 ARG cc_start: 0.6896 (ptm160) cc_final: 0.6635 (ttp-170) outliers start: 35 outliers final: 26 residues processed: 117 average time/residue: 0.1929 time to fit residues: 33.7141 Evaluate side-chains 118 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 90 time to evaluate : 1.096 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 263 LEU Chi-restraints excluded: chain A residue 267 ILE Chi-restraints excluded: chain A residue 351 SER Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain A residue 491 SER Chi-restraints excluded: chain A residue 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 289 ILE Chi-restraints excluded: chain B residue 351 SER Chi-restraints excluded: chain B residue 425 LEU Chi-restraints excluded: chain B residue 458 LEU Chi-restraints excluded: chain B residue 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 710 MET Chi-restraints excluded: chain B residue 781 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 70 optimal weight: 0.1980 chunk 45 optimal weight: 1.9990 chunk 67 optimal weight: 5.9990 chunk 34 optimal weight: 0.8980 chunk 22 optimal weight: 1.9990 chunk 72 optimal weight: 5.9990 chunk 77 optimal weight: 1.9990 chunk 56 optimal weight: 10.0000 chunk 10 optimal weight: 1.9990 chunk 89 optimal weight: 0.6980 chunk 103 optimal weight: 0.8980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8230 moved from start: 0.3875 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 : 0.503 10.941 13012 Z= 0.255 Chirality : 0.039 0.131 1496 Planarity : 0.002 0.023 1632 Dihedral : 6.493 87.662 1374 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 3.23 % Allowed : 14.11 % 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: -0.80 (0.25), residues: 1176 helix: -0.42 (0.20), residues: 736 sheet: 1.01 (0.58), residues: 84 loop : -0.81 (0.31), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 822 HIS 0.003 0.001 HIS A 808 PHE 0.007 0.001 PHE A 611 TYR 0.012 0.001 TYR A 818 ARG 0.009 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 133 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 101 time to evaluate : 1.089 Fit side-chains REVERT: A 272 MET cc_start: 0.7784 (ttm) cc_final: 0.7568 (mtp) REVERT: A 455 ASP cc_start: 0.8324 (t70) cc_final: 0.7696 (t0) REVERT: A 498 ASN cc_start: 0.8413 (OUTLIER) cc_final: 0.7938 (m-40) REVERT: A 503 LEU cc_start: 0.8498 (OUTLIER) cc_final: 0.8155 (tp) REVERT: A 603 ARG cc_start: 0.6906 (ptm160) cc_final: 0.6661 (ttp-170) REVERT: B 272 MET cc_start: 0.7962 (ttm) cc_final: 0.7673 (mtp) REVERT: B 322 SER cc_start: 0.8433 (t) cc_final: 0.7989 (p) REVERT: B 455 ASP cc_start: 0.8342 (t70) cc_final: 0.7694 (t0) REVERT: B 503 LEU cc_start: 0.8458 (OUTLIER) cc_final: 0.8144 (tp) REVERT: B 603 ARG cc_start: 0.6871 (ptm160) cc_final: 0.6621 (ttp-170) outliers start: 32 outliers final: 26 residues processed: 126 average time/residue: 0.1749 time to fit residues: 33.7891 Evaluate side-chains 122 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 93 time to evaluate : 1.069 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 263 LEU Chi-restraints excluded: chain A residue 267 ILE Chi-restraints excluded: chain A residue 351 SER Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain A residue 458 LEU Chi-restraints excluded: chain A residue 491 SER Chi-restraints excluded: chain A residue 498 ASN Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 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 289 ILE Chi-restraints excluded: chain B residue 351 SER Chi-restraints excluded: chain B residue 425 LEU Chi-restraints excluded: chain B residue 458 LEU Chi-restraints excluded: chain B residue 491 SER Chi-restraints excluded: chain B residue 503 LEU Chi-restraints excluded: chain B residue 668 VAL Chi-restraints excluded: chain B residue 669 VAL Chi-restraints excluded: chain B residue 680 ILE Chi-restraints excluded: chain B residue 697 GLU Chi-restraints excluded: chain B residue 781 VAL Chi-restraints excluded: chain B residue 785 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 108 optimal weight: 4.9990 chunk 99 optimal weight: 0.9990 chunk 105 optimal weight: 0.9990 chunk 63 optimal weight: 0.9980 chunk 46 optimal weight: 1.9990 chunk 83 optimal weight: 3.9990 chunk 32 optimal weight: 0.9980 chunk 95 optimal weight: 0.0770 chunk 100 optimal weight: 0.0470 chunk 69 optimal weight: 0.9980 chunk 112 optimal weight: 1.9990 overall best weight: 0.6236 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8202 moved from start: 0.3978 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= 0.123 Angle : 0.486 11.368 13012 Z= 0.245 Chirality : 0.039 0.138 1496 Planarity : 0.002 0.023 1632 Dihedral : 6.345 86.849 1374 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 2.82 % Allowed : 14.72 % Favored : 82.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.56 (0.25), residues: 1176 helix: -0.23 (0.20), residues: 758 sheet: 1.10 (0.59), residues: 84 loop : -0.75 (0.32), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 546 HIS 0.003 0.001 HIS A 808 PHE 0.007 0.001 PHE A 676 TYR 0.008 0.001 TYR B 530 ARG 0.008 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 131 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 103 time to evaluate : 1.064 Fit side-chains REVERT: A 455 ASP cc_start: 0.8338 (t70) cc_final: 0.7717 (t0) REVERT: A 498 ASN cc_start: 0.8345 (OUTLIER) cc_final: 0.7969 (m-40) REVERT: A 503 LEU cc_start: 0.8406 (OUTLIER) cc_final: 0.8095 (tp) REVERT: A 603 ARG cc_start: 0.6931 (ptm160) cc_final: 0.6705 (ttp-170) REVERT: B 272 MET cc_start: 0.7916 (ttm) cc_final: 0.7701 (mtp) REVERT: B 322 SER cc_start: 0.8300 (t) cc_final: 0.7975 (p) REVERT: B 455 ASP cc_start: 0.8367 (t70) cc_final: 0.7731 (t0) REVERT: B 498 ASN cc_start: 0.8320 (OUTLIER) cc_final: 0.7950 (m-40) REVERT: B 503 LEU cc_start: 0.8405 (OUTLIER) cc_final: 0.8147 (tp) REVERT: B 603 ARG cc_start: 0.6897 (ptm160) cc_final: 0.6679 (ttp-170) outliers start: 28 outliers final: 22 residues processed: 126 average time/residue: 0.1811 time to fit residues: 34.8119 Evaluate side-chains 126 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 100 time to evaluate : 1.065 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 263 LEU Chi-restraints excluded: chain A residue 267 ILE Chi-restraints excluded: chain A residue 351 SER Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain A residue 498 ASN 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 289 ILE Chi-restraints excluded: chain B residue 425 LEU Chi-restraints excluded: chain B residue 491 SER Chi-restraints excluded: chain B residue 498 ASN Chi-restraints excluded: chain B residue 503 LEU Chi-restraints excluded: chain B residue 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 Chi-restraints excluded: chain B residue 785 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 68 optimal weight: 0.9980 chunk 53 optimal weight: 9.9990 chunk 77 optimal weight: 2.9990 chunk 117 optimal weight: 1.9990 chunk 108 optimal weight: 3.9990 chunk 93 optimal weight: 0.4980 chunk 9 optimal weight: 2.9990 chunk 72 optimal weight: 0.9990 chunk 57 optimal weight: 9.9990 chunk 74 optimal weight: 0.5980 chunk 99 optimal weight: 3.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8222 moved from start: 0.4017 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= 0.156 Angle : 0.497 11.008 13012 Z= 0.251 Chirality : 0.040 0.187 1496 Planarity : 0.002 0.023 1632 Dihedral : 6.412 89.564 1374 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 2.82 % Allowed : 14.72 % Favored : 82.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.38 (0.26), residues: 1176 helix: -0.10 (0.21), residues: 748 sheet: 1.09 (0.59), residues: 84 loop : -0.60 (0.33), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 546 HIS 0.003 0.001 HIS A 808 PHE 0.008 0.001 PHE B 676 TYR 0.009 0.001 TYR B 530 ARG 0.008 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 122 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 94 time to evaluate : 1.128 Fit side-chains REVERT: A 455 ASP cc_start: 0.8330 (t70) cc_final: 0.7718 (t0) REVERT: A 503 LEU cc_start: 0.8453 (OUTLIER) cc_final: 0.8131 (tp) REVERT: A 603 ARG cc_start: 0.6956 (ptm160) cc_final: 0.6708 (ttp-170) REVERT: B 272 MET cc_start: 0.7937 (ttm) cc_final: 0.7685 (mtp) REVERT: B 322 SER cc_start: 0.8355 (t) cc_final: 0.7926 (p) REVERT: B 455 ASP cc_start: 0.8349 (t70) cc_final: 0.7733 (t0) REVERT: B 503 LEU cc_start: 0.8458 (OUTLIER) cc_final: 0.8187 (tp) REVERT: B 603 ARG cc_start: 0.6936 (ptm160) cc_final: 0.6693 (ttp-170) outliers start: 28 outliers final: 23 residues processed: 116 average time/residue: 0.1791 time to fit residues: 31.5960 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 : 1.067 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 263 LEU Chi-restraints excluded: chain A residue 267 ILE Chi-restraints excluded: chain A residue 351 SER Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain A residue 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 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 781 VAL Chi-restraints excluded: chain B residue 785 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 28 optimal weight: 2.9990 chunk 86 optimal weight: 3.9990 chunk 13 optimal weight: 0.0170 chunk 26 optimal weight: 1.9990 chunk 93 optimal weight: 0.8980 chunk 39 optimal weight: 0.9980 chunk 96 optimal weight: 0.3980 chunk 11 optimal weight: 2.9990 chunk 17 optimal weight: 4.9990 chunk 82 optimal weight: 0.5980 chunk 5 optimal weight: 4.9990 overall best weight: 0.5818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 338 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.124229 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.103670 restraints weight = 12367.733| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.106288 restraints weight = 7551.314| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.107990 restraints weight = 5483.431| |-----------------------------------------------------------------------------| r_work (final): 0.3227 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8203 moved from start: 0.4083 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= 0.116 Angle : 0.486 11.366 13012 Z= 0.246 Chirality : 0.039 0.171 1496 Planarity : 0.002 0.023 1632 Dihedral : 6.292 87.361 1374 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 2.82 % Allowed : 15.12 % Favored : 82.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.26 (0.26), residues: 1176 helix: 0.02 (0.21), residues: 762 sheet: 1.13 (0.59), residues: 84 loop : -0.66 (0.33), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 546 HIS 0.003 0.001 HIS A 808 PHE 0.006 0.001 PHE A 611 TYR 0.009 0.001 TYR B 530 ARG 0.007 0.000 ARG B 589 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1760.89 seconds wall clock time: 33 minutes 6.21 seconds (1986.21 seconds total)