Starting phenix.real_space_refine on Thu Mar 13 19:33:04 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6v6b_21067/03_2025/6v6b_21067.cif Found real_map, /net/cci-nas-00/data/ceres_data/6v6b_21067/03_2025/6v6b_21067.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6v6b_21067/03_2025/6v6b_21067.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6v6b_21067/03_2025/6v6b_21067.map" model { file = "/net/cci-nas-00/data/ceres_data/6v6b_21067/03_2025/6v6b_21067.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6v6b_21067/03_2025/6v6b_21067.cif" } resolution = 3.8 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= 0.002 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: 4 Type Number sf(0) Gaussians S 55 5.16 5 C 5859 2.51 5 N 1553 2.21 5 O 1648 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 34 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 9115 Number of models: 1 Model: "" Number of chains: 2 Chain: "B" Number of atoms: 4744 Number of conformers: 1 Conformer: "" Number of residues, atoms: 572, 4744 Classifications: {'peptide': 572} Link IDs: {'PTRANS': 11, 'TRANS': 560} Chain breaks: 9 Chain: "C" Number of atoms: 4371 Number of conformers: 1 Conformer: "" Number of residues, atoms: 539, 4371 Classifications: {'peptide': 539} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 16, 'TRANS': 522} Chain breaks: 8 Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 Time building chain proxies: 6.75, per 1000 atoms: 0.74 Number of scatterers: 9115 At special positions: 0 Unit cell: (116.145, 152.19, 120.15, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 55 16.00 O 1648 8.00 N 1553 7.00 C 5859 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: 2.39 Conformation dependent library (CDL) restraints added in 1.4 seconds 2146 Ramachandran restraints generated. 1073 Oldfield, 0 Emsley, 1073 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2144 Finding SS restraints... Secondary structure from input PDB file: 62 helices and 5 sheets defined 69.7% alpha, 1.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.98 Creating SS restraints... Processing helix chain 'B' and resid 246 through 258 removed outlier: 3.814A pdb=" N LEU B 250 " --> pdb=" O THR B 246 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N TYR B 256 " --> pdb=" O ARG B 252 " (cutoff:3.500A) Processing helix chain 'B' and resid 284 through 296 removed outlier: 4.250A pdb=" N THR B 290 " --> pdb=" O SER B 286 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N GLU B 296 " --> pdb=" O VAL B 292 " (cutoff:3.500A) Processing helix chain 'B' and resid 297 through 311 removed outlier: 3.609A pdb=" N LYS B 303 " --> pdb=" O TRP B 299 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ILE B 304 " --> pdb=" O LEU B 300 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N TYR B 307 " --> pdb=" O LYS B 303 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N THR B 308 " --> pdb=" O ILE B 304 " (cutoff:3.500A) Processing helix chain 'B' and resid 319 through 326 removed outlier: 3.664A pdb=" N SER B 323 " --> pdb=" O LEU B 319 " (cutoff:3.500A) Processing helix chain 'B' and resid 329 through 345 removed outlier: 4.063A pdb=" N GLU B 334 " --> pdb=" O GLN B 330 " (cutoff:3.500A) removed outlier: 4.694A pdb=" N TYR B 335 " --> pdb=" O GLU B 331 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N LEU B 339 " --> pdb=" O TYR B 335 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N GLN B 345 " --> pdb=" O VAL B 341 " (cutoff:3.500A) Processing helix chain 'B' and resid 363 through 371 removed outlier: 4.784A pdb=" N VAL B 369 " --> pdb=" O ARG B 365 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N TRP B 370 " --> pdb=" O ARG B 366 " (cutoff:3.500A) Processing helix chain 'B' and resid 376 through 388 removed outlier: 4.191A pdb=" N ALA B 382 " --> pdb=" O LEU B 378 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N ALA B 383 " --> pdb=" O LYS B 379 " (cutoff:3.500A) removed outlier: 4.833A pdb=" N ASP B 386 " --> pdb=" O ALA B 382 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N HIS B 387 " --> pdb=" O ALA B 383 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N CYS B 388 " --> pdb=" O LEU B 384 " (cutoff:3.500A) Processing helix chain 'B' and resid 393 through 398 removed outlier: 3.731A pdb=" N ALA B 397 " --> pdb=" O GLY B 393 " (cutoff:3.500A) Processing helix chain 'B' and resid 414 through 434 removed outlier: 4.167A pdb=" N SER B 420 " --> pdb=" O GLN B 416 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N HIS B 424 " --> pdb=" O SER B 420 " (cutoff:3.500A) Proline residue: B 425 - end of helix removed outlier: 3.675A pdb=" N TYR B 431 " --> pdb=" O LEU B 427 " (cutoff:3.500A) Processing helix chain 'B' and resid 479 through 495 removed outlier: 3.558A pdb=" N VAL B 483 " --> pdb=" O GLN B 479 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N LEU B 484 " --> pdb=" O SER B 480 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N LEU B 485 " --> pdb=" O ARG B 481 " (cutoff:3.500A) Processing helix chain 'B' and resid 528 through 552 removed outlier: 3.750A pdb=" N GLU B 540 " --> pdb=" O ALA B 536 " (cutoff:3.500A) removed outlier: 4.718A pdb=" N LYS B 543 " --> pdb=" O PHE B 539 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ASP B 547 " --> pdb=" O LYS B 543 " (cutoff:3.500A) Processing helix chain 'B' and resid 554 through 565 removed outlier: 3.538A pdb=" N MET B 559 " --> pdb=" O LEU B 555 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ALA B 561 " --> pdb=" O ASP B 557 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N TYR B 565 " --> pdb=" O ALA B 561 " (cutoff:3.500A) Processing helix chain 'B' and resid 571 through 581 removed outlier: 3.673A pdb=" N HIS B 576 " --> pdb=" O ASP B 572 " (cutoff:3.500A) Processing helix chain 'B' and resid 581 through 586 removed outlier: 3.762A pdb=" N VAL B 586 " --> pdb=" O LYS B 582 " (cutoff:3.500A) Processing helix chain 'B' and resid 588 through 592 removed outlier: 3.521A pdb=" N THR B 591 " --> pdb=" O PRO B 588 " (cutoff:3.500A) Processing helix chain 'B' and resid 593 through 608 removed outlier: 4.065A pdb=" N LEU B 597 " --> pdb=" O TYR B 593 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N THR B 598 " --> pdb=" O GLN B 594 " (cutoff:3.500A) removed outlier: 4.744A pdb=" N GLY B 599 " --> pdb=" O HIS B 595 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N ILE B 600 " --> pdb=" O ASN B 596 " (cutoff:3.500A) Processing helix chain 'B' and resid 609 through 612 removed outlier: 3.508A pdb=" N PHE B 612 " --> pdb=" O ASN B 609 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 609 through 612' Processing helix chain 'B' and resid 614 through 621 removed outlier: 3.849A pdb=" N ARG B 620 " --> pdb=" O GLU B 616 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N LEU B 621 " --> pdb=" O ILE B 617 " (cutoff:3.500A) Processing helix chain 'B' and resid 633 through 637 removed outlier: 3.695A pdb=" N VAL B 637 " --> pdb=" O THR B 633 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 633 through 637' Processing helix chain 'B' and resid 648 through 653 removed outlier: 4.011A pdb=" N PHE B 652 " --> pdb=" O ILE B 648 " (cutoff:3.500A) Processing helix chain 'B' and resid 655 through 676 removed outlier: 4.027A pdb=" N LEU B 661 " --> pdb=" O MET B 657 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N ARG B 662 " --> pdb=" O SER B 658 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N PHE B 666 " --> pdb=" O ARG B 662 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N GLU B 674 " --> pdb=" O ALA B 670 " (cutoff:3.500A) Processing helix chain 'B' and resid 676 through 688 removed outlier: 3.899A pdb=" N MET B 685 " --> pdb=" O ARG B 681 " (cutoff:3.500A) Processing helix chain 'B' and resid 697 through 725 removed outlier: 4.380A pdb=" N GLN B 703 " --> pdb=" O GLY B 699 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N CYS B 704 " --> pdb=" O VAL B 700 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ALA B 708 " --> pdb=" O CYS B 704 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N HIS B 713 " --> pdb=" O SER B 709 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N PHE B 714 " --> pdb=" O GLU B 710 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N TYR B 720 " --> pdb=" O HIS B 716 " (cutoff:3.500A) Processing helix chain 'B' and resid 726 through 731 removed outlier: 3.548A pdb=" N SER B 730 " --> pdb=" O VAL B 726 " (cutoff:3.500A) Processing helix chain 'B' and resid 731 through 736 Processing helix chain 'B' and resid 744 through 762 removed outlier: 3.750A pdb=" N ILE B 748 " --> pdb=" O LEU B 744 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ALA B 749 " --> pdb=" O ASP B 745 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N VAL B 753 " --> pdb=" O ALA B 749 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N PHE B 754 " --> pdb=" O ALA B 750 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N LEU B 755 " --> pdb=" O HIS B 751 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N ILE B 758 " --> pdb=" O PHE B 754 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ILE B 759 " --> pdb=" O LEU B 755 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N SER B 760 " --> pdb=" O ASP B 756 " (cutoff:3.500A) Processing helix chain 'B' and resid 768 through 809 removed outlier: 3.539A pdb=" N GLN B 774 " --> pdb=" O ALA B 770 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ALA B 777 " --> pdb=" O ASN B 773 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N VAL B 778 " --> pdb=" O GLN B 774 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ILE B 782 " --> pdb=" O VAL B 778 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N ILE B 783 " --> pdb=" O PHE B 779 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N ASP B 790 " --> pdb=" O GLN B 786 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N ALA B 791 " --> pdb=" O ASN B 787 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N ILE B 792 " --> pdb=" O ALA B 788 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ALA B 796 " --> pdb=" O ILE B 792 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N GLU B 799 " --> pdb=" O ALA B 795 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N GLU B 807 " --> pdb=" O ARG B 803 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N LYS B 809 " --> pdb=" O GLN B 805 " (cutoff:3.500A) Processing helix chain 'B' and resid 826 through 839 removed outlier: 3.894A pdb=" N ASN B 830 " --> pdb=" O GLU B 826 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N LYS B 831 " --> pdb=" O GLU B 827 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N ARG B 832 " --> pdb=" O GLU B 828 " (cutoff:3.500A) Processing helix chain 'B' and resid 839 through 866 removed outlier: 3.601A pdb=" N GLN B 846 " --> pdb=" O LYS B 842 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N HIS B 852 " --> pdb=" O ARG B 848 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N GLY B 856 " --> pdb=" O HIS B 852 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N GLN B 860 " --> pdb=" O GLY B 856 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N VAL B 863 " --> pdb=" O GLN B 859 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LEU B 864 " --> pdb=" O GLN B 860 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N LEU B 865 " --> pdb=" O PHE B 861 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N THR B 866 " --> pdb=" O LEU B 862 " (cutoff:3.500A) Processing helix chain 'B' and resid 873 through 881 removed outlier: 3.541A pdb=" N PHE B 878 " --> pdb=" O ARG B 874 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ARG B 879 " --> pdb=" O PHE B 875 " (cutoff:3.500A) Processing helix chain 'B' and resid 882 through 885 removed outlier: 3.671A pdb=" N HIS B 885 " --> pdb=" O PHE B 882 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 882 through 885' Processing helix chain 'C' and resid 232 through 236 removed outlier: 3.518A pdb=" N THR C 235 " --> pdb=" O LEU C 232 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LEU C 236 " --> pdb=" O PRO C 233 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 232 through 236' Processing helix chain 'C' and resid 237 through 253 removed outlier: 3.526A pdb=" N GLU C 242 " --> pdb=" O LEU C 238 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N SER C 243 " --> pdb=" O ALA C 239 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N GLU C 247 " --> pdb=" O SER C 243 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N TYR C 251 " --> pdb=" O GLU C 247 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N VAL C 252 " --> pdb=" O ASP C 248 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N LEU C 253 " --> pdb=" O LEU C 249 " (cutoff:3.500A) Processing helix chain 'C' and resid 281 through 289 removed outlier: 3.501A pdb=" N GLU C 286 " --> pdb=" O LEU C 282 " (cutoff:3.500A) removed outlier: 4.753A pdb=" N LEU C 287 " --> pdb=" O SER C 283 " (cutoff:3.500A) Processing helix chain 'C' and resid 290 through 295 Proline residue: C 293 - end of helix No H-bonds generated for 'chain 'C' and resid 290 through 295' Processing helix chain 'C' and resid 301 through 306 Processing helix chain 'C' and resid 310 through 314 removed outlier: 4.085A pdb=" N TYR C 313 " --> pdb=" O SER C 310 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N GLY C 314 " --> pdb=" O PHE C 311 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 310 through 314' Processing helix chain 'C' and resid 318 through 323 Processing helix chain 'C' and resid 325 through 335 removed outlier: 3.673A pdb=" N LEU C 334 " --> pdb=" O GLU C 330 " (cutoff:3.500A) Processing helix chain 'C' and resid 335 through 342 Processing helix chain 'C' and resid 348 through 356 removed outlier: 4.032A pdb=" N PHE C 354 " --> pdb=" O GLN C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 356 through 363 removed outlier: 3.692A pdb=" N MET C 363 " --> pdb=" O ALA C 359 " (cutoff:3.500A) Processing helix chain 'C' and resid 365 through 373 removed outlier: 4.340A pdb=" N THR C 371 " --> pdb=" O ALA C 367 " (cutoff:3.500A) Processing helix chain 'C' and resid 381 through 390 removed outlier: 4.748A pdb=" N LEU C 387 " --> pdb=" O THR C 383 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N HIS C 388 " --> pdb=" O LEU C 384 " (cutoff:3.500A) Processing helix chain 'C' and resid 400 through 409 removed outlier: 3.868A pdb=" N CYS C 404 " --> pdb=" O ALA C 400 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N TYR C 406 " --> pdb=" O GLU C 402 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N THR C 408 " --> pdb=" O CYS C 404 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N LYS C 409 " --> pdb=" O LEU C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 412 through 423 removed outlier: 3.638A pdb=" N VAL C 418 " --> pdb=" O PRO C 414 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LEU C 419 " --> pdb=" O TYR C 415 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLU C 420 " --> pdb=" O PHE C 416 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N LYS C 421 " --> pdb=" O GLU C 417 " (cutoff:3.500A) Processing helix chain 'C' and resid 471 through 473 No H-bonds generated for 'chain 'C' and resid 471 through 473' Processing helix chain 'C' and resid 474 through 490 removed outlier: 4.340A pdb=" N LEU C 479 " --> pdb=" O ALA C 475 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N GLY C 482 " --> pdb=" O ILE C 478 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N TYR C 484 " --> pdb=" O SER C 480 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N VAL C 487 " --> pdb=" O LYS C 483 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N VAL C 488 " --> pdb=" O TYR C 484 " (cutoff:3.500A) Processing helix chain 'C' and resid 512 through 533 removed outlier: 3.741A pdb=" N GLU C 517 " --> pdb=" O VAL C 513 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ALA C 519 " --> pdb=" O GLN C 515 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N TYR C 522 " --> pdb=" O LYS C 518 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N LYS C 525 " --> pdb=" O ASN C 521 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N LEU C 527 " --> pdb=" O ALA C 523 " (cutoff:3.500A) Processing helix chain 'C' and resid 537 through 546 removed outlier: 3.554A pdb=" N ARG C 542 " --> pdb=" O VAL C 538 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N SER C 543 " --> pdb=" O ALA C 539 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N ILE C 544 " --> pdb=" O HIS C 540 " (cutoff:3.500A) Processing helix chain 'C' and resid 552 through 563 removed outlier: 4.132A pdb=" N PHE C 556 " --> pdb=" O GLN C 552 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N HIS C 558 " --> pdb=" O ASP C 554 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N ASP C 561 " --> pdb=" O VAL C 557 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N LEU C 562 " --> pdb=" O HIS C 558 " (cutoff:3.500A) Processing helix chain 'C' and resid 575 through 590 removed outlier: 3.501A pdb=" N LEU C 579 " --> pdb=" O THR C 575 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N ALA C 581 " --> pdb=" O PRO C 577 " (cutoff:3.500A) Processing helix chain 'C' and resid 597 through 599 No H-bonds generated for 'chain 'C' and resid 597 through 599' Processing helix chain 'C' and resid 652 through 657 removed outlier: 3.756A pdb=" N LEU C 656 " --> pdb=" O PRO C 653 " (cutoff:3.500A) Processing helix chain 'C' and resid 663 through 691 removed outlier: 4.013A pdb=" N ARG C 671 " --> pdb=" O GLN C 667 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N HIS C 672 " --> pdb=" O MET C 668 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N MET C 673 " --> pdb=" O LEU C 669 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N CYS C 676 " --> pdb=" O HIS C 672 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N GLU C 680 " --> pdb=" O CYS C 676 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N CYS C 684 " --> pdb=" O GLU C 680 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N SER C 685 " --> pdb=" O ARG C 681 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N TRP C 687 " --> pdb=" O LEU C 683 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N ILE C 688 " --> pdb=" O CYS C 684 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N SER C 689 " --> pdb=" O SER C 685 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N LYS C 691 " --> pdb=" O TRP C 687 " (cutoff:3.500A) Processing helix chain 'C' and resid 707 through 719 removed outlier: 4.045A pdb=" N ARG C 713 " --> pdb=" O THR C 709 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N PHE C 717 " --> pdb=" O ARG C 713 " (cutoff:3.500A) Processing helix chain 'C' and resid 721 through 728 removed outlier: 3.518A pdb=" N GLU C 728 " --> pdb=" O TYR C 724 " (cutoff:3.500A) Processing helix chain 'C' and resid 730 through 741 removed outlier: 3.511A pdb=" N LYS C 739 " --> pdb=" O HIS C 735 " (cutoff:3.500A) Processing helix chain 'C' and resid 746 through 765 removed outlier: 4.043A pdb=" N GLY C 752 " --> pdb=" O ASP C 748 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N THR C 755 " --> pdb=" O LEU C 751 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N PHE C 757 " --> pdb=" O HIS C 753 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N THR C 760 " --> pdb=" O GLY C 756 " (cutoff:3.500A) Processing helix chain 'C' and resid 774 through 791 removed outlier: 3.926A pdb=" N VAL C 782 " --> pdb=" O LYS C 778 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N CYS C 783 " --> pdb=" O LEU C 779 " (cutoff:3.500A) Processing helix chain 'C' and resid 847 through 870 removed outlier: 4.239A pdb=" N ASN C 851 " --> pdb=" O GLU C 847 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N LYS C 852 " --> pdb=" O ALA C 848 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ALA C 859 " --> pdb=" O LYS C 855 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ILE C 870 " --> pdb=" O ALA C 866 " (cutoff:3.500A) Processing helix chain 'C' and resid 881 through 888 removed outlier: 4.301A pdb=" N SER C 885 " --> pdb=" O ALA C 881 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 448 through 450 Processing sheet with id=AA2, first strand: chain 'B' and resid 623 through 625 removed outlier: 3.534A pdb=" N SER B 639 " --> pdb=" O ARG B 624 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 262 through 263 Processing sheet with id=AA4, first strand: chain 'C' and resid 437 through 438 removed outlier: 3.540A pdb=" N GLU C 438 " --> pdb=" O THR C 461 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 601 through 604 376 hydrogen bonds defined for protein. 1110 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: 2.56 Time building geometry restraints manager: 2.86 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 2804 1.33 - 1.45: 1367 1.45 - 1.57: 5038 1.57 - 1.69: 0 1.69 - 1.81: 91 Bond restraints: 9300 Sorted by residual: bond pdb=" CA THR B 308 " pdb=" C THR B 308 " ideal model delta sigma weight residual 1.523 1.487 0.037 1.80e-02 3.09e+03 4.12e+00 bond pdb=" CA ILE B 471 " pdb=" CB ILE B 471 " ideal model delta sigma weight residual 1.537 1.523 0.015 1.29e-02 6.01e+03 1.29e+00 bond pdb=" CA THR C 383 " pdb=" C THR C 383 " ideal model delta sigma weight residual 1.523 1.506 0.017 1.56e-02 4.11e+03 1.24e+00 bond pdb=" N ASP B 743 " pdb=" CA ASP B 743 " ideal model delta sigma weight residual 1.457 1.470 -0.013 1.29e-02 6.01e+03 1.03e+00 bond pdb=" CA ASN B 883 " pdb=" CB ASN B 883 " ideal model delta sigma weight residual 1.533 1.550 -0.017 1.66e-02 3.63e+03 9.97e-01 ... (remaining 9295 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.12: 11930 1.12 - 2.23: 511 2.23 - 3.35: 66 3.35 - 4.47: 16 4.47 - 5.58: 19 Bond angle restraints: 12542 Sorted by residual: angle pdb=" C ASP C 397 " pdb=" N SER C 398 " pdb=" CA SER C 398 " ideal model delta sigma weight residual 121.54 126.55 -5.01 1.91e+00 2.74e-01 6.88e+00 angle pdb=" C GLN B 742 " pdb=" N ASP B 743 " pdb=" CA ASP B 743 " ideal model delta sigma weight residual 121.54 126.37 -4.83 1.91e+00 2.74e-01 6.39e+00 angle pdb=" N ASP B 622 " pdb=" CA ASP B 622 " pdb=" C ASP B 622 " ideal model delta sigma weight residual 108.34 111.45 -3.11 1.31e+00 5.83e-01 5.62e+00 angle pdb=" CA TRP C 353 " pdb=" CB TRP C 353 " pdb=" CG TRP C 353 " ideal model delta sigma weight residual 113.60 118.07 -4.47 1.90e+00 2.77e-01 5.55e+00 angle pdb=" N LEU C 384 " pdb=" CA LEU C 384 " pdb=" C LEU C 384 " ideal model delta sigma weight residual 114.31 111.50 2.81 1.29e+00 6.01e-01 4.74e+00 ... (remaining 12537 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.89: 4952 16.89 - 33.78: 490 33.78 - 50.67: 117 50.67 - 67.56: 14 67.56 - 84.45: 9 Dihedral angle restraints: 5582 sinusoidal: 2298 harmonic: 3284 Sorted by residual: dihedral pdb=" CA PHE B 652 " pdb=" C PHE B 652 " pdb=" N THR B 653 " pdb=" CA THR B 653 " ideal model delta harmonic sigma weight residual 180.00 161.11 18.89 0 5.00e+00 4.00e-02 1.43e+01 dihedral pdb=" CA SER C 469 " pdb=" C SER C 469 " pdb=" N PHE C 470 " pdb=" CA PHE C 470 " ideal model delta harmonic sigma weight residual 180.00 161.95 18.05 0 5.00e+00 4.00e-02 1.30e+01 dihedral pdb=" CA ASP B 745 " pdb=" C ASP B 745 " pdb=" N HIS B 746 " pdb=" CA HIS B 746 " ideal model delta harmonic sigma weight residual 180.00 162.23 17.77 0 5.00e+00 4.00e-02 1.26e+01 ... (remaining 5579 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 727 0.030 - 0.060: 512 0.060 - 0.090: 114 0.090 - 0.120: 46 0.120 - 0.150: 6 Chirality restraints: 1405 Sorted by residual: chirality pdb=" CA ASN B 883 " pdb=" N ASN B 883 " pdb=" C ASN B 883 " pdb=" CB ASN B 883 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.61e-01 chirality pdb=" CB VAL C 571 " pdb=" CA VAL C 571 " pdb=" CG1 VAL C 571 " pdb=" CG2 VAL C 571 " both_signs ideal model delta sigma weight residual False -2.63 -2.49 -0.14 2.00e-01 2.50e+01 4.96e-01 chirality pdb=" CA ASP B 743 " pdb=" N ASP B 743 " pdb=" C ASP B 743 " pdb=" CB ASP B 743 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.66e-01 ... (remaining 1402 not shown) Planarity restraints: 1576 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU C 292 " -0.046 5.00e-02 4.00e+02 6.96e-02 7.74e+00 pdb=" N PRO C 293 " 0.120 5.00e-02 4.00e+02 pdb=" CA PRO C 293 " -0.035 5.00e-02 4.00e+02 pdb=" CD PRO C 293 " -0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO C 576 " 0.031 5.00e-02 4.00e+02 4.64e-02 3.45e+00 pdb=" N PRO C 577 " -0.080 5.00e-02 4.00e+02 pdb=" CA PRO C 577 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO C 577 " 0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR C 575 " 0.026 5.00e-02 4.00e+02 3.95e-02 2.49e+00 pdb=" N PRO C 576 " -0.068 5.00e-02 4.00e+02 pdb=" CA PRO C 576 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO C 576 " 0.022 5.00e-02 4.00e+02 ... (remaining 1573 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 1380 2.75 - 3.29: 8948 3.29 - 3.82: 13207 3.82 - 4.36: 16502 4.36 - 4.90: 27049 Nonbonded interactions: 67086 Sorted by model distance: nonbonded pdb=" OE2 GLU B 247 " pdb=" OG1 THR B 363 " model vdw 2.211 3.040 nonbonded pdb=" NE2 GLN B 259 " pdb=" OE1 GLN C 350 " model vdw 2.232 3.120 nonbonded pdb=" OH TYR B 464 " pdb=" ND2 ASN B 491 " model vdw 2.237 3.120 nonbonded pdb=" O SER C 299 " pdb=" OG SER C 299 " model vdw 2.284 3.040 nonbonded pdb=" O LYS C 774 " pdb=" OG SER C 777 " model vdw 2.285 3.040 ... (remaining 67081 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 6.510 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.330 Check model and map are aligned: 0.060 Set scattering table: 0.090 Process input model: 25.460 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.030 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:2.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.540 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8272 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 0.039 9300 Z= 0.292 Angle : 0.553 5.584 12542 Z= 0.311 Chirality : 0.041 0.150 1405 Planarity : 0.004 0.070 1576 Dihedral : 14.359 84.449 3438 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer: Outliers : 0.00 % Allowed : 7.80 % Favored : 92.20 % 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: -5.29 (0.20), residues: 1073 helix: -3.88 (0.13), residues: 693 sheet: -2.57 (0.91), residues: 34 loop : -2.20 (0.33), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 652 HIS 0.004 0.001 HIS B 301 PHE 0.020 0.001 PHE B 317 TYR 0.013 0.001 TYR C 355 ARG 0.004 0.000 ARG B 391 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2146 Ramachandran restraints generated. 1073 Oldfield, 0 Emsley, 1073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2146 Ramachandran restraints generated. 1073 Oldfield, 0 Emsley, 1073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 159 time to evaluate : 1.073 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 379 LYS cc_start: 0.8622 (tttt) cc_final: 0.8401 (tttm) REVERT: B 543 LYS cc_start: 0.9002 (tmtt) cc_final: 0.8790 (tmtt) REVERT: B 573 PHE cc_start: 0.8851 (t80) cc_final: 0.8466 (t80) REVERT: B 772 LEU cc_start: 0.8667 (tp) cc_final: 0.8337 (tt) REVERT: B 843 MET cc_start: 0.9120 (mtm) cc_final: 0.8850 (mtm) REVERT: C 405 LEU cc_start: 0.9227 (tp) cc_final: 0.9026 (tt) REVERT: C 409 LYS cc_start: 0.9493 (tttt) cc_final: 0.9285 (tttm) REVERT: C 456 TRP cc_start: 0.6611 (p-90) cc_final: 0.6079 (m-10) REVERT: C 589 MET cc_start: 0.7634 (mmt) cc_final: 0.6972 (mmt) REVERT: C 656 LEU cc_start: 0.8341 (mp) cc_final: 0.7873 (mp) REVERT: C 716 ASN cc_start: 0.8266 (t0) cc_final: 0.7735 (t0) REVERT: C 751 LEU cc_start: 0.9253 (mt) cc_final: 0.8908 (tt) outliers start: 0 outliers final: 0 residues processed: 159 average time/residue: 0.2507 time to fit residues: 54.4321 Evaluate side-chains 120 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 120 time to evaluate : 1.154 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 92 optimal weight: 4.9990 chunk 83 optimal weight: 1.9990 chunk 46 optimal weight: 0.9990 chunk 28 optimal weight: 0.5980 chunk 56 optimal weight: 2.9990 chunk 44 optimal weight: 1.9990 chunk 86 optimal weight: 2.9990 chunk 33 optimal weight: 0.2980 chunk 52 optimal weight: 0.0030 chunk 64 optimal weight: 0.6980 chunk 99 optimal weight: 0.9980 overall best weight: 0.5190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 259 GLN B 345 GLN B 401 HIS B 491 ASN B 643 HIS B 739 GLN B 751 HIS B 830 ASN B 846 GLN C 264 GLN C 342 HIS C 350 GLN C 486 ASN C 540 HIS C 667 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.121509 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.094570 restraints weight = 14914.518| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.095714 restraints weight = 11241.268| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.095894 restraints weight = 9184.247| |-----------------------------------------------------------------------------| r_work (final): 0.3085 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8184 moved from start: 0.1714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9300 Z= 0.193 Angle : 0.573 7.689 12542 Z= 0.302 Chirality : 0.040 0.158 1405 Planarity : 0.004 0.071 1576 Dihedral : 4.462 18.210 1208 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 1.30 % Allowed : 14.00 % Favored : 84.70 % 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: -3.82 (0.22), residues: 1073 helix: -2.52 (0.16), residues: 731 sheet: -3.07 (0.84), residues: 24 loop : -1.94 (0.35), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 687 HIS 0.006 0.001 HIS C 735 PHE 0.025 0.001 PHE B 836 TYR 0.012 0.001 TYR B 793 ARG 0.004 0.000 ARG B 654 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2146 Ramachandran restraints generated. 1073 Oldfield, 0 Emsley, 1073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2146 Ramachandran restraints generated. 1073 Oldfield, 0 Emsley, 1073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 141 time to evaluate : 1.058 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 261 ILE cc_start: 0.8951 (mp) cc_final: 0.8714 (mt) REVERT: B 543 LYS cc_start: 0.9092 (tmtt) cc_final: 0.8807 (tmtt) REVERT: B 673 MET cc_start: 0.8964 (mmt) cc_final: 0.8397 (mmm) REVERT: B 763 LEU cc_start: 0.7835 (mp) cc_final: 0.7626 (mp) REVERT: B 782 ILE cc_start: 0.9005 (mt) cc_final: 0.8674 (mp) REVERT: C 409 LYS cc_start: 0.9471 (tttt) cc_final: 0.9263 (tttm) REVERT: C 532 MET cc_start: 0.9157 (mmt) cc_final: 0.8756 (mmp) REVERT: C 656 LEU cc_start: 0.8365 (mp) cc_final: 0.8004 (mp) REVERT: C 680 GLU cc_start: 0.8910 (pp20) cc_final: 0.8428 (tm-30) REVERT: C 716 ASN cc_start: 0.8320 (t0) cc_final: 0.7835 (t0) REVERT: C 751 LEU cc_start: 0.9128 (mt) cc_final: 0.8804 (tt) outliers start: 13 outliers final: 7 residues processed: 148 average time/residue: 0.1779 time to fit residues: 38.6100 Evaluate side-chains 131 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 124 time to evaluate : 0.994 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 277 VAL Chi-restraints excluded: chain B residue 491 ASN Chi-restraints excluded: chain B residue 592 LEU Chi-restraints excluded: chain C residue 256 VAL Chi-restraints excluded: chain C residue 427 ILE Chi-restraints excluded: chain C residue 557 VAL Chi-restraints excluded: chain C residue 789 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 51 optimal weight: 0.9990 chunk 32 optimal weight: 5.9990 chunk 109 optimal weight: 0.7980 chunk 39 optimal weight: 0.9980 chunk 30 optimal weight: 0.9990 chunk 24 optimal weight: 0.2980 chunk 80 optimal weight: 1.9990 chunk 9 optimal weight: 0.7980 chunk 26 optimal weight: 1.9990 chunk 42 optimal weight: 1.9990 chunk 95 optimal weight: 1.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 665 ASN C 241 GLN C 672 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.120919 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.095004 restraints weight = 15129.595| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.096218 restraints weight = 11236.988| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.096898 restraints weight = 10253.344| |-----------------------------------------------------------------------------| r_work (final): 0.3127 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8192 moved from start: 0.2021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 9300 Z= 0.234 Angle : 0.548 7.452 12542 Z= 0.285 Chirality : 0.041 0.155 1405 Planarity : 0.004 0.070 1576 Dihedral : 4.379 18.358 1208 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 2.60 % Allowed : 15.50 % Favored : 81.90 % 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: -2.96 (0.24), residues: 1073 helix: -1.78 (0.18), residues: 731 sheet: -3.06 (0.78), residues: 24 loop : -1.83 (0.35), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 687 HIS 0.003 0.001 HIS C 735 PHE 0.014 0.001 PHE C 470 TYR 0.010 0.001 TYR C 675 ARG 0.002 0.000 ARG B 563 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2146 Ramachandran restraints generated. 1073 Oldfield, 0 Emsley, 1073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2146 Ramachandran restraints generated. 1073 Oldfield, 0 Emsley, 1073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 130 time to evaluate : 1.007 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 297 LEU cc_start: 0.9580 (OUTLIER) cc_final: 0.9301 (tp) REVERT: B 543 LYS cc_start: 0.9009 (tmtt) cc_final: 0.8748 (tmtt) REVERT: B 594 GLN cc_start: 0.8183 (tt0) cc_final: 0.7895 (tm-30) REVERT: B 673 MET cc_start: 0.8947 (mmt) cc_final: 0.8434 (mmm) REVERT: B 702 HIS cc_start: 0.8436 (t-90) cc_final: 0.8102 (t-90) REVERT: B 763 LEU cc_start: 0.7660 (mp) cc_final: 0.7435 (mp) REVERT: C 409 LYS cc_start: 0.9479 (tttt) cc_final: 0.9256 (tttm) REVERT: C 532 MET cc_start: 0.9200 (mmt) cc_final: 0.8808 (mmp) REVERT: C 590 SER cc_start: 0.9275 (OUTLIER) cc_final: 0.8923 (t) REVERT: C 656 LEU cc_start: 0.8412 (mp) cc_final: 0.8021 (mp) REVERT: C 680 GLU cc_start: 0.8923 (pp20) cc_final: 0.8397 (tm-30) REVERT: C 716 ASN cc_start: 0.8327 (t0) cc_final: 0.7842 (t0) REVERT: C 751 LEU cc_start: 0.9135 (mt) cc_final: 0.8842 (tt) REVERT: C 785 MET cc_start: 0.8139 (mmm) cc_final: 0.7915 (mmm) outliers start: 26 outliers final: 15 residues processed: 144 average time/residue: 0.1705 time to fit residues: 36.4822 Evaluate side-chains 139 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 122 time to evaluate : 1.009 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 254 ILE Chi-restraints excluded: chain B residue 277 VAL Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain B residue 400 VAL Chi-restraints excluded: chain B residue 406 THR Chi-restraints excluded: chain B residue 592 LEU Chi-restraints excluded: chain B residue 643 HIS Chi-restraints excluded: chain C residue 256 VAL Chi-restraints excluded: chain C residue 427 ILE Chi-restraints excluded: chain C residue 554 ASP Chi-restraints excluded: chain C residue 557 VAL Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain C residue 590 SER Chi-restraints excluded: chain C residue 729 VAL Chi-restraints excluded: chain C residue 760 THR Chi-restraints excluded: chain C residue 789 CYS Chi-restraints excluded: chain C residue 868 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 82 optimal weight: 0.0970 chunk 29 optimal weight: 5.9990 chunk 63 optimal weight: 0.6980 chunk 78 optimal weight: 0.9990 chunk 9 optimal weight: 0.2980 chunk 72 optimal weight: 1.9990 chunk 6 optimal weight: 0.2980 chunk 109 optimal weight: 5.9990 chunk 73 optimal weight: 0.5980 chunk 89 optimal weight: 0.6980 chunk 64 optimal weight: 0.7980 overall best weight: 0.3978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 491 ASN C 678 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.123087 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.096515 restraints weight = 14727.989| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.097332 restraints weight = 10862.928| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.097555 restraints weight = 9501.888| |-----------------------------------------------------------------------------| r_work (final): 0.3131 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8159 moved from start: 0.2379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 9300 Z= 0.159 Angle : 0.515 8.457 12542 Z= 0.266 Chirality : 0.039 0.168 1405 Planarity : 0.004 0.069 1576 Dihedral : 4.157 17.349 1208 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 2.50 % Allowed : 17.50 % Favored : 80.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -2.33 (0.25), residues: 1073 helix: -1.26 (0.19), residues: 733 sheet: -2.68 (0.87), residues: 22 loop : -1.76 (0.35), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 687 HIS 0.002 0.000 HIS C 735 PHE 0.012 0.001 PHE C 470 TYR 0.008 0.001 TYR C 675 ARG 0.002 0.000 ARG B 654 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2146 Ramachandran restraints generated. 1073 Oldfield, 0 Emsley, 1073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2146 Ramachandran restraints generated. 1073 Oldfield, 0 Emsley, 1073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 135 time to evaluate : 1.150 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 297 LEU cc_start: 0.9527 (OUTLIER) cc_final: 0.9241 (tp) REVERT: B 594 GLN cc_start: 0.8139 (tt0) cc_final: 0.7857 (tm-30) REVERT: B 673 MET cc_start: 0.8908 (mmt) cc_final: 0.8375 (mmm) REVERT: B 702 HIS cc_start: 0.8389 (t-90) cc_final: 0.8047 (t-90) REVERT: B 843 MET cc_start: 0.8990 (mtm) cc_final: 0.8711 (ptp) REVERT: C 409 LYS cc_start: 0.9439 (tttt) cc_final: 0.9215 (tttm) REVERT: C 502 GLU cc_start: 0.5419 (tp30) cc_final: 0.4799 (tp30) REVERT: C 532 MET cc_start: 0.9135 (mmt) cc_final: 0.8671 (mmp) REVERT: C 589 MET cc_start: 0.7685 (mmt) cc_final: 0.7189 (mmt) REVERT: C 590 SER cc_start: 0.9323 (OUTLIER) cc_final: 0.9006 (t) REVERT: C 656 LEU cc_start: 0.8411 (mp) cc_final: 0.8038 (mp) REVERT: C 680 GLU cc_start: 0.8862 (pp20) cc_final: 0.8192 (tm-30) REVERT: C 716 ASN cc_start: 0.8354 (t0) cc_final: 0.7890 (t0) REVERT: C 751 LEU cc_start: 0.9033 (mt) cc_final: 0.8769 (tt) REVERT: C 785 MET cc_start: 0.8378 (mmm) cc_final: 0.8094 (mmm) outliers start: 25 outliers final: 16 residues processed: 150 average time/residue: 0.1876 time to fit residues: 42.1476 Evaluate side-chains 141 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 123 time to evaluate : 1.014 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 277 VAL Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain B residue 406 THR Chi-restraints excluded: chain B residue 491 ASN Chi-restraints excluded: chain B residue 592 LEU Chi-restraints excluded: chain B residue 643 HIS Chi-restraints excluded: chain C residue 256 VAL Chi-restraints excluded: chain C residue 277 ASP Chi-restraints excluded: chain C residue 338 LEU Chi-restraints excluded: chain C residue 427 ILE Chi-restraints excluded: chain C residue 554 ASP Chi-restraints excluded: chain C residue 557 VAL Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain C residue 590 SER Chi-restraints excluded: chain C residue 604 ASP Chi-restraints excluded: chain C residue 650 VAL Chi-restraints excluded: chain C residue 760 THR Chi-restraints excluded: chain C residue 789 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 81 optimal weight: 0.5980 chunk 11 optimal weight: 1.9990 chunk 94 optimal weight: 0.0870 chunk 16 optimal weight: 0.9980 chunk 104 optimal weight: 1.9990 chunk 83 optimal weight: 0.5980 chunk 38 optimal weight: 6.9990 chunk 73 optimal weight: 0.4980 chunk 58 optimal weight: 0.6980 chunk 53 optimal weight: 0.9990 chunk 68 optimal weight: 0.3980 overall best weight: 0.4358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 486 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.122695 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.096414 restraints weight = 14805.477| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.097958 restraints weight = 10767.111| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.098906 restraints weight = 7947.414| |-----------------------------------------------------------------------------| r_work (final): 0.3158 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8156 moved from start: 0.2524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9300 Z= 0.163 Angle : 0.514 9.324 12542 Z= 0.264 Chirality : 0.040 0.210 1405 Planarity : 0.004 0.068 1576 Dihedral : 4.077 17.011 1208 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 2.70 % Allowed : 18.10 % Favored : 79.20 % 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: -1.96 (0.25), residues: 1073 helix: -0.96 (0.19), residues: 740 sheet: -2.33 (0.94), residues: 22 loop : -1.66 (0.36), residues: 311 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 687 HIS 0.002 0.000 HIS C 678 PHE 0.017 0.001 PHE B 836 TYR 0.008 0.001 TYR C 460 ARG 0.001 0.000 ARG B 654 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2146 Ramachandran restraints generated. 1073 Oldfield, 0 Emsley, 1073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2146 Ramachandran restraints generated. 1073 Oldfield, 0 Emsley, 1073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 132 time to evaluate : 1.344 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 297 LEU cc_start: 0.9539 (OUTLIER) cc_final: 0.9239 (tp) REVERT: B 594 GLN cc_start: 0.8015 (tt0) cc_final: 0.7814 (tm-30) REVERT: B 673 MET cc_start: 0.8915 (mmt) cc_final: 0.8409 (mmm) REVERT: C 409 LYS cc_start: 0.9456 (tttt) cc_final: 0.9237 (tttm) REVERT: C 515 GLN cc_start: 0.8579 (tt0) cc_final: 0.8300 (tt0) REVERT: C 532 MET cc_start: 0.9150 (mmt) cc_final: 0.8678 (mmp) REVERT: C 589 MET cc_start: 0.7892 (mmt) cc_final: 0.7373 (mmt) REVERT: C 590 SER cc_start: 0.9325 (OUTLIER) cc_final: 0.8991 (t) REVERT: C 656 LEU cc_start: 0.8386 (mp) cc_final: 0.8011 (mp) REVERT: C 680 GLU cc_start: 0.8881 (pp20) cc_final: 0.8335 (tm-30) REVERT: C 716 ASN cc_start: 0.8485 (t0) cc_final: 0.8040 (t0) REVERT: C 746 ASN cc_start: 0.8869 (OUTLIER) cc_final: 0.8363 (p0) REVERT: C 751 LEU cc_start: 0.9052 (mt) cc_final: 0.8747 (tt) REVERT: C 785 MET cc_start: 0.8322 (mmm) cc_final: 0.7992 (mmm) outliers start: 27 outliers final: 20 residues processed: 148 average time/residue: 0.1858 time to fit residues: 40.4082 Evaluate side-chains 146 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 123 time to evaluate : 1.090 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 254 ILE Chi-restraints excluded: chain B residue 277 VAL Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain B residue 304 ILE Chi-restraints excluded: chain B residue 400 VAL Chi-restraints excluded: chain B residue 406 THR Chi-restraints excluded: chain B residue 592 LEU Chi-restraints excluded: chain B residue 643 HIS Chi-restraints excluded: chain C residue 256 VAL Chi-restraints excluded: chain C residue 277 ASP Chi-restraints excluded: chain C residue 338 LEU Chi-restraints excluded: chain C residue 427 ILE Chi-restraints excluded: chain C residue 485 LEU Chi-restraints excluded: chain C residue 486 ASN Chi-restraints excluded: chain C residue 554 ASP Chi-restraints excluded: chain C residue 557 VAL Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain C residue 590 SER Chi-restraints excluded: chain C residue 604 ASP Chi-restraints excluded: chain C residue 650 VAL Chi-restraints excluded: chain C residue 746 ASN Chi-restraints excluded: chain C residue 760 THR Chi-restraints excluded: chain C residue 789 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 7 optimal weight: 0.9990 chunk 69 optimal weight: 0.7980 chunk 77 optimal weight: 0.9990 chunk 30 optimal weight: 0.7980 chunk 33 optimal weight: 2.9990 chunk 102 optimal weight: 0.6980 chunk 104 optimal weight: 0.9980 chunk 88 optimal weight: 0.9990 chunk 63 optimal weight: 0.8980 chunk 97 optimal weight: 3.9990 chunk 42 optimal weight: 0.6980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 491 ASN C 486 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.121573 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.095325 restraints weight = 14890.160| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.096286 restraints weight = 10946.177| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.096711 restraints weight = 10448.670| |-----------------------------------------------------------------------------| r_work (final): 0.3118 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8191 moved from start: 0.2575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 9300 Z= 0.234 Angle : 0.545 8.470 12542 Z= 0.276 Chirality : 0.041 0.192 1405 Planarity : 0.004 0.070 1576 Dihedral : 4.117 17.879 1208 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 2.90 % Allowed : 19.30 % Favored : 77.80 % 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: -1.72 (0.26), residues: 1073 helix: -0.77 (0.19), residues: 740 sheet: -2.22 (0.95), residues: 22 loop : -1.61 (0.36), residues: 311 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 687 HIS 0.002 0.001 HIS C 678 PHE 0.012 0.001 PHE C 470 TYR 0.009 0.001 TYR C 675 ARG 0.002 0.000 ARG C 660 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2146 Ramachandran restraints generated. 1073 Oldfield, 0 Emsley, 1073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2146 Ramachandran restraints generated. 1073 Oldfield, 0 Emsley, 1073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 124 time to evaluate : 1.085 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 477 MET cc_start: 0.8782 (tpp) cc_final: 0.8560 (tpt) REVERT: B 594 GLN cc_start: 0.8085 (tt0) cc_final: 0.7849 (tm-30) REVERT: B 673 MET cc_start: 0.8939 (mmt) cc_final: 0.8410 (mmm) REVERT: C 409 LYS cc_start: 0.9451 (tttt) cc_final: 0.9227 (tttm) REVERT: C 589 MET cc_start: 0.7883 (mmt) cc_final: 0.7379 (mmt) REVERT: C 656 LEU cc_start: 0.8443 (mp) cc_final: 0.8040 (mp) REVERT: C 680 GLU cc_start: 0.8862 (pp20) cc_final: 0.8287 (tm-30) REVERT: C 716 ASN cc_start: 0.8450 (t0) cc_final: 0.7969 (t0) REVERT: C 746 ASN cc_start: 0.8860 (OUTLIER) cc_final: 0.8312 (p0) REVERT: C 751 LEU cc_start: 0.9107 (mt) cc_final: 0.8691 (tt) REVERT: C 785 MET cc_start: 0.8237 (mmm) cc_final: 0.7915 (mmm) outliers start: 29 outliers final: 23 residues processed: 141 average time/residue: 0.1749 time to fit residues: 36.9321 Evaluate side-chains 145 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 121 time to evaluate : 0.988 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 254 ILE Chi-restraints excluded: chain B residue 277 VAL Chi-restraints excluded: chain B residue 304 ILE Chi-restraints excluded: chain B residue 367 LEU Chi-restraints excluded: chain B residue 400 VAL Chi-restraints excluded: chain B residue 406 THR Chi-restraints excluded: chain B residue 592 LEU Chi-restraints excluded: chain B residue 643 HIS Chi-restraints excluded: chain B residue 661 LEU Chi-restraints excluded: chain C residue 256 VAL Chi-restraints excluded: chain C residue 277 ASP Chi-restraints excluded: chain C residue 427 ILE Chi-restraints excluded: chain C residue 485 LEU Chi-restraints excluded: chain C residue 486 ASN Chi-restraints excluded: chain C residue 554 ASP Chi-restraints excluded: chain C residue 557 VAL Chi-restraints excluded: chain C residue 574 ILE Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain C residue 590 SER Chi-restraints excluded: chain C residue 604 ASP Chi-restraints excluded: chain C residue 650 VAL Chi-restraints excluded: chain C residue 746 ASN Chi-restraints excluded: chain C residue 760 THR Chi-restraints excluded: chain C residue 789 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 47 optimal weight: 0.8980 chunk 1 optimal weight: 0.8980 chunk 3 optimal weight: 0.7980 chunk 100 optimal weight: 1.9990 chunk 41 optimal weight: 0.6980 chunk 27 optimal weight: 1.9990 chunk 58 optimal weight: 0.0270 chunk 71 optimal weight: 0.5980 chunk 37 optimal weight: 0.9990 chunk 49 optimal weight: 4.9990 chunk 75 optimal weight: 0.5980 overall best weight: 0.5438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 486 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.121862 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.095469 restraints weight = 15082.138| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.097285 restraints weight = 10540.807| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.097559 restraints weight = 9440.144| |-----------------------------------------------------------------------------| r_work (final): 0.3170 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8190 moved from start: 0.2697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9300 Z= 0.186 Angle : 0.526 8.046 12542 Z= 0.269 Chirality : 0.040 0.222 1405 Planarity : 0.004 0.069 1576 Dihedral : 4.049 17.639 1208 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.82 % Favored : 96.09 % Rotamer: Outliers : 3.10 % Allowed : 19.40 % Favored : 77.50 % 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: -1.46 (0.26), residues: 1073 helix: -0.57 (0.19), residues: 741 sheet: -2.11 (0.96), residues: 22 loop : -1.54 (0.36), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 687 HIS 0.006 0.001 HIS B 558 PHE 0.012 0.001 PHE C 556 TYR 0.007 0.001 TYR C 675 ARG 0.003 0.000 ARG C 660 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2146 Ramachandran restraints generated. 1073 Oldfield, 0 Emsley, 1073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2146 Ramachandran restraints generated. 1073 Oldfield, 0 Emsley, 1073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 129 time to evaluate : 1.175 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 477 MET cc_start: 0.8792 (tpp) cc_final: 0.8545 (tpt) REVERT: B 594 GLN cc_start: 0.8070 (tt0) cc_final: 0.7819 (tm-30) REVERT: B 673 MET cc_start: 0.8930 (mmt) cc_final: 0.8426 (mmm) REVERT: B 725 GLU cc_start: 0.6032 (mm-30) cc_final: 0.5811 (mm-30) REVERT: C 409 LYS cc_start: 0.9451 (tttt) cc_final: 0.9222 (tttm) REVERT: C 550 MET cc_start: 0.8778 (mmm) cc_final: 0.8430 (mmm) REVERT: C 589 MET cc_start: 0.7956 (mmt) cc_final: 0.7441 (mmt) REVERT: C 656 LEU cc_start: 0.8398 (mp) cc_final: 0.7984 (mp) REVERT: C 680 GLU cc_start: 0.8876 (pp20) cc_final: 0.8593 (tm-30) REVERT: C 716 ASN cc_start: 0.8509 (t0) cc_final: 0.8053 (t0) REVERT: C 746 ASN cc_start: 0.8867 (OUTLIER) cc_final: 0.8341 (p0) REVERT: C 751 LEU cc_start: 0.9154 (mt) cc_final: 0.8707 (tt) REVERT: C 785 MET cc_start: 0.8102 (mmm) cc_final: 0.7848 (mmm) outliers start: 31 outliers final: 25 residues processed: 149 average time/residue: 0.1741 time to fit residues: 38.7630 Evaluate side-chains 149 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 123 time to evaluate : 1.103 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 254 ILE Chi-restraints excluded: chain B residue 277 VAL Chi-restraints excluded: chain B residue 304 ILE Chi-restraints excluded: chain B residue 340 SER Chi-restraints excluded: chain B residue 400 VAL Chi-restraints excluded: chain B residue 406 THR Chi-restraints excluded: chain B residue 414 LEU Chi-restraints excluded: chain B residue 592 LEU Chi-restraints excluded: chain B residue 643 HIS Chi-restraints excluded: chain B residue 661 LEU Chi-restraints excluded: chain B residue 743 ASP Chi-restraints excluded: chain C residue 236 LEU Chi-restraints excluded: chain C residue 256 VAL Chi-restraints excluded: chain C residue 277 ASP Chi-restraints excluded: chain C residue 338 LEU Chi-restraints excluded: chain C residue 427 ILE Chi-restraints excluded: chain C residue 485 LEU Chi-restraints excluded: chain C residue 486 ASN Chi-restraints excluded: chain C residue 554 ASP Chi-restraints excluded: chain C residue 557 VAL Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain C residue 604 ASP Chi-restraints excluded: chain C residue 650 VAL Chi-restraints excluded: chain C residue 746 ASN Chi-restraints excluded: chain C residue 760 THR Chi-restraints excluded: chain C residue 789 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 80 optimal weight: 2.9990 chunk 78 optimal weight: 0.5980 chunk 60 optimal weight: 0.8980 chunk 34 optimal weight: 0.0050 chunk 69 optimal weight: 0.9980 chunk 51 optimal weight: 0.9990 chunk 82 optimal weight: 0.7980 chunk 22 optimal weight: 0.8980 chunk 89 optimal weight: 1.9990 chunk 95 optimal weight: 2.9990 chunk 28 optimal weight: 2.9990 overall best weight: 0.6394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 486 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.121705 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.095397 restraints weight = 15113.241| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.096099 restraints weight = 11018.753| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.096492 restraints weight = 11009.006| |-----------------------------------------------------------------------------| r_work (final): 0.3108 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8186 moved from start: 0.2773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9300 Z= 0.205 Angle : 0.535 9.089 12542 Z= 0.272 Chirality : 0.040 0.221 1405 Planarity : 0.004 0.070 1576 Dihedral : 4.052 17.861 1208 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 3.60 % Allowed : 19.20 % Favored : 77.20 % 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: -1.25 (0.26), residues: 1073 helix: -0.41 (0.19), residues: 742 sheet: -2.69 (1.65), residues: 10 loop : -1.46 (0.35), residues: 321 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP C 687 HIS 0.005 0.001 HIS B 558 PHE 0.011 0.001 PHE C 470 TYR 0.007 0.001 TYR C 675 ARG 0.002 0.000 ARG C 660 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2146 Ramachandran restraints generated. 1073 Oldfield, 0 Emsley, 1073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2146 Ramachandran restraints generated. 1073 Oldfield, 0 Emsley, 1073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 129 time to evaluate : 1.017 Fit side-chains revert: symmetry clash REVERT: B 446 PHE cc_start: 0.8853 (OUTLIER) cc_final: 0.8282 (t80) REVERT: B 477 MET cc_start: 0.8754 (tpp) cc_final: 0.8532 (tpt) REVERT: B 594 GLN cc_start: 0.8174 (tt0) cc_final: 0.7854 (tm-30) REVERT: B 673 MET cc_start: 0.8978 (mmt) cc_final: 0.8410 (mmm) REVERT: B 711 MET cc_start: 0.8434 (mtt) cc_final: 0.8180 (mtt) REVERT: B 725 GLU cc_start: 0.6011 (mm-30) cc_final: 0.5774 (mm-30) REVERT: C 409 LYS cc_start: 0.9442 (tttt) cc_final: 0.9221 (tttm) REVERT: C 456 TRP cc_start: 0.6779 (p-90) cc_final: 0.6538 (p-90) REVERT: C 550 MET cc_start: 0.8765 (mmm) cc_final: 0.8388 (mmm) REVERT: C 589 MET cc_start: 0.8007 (mmt) cc_final: 0.7509 (mmt) REVERT: C 656 LEU cc_start: 0.8442 (mp) cc_final: 0.7976 (mp) REVERT: C 680 GLU cc_start: 0.8857 (pp20) cc_final: 0.8592 (tm-30) REVERT: C 714 MET cc_start: 0.8242 (mtt) cc_final: 0.7911 (mtp) REVERT: C 716 ASN cc_start: 0.8475 (t0) cc_final: 0.8015 (t0) REVERT: C 746 ASN cc_start: 0.8823 (OUTLIER) cc_final: 0.8300 (p0) REVERT: C 751 LEU cc_start: 0.9125 (mt) cc_final: 0.8679 (tt) REVERT: C 785 MET cc_start: 0.8174 (mmm) cc_final: 0.7882 (mmm) outliers start: 36 outliers final: 30 residues processed: 153 average time/residue: 0.1700 time to fit residues: 39.2860 Evaluate side-chains 155 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 123 time to evaluate : 1.016 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 254 ILE Chi-restraints excluded: chain B residue 277 VAL Chi-restraints excluded: chain B residue 304 ILE Chi-restraints excluded: chain B residue 340 SER Chi-restraints excluded: chain B residue 367 LEU Chi-restraints excluded: chain B residue 400 VAL Chi-restraints excluded: chain B residue 406 THR Chi-restraints excluded: chain B residue 414 LEU Chi-restraints excluded: chain B residue 446 PHE Chi-restraints excluded: chain B residue 592 LEU Chi-restraints excluded: chain B residue 643 HIS Chi-restraints excluded: chain B residue 661 LEU Chi-restraints excluded: chain B residue 743 ASP Chi-restraints excluded: chain C residue 236 LEU Chi-restraints excluded: chain C residue 256 VAL Chi-restraints excluded: chain C residue 277 ASP Chi-restraints excluded: chain C residue 338 LEU Chi-restraints excluded: chain C residue 418 VAL Chi-restraints excluded: chain C residue 427 ILE Chi-restraints excluded: chain C residue 485 LEU Chi-restraints excluded: chain C residue 486 ASN Chi-restraints excluded: chain C residue 554 ASP Chi-restraints excluded: chain C residue 557 VAL Chi-restraints excluded: chain C residue 574 ILE Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain C residue 590 SER Chi-restraints excluded: chain C residue 650 VAL Chi-restraints excluded: chain C residue 729 VAL Chi-restraints excluded: chain C residue 736 ILE Chi-restraints excluded: chain C residue 746 ASN Chi-restraints excluded: chain C residue 760 THR Chi-restraints excluded: chain C residue 789 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 62 optimal weight: 0.0270 chunk 7 optimal weight: 0.8980 chunk 17 optimal weight: 3.9990 chunk 40 optimal weight: 2.9990 chunk 61 optimal weight: 1.9990 chunk 8 optimal weight: 0.3980 chunk 46 optimal weight: 0.9980 chunk 30 optimal weight: 0.9980 chunk 10 optimal weight: 0.8980 chunk 34 optimal weight: 0.0770 chunk 105 optimal weight: 0.7980 overall best weight: 0.4396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 486 ASN C 753 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.122726 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.096657 restraints weight = 14890.622| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.097207 restraints weight = 10879.875| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.098072 restraints weight = 8895.811| |-----------------------------------------------------------------------------| r_work (final): 0.3129 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8163 moved from start: 0.2877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9300 Z= 0.168 Angle : 0.525 7.910 12542 Z= 0.268 Chirality : 0.040 0.221 1405 Planarity : 0.004 0.068 1576 Dihedral : 3.969 17.318 1208 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.26 % Favored : 96.64 % Rotamer: Outliers : 3.60 % Allowed : 19.20 % Favored : 77.20 % 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: -1.01 (0.26), residues: 1073 helix: -0.22 (0.20), residues: 744 sheet: -2.35 (1.75), residues: 10 loop : -1.41 (0.36), residues: 319 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP C 687 HIS 0.005 0.000 HIS B 558 PHE 0.011 0.001 PHE C 470 TYR 0.006 0.001 TYR C 675 ARG 0.002 0.000 ARG C 660 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2146 Ramachandran restraints generated. 1073 Oldfield, 0 Emsley, 1073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2146 Ramachandran restraints generated. 1073 Oldfield, 0 Emsley, 1073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 132 time to evaluate : 1.037 Fit side-chains revert: symmetry clash REVERT: B 477 MET cc_start: 0.8776 (tpp) cc_final: 0.8566 (tpt) REVERT: B 594 GLN cc_start: 0.8127 (tt0) cc_final: 0.7822 (tm-30) REVERT: B 673 MET cc_start: 0.8966 (mmt) cc_final: 0.8391 (mmm) REVERT: B 711 MET cc_start: 0.8402 (mtt) cc_final: 0.8159 (mtt) REVERT: B 725 GLU cc_start: 0.5893 (mm-30) cc_final: 0.5635 (mm-30) REVERT: C 409 LYS cc_start: 0.9439 (tttt) cc_final: 0.9212 (tttm) REVERT: C 458 GLN cc_start: 0.7562 (pm20) cc_final: 0.7351 (pm20) REVERT: C 502 GLU cc_start: 0.5401 (tp30) cc_final: 0.4964 (tp30) REVERT: C 550 MET cc_start: 0.8744 (mmm) cc_final: 0.8371 (mmm) REVERT: C 560 MET cc_start: 0.8968 (tpp) cc_final: 0.8725 (tpp) REVERT: C 588 ARG cc_start: 0.8943 (mtt90) cc_final: 0.7428 (ttt180) REVERT: C 589 MET cc_start: 0.7985 (mmt) cc_final: 0.7517 (mmt) REVERT: C 656 LEU cc_start: 0.8407 (mp) cc_final: 0.7981 (mp) REVERT: C 714 MET cc_start: 0.8209 (mtt) cc_final: 0.7884 (mtp) REVERT: C 716 ASN cc_start: 0.8454 (t0) cc_final: 0.7985 (t0) REVERT: C 746 ASN cc_start: 0.8791 (OUTLIER) cc_final: 0.8235 (p0) REVERT: C 751 LEU cc_start: 0.8968 (mt) cc_final: 0.8618 (tt) REVERT: C 785 MET cc_start: 0.8176 (mmm) cc_final: 0.7889 (mmm) outliers start: 36 outliers final: 30 residues processed: 157 average time/residue: 0.1786 time to fit residues: 41.6269 Evaluate side-chains 158 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 127 time to evaluate : 1.012 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 254 ILE Chi-restraints excluded: chain B residue 277 VAL Chi-restraints excluded: chain B residue 304 ILE Chi-restraints excluded: chain B residue 340 SER Chi-restraints excluded: chain B residue 367 LEU Chi-restraints excluded: chain B residue 400 VAL Chi-restraints excluded: chain B residue 406 THR Chi-restraints excluded: chain B residue 414 LEU Chi-restraints excluded: chain B residue 592 LEU Chi-restraints excluded: chain B residue 643 HIS Chi-restraints excluded: chain B residue 661 LEU Chi-restraints excluded: chain B residue 743 ASP Chi-restraints excluded: chain C residue 236 LEU Chi-restraints excluded: chain C residue 256 VAL Chi-restraints excluded: chain C residue 277 ASP Chi-restraints excluded: chain C residue 338 LEU Chi-restraints excluded: chain C residue 418 VAL Chi-restraints excluded: chain C residue 427 ILE Chi-restraints excluded: chain C residue 485 LEU Chi-restraints excluded: chain C residue 486 ASN Chi-restraints excluded: chain C residue 554 ASP Chi-restraints excluded: chain C residue 557 VAL Chi-restraints excluded: chain C residue 574 ILE Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain C residue 590 SER Chi-restraints excluded: chain C residue 650 VAL Chi-restraints excluded: chain C residue 729 VAL Chi-restraints excluded: chain C residue 736 ILE Chi-restraints excluded: chain C residue 746 ASN Chi-restraints excluded: chain C residue 760 THR Chi-restraints excluded: chain C residue 789 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 95 optimal weight: 1.9990 chunk 106 optimal weight: 5.9990 chunk 69 optimal weight: 0.1980 chunk 99 optimal weight: 0.9980 chunk 80 optimal weight: 0.7980 chunk 54 optimal weight: 0.4980 chunk 0 optimal weight: 2.9990 chunk 96 optimal weight: 0.8980 chunk 53 optimal weight: 1.9990 chunk 98 optimal weight: 0.9980 chunk 40 optimal weight: 1.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 486 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.121820 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.094966 restraints weight = 15116.545| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.096796 restraints weight = 10965.227| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.097447 restraints weight = 8423.183| |-----------------------------------------------------------------------------| r_work (final): 0.3164 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8195 moved from start: 0.2916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9300 Z= 0.217 Angle : 0.557 9.263 12542 Z= 0.282 Chirality : 0.041 0.223 1405 Planarity : 0.004 0.067 1576 Dihedral : 4.005 18.028 1208 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.73 % Favored : 96.18 % Rotamer: Outliers : 3.30 % Allowed : 19.30 % Favored : 77.40 % 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: -0.94 (0.26), residues: 1073 helix: -0.14 (0.20), residues: 744 sheet: -1.87 (0.98), residues: 22 loop : -1.45 (0.37), residues: 307 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP C 456 HIS 0.005 0.001 HIS B 558 PHE 0.011 0.001 PHE C 470 TYR 0.007 0.001 TYR C 675 ARG 0.002 0.000 ARG C 660 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2146 Ramachandran restraints generated. 1073 Oldfield, 0 Emsley, 1073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2146 Ramachandran restraints generated. 1073 Oldfield, 0 Emsley, 1073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 124 time to evaluate : 1.128 Fit side-chains revert: symmetry clash REVERT: B 477 MET cc_start: 0.8749 (tpp) cc_final: 0.8502 (tpt) REVERT: B 594 GLN cc_start: 0.8069 (tt0) cc_final: 0.7823 (tm-30) REVERT: B 673 MET cc_start: 0.8970 (mmt) cc_final: 0.8492 (mmm) REVERT: C 409 LYS cc_start: 0.9441 (tttt) cc_final: 0.9209 (tttm) REVERT: C 456 TRP cc_start: 0.7096 (p-90) cc_final: 0.6875 (p-90) REVERT: C 458 GLN cc_start: 0.7616 (pm20) cc_final: 0.7223 (pm20) REVERT: C 502 GLU cc_start: 0.5470 (tp30) cc_final: 0.5097 (tp30) REVERT: C 550 MET cc_start: 0.8749 (mmm) cc_final: 0.8403 (mmm) REVERT: C 560 MET cc_start: 0.8990 (tpp) cc_final: 0.8734 (tpp) REVERT: C 589 MET cc_start: 0.7996 (mmt) cc_final: 0.7493 (mmt) REVERT: C 656 LEU cc_start: 0.8389 (mp) cc_final: 0.7905 (mp) REVERT: C 680 GLU cc_start: 0.8703 (tm-30) cc_final: 0.8249 (tm-30) REVERT: C 714 MET cc_start: 0.8235 (mtt) cc_final: 0.7908 (mtp) REVERT: C 716 ASN cc_start: 0.8500 (t0) cc_final: 0.8026 (t0) REVERT: C 746 ASN cc_start: 0.8828 (OUTLIER) cc_final: 0.8298 (p0) REVERT: C 751 LEU cc_start: 0.9011 (mt) cc_final: 0.8641 (tt) REVERT: C 785 MET cc_start: 0.8116 (mmm) cc_final: 0.7840 (mmm) outliers start: 33 outliers final: 29 residues processed: 147 average time/residue: 0.1764 time to fit residues: 38.6064 Evaluate side-chains 152 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 122 time to evaluate : 1.040 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 254 ILE Chi-restraints excluded: chain B residue 277 VAL Chi-restraints excluded: chain B residue 304 ILE Chi-restraints excluded: chain B residue 340 SER Chi-restraints excluded: chain B residue 367 LEU Chi-restraints excluded: chain B residue 400 VAL Chi-restraints excluded: chain B residue 406 THR Chi-restraints excluded: chain B residue 414 LEU Chi-restraints excluded: chain B residue 592 LEU Chi-restraints excluded: chain B residue 643 HIS Chi-restraints excluded: chain B residue 661 LEU Chi-restraints excluded: chain B residue 743 ASP Chi-restraints excluded: chain C residue 236 LEU Chi-restraints excluded: chain C residue 256 VAL Chi-restraints excluded: chain C residue 277 ASP Chi-restraints excluded: chain C residue 338 LEU Chi-restraints excluded: chain C residue 418 VAL Chi-restraints excluded: chain C residue 427 ILE Chi-restraints excluded: chain C residue 485 LEU Chi-restraints excluded: chain C residue 486 ASN Chi-restraints excluded: chain C residue 554 ASP Chi-restraints excluded: chain C residue 557 VAL Chi-restraints excluded: chain C residue 574 ILE Chi-restraints excluded: chain C residue 590 SER Chi-restraints excluded: chain C residue 650 VAL Chi-restraints excluded: chain C residue 729 VAL Chi-restraints excluded: chain C residue 736 ILE Chi-restraints excluded: chain C residue 746 ASN Chi-restraints excluded: chain C residue 760 THR Chi-restraints excluded: chain C residue 789 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 61 optimal weight: 1.9990 chunk 42 optimal weight: 1.9990 chunk 46 optimal weight: 3.9990 chunk 95 optimal weight: 1.9990 chunk 9 optimal weight: 0.6980 chunk 31 optimal weight: 0.7980 chunk 26 optimal weight: 0.0770 chunk 37 optimal weight: 0.7980 chunk 13 optimal weight: 0.7980 chunk 103 optimal weight: 0.7980 chunk 60 optimal weight: 0.4980 overall best weight: 0.5738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.122275 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.095346 restraints weight = 14954.941| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.097017 restraints weight = 10633.207| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.096991 restraints weight = 8259.674| |-----------------------------------------------------------------------------| r_work (final): 0.3160 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8190 moved from start: 0.2946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9300 Z= 0.192 Angle : 0.540 7.840 12542 Z= 0.276 Chirality : 0.041 0.222 1405 Planarity : 0.004 0.067 1576 Dihedral : 3.970 17.765 1208 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.36 % Favored : 96.55 % Rotamer: Outliers : 3.10 % Allowed : 20.40 % Favored : 76.50 % 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: -0.83 (0.27), residues: 1073 helix: -0.03 (0.20), residues: 748 sheet: -1.79 (0.99), residues: 22 loop : -1.52 (0.37), residues: 303 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP C 687 HIS 0.005 0.001 HIS B 558 PHE 0.011 0.001 PHE C 470 TYR 0.006 0.001 TYR C 675 ARG 0.002 0.000 ARG C 660 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2870.77 seconds wall clock time: 51 minutes 20.86 seconds (3080.86 seconds total)