Starting phenix.real_space_refine on Thu Feb 13 16:31:44 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6v6b_21067/02_2025/6v6b_21067.cif Found real_map, /net/cci-nas-00/data/ceres_data/6v6b_21067/02_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_21067/02_2025/6v6b_21067.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6v6b_21067/02_2025/6v6b_21067.map" model { file = "/net/cci-nas-00/data/ceres_data/6v6b_21067/02_2025/6v6b_21067.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6v6b_21067/02_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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/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: 6.21, per 1000 atoms: 0.68 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: 2.20 Conformation dependent library (CDL) restraints added in 993.3 milliseconds 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: 0.91 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: 2.36 Time building geometry restraints manager: 2.52 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.400 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: 0.380 Check model and map are aligned: 0.070 Set scattering table: 0.100 Process input model: 23.260 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.040 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:2.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.270 ------------------------------------------------------------------------------- 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 : 0.976 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: 0.2552 time to fit residues: 55.2223 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 : 1.119 ------------------------------------------------------------------------------- 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 = 0.121527 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.094601 restraints weight = 14902.587| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.095799 restraints weight = 11214.623| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.095960 restraints weight = 9128.425| |-----------------------------------------------------------------------------| r_work (final): 0.3085 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8183 moved from start: 0.1711 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= 0.192 Angle : 0.573 7.690 12542 Z= 0.302 Chirality : 0.040 0.158 1405 Planarity : 0.004 0.071 1576 Dihedral : 4.464 18.214 1208 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 1.30 % Allowed : 14.20 % Favored : 84.50 % 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: -3.82 (0.22), residues: 1073 helix: -2.52 (0.16), residues: 731 sheet: -3.07 (0.84), residues: 24 loop : -1.93 (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 0.003 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 : 1.250 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 261 ILE cc_start: 0.8951 (mp) cc_final: 0.8713 (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: 0.8399 (mmm) REVERT: B 763 LEU cc_start: 0.7839 (mp) cc_final: 0.7630 (mp) REVERT: B 782 ILE cc_start: 0.9006 (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: 0.9156 (mmt) cc_final: 0.8757 (mmp) REVERT: C 656 LEU cc_start: 0.8363 (mp) cc_final: 0.8002 (mp) REVERT: C 680 GLU cc_start: 0.8912 (pp20) cc_final: 0.8432 (tm-30) REVERT: C 716 ASN cc_start: 0.8320 (t0) cc_final: 0.7835 (t0) REVERT: C 751 LEU cc_start: 0.9129 (mt) cc_final: 0.8804 (tt) outliers start: 13 outliers final: 7 residues processed: 148 average time/residue: 0.1930 time to fit residues: 42.2032 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 : 1.135 ------------------------------------------------------------------------------- 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: 5.9990 chunk 32 optimal weight: 5.9990 chunk 109 optimal weight: 0.9980 chunk 39 optimal weight: 0.2980 chunk 30 optimal weight: 0.6980 chunk 24 optimal weight: 0.0870 chunk 80 optimal weight: 1.9990 chunk 9 optimal weight: 0.5980 chunk 26 optimal weight: 1.9990 chunk 42 optimal weight: 1.9990 chunk 95 optimal weight: 1.9990 overall best weight: 0.5358 ------------------------------------------------------------------------------- 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 = 0.3514 r_free = 0.3514 target = 0.121929 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.095360 restraints weight = 15088.616| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.096963 restraints weight = 10815.038| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.097304 restraints weight = 9931.621| |-----------------------------------------------------------------------------| r_work (final): 0.3133 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8183 moved from start: 0.2097 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= 0.182 Angle : 0.524 7.336 12542 Z= 0.273 Chirality : 0.039 0.153 1405 Planarity : 0.004 0.069 1576 Dihedral : 4.276 17.612 1208 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 2.20 % Allowed : 15.80 % Favored : 82.00 % 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: -2.88 (0.24), residues: 1073 helix: -1.72 (0.18), residues: 735 sheet: -3.02 (0.78), residues: 24 loop : -1.78 (0.36), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 687 HIS 0.003 0.000 HIS C 735 PHE 0.013 0.001 PHE C 470 TYR 0.010 0.001 TYR C 675 ARG 0.002 0.000 ARG B 654 *********************** 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: 22 poor density : 134 time to evaluate : 1.029 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 297 LEU cc_start: 0.9547 (OUTLIER) cc_final: 0.9280 (tp) REVERT: B 594 GLN cc_start: 0.8071 (tt0) cc_final: 0.7858 (tm-30) REVERT: B 673 MET cc_start: 0.8926 (mmt) cc_final: 0.8402 (mmm) REVERT: B 702 HIS cc_start: 0.8395 (t-90) cc_final: 0.8051 (t-90) REVERT: B 763 LEU cc_start: 0.7477 (mp) cc_final: 0.7217 (mp) REVERT: C 409 LYS cc_start: 0.9486 (tttt) cc_final: 0.9269 (tttm) REVERT: C 532 MET cc_start: 0.9225 (mmt) cc_final: 0.8792 (mmp) REVERT: C 590 SER cc_start: 0.9266 (OUTLIER) cc_final: 0.8918 (t) REVERT: C 656 LEU cc_start: 0.8348 (mp) cc_final: 0.7977 (mp) REVERT: C 680 GLU cc_start: 0.8861 (pp20) cc_final: 0.8371 (tm-30) REVERT: C 716 ASN cc_start: 0.8301 (t0) cc_final: 0.7813 (t0) REVERT: C 751 LEU cc_start: 0.9089 (mt) cc_final: 0.8821 (tt) REVERT: C 785 MET cc_start: 0.8162 (mmm) cc_final: 0.7906 (mmm) outliers start: 22 outliers final: 13 residues processed: 146 average time/residue: 0.1643 time to fit residues: 35.8314 Evaluate side-chains 135 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 120 time to evaluate : 1.132 ------------------------------------------------------------------------------- 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 434 ILE 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 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: 0.7980 chunk 29 optimal weight: 6.9990 chunk 63 optimal weight: 0.6980 chunk 78 optimal weight: 0.9980 chunk 9 optimal weight: 0.4980 chunk 72 optimal weight: 0.4980 chunk 6 optimal weight: 0.9990 chunk 109 optimal weight: 5.9990 chunk 73 optimal weight: 0.9980 chunk 89 optimal weight: 0.5980 chunk 64 optimal weight: 0.6980 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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 = 0.3515 r_free = 0.3515 target = 0.122099 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.095488 restraints weight = 14793.233| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.097114 restraints weight = 10831.249| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.097663 restraints weight = 8686.237| |-----------------------------------------------------------------------------| r_work (final): 0.3129 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8184 moved from start: 0.2374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9300 Z= 0.194 Angle : 0.528 8.355 12542 Z= 0.271 Chirality : 0.040 0.152 1405 Planarity : 0.004 0.070 1576 Dihedral : 4.190 17.681 1208 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 3.00 % Allowed : 17.30 % Favored : 79.70 % 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: -2.32 (0.25), residues: 1073 helix: -1.26 (0.19), residues: 735 sheet: -2.56 (0.91), residues: 22 loop : -1.74 (0.35), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 687 HIS 0.002 0.000 HIS C 735 PHE 0.012 0.001 PHE C 470 TYR 0.009 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 159 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 129 time to evaluate : 1.066 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 673 MET cc_start: 0.8907 (mmt) cc_final: 0.8423 (mmm) REVERT: C 409 LYS cc_start: 0.9482 (tttt) cc_final: 0.9260 (tttm) REVERT: C 502 GLU cc_start: 0.5701 (tp30) cc_final: 0.5065 (tp30) REVERT: C 532 MET cc_start: 0.9191 (mmt) cc_final: 0.8749 (mmp) REVERT: C 589 MET cc_start: 0.7701 (mmt) cc_final: 0.7195 (mmt) REVERT: C 590 SER cc_start: 0.9339 (OUTLIER) cc_final: 0.9015 (t) REVERT: C 656 LEU cc_start: 0.8401 (mp) cc_final: 0.8020 (mp) REVERT: C 680 GLU cc_start: 0.8929 (pp20) cc_final: 0.8208 (tm-30) REVERT: C 716 ASN cc_start: 0.8372 (t0) cc_final: 0.7904 (t0) REVERT: C 746 ASN cc_start: 0.8891 (OUTLIER) cc_final: 0.8388 (p0) REVERT: C 751 LEU cc_start: 0.9079 (mt) cc_final: 0.8764 (tt) REVERT: C 785 MET cc_start: 0.8306 (mmm) cc_final: 0.8016 (mmm) outliers start: 30 outliers final: 18 residues processed: 147 average time/residue: 0.1799 time to fit residues: 38.9301 Evaluate side-chains 142 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 122 time to evaluate : 1.027 ------------------------------------------------------------------------------- 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 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 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 668 MET 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 81 optimal weight: 0.4980 chunk 11 optimal weight: 0.5980 chunk 94 optimal weight: 0.4980 chunk 16 optimal weight: 0.7980 chunk 104 optimal weight: 0.8980 chunk 83 optimal weight: 0.6980 chunk 38 optimal weight: 6.9990 chunk 73 optimal weight: 0.6980 chunk 58 optimal weight: 0.9980 chunk 53 optimal weight: 0.9990 chunk 68 optimal weight: 0.1980 overall best weight: 0.4980 ------------------------------------------------------------------------------- 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 = 0.3524 r_free = 0.3524 target = 0.122704 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.095847 restraints weight = 14827.136| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.096776 restraints weight = 10879.952| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.097135 restraints weight = 8589.252| |-----------------------------------------------------------------------------| r_work (final): 0.3154 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8166 moved from start: 0.2584 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= 0.173 Angle : 0.516 9.271 12542 Z= 0.265 Chirality : 0.040 0.205 1405 Planarity : 0.004 0.069 1576 Dihedral : 4.086 17.190 1208 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 2.60 % Allowed : 18.60 % Favored : 78.80 % 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: -1.87 (0.25), residues: 1073 helix: -0.88 (0.19), residues: 740 sheet: -2.23 (0.97), residues: 22 loop : -1.67 (0.36), residues: 311 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP C 687 HIS 0.003 0.000 HIS C 678 PHE 0.018 0.001 PHE B 836 TYR 0.008 0.001 TYR B 793 ARG 0.003 0.000 ARG C 660 *********************** 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 157 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 131 time to evaluate : 1.130 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 673 MET cc_start: 0.8924 (mmt) cc_final: 0.8382 (mmm) REVERT: C 409 LYS cc_start: 0.9438 (tttt) cc_final: 0.9215 (tttm) REVERT: C 502 GLU cc_start: 0.5438 (tp30) cc_final: 0.5201 (tp30) REVERT: C 532 MET cc_start: 0.9133 (mmt) cc_final: 0.8536 (mmp) REVERT: C 589 MET cc_start: 0.7846 (mmt) cc_final: 0.7342 (mmt) REVERT: C 590 SER cc_start: 0.9321 (OUTLIER) cc_final: 0.9007 (t) REVERT: C 600 ASP cc_start: 0.6022 (t70) cc_final: 0.5791 (t70) REVERT: C 656 LEU cc_start: 0.8429 (mp) cc_final: 0.8040 (mp) REVERT: C 680 GLU cc_start: 0.8872 (pp20) cc_final: 0.8599 (tm-30) REVERT: C 716 ASN cc_start: 0.8468 (t0) cc_final: 0.8028 (t0) REVERT: C 746 ASN cc_start: 0.8797 (OUTLIER) cc_final: 0.8312 (p0) REVERT: C 751 LEU cc_start: 0.8979 (mt) cc_final: 0.8655 (tt) REVERT: C 785 MET cc_start: 0.8291 (mmm) cc_final: 0.7948 (mmm) outliers start: 26 outliers final: 18 residues processed: 144 average time/residue: 0.1947 time to fit residues: 41.6607 Evaluate side-chains 141 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 121 time to evaluate : 1.044 ------------------------------------------------------------------------------- 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 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 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 729 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: 0.9980 chunk 69 optimal weight: 0.9990 chunk 77 optimal weight: 1.9990 chunk 30 optimal weight: 0.6980 chunk 33 optimal weight: 2.9990 chunk 102 optimal weight: 0.9990 chunk 104 optimal weight: 1.9990 chunk 88 optimal weight: 2.9990 chunk 63 optimal weight: 0.7980 chunk 97 optimal weight: 3.9990 chunk 42 optimal weight: 0.6980 overall best weight: 0.8382 ------------------------------------------------------------------------------- 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 = 0.3503 r_free = 0.3503 target = 0.121120 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.095247 restraints weight = 14908.016| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.095193 restraints weight = 11422.807| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.095901 restraints weight = 11441.677| |-----------------------------------------------------------------------------| r_work (final): 0.3098 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8189 moved from start: 0.2620 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= 0.249 Angle : 0.556 8.643 12542 Z= 0.283 Chirality : 0.041 0.202 1405 Planarity : 0.004 0.071 1576 Dihedral : 4.154 18.384 1208 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 3.00 % Allowed : 19.20 % 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: -1.63 (0.26), residues: 1073 helix: -0.69 (0.19), residues: 742 sheet: -2.33 (0.93), residues: 22 loop : -1.59 (0.36), residues: 309 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP C 687 HIS 0.006 0.001 HIS B 558 PHE 0.014 0.001 PHE C 470 TYR 0.009 0.001 TYR C 675 ARG 0.003 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 150 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 120 time to evaluate : 1.096 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 477 MET cc_start: 0.8741 (tpp) cc_final: 0.8524 (tpt) REVERT: B 673 MET cc_start: 0.8946 (mmt) cc_final: 0.8395 (mmm) REVERT: C 409 LYS cc_start: 0.9436 (tttt) cc_final: 0.9202 (tttm) REVERT: C 589 MET cc_start: 0.8027 (mmt) cc_final: 0.7533 (mmt) REVERT: C 590 SER cc_start: 0.9297 (OUTLIER) cc_final: 0.8999 (t) REVERT: C 656 LEU cc_start: 0.8470 (mp) cc_final: 0.8077 (mp) REVERT: C 680 GLU cc_start: 0.8894 (pp20) cc_final: 0.8579 (tm-30) REVERT: C 716 ASN cc_start: 0.8441 (t0) cc_final: 0.7966 (t0) REVERT: C 751 LEU cc_start: 0.9069 (mt) cc_final: 0.8668 (tt) REVERT: C 785 MET cc_start: 0.8182 (mmm) cc_final: 0.7893 (mmm) outliers start: 30 outliers final: 23 residues processed: 136 average time/residue: 0.1795 time to fit residues: 36.4211 Evaluate side-chains 141 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 117 time to evaluate : 1.135 ------------------------------------------------------------------------------- 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 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 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 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: 0.9980 chunk 1 optimal weight: 0.9990 chunk 3 optimal weight: 0.7980 chunk 100 optimal weight: 0.8980 chunk 41 optimal weight: 0.7980 chunk 27 optimal weight: 1.9990 chunk 58 optimal weight: 0.1980 chunk 71 optimal weight: 0.3980 chunk 37 optimal weight: 0.6980 chunk 49 optimal weight: 4.9990 chunk 75 optimal weight: 0.6980 overall best weight: 0.5580 ------------------------------------------------------------------------------- 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 = 0.3512 r_free = 0.3512 target = 0.121857 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.096155 restraints weight = 15054.796| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.096917 restraints weight = 10648.182| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.097766 restraints weight = 10270.853| |-----------------------------------------------------------------------------| r_work (final): 0.3125 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8164 moved from start: 0.2748 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= 0.187 Angle : 0.523 7.687 12542 Z= 0.268 Chirality : 0.040 0.192 1405 Planarity : 0.004 0.069 1576 Dihedral : 4.086 18.054 1208 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 3.50 % Allowed : 19.70 % Favored : 76.80 % 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: -1.42 (0.26), residues: 1073 helix: -0.51 (0.19), residues: 741 sheet: -2.37 (0.89), residues: 22 loop : -1.57 (0.36), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 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 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 163 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 128 time to evaluate : 1.186 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 477 MET cc_start: 0.8753 (tpp) cc_final: 0.8513 (tpt) REVERT: B 673 MET cc_start: 0.8936 (mmt) cc_final: 0.8401 (mmm) REVERT: C 409 LYS cc_start: 0.9424 (tttt) cc_final: 0.9198 (tttm) REVERT: C 456 TRP cc_start: 0.6786 (p-90) cc_final: 0.5894 (m100) REVERT: C 550 MET cc_start: 0.8754 (mmm) cc_final: 0.8404 (mmm) REVERT: C 589 MET cc_start: 0.7996 (mmt) cc_final: 0.7491 (mmt) REVERT: C 590 SER cc_start: 0.9469 (OUTLIER) cc_final: 0.9108 (t) REVERT: C 656 LEU cc_start: 0.8418 (mp) cc_final: 0.7854 (mp) REVERT: C 680 GLU cc_start: 0.8891 (pp20) cc_final: 0.8629 (tm-30) REVERT: C 716 ASN cc_start: 0.8477 (t0) cc_final: 0.8018 (t0) REVERT: C 751 LEU cc_start: 0.9114 (mt) cc_final: 0.8706 (tt) REVERT: C 785 MET cc_start: 0.8167 (mmm) cc_final: 0.7875 (mmm) outliers start: 35 outliers final: 30 residues processed: 151 average time/residue: 0.1771 time to fit residues: 39.8209 Evaluate side-chains 157 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 126 time to evaluate : 1.231 ------------------------------------------------------------------------------- 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 434 ILE 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 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 604 ASP 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 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: 2.9990 chunk 60 optimal weight: 0.7980 chunk 34 optimal weight: 1.9990 chunk 69 optimal weight: 0.5980 chunk 51 optimal weight: 1.9990 chunk 82 optimal weight: 0.8980 chunk 22 optimal weight: 0.1980 chunk 89 optimal weight: 1.9990 chunk 95 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- 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 = 0.3495 r_free = 0.3495 target = 0.120549 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.094756 restraints weight = 15186.941| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.095732 restraints weight = 10857.785| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.096485 restraints weight = 9954.044| |-----------------------------------------------------------------------------| r_work (final): 0.3107 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8190 moved from start: 0.2765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 9300 Z= 0.261 Angle : 0.564 8.784 12542 Z= 0.284 Chirality : 0.042 0.184 1405 Planarity : 0.004 0.072 1576 Dihedral : 4.171 19.057 1208 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 3.60 % Allowed : 19.70 % Favored : 76.70 % 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: -1.30 (0.26), residues: 1073 helix: -0.42 (0.20), residues: 740 sheet: -2.17 (0.93), residues: 22 loop : -1.53 (0.36), residues: 311 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 687 HIS 0.004 0.001 HIS B 558 PHE 0.013 0.001 PHE C 470 TYR 0.009 0.001 TYR C 355 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 163 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 127 time to evaluate : 1.126 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 315 ARG cc_start: 0.7070 (mmt180) cc_final: 0.6789 (mmt180) REVERT: B 446 PHE cc_start: 0.8882 (OUTLIER) cc_final: 0.8277 (t80) REVERT: B 673 MET cc_start: 0.8995 (mmt) cc_final: 0.8451 (mmm) REVERT: C 399 GLN cc_start: 0.7651 (tm-30) cc_final: 0.6927 (tm-30) REVERT: C 409 LYS cc_start: 0.9415 (tttt) cc_final: 0.9181 (tttm) REVERT: C 420 GLU cc_start: 0.7154 (mt-10) cc_final: 0.6786 (mp0) REVERT: C 456 TRP cc_start: 0.6797 (p-90) cc_final: 0.6564 (p-90) REVERT: C 458 GLN cc_start: 0.7513 (pm20) cc_final: 0.7270 (pm20) REVERT: C 550 MET cc_start: 0.8784 (mmm) cc_final: 0.8419 (mmm) REVERT: C 589 MET cc_start: 0.8024 (mmt) cc_final: 0.7517 (mmt) REVERT: C 656 LEU cc_start: 0.8450 (mp) cc_final: 0.8011 (mp) REVERT: C 680 GLU cc_start: 0.8934 (pp20) cc_final: 0.8653 (tm-30) REVERT: C 716 ASN cc_start: 0.8462 (t0) cc_final: 0.7984 (t0) REVERT: C 746 ASN cc_start: 0.8823 (OUTLIER) cc_final: 0.8316 (p0) REVERT: C 751 LEU cc_start: 0.9138 (mt) cc_final: 0.8693 (tt) REVERT: C 785 MET cc_start: 0.8173 (mmm) cc_final: 0.7881 (mmm) outliers start: 36 outliers final: 29 residues processed: 153 average time/residue: 0.1863 time to fit residues: 41.8909 Evaluate side-chains 154 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 123 time to evaluate : 1.086 ------------------------------------------------------------------------------- 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 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 604 ASP 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: 0.4980 chunk 7 optimal weight: 0.8980 chunk 17 optimal weight: 0.5980 chunk 40 optimal weight: 2.9990 chunk 61 optimal weight: 1.9990 chunk 8 optimal weight: 0.1980 chunk 46 optimal weight: 0.8980 chunk 30 optimal weight: 0.6980 chunk 10 optimal weight: 0.6980 chunk 34 optimal weight: 2.9990 chunk 105 optimal weight: 3.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- 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 = 0.3512 r_free = 0.3512 target = 0.121845 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.095470 restraints weight = 14930.751| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.096307 restraints weight = 11022.703| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.096490 restraints weight = 9724.418| |-----------------------------------------------------------------------------| r_work (final): 0.3102 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8172 moved from start: 0.2857 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= 0.184 Angle : 0.528 7.222 12542 Z= 0.269 Chirality : 0.040 0.177 1405 Planarity : 0.004 0.069 1576 Dihedral : 4.055 18.262 1208 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 3.20 % Allowed : 20.30 % 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: -1.07 (0.26), residues: 1073 helix: -0.25 (0.20), residues: 746 sheet: -2.51 (1.71), residues: 10 loop : -1.49 (0.35), residues: 317 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 687 HIS 0.005 0.000 HIS B 558 PHE 0.010 0.001 PHE C 470 TYR 0.006 0.001 TYR C 675 ARG 0.002 0.000 ARG B 285 *********************** 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 161 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 129 time to evaluate : 1.084 Fit side-chains revert: symmetry clash REVERT: B 446 PHE cc_start: 0.8831 (OUTLIER) cc_final: 0.8120 (t80) REVERT: B 673 MET cc_start: 0.8925 (mmt) cc_final: 0.8381 (mmm) REVERT: C 409 LYS cc_start: 0.9424 (tttt) cc_final: 0.9198 (tttm) REVERT: C 456 TRP cc_start: 0.6779 (p-90) cc_final: 0.6575 (p-90) REVERT: C 458 GLN cc_start: 0.7473 (pm20) cc_final: 0.7221 (pm20) REVERT: C 477 LYS cc_start: 0.8551 (mttt) cc_final: 0.8322 (ttmt) REVERT: C 550 MET cc_start: 0.8749 (mmm) cc_final: 0.8373 (mmm) REVERT: C 588 ARG cc_start: 0.8963 (mtt90) cc_final: 0.7407 (ttt180) REVERT: C 589 MET cc_start: 0.7988 (mmt) cc_final: 0.7510 (mmt) REVERT: C 590 SER cc_start: 0.9460 (t) cc_final: 0.9112 (t) REVERT: C 656 LEU cc_start: 0.8453 (mp) cc_final: 0.8026 (mp) REVERT: C 680 GLU cc_start: 0.8872 (pp20) cc_final: 0.8632 (tm-30) REVERT: C 714 MET cc_start: 0.8211 (mtt) cc_final: 0.7878 (mtp) REVERT: C 716 ASN cc_start: 0.8461 (t0) cc_final: 0.7990 (t0) REVERT: C 751 LEU cc_start: 0.9068 (mt) cc_final: 0.8640 (tt) REVERT: C 785 MET cc_start: 0.8208 (mmm) cc_final: 0.7909 (mmm) outliers start: 32 outliers final: 28 residues processed: 153 average time/residue: 0.1769 time to fit residues: 39.7636 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 : 1.074 ------------------------------------------------------------------------------- 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 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 650 VAL Chi-restraints excluded: chain C residue 729 VAL Chi-restraints excluded: chain C residue 736 ILE 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: 0.2980 chunk 99 optimal weight: 0.8980 chunk 80 optimal weight: 0.9990 chunk 54 optimal weight: 0.7980 chunk 0 optimal weight: 2.9990 chunk 96 optimal weight: 0.9980 chunk 53 optimal weight: 0.6980 chunk 98 optimal weight: 0.6980 chunk 40 optimal weight: 0.7980 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 = 0.3501 r_free = 0.3501 target = 0.121069 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.095377 restraints weight = 15137.443| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.094941 restraints weight = 12136.171| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.095812 restraints weight = 11909.078| |-----------------------------------------------------------------------------| r_work (final): 0.3118 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8196 moved from start: 0.2907 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= 0.209 Angle : 0.547 9.336 12542 Z= 0.276 Chirality : 0.041 0.205 1405 Planarity : 0.004 0.070 1576 Dihedral : 4.055 18.406 1208 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 3.00 % Allowed : 20.90 % Favored : 76.10 % 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: -1.00 (0.26), residues: 1073 helix: -0.17 (0.20), residues: 746 sheet: -2.06 (0.95), residues: 22 loop : -1.52 (0.36), residues: 305 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 687 HIS 0.004 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 B 285 ********************** 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 155 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 125 time to evaluate : 1.112 Fit side-chains revert: symmetry clash REVERT: B 446 PHE cc_start: 0.8834 (OUTLIER) cc_final: 0.8140 (t80) REVERT: B 673 MET cc_start: 0.8990 (mmt) cc_final: 0.8438 (mmm) REVERT: C 409 LYS cc_start: 0.9402 (tttt) cc_final: 0.9171 (tttm) REVERT: C 420 GLU cc_start: 0.7083 (mt-10) cc_final: 0.6598 (mp0) REVERT: C 458 GLN cc_start: 0.7547 (pm20) cc_final: 0.7326 (pm20) REVERT: C 550 MET cc_start: 0.8768 (mmm) cc_final: 0.8399 (mmm) REVERT: C 588 ARG cc_start: 0.8969 (mtt90) cc_final: 0.7451 (ttt180) REVERT: C 589 MET cc_start: 0.8003 (mmt) cc_final: 0.7522 (mmt) REVERT: C 600 ASP cc_start: 0.7032 (t0) cc_final: 0.6195 (t70) REVERT: C 656 LEU cc_start: 0.8462 (mp) cc_final: 0.8022 (mp) REVERT: C 680 GLU cc_start: 0.8882 (pp20) cc_final: 0.8630 (tm-30) REVERT: C 714 MET cc_start: 0.8232 (mtt) cc_final: 0.7907 (mtp) REVERT: C 716 ASN cc_start: 0.8468 (t0) cc_final: 0.8003 (t0) REVERT: C 751 LEU cc_start: 0.9033 (mt) cc_final: 0.8662 (tt) REVERT: C 785 MET cc_start: 0.8208 (mmm) cc_final: 0.7904 (mmm) outliers start: 30 outliers final: 28 residues processed: 147 average time/residue: 0.1857 time to fit residues: 40.3618 Evaluate side-chains 149 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 120 time to evaluate : 1.142 ------------------------------------------------------------------------------- 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 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 650 VAL Chi-restraints excluded: chain C residue 729 VAL Chi-restraints excluded: chain C residue 736 ILE 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: 0.7980 chunk 46 optimal weight: 2.9990 chunk 95 optimal weight: 1.9990 chunk 9 optimal weight: 0.0970 chunk 31 optimal weight: 3.9990 chunk 26 optimal weight: 0.5980 chunk 37 optimal weight: 0.0000 chunk 13 optimal weight: 0.2980 chunk 103 optimal weight: 0.6980 chunk 60 optimal weight: 0.0870 overall best weight: 0.2160 ------------------------------------------------------------------------------- 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 = 0.3531 r_free = 0.3531 target = 0.123466 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.098025 restraints weight = 14853.814| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.098024 restraints weight = 10495.065| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.099193 restraints weight = 8903.520| |-----------------------------------------------------------------------------| r_work (final): 0.3187 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8154 moved from start: 0.3063 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= 0.143 Angle : 0.524 7.466 12542 Z= 0.268 Chirality : 0.039 0.215 1405 Planarity : 0.004 0.067 1576 Dihedral : 3.917 17.093 1208 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 2.50 % Allowed : 21.90 % Favored : 75.60 % 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: -0.66 (0.27), residues: 1073 helix: 0.08 (0.20), residues: 739 sheet: -2.22 (1.73), residues: 10 loop : -1.37 (0.35), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP C 456 HIS 0.005 0.000 HIS B 558 PHE 0.011 0.001 PHE B 714 TYR 0.007 0.001 TYR C 460 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: 2653.62 seconds wall clock time: 48 minutes 36.59 seconds (2916.59 seconds total)