Starting phenix.real_space_refine on Sat Aug 3 23:43:44 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v6b_21067/08_2024/6v6b_21067.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v6b_21067/08_2024/6v6b_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v6b_21067/08_2024/6v6b_21067.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v6b_21067/08_2024/6v6b_21067.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v6b_21067/08_2024/6v6b_21067.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v6b_21067/08_2024/6v6b_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 Residue "B GLU 247": "OE1" <-> "OE2" Residue "B ARG 285": "NH1" <-> "NH2" Residue "B ARG 337": "NH1" <-> "NH2" Residue "B ARG 366": "NH1" <-> "NH2" Residue "B ARG 391": "NH1" <-> "NH2" Residue "B GLU 440": "OE1" <-> "OE2" Residue "B GLU 602": "OE1" <-> "OE2" Residue "B ARG 619": "NH1" <-> "NH2" Residue "B ARG 624": "NH1" <-> "NH2" Residue "B GLU 627": "OE1" <-> "OE2" Residue "B ARG 654": "NH1" <-> "NH2" Residue "B ARG 692": "NH1" <-> "NH2" Residue "B GLU 784": "OE1" <-> "OE2" Residue "B TYR 793": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 798": "OE1" <-> "OE2" Residue "B ARG 802": "NH1" <-> "NH2" Residue "B ARG 803": "NH1" <-> "NH2" Residue "B GLU 827": "OE1" <-> "OE2" Residue "B ARG 879": "NH1" <-> "NH2" Residue "C ARG 325": "NH1" <-> "NH2" Residue "C ARG 343": "NH1" <-> "NH2" Residue "C ARG 425": "NH1" <-> "NH2" Residue "C GLU 439": "OE1" <-> "OE2" Residue "C ARG 510": "NH1" <-> "NH2" Residue "C TYR 512": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 565": "OE1" <-> "OE2" Residue "C ARG 578": "NH1" <-> "NH2" Residue "C GLU 580": "OE1" <-> "OE2" Residue "C ARG 660": "NH1" <-> "NH2" Residue "C ARG 671": "NH1" <-> "NH2" Residue "C ARG 713": "NH1" <-> "NH2" Residue "C GLU 731": "OE1" <-> "OE2" Residue "C GLU 738": "OE1" <-> "OE2" Residue "C ARG 886": "NH1" <-> "NH2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/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: 5.25, per 1000 atoms: 0.58 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 - 3.50 Amino acid : False - 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: 3.10 Conformation dependent library (CDL) restraints added in 1.4 seconds 2146 Ramachandran restraints generated. 1073 Oldfield, 0 Emsley, 1073 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2144 Finding SS restraints... Secondary structure from input PDB file: 62 helices and 5 sheets defined 69.7% alpha, 1.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.84 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: 2.11 Time building geometry restraints manager: 3.42 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: 99.60 - 106.52: 197 106.52 - 113.43: 5105 113.43 - 120.35: 3861 120.35 - 127.26: 3287 127.26 - 134.18: 92 Bond angle restraints: 12542 Sorted by residual: angle pdb=" C ASP C 397 " pdb=" N SER C 398 " pdb=" CA SER C 398 " ideal model delta sigma weight residual 121.54 126.55 -5.01 1.91e+00 2.74e-01 6.88e+00 angle pdb=" C GLN B 742 " pdb=" N ASP B 743 " pdb=" CA ASP B 743 " ideal model delta sigma weight residual 121.54 126.37 -4.83 1.91e+00 2.74e-01 6.39e+00 angle pdb=" N ASP B 622 " pdb=" CA ASP B 622 " pdb=" C ASP B 622 " ideal model delta sigma weight residual 108.34 111.45 -3.11 1.31e+00 5.83e-01 5.62e+00 angle pdb=" CA TRP C 353 " pdb=" CB TRP C 353 " pdb=" CG TRP C 353 " ideal model delta sigma weight residual 113.60 118.07 -4.47 1.90e+00 2.77e-01 5.55e+00 angle pdb=" N LEU C 384 " pdb=" CA LEU C 384 " pdb=" C LEU C 384 " ideal model delta sigma weight residual 114.31 111.50 2.81 1.29e+00 6.01e-01 4.74e+00 ... (remaining 12537 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.89: 4952 16.89 - 33.78: 490 33.78 - 50.67: 117 50.67 - 67.56: 14 67.56 - 84.45: 9 Dihedral angle restraints: 5582 sinusoidal: 2298 harmonic: 3284 Sorted by residual: dihedral pdb=" CA PHE B 652 " pdb=" C PHE B 652 " pdb=" N THR B 653 " pdb=" CA THR B 653 " ideal model delta harmonic sigma weight residual 180.00 161.11 18.89 0 5.00e+00 4.00e-02 1.43e+01 dihedral pdb=" CA SER C 469 " pdb=" C SER C 469 " pdb=" N PHE C 470 " pdb=" CA PHE C 470 " ideal model delta harmonic sigma weight residual 180.00 161.95 18.05 0 5.00e+00 4.00e-02 1.30e+01 dihedral pdb=" CA ASP B 745 " pdb=" C ASP B 745 " pdb=" N HIS B 746 " pdb=" CA HIS B 746 " ideal model delta harmonic sigma weight residual 180.00 162.23 17.77 0 5.00e+00 4.00e-02 1.26e+01 ... (remaining 5579 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 727 0.030 - 0.060: 512 0.060 - 0.090: 114 0.090 - 0.120: 46 0.120 - 0.150: 6 Chirality restraints: 1405 Sorted by residual: chirality pdb=" CA ASN B 883 " pdb=" N ASN B 883 " pdb=" C ASN B 883 " pdb=" CB ASN B 883 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.61e-01 chirality pdb=" CB VAL C 571 " pdb=" CA VAL C 571 " pdb=" CG1 VAL C 571 " pdb=" CG2 VAL C 571 " both_signs ideal model delta sigma weight residual False -2.63 -2.49 -0.14 2.00e-01 2.50e+01 4.96e-01 chirality pdb=" CA ASP B 743 " pdb=" N ASP B 743 " pdb=" C ASP B 743 " pdb=" CB ASP B 743 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.66e-01 ... (remaining 1402 not shown) Planarity restraints: 1576 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU C 292 " -0.046 5.00e-02 4.00e+02 6.96e-02 7.74e+00 pdb=" N PRO C 293 " 0.120 5.00e-02 4.00e+02 pdb=" CA PRO C 293 " -0.035 5.00e-02 4.00e+02 pdb=" CD PRO C 293 " -0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO C 576 " 0.031 5.00e-02 4.00e+02 4.64e-02 3.45e+00 pdb=" N PRO C 577 " -0.080 5.00e-02 4.00e+02 pdb=" CA PRO C 577 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO C 577 " 0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR C 575 " 0.026 5.00e-02 4.00e+02 3.95e-02 2.49e+00 pdb=" N PRO C 576 " -0.068 5.00e-02 4.00e+02 pdb=" CA PRO C 576 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO C 576 " 0.022 5.00e-02 4.00e+02 ... (remaining 1573 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 1380 2.75 - 3.29: 8948 3.29 - 3.82: 13207 3.82 - 4.36: 16502 4.36 - 4.90: 27049 Nonbonded interactions: 67086 Sorted by model distance: nonbonded pdb=" OE2 GLU B 247 " pdb=" OG1 THR B 363 " model vdw 2.211 3.040 nonbonded pdb=" NE2 GLN B 259 " pdb=" OE1 GLN C 350 " model vdw 2.232 3.120 nonbonded pdb=" OH TYR B 464 " pdb=" ND2 ASN B 491 " model vdw 2.237 3.120 nonbonded pdb=" O SER C 299 " pdb=" OG SER C 299 " model vdw 2.284 3.040 nonbonded pdb=" O LYS C 774 " pdb=" OG SER C 777 " model vdw 2.285 3.040 ... (remaining 67081 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.670 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.310 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 24.440 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.570 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.290 ------------------------------------------------------------------------------- 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 fitting. rotamer outliers: 0 poor density : 159 time to evaluate : 1.101 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: 0.2276 time to fit residues: 49.2193 Evaluate side-chains 120 residues out of total 1004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 120 time to evaluate : 1.082 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8215 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 fitting. rotamer outliers: 13 poor density : 141 time to evaluate : 1.093 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 261 ILE cc_start: 0.8943 (mp) cc_final: 0.8698 (mt) REVERT: B 543 LYS cc_start: 0.9051 (tmtt) cc_final: 0.8793 (tmtt) REVERT: B 673 MET cc_start: 0.8981 (mmt) cc_final: 0.8422 (mmm) REVERT: B 763 LEU cc_start: 0.7814 (mp) cc_final: 0.7613 (mp) REVERT: B 782 ILE cc_start: 0.9009 (mt) cc_final: 0.8677 (mp) REVERT: C 532 MET cc_start: 0.9176 (mmt) cc_final: 0.8768 (mmp) REVERT: C 656 LEU cc_start: 0.8342 (mp) cc_final: 0.7965 (mp) REVERT: C 680 GLU cc_start: 0.8910 (pp20) cc_final: 0.8427 (tm-30) REVERT: C 716 ASN cc_start: 0.8330 (t0) cc_final: 0.7845 (t0) REVERT: C 751 LEU cc_start: 0.9190 (mt) cc_final: 0.8847 (tt) outliers start: 13 outliers final: 7 residues processed: 148 average time/residue: 0.1835 time to fit residues: 39.7540 Evaluate side-chains 130 residues out of total 1004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 123 time to evaluate : 1.068 ------------------------------------------------------------------------------- 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 55 optimal weight: 0.7980 chunk 31 optimal weight: 2.9990 chunk 83 optimal weight: 1.9990 chunk 68 optimal weight: 0.9980 chunk 27 optimal weight: 1.9990 chunk 100 optimal weight: 0.9980 chunk 108 optimal weight: 2.9990 chunk 89 optimal weight: 0.5980 chunk 99 optimal weight: 0.9980 chunk 34 optimal weight: 0.6980 chunk 80 optimal weight: 1.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8230 moved from start: 0.2014 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= 0.241 Angle : 0.553 7.760 12542 Z= 0.288 Chirality : 0.041 0.152 1405 Planarity : 0.004 0.071 1576 Dihedral : 4.393 18.470 1208 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 2.60 % Allowed : 15.60 % Favored : 81.80 % 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: -2.97 (0.24), residues: 1073 helix: -1.78 (0.18), residues: 731 sheet: -3.06 (0.78), residues: 24 loop : -1.83 (0.35), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 687 HIS 0.003 0.001 HIS C 735 PHE 0.014 0.001 PHE C 470 TYR 0.011 0.001 TYR C 675 ARG 0.002 0.000 ARG B 563 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2146 Ramachandran restraints generated. 1073 Oldfield, 0 Emsley, 1073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2146 Ramachandran restraints generated. 1073 Oldfield, 0 Emsley, 1073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 130 time to evaluate : 1.061 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 297 LEU cc_start: 0.9600 (OUTLIER) cc_final: 0.9326 (tp) REVERT: B 543 LYS cc_start: 0.9018 (tmtt) cc_final: 0.8761 (tmtt) REVERT: B 594 GLN cc_start: 0.8211 (tt0) cc_final: 0.7891 (tm-30) REVERT: B 673 MET cc_start: 0.8979 (mmt) cc_final: 0.8423 (mmm) REVERT: B 702 HIS cc_start: 0.8408 (t-90) cc_final: 0.7960 (t-90) REVERT: B 763 LEU cc_start: 0.7665 (mp) cc_final: 0.7433 (mp) REVERT: C 532 MET cc_start: 0.9194 (mmt) cc_final: 0.8809 (mmp) REVERT: C 590 SER cc_start: 0.9264 (OUTLIER) cc_final: 0.8914 (t) REVERT: C 656 LEU cc_start: 0.8426 (mp) cc_final: 0.8030 (mp) REVERT: C 680 GLU cc_start: 0.8913 (pp20) cc_final: 0.8405 (tm-30) REVERT: C 716 ASN cc_start: 0.8305 (t0) cc_final: 0.7820 (t0) REVERT: C 751 LEU cc_start: 0.9151 (mt) cc_final: 0.8856 (tt) REVERT: C 785 MET cc_start: 0.8242 (mmm) cc_final: 0.7963 (mmm) outliers start: 26 outliers final: 15 residues processed: 143 average time/residue: 0.1694 time to fit residues: 36.2083 Evaluate side-chains 136 residues out of total 1004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 119 time to evaluate : 1.034 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 254 ILE Chi-restraints excluded: chain B residue 277 VAL Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain B residue 400 VAL Chi-restraints excluded: chain B residue 406 THR Chi-restraints excluded: chain B residue 592 LEU Chi-restraints excluded: chain B residue 643 HIS Chi-restraints excluded: chain C residue 256 VAL Chi-restraints excluded: chain C residue 427 ILE Chi-restraints excluded: chain C residue 554 ASP Chi-restraints excluded: chain C residue 557 VAL Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain C residue 590 SER Chi-restraints excluded: chain C residue 729 VAL Chi-restraints excluded: chain C residue 760 THR Chi-restraints excluded: chain C residue 789 CYS Chi-restraints excluded: chain C residue 868 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 98 optimal weight: 1.9990 chunk 75 optimal weight: 0.9980 chunk 51 optimal weight: 0.8980 chunk 11 optimal weight: 0.6980 chunk 47 optimal weight: 3.9990 chunk 67 optimal weight: 0.6980 chunk 100 optimal weight: 0.5980 chunk 106 optimal weight: 0.9980 chunk 52 optimal weight: 0.4980 chunk 95 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 491 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8218 moved from start: 0.2300 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= 0.210 Angle : 0.536 8.055 12542 Z= 0.276 Chirality : 0.040 0.168 1405 Planarity : 0.004 0.071 1576 Dihedral : 4.269 18.414 1208 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 3.10 % Allowed : 17.70 % Favored : 79.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.40 (0.25), residues: 1073 helix: -1.31 (0.18), residues: 734 sheet: -2.92 (0.84), residues: 22 loop : -1.76 (0.35), residues: 317 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 687 HIS 0.002 0.000 HIS C 735 PHE 0.013 0.001 PHE C 470 TYR 0.010 0.001 TYR B 660 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 158 residues out of total 1004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 127 time to evaluate : 1.145 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 594 GLN cc_start: 0.8186 (tt0) cc_final: 0.7868 (tm-30) REVERT: B 673 MET cc_start: 0.8945 (mmt) cc_final: 0.8420 (mmm) REVERT: B 702 HIS cc_start: 0.8390 (t-90) cc_final: 0.8056 (t-90) REVERT: B 843 MET cc_start: 0.8991 (mtm) cc_final: 0.8712 (ptp) REVERT: C 456 TRP cc_start: 0.6504 (p-90) cc_final: 0.5978 (m-10) REVERT: C 502 GLU cc_start: 0.5929 (tp30) cc_final: 0.5618 (tp30) REVERT: C 532 MET cc_start: 0.9175 (mmt) cc_final: 0.8758 (mmp) REVERT: C 589 MET cc_start: 0.7658 (mmt) cc_final: 0.7179 (mmt) REVERT: C 590 SER cc_start: 0.9337 (OUTLIER) cc_final: 0.9064 (t) REVERT: C 656 LEU cc_start: 0.8423 (mp) cc_final: 0.7846 (mp) REVERT: C 680 GLU cc_start: 0.8951 (pp20) cc_final: 0.8245 (tm-30) REVERT: C 716 ASN cc_start: 0.8376 (t0) cc_final: 0.7907 (t0) REVERT: C 746 ASN cc_start: 0.8913 (OUTLIER) cc_final: 0.8408 (p0) REVERT: C 751 LEU cc_start: 0.9119 (mt) cc_final: 0.8794 (tt) REVERT: C 785 MET cc_start: 0.8320 (mmm) cc_final: 0.8026 (mmm) outliers start: 31 outliers final: 21 residues processed: 145 average time/residue: 0.1678 time to fit residues: 36.2199 Evaluate side-chains 144 residues out of total 1004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 121 time to evaluate : 1.112 ------------------------------------------------------------------------------- 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 491 ASN Chi-restraints excluded: chain B residue 592 LEU Chi-restraints excluded: chain B residue 643 HIS Chi-restraints excluded: chain C residue 256 VAL Chi-restraints excluded: chain C residue 277 ASP Chi-restraints excluded: chain C residue 338 LEU Chi-restraints excluded: chain C residue 427 ILE Chi-restraints excluded: chain C residue 554 ASP Chi-restraints excluded: chain C residue 557 VAL Chi-restraints excluded: chain C residue 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 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 88 optimal weight: 0.0020 chunk 60 optimal weight: 0.0670 chunk 1 optimal weight: 0.5980 chunk 79 optimal weight: 0.9990 chunk 43 optimal weight: 0.0030 chunk 90 optimal weight: 1.9990 chunk 73 optimal weight: 1.9990 chunk 0 optimal weight: 0.5980 chunk 54 optimal weight: 1.9990 chunk 95 optimal weight: 0.9980 chunk 26 optimal weight: 0.5980 overall best weight: 0.2536 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 678 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8173 moved from start: 0.2575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 9300 Z= 0.139 Angle : 0.502 9.416 12542 Z= 0.259 Chirality : 0.039 0.207 1405 Planarity : 0.004 0.067 1576 Dihedral : 4.059 16.731 1208 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 2.00 % Allowed : 18.90 % Favored : 79.10 % 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: -1.91 (0.25), residues: 1073 helix: -0.90 (0.19), residues: 738 sheet: -2.57 (0.89), residues: 22 loop : -1.69 (0.36), residues: 313 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 687 HIS 0.002 0.000 HIS C 735 PHE 0.017 0.001 PHE B 836 TYR 0.009 0.001 TYR B 660 ARG 0.002 0.000 ARG B 654 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2146 Ramachandran restraints generated. 1073 Oldfield, 0 Emsley, 1073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2146 Ramachandran restraints generated. 1073 Oldfield, 0 Emsley, 1073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 139 time to evaluate : 0.957 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 594 GLN cc_start: 0.8027 (tt0) cc_final: 0.7802 (tm-30) REVERT: B 673 MET cc_start: 0.8932 (mmt) cc_final: 0.8391 (mmm) REVERT: C 502 GLU cc_start: 0.5807 (tp30) cc_final: 0.5413 (tp30) REVERT: C 532 MET cc_start: 0.9143 (mmt) cc_final: 0.8586 (mmp) REVERT: C 589 MET cc_start: 0.7821 (mmt) cc_final: 0.7316 (mmt) REVERT: C 590 SER cc_start: 0.9305 (OUTLIER) cc_final: 0.8988 (t) REVERT: C 656 LEU cc_start: 0.8385 (mp) cc_final: 0.7987 (mp) REVERT: C 680 GLU cc_start: 0.8824 (pp20) cc_final: 0.8122 (tm-30) REVERT: C 716 ASN cc_start: 0.8474 (t0) cc_final: 0.8014 (t0) REVERT: C 751 LEU cc_start: 0.9096 (mt) cc_final: 0.8724 (tt) REVERT: C 785 MET cc_start: 0.8321 (mmm) cc_final: 0.7963 (mmm) outliers start: 20 outliers final: 16 residues processed: 150 average time/residue: 0.1954 time to fit residues: 42.4621 Evaluate side-chains 144 residues out of total 1004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 127 time to evaluate : 1.089 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 277 VAL 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 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 554 ASP Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain C residue 590 SER Chi-restraints excluded: chain C residue 604 ASP Chi-restraints excluded: chain C residue 650 VAL Chi-restraints excluded: chain C residue 760 THR Chi-restraints excluded: chain C residue 789 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 35 optimal weight: 1.9990 chunk 95 optimal weight: 0.2980 chunk 21 optimal weight: 0.8980 chunk 62 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 106 optimal weight: 6.9990 chunk 88 optimal weight: 2.9990 chunk 49 optimal weight: 0.9990 chunk 8 optimal weight: 0.9990 chunk 55 optimal weight: 2.9990 chunk 102 optimal weight: 1.9990 overall best weight: 1.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 491 ASN C 486 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8233 moved from start: 0.2556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 9300 Z= 0.293 Angle : 0.575 8.320 12542 Z= 0.293 Chirality : 0.043 0.189 1405 Planarity : 0.004 0.070 1576 Dihedral : 4.253 18.922 1208 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 3.60 % Allowed : 19.00 % Favored : 77.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.75 (0.26), residues: 1073 helix: -0.79 (0.19), residues: 740 sheet: -2.36 (0.94), residues: 22 loop : -1.62 (0.36), residues: 311 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP C 687 HIS 0.003 0.001 HIS C 678 PHE 0.027 0.002 PHE B 638 TYR 0.010 0.001 TYR C 355 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 157 residues out of total 1004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 121 time to evaluate : 1.095 Fit side-chains revert: symmetry clash REVERT: B 594 GLN cc_start: 0.8103 (tt0) cc_final: 0.7790 (tm-30) REVERT: B 673 MET cc_start: 0.8967 (mmt) cc_final: 0.8418 (mmm) REVERT: C 456 TRP cc_start: 0.6815 (p-90) cc_final: 0.6499 (p-90) REVERT: C 502 GLU cc_start: 0.5874 (tp30) cc_final: 0.5627 (tp30) REVERT: C 589 MET cc_start: 0.8023 (mmt) cc_final: 0.7524 (mmt) REVERT: C 590 SER cc_start: 0.9304 (OUTLIER) cc_final: 0.8989 (t) REVERT: C 656 LEU cc_start: 0.8468 (mp) cc_final: 0.8001 (mp) REVERT: C 680 GLU cc_start: 0.8964 (pp20) cc_final: 0.8370 (tm-30) REVERT: C 716 ASN cc_start: 0.8453 (t0) cc_final: 0.7982 (t0) REVERT: C 746 ASN cc_start: 0.8900 (OUTLIER) cc_final: 0.8419 (p0) REVERT: C 751 LEU cc_start: 0.9098 (mt) cc_final: 0.8667 (tt) REVERT: C 785 MET cc_start: 0.8249 (mmm) cc_final: 0.7941 (mmm) outliers start: 36 outliers final: 26 residues processed: 143 average time/residue: 0.1673 time to fit residues: 36.0333 Evaluate side-chains 148 residues out of total 1004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 120 time to evaluate : 1.225 ------------------------------------------------------------------------------- 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 667 LEU Chi-restraints excluded: chain B residue 743 ASP Chi-restraints excluded: chain C residue 256 VAL Chi-restraints excluded: chain C residue 277 ASP Chi-restraints excluded: chain C residue 427 ILE Chi-restraints excluded: chain C residue 485 LEU Chi-restraints excluded: chain C residue 486 ASN Chi-restraints excluded: chain C residue 554 ASP Chi-restraints excluded: chain C residue 557 VAL Chi-restraints excluded: chain C residue 574 ILE Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain C residue 590 SER Chi-restraints excluded: chain C residue 604 ASP Chi-restraints excluded: chain C residue 650 VAL Chi-restraints excluded: chain C residue 668 MET 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 11 optimal weight: 0.9980 chunk 60 optimal weight: 0.0070 chunk 77 optimal weight: 0.9980 chunk 89 optimal weight: 0.6980 chunk 59 optimal weight: 1.9990 chunk 106 optimal weight: 5.9990 chunk 66 optimal weight: 0.9980 chunk 64 optimal weight: 0.5980 chunk 48 optimal weight: 2.9990 chunk 65 optimal weight: 0.4980 chunk 42 optimal weight: 0.6980 overall best weight: 0.4998 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8199 moved from start: 0.2722 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= 0.177 Angle : 0.528 7.153 12542 Z= 0.269 Chirality : 0.040 0.192 1405 Planarity : 0.004 0.070 1576 Dihedral : 4.121 18.091 1208 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 3.60 % Allowed : 19.50 % Favored : 76.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.50 (0.26), residues: 1073 helix: -0.59 (0.19), residues: 740 sheet: -2.19 (0.93), residues: 22 loop : -1.56 (0.36), residues: 311 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 687 HIS 0.003 0.000 HIS C 678 PHE 0.016 0.001 PHE B 638 TYR 0.010 0.001 TYR B 793 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 164 residues out of total 1004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 128 time to evaluate : 1.094 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 446 PHE cc_start: 0.8821 (OUTLIER) cc_final: 0.8166 (t80) REVERT: B 477 MET cc_start: 0.8848 (tpp) cc_final: 0.8532 (tpt) REVERT: B 594 GLN cc_start: 0.8125 (tt0) cc_final: 0.7828 (tm-30) REVERT: B 673 MET cc_start: 0.8951 (mmt) cc_final: 0.8402 (mmm) REVERT: C 456 TRP cc_start: 0.6750 (p-90) cc_final: 0.6515 (p-90) REVERT: C 550 MET cc_start: 0.8768 (mmm) cc_final: 0.8414 (mmm) REVERT: C 560 MET cc_start: 0.8910 (tpp) cc_final: 0.8693 (tpp) REVERT: C 589 MET cc_start: 0.7980 (mmt) cc_final: 0.7464 (mmt) REVERT: C 590 SER cc_start: 0.9459 (OUTLIER) cc_final: 0.9088 (t) REVERT: C 656 LEU cc_start: 0.8414 (mp) cc_final: 0.7964 (mp) REVERT: C 680 GLU cc_start: 0.8880 (pp20) cc_final: 0.8335 (tm-30) REVERT: C 716 ASN cc_start: 0.8471 (t0) cc_final: 0.8014 (t0) REVERT: C 746 ASN cc_start: 0.8854 (OUTLIER) cc_final: 0.8339 (p0) REVERT: C 751 LEU cc_start: 0.9150 (mt) cc_final: 0.8705 (tt) REVERT: C 785 MET cc_start: 0.8243 (mmm) cc_final: 0.7911 (mmm) outliers start: 36 outliers final: 26 residues processed: 150 average time/residue: 0.1679 time to fit residues: 37.4397 Evaluate side-chains 155 residues out of total 1004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 126 time to evaluate : 1.047 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 446 PHE Chi-restraints excluded: chain B residue 592 LEU Chi-restraints excluded: chain B residue 643 HIS Chi-restraints excluded: chain B residue 661 LEU Chi-restraints excluded: chain B residue 743 ASP Chi-restraints excluded: chain B residue 800 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 486 ASN Chi-restraints excluded: chain C residue 554 ASP Chi-restraints excluded: chain C residue 557 VAL Chi-restraints excluded: chain C residue 574 ILE Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain C residue 590 SER Chi-restraints excluded: chain C residue 604 ASP Chi-restraints excluded: chain C residue 650 VAL Chi-restraints excluded: chain C residue 746 ASN Chi-restraints excluded: chain C residue 760 THR Chi-restraints excluded: chain C residue 789 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 63 optimal weight: 0.0470 chunk 31 optimal weight: 0.4980 chunk 20 optimal weight: 0.9980 chunk 67 optimal weight: 0.9980 chunk 72 optimal weight: 0.9990 chunk 52 optimal weight: 0.9980 chunk 9 optimal weight: 0.6980 chunk 83 optimal weight: 0.9980 chunk 96 optimal weight: 0.0570 chunk 101 optimal weight: 0.6980 chunk 92 optimal weight: 0.6980 overall best weight: 0.3996 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8182 moved from start: 0.2886 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= 0.161 Angle : 0.528 9.196 12542 Z= 0.267 Chirality : 0.040 0.203 1405 Planarity : 0.004 0.069 1576 Dihedral : 4.003 17.376 1208 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 3.40 % Allowed : 20.00 % Favored : 76.60 % 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: -1.19 (0.26), residues: 1073 helix: -0.35 (0.20), residues: 742 sheet: -2.04 (0.94), residues: 22 loop : -1.49 (0.36), residues: 309 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 687 HIS 0.002 0.000 HIS C 678 PHE 0.012 0.001 PHE B 638 TYR 0.009 0.001 TYR B 660 ARG 0.002 0.000 ARG C 660 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2146 Ramachandran restraints generated. 1073 Oldfield, 0 Emsley, 1073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2146 Ramachandran restraints generated. 1073 Oldfield, 0 Emsley, 1073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 131 time to evaluate : 1.115 Fit side-chains revert: symmetry clash REVERT: B 446 PHE cc_start: 0.8792 (OUTLIER) cc_final: 0.8148 (t80) REVERT: B 477 MET cc_start: 0.8843 (tpp) cc_final: 0.8541 (tpt) REVERT: B 594 GLN cc_start: 0.8089 (tt0) cc_final: 0.7799 (tm-30) REVERT: B 673 MET cc_start: 0.8928 (mmt) cc_final: 0.8352 (mmm) REVERT: B 711 MET cc_start: 0.8389 (mtt) cc_final: 0.8142 (mtt) REVERT: C 477 LYS cc_start: 0.8872 (mttt) cc_final: 0.8507 (ttmt) REVERT: C 518 LYS cc_start: 0.9014 (ttmm) cc_final: 0.8730 (ttmm) REVERT: C 550 MET cc_start: 0.8750 (mmm) cc_final: 0.8412 (mmm) REVERT: C 560 MET cc_start: 0.8964 (tpp) cc_final: 0.8751 (tpp) REVERT: C 589 MET cc_start: 0.7962 (mmt) cc_final: 0.7450 (mmt) REVERT: C 656 LEU cc_start: 0.8395 (mp) cc_final: 0.7945 (mp) REVERT: C 680 GLU cc_start: 0.8812 (pp20) cc_final: 0.8609 (tm-30) REVERT: C 714 MET cc_start: 0.8205 (mtt) cc_final: 0.7865 (mtp) REVERT: C 716 ASN cc_start: 0.8461 (t0) cc_final: 0.7993 (t0) REVERT: C 746 ASN cc_start: 0.8830 (OUTLIER) cc_final: 0.8323 (p0) REVERT: C 751 LEU cc_start: 0.9019 (mt) cc_final: 0.8654 (tt) REVERT: C 785 MET cc_start: 0.8247 (mmm) cc_final: 0.7904 (mmm) outliers start: 34 outliers final: 26 residues processed: 152 average time/residue: 0.1704 time to fit residues: 38.7655 Evaluate side-chains 158 residues out of total 1004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 130 time to evaluate : 1.132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 446 PHE Chi-restraints excluded: chain B residue 592 LEU Chi-restraints excluded: chain B residue 643 HIS Chi-restraints excluded: chain B residue 743 ASP Chi-restraints excluded: chain B residue 800 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 486 ASN Chi-restraints excluded: chain C residue 549 LEU 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 650 VAL Chi-restraints excluded: chain C residue 746 ASN Chi-restraints excluded: chain C residue 760 THR Chi-restraints excluded: chain C residue 789 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 98 optimal weight: 1.9990 chunk 101 optimal weight: 0.9990 chunk 59 optimal weight: 0.9990 chunk 43 optimal weight: 0.0020 chunk 77 optimal weight: 0.5980 chunk 30 optimal weight: 1.9990 chunk 89 optimal weight: 0.8980 chunk 93 optimal weight: 0.7980 chunk 64 optimal weight: 0.0670 chunk 104 optimal weight: 0.5980 chunk 63 optimal weight: 0.9990 overall best weight: 0.4126 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8175 moved from start: 0.2975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9300 Z= 0.163 Angle : 0.525 7.676 12542 Z= 0.267 Chirality : 0.040 0.192 1405 Planarity : 0.004 0.066 1576 Dihedral : 3.941 17.011 1208 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 3.30 % Allowed : 20.20 % Favored : 76.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.97 (0.26), residues: 1073 helix: -0.15 (0.20), residues: 745 sheet: -2.56 (1.65), residues: 10 loop : -1.52 (0.35), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP C 456 HIS 0.002 0.000 HIS C 678 PHE 0.011 0.001 PHE B 638 TYR 0.009 0.001 TYR B 660 ARG 0.002 0.000 ARG C 660 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2146 Ramachandran restraints generated. 1073 Oldfield, 0 Emsley, 1073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2146 Ramachandran restraints generated. 1073 Oldfield, 0 Emsley, 1073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 137 time to evaluate : 1.359 Fit side-chains revert: symmetry clash REVERT: B 446 PHE cc_start: 0.8782 (OUTLIER) cc_final: 0.8153 (t80) REVERT: B 477 MET cc_start: 0.8833 (tpp) cc_final: 0.8549 (tpt) REVERT: B 594 GLN cc_start: 0.8070 (tt0) cc_final: 0.7787 (tm-30) REVERT: B 673 MET cc_start: 0.8983 (mmt) cc_final: 0.8420 (mmm) REVERT: B 711 MET cc_start: 0.8427 (mtt) cc_final: 0.8201 (mtt) REVERT: C 458 GLN cc_start: 0.7602 (pm20) cc_final: 0.7214 (pm20) REVERT: C 477 LYS cc_start: 0.8883 (mttt) cc_final: 0.8495 (ttmt) REVERT: C 517 GLU cc_start: 0.8088 (mm-30) cc_final: 0.7873 (mm-30) REVERT: C 550 MET cc_start: 0.8732 (mmm) cc_final: 0.8368 (mmm) REVERT: C 588 ARG cc_start: 0.8907 (mtt90) cc_final: 0.7432 (ttt180) REVERT: C 589 MET cc_start: 0.7962 (mmt) cc_final: 0.7475 (mmt) REVERT: C 656 LEU cc_start: 0.8378 (mp) cc_final: 0.7907 (mp) REVERT: C 714 MET cc_start: 0.8174 (mtt) cc_final: 0.7844 (mtp) REVERT: C 716 ASN cc_start: 0.8443 (t0) cc_final: 0.7978 (t0) REVERT: C 746 ASN cc_start: 0.8828 (OUTLIER) cc_final: 0.8295 (p0) REVERT: C 751 LEU cc_start: 0.8988 (mt) cc_final: 0.8612 (tt) REVERT: C 785 MET cc_start: 0.8300 (mmm) cc_final: 0.7951 (mmm) outliers start: 33 outliers final: 26 residues processed: 159 average time/residue: 0.1863 time to fit residues: 43.5557 Evaluate side-chains 155 residues out of total 1004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 127 time to evaluate : 1.123 ------------------------------------------------------------------------------- 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 446 PHE Chi-restraints excluded: chain B residue 592 LEU Chi-restraints excluded: chain B residue 643 HIS Chi-restraints excluded: chain B residue 743 ASP Chi-restraints excluded: chain B residue 800 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 486 ASN Chi-restraints excluded: chain C residue 549 LEU Chi-restraints excluded: chain C residue 554 ASP Chi-restraints excluded: chain C residue 557 VAL Chi-restraints excluded: chain C residue 650 VAL Chi-restraints excluded: chain C residue 746 ASN Chi-restraints excluded: chain C residue 760 THR Chi-restraints excluded: chain C residue 789 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 49 optimal weight: 0.8980 chunk 72 optimal weight: 0.9990 chunk 109 optimal weight: 1.9990 chunk 100 optimal weight: 1.9990 chunk 87 optimal weight: 0.4980 chunk 9 optimal weight: 0.5980 chunk 67 optimal weight: 0.7980 chunk 53 optimal weight: 4.9990 chunk 69 optimal weight: 0.5980 chunk 92 optimal weight: 4.9990 chunk 26 optimal weight: 0.6980 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8191 moved from start: 0.3024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9300 Z= 0.205 Angle : 0.548 9.444 12542 Z= 0.276 Chirality : 0.041 0.198 1405 Planarity : 0.004 0.067 1576 Dihedral : 3.970 17.769 1208 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 3.50 % Allowed : 20.40 % 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: -0.86 (0.26), residues: 1073 helix: -0.07 (0.20), residues: 745 sheet: -2.34 (1.71), residues: 10 loop : -1.49 (0.35), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP C 456 HIS 0.002 0.000 HIS C 678 PHE 0.011 0.001 PHE B 638 TYR 0.009 0.001 TYR B 660 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 167 residues out of total 1004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 132 time to evaluate : 1.081 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 315 ARG cc_start: 0.7091 (mmt180) cc_final: 0.6819 (mmt180) REVERT: B 446 PHE cc_start: 0.8818 (OUTLIER) cc_final: 0.8126 (t80) REVERT: B 594 GLN cc_start: 0.8097 (tt0) cc_final: 0.7808 (tm-30) REVERT: B 673 MET cc_start: 0.9062 (mmt) cc_final: 0.8516 (mmm) REVERT: C 420 GLU cc_start: 0.7148 (mt-10) cc_final: 0.6797 (mp0) REVERT: C 458 GLN cc_start: 0.7570 (pm20) cc_final: 0.7212 (pm20) REVERT: C 550 MET cc_start: 0.8760 (mmm) cc_final: 0.8411 (mmm) REVERT: C 588 ARG cc_start: 0.8952 (mtt90) cc_final: 0.7476 (ttt180) REVERT: C 589 MET cc_start: 0.7990 (mmt) cc_final: 0.7505 (mmt) REVERT: C 656 LEU cc_start: 0.8489 (mp) cc_final: 0.8038 (mp) REVERT: C 714 MET cc_start: 0.8188 (mtt) cc_final: 0.7856 (mtp) REVERT: C 716 ASN cc_start: 0.8451 (t0) cc_final: 0.7987 (t0) REVERT: C 746 ASN cc_start: 0.8823 (OUTLIER) cc_final: 0.8218 (p0) REVERT: C 751 LEU cc_start: 0.8989 (mt) cc_final: 0.8613 (tt) REVERT: C 785 MET cc_start: 0.8325 (mmm) cc_final: 0.7952 (mmm) outliers start: 35 outliers final: 31 residues processed: 156 average time/residue: 0.1880 time to fit residues: 42.3608 Evaluate side-chains 159 residues out of total 1004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 126 time to evaluate : 1.012 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 254 ILE Chi-restraints excluded: chain B residue 277 VAL Chi-restraints excluded: chain B residue 304 ILE Chi-restraints excluded: chain B residue 340 SER Chi-restraints excluded: chain B residue 367 LEU Chi-restraints excluded: chain B residue 400 VAL Chi-restraints excluded: chain B residue 406 THR Chi-restraints excluded: chain B residue 414 LEU Chi-restraints excluded: chain B residue 434 ILE 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 743 ASP Chi-restraints excluded: chain B residue 800 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 432 TYR Chi-restraints excluded: chain C residue 485 LEU Chi-restraints excluded: chain C residue 486 ASN Chi-restraints excluded: chain C residue 549 LEU 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 650 VAL Chi-restraints excluded: chain C residue 729 VAL Chi-restraints excluded: chain C residue 736 ILE Chi-restraints excluded: chain C residue 746 ASN Chi-restraints excluded: chain C residue 760 THR Chi-restraints excluded: chain C residue 789 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/programs/real_space_refine.py", line 200, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 766, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 63.9253 > 50: distance: 37 - 42: 5.268 distance: 42 - 43: 8.067 distance: 43 - 44: 10.342 distance: 43 - 46: 16.175 distance: 44 - 45: 5.512 distance: 44 - 50: 5.904 distance: 46 - 47: 18.410 distance: 47 - 48: 14.615 distance: 47 - 49: 14.607 distance: 50 - 51: 4.144 distance: 51 - 52: 11.073 distance: 51 - 54: 5.195 distance: 52 - 53: 27.057 distance: 52 - 60: 17.737 distance: 54 - 55: 27.603 distance: 55 - 56: 13.533 distance: 55 - 57: 13.529 distance: 56 - 58: 14.526 distance: 57 - 59: 10.731 distance: 58 - 59: 12.444 distance: 60 - 61: 8.490 distance: 61 - 62: 23.775 distance: 61 - 64: 28.046 distance: 62 - 63: 26.758 distance: 62 - 66: 28.158 distance: 64 - 65: 18.022 distance: 66 - 67: 6.792 distance: 67 - 68: 27.829 distance: 67 - 70: 15.316 distance: 68 - 69: 45.100 distance: 70 - 71: 29.178 distance: 71 - 72: 16.343 distance: 72 - 73: 19.539 distance: 72 - 74: 20.840 distance: 75 - 76: 20.849 distance: 76 - 77: 33.722 distance: 77 - 78: 28.983 distance: 77 - 79: 15.332 distance: 79 - 80: 14.579 distance: 80 - 81: 14.065 distance: 80 - 83: 18.452 distance: 81 - 82: 25.294 distance: 81 - 90: 7.854 distance: 83 - 84: 12.339 distance: 84 - 85: 4.869 distance: 85 - 86: 19.988 distance: 86 - 87: 10.297 distance: 87 - 88: 17.508 distance: 87 - 89: 34.875 distance: 90 - 91: 27.442 distance: 91 - 92: 20.169 distance: 91 - 94: 26.700 distance: 92 - 93: 3.691 distance: 92 - 99: 20.174 distance: 94 - 95: 23.915 distance: 95 - 96: 13.009 distance: 96 - 97: 10.318 distance: 97 - 98: 23.815 distance: 99 - 100: 22.195 distance: 100 - 101: 24.605 distance: 101 - 102: 24.834 distance: 101 - 103: 21.520 distance: 103 - 104: 18.862 distance: 104 - 105: 10.941 distance: 105 - 106: 10.720 distance: 105 - 107: 5.399 distance: 106 - 129: 31.828 distance: 107 - 108: 11.415 distance: 108 - 109: 22.095 distance: 108 - 111: 21.074 distance: 109 - 110: 4.801 distance: 109 - 116: 27.300 distance: 111 - 112: 13.571 distance: 112 - 113: 12.829 distance: 113 - 114: 10.006 distance: 113 - 115: 17.451