Starting phenix.real_space_refine (version: dev) on Sun Feb 19 01:10:35 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v6b_21067/02_2023/6v6b_21067.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v6b_21067/02_2023/6v6b_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_21067/02_2023/6v6b_21067.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v6b_21067/02_2023/6v6b_21067.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v6b_21067/02_2023/6v6b_21067.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v6b_21067/02_2023/6v6b_21067.pdb" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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 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-4877/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: 5.69, per 1000 atoms: 0.62 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: 3.58 Conformation dependent library (CDL) restraints added in 1.5 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: 0.47 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: 2.29 Time building geometry restraints manager: 3.87 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 2.440 nonbonded pdb=" NE2 GLN B 259 " pdb=" OE1 GLN C 350 " model vdw 2.232 2.520 nonbonded pdb=" OH TYR B 464 " pdb=" ND2 ASN B 491 " model vdw 2.237 2.520 nonbonded pdb=" O SER C 299 " pdb=" OG SER C 299 " model vdw 2.284 2.440 nonbonded pdb=" O LYS C 774 " pdb=" OG SER C 777 " model vdw 2.285 2.440 ... (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 ========== 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 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. 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: 2.150 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: 10.470 Check model and map are aligned: 0.150 Process input model: 26.640 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Set scattering table: 0.080 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:2.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.550 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8429 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 % 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 *********************** 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 : 1.145 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 159 average time/residue: 0.2482 time to fit residues: 53.4373 Evaluate side-chains 116 residues out of total 1004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 116 time to evaluate : 0.972 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.4678 ------------------------------------------------------------------------------- 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: 0.9980 chunk 28 optimal weight: 0.8980 chunk 56 optimal weight: 2.9990 chunk 44 optimal weight: 1.9990 chunk 86 optimal weight: 2.9990 chunk 33 optimal weight: 0.9980 chunk 52 optimal weight: 3.9990 chunk 64 optimal weight: 0.5980 chunk 99 optimal weight: 0.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 345 GLN B 401 HIS B 491 ASN B 643 HIS B 665 ASN B 739 GLN ** B 751 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 830 ASN B 846 GLN C 264 GLN C 317 ASN C 342 HIS C 486 ASN C 540 HIS C 667 GLN C 682 GLN ** C 720 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8407 moved from start: 0.1726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.045 9300 Z= 0.263 Angle : 0.601 7.359 12542 Z= 0.313 Chirality : 0.042 0.152 1405 Planarity : 0.004 0.069 1576 Dihedral : 4.630 18.749 1208 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer Outliers : 1.40 % 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: -3.90 (0.22), residues: 1073 helix: -2.58 (0.16), residues: 726 sheet: -3.05 (0.86), residues: 24 loop : -2.00 (0.34), residues: 323 *********************** 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 146 residues out of total 1004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 132 time to evaluate : 1.066 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 14 outliers final: 8 residues processed: 140 average time/residue: 0.1719 time to fit residues: 36.0917 Evaluate side-chains 124 residues out of total 1004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 116 time to evaluate : 1.245 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.0899 time to fit residues: 2.9917 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 55 optimal weight: 0.1980 chunk 31 optimal weight: 0.9980 chunk 83 optimal weight: 0.7980 chunk 68 optimal weight: 0.9980 chunk 27 optimal weight: 0.9980 chunk 100 optimal weight: 0.9990 chunk 108 optimal weight: 4.9990 chunk 89 optimal weight: 0.8980 chunk 99 optimal weight: 1.9990 chunk 34 optimal weight: 2.9990 chunk 80 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 241 GLN ** C 720 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8398 moved from start: 0.2048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.046 9300 Z= 0.235 Angle : 0.554 7.710 12542 Z= 0.284 Chirality : 0.041 0.149 1405 Planarity : 0.004 0.068 1576 Dihedral : 4.473 18.001 1208 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer Outliers : 2.40 % 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: -2.96 (0.24), residues: 1073 helix: -1.75 (0.18), residues: 731 sheet: -2.60 (0.81), residues: 34 loop : -1.92 (0.36), residues: 308 *********************** 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 149 residues out of total 1004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 125 time to evaluate : 1.089 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 24 outliers final: 12 residues processed: 140 average time/residue: 0.1698 time to fit residues: 35.7383 Evaluate side-chains 125 residues out of total 1004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 113 time to evaluate : 0.979 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.0792 time to fit residues: 3.0965 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 98 optimal weight: 3.9990 chunk 75 optimal weight: 1.9990 chunk 51 optimal weight: 3.9990 chunk 11 optimal weight: 1.9990 chunk 47 optimal weight: 0.5980 chunk 67 optimal weight: 1.9990 chunk 100 optimal weight: 0.7980 chunk 106 optimal weight: 6.9990 chunk 52 optimal weight: 1.9990 chunk 95 optimal weight: 0.9980 chunk 28 optimal weight: 2.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 751 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 720 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8431 moved from start: 0.2243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.041 9300 Z= 0.350 Angle : 0.614 7.609 12542 Z= 0.312 Chirality : 0.044 0.144 1405 Planarity : 0.004 0.071 1576 Dihedral : 4.650 19.267 1208 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Rotamer Outliers : 2.10 % 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: -2.59 (0.25), residues: 1073 helix: -1.45 (0.19), residues: 731 sheet: -2.51 (0.82), residues: 34 loop : -1.83 (0.36), residues: 308 *********************** 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 140 residues out of total 1004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 119 time to evaluate : 1.426 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 21 outliers final: 12 residues processed: 133 average time/residue: 0.1855 time to fit residues: 37.2774 Evaluate side-chains 123 residues out of total 1004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 111 time to evaluate : 1.230 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.0915 time to fit residues: 3.5582 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 88 optimal weight: 2.9990 chunk 60 optimal weight: 1.9990 chunk 1 optimal weight: 0.7980 chunk 79 optimal weight: 0.3980 chunk 43 optimal weight: 0.0050 chunk 90 optimal weight: 0.5980 chunk 73 optimal weight: 0.1980 chunk 0 optimal weight: 0.9990 chunk 54 optimal weight: 0.9980 chunk 95 optimal weight: 2.9990 chunk 26 optimal weight: 1.9990 overall best weight: 0.3994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 751 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 720 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8369 moved from start: 0.2511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.028 9300 Z= 0.159 Angle : 0.515 6.670 12542 Z= 0.265 Chirality : 0.039 0.179 1405 Planarity : 0.004 0.068 1576 Dihedral : 4.264 17.160 1208 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer Outliers : 1.60 % 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: -2.05 (0.26), residues: 1073 helix: -1.00 (0.19), residues: 737 sheet: -2.93 (0.86), residues: 22 loop : -1.72 (0.36), residues: 314 *********************** 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 141 residues out of total 1004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 125 time to evaluate : 1.210 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 16 outliers final: 9 residues processed: 137 average time/residue: 0.1950 time to fit residues: 39.3258 Evaluate side-chains 124 residues out of total 1004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 115 time to evaluate : 1.184 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.0934 time to fit residues: 3.1467 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.8980 chunk 21 optimal weight: 0.0170 chunk 62 optimal weight: 0.1980 chunk 26 optimal weight: 0.0870 chunk 106 optimal weight: 0.0370 chunk 88 optimal weight: 4.9990 chunk 49 optimal weight: 1.9990 chunk 8 optimal weight: 0.8980 chunk 55 optimal weight: 0.0980 chunk 102 optimal weight: 1.9990 overall best weight: 0.0874 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 751 HIS ** C 659 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8316 moved from start: 0.2895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.028 9300 Z= 0.127 Angle : 0.509 8.900 12542 Z= 0.255 Chirality : 0.038 0.171 1405 Planarity : 0.004 0.062 1576 Dihedral : 3.943 14.152 1208 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer Outliers : 0.90 % 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: -1.39 (0.26), residues: 1073 helix: -0.51 (0.20), residues: 741 sheet: -2.39 (0.93), residues: 22 loop : -1.48 (0.37), residues: 310 *********************** 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 145 residues out of total 1004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 136 time to evaluate : 1.192 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 4 residues processed: 143 average time/residue: 0.2039 time to fit residues: 42.3100 Evaluate side-chains 124 residues out of total 1004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 120 time to evaluate : 1.020 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0955 time to fit residues: 2.1218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 11 optimal weight: 0.8980 chunk 60 optimal weight: 1.9990 chunk 77 optimal weight: 0.8980 chunk 89 optimal weight: 1.9990 chunk 59 optimal weight: 0.0470 chunk 106 optimal weight: 6.9990 chunk 66 optimal weight: 0.4980 chunk 64 optimal weight: 0.8980 chunk 48 optimal weight: 2.9990 chunk 65 optimal weight: 0.6980 chunk 42 optimal weight: 0.6980 overall best weight: 0.5678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 659 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 672 HIS C 678 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8352 moved from start: 0.2979 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= 0.191 Angle : 0.530 8.289 12542 Z= 0.268 Chirality : 0.040 0.170 1405 Planarity : 0.004 0.061 1576 Dihedral : 3.989 15.218 1208 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer Outliers : 1.00 % 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: -1.12 (0.26), residues: 1073 helix: -0.30 (0.20), residues: 741 sheet: -2.16 (0.96), residues: 22 loop : -1.44 (0.37), residues: 310 *********************** 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 131 residues out of total 1004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 121 time to evaluate : 1.061 Fit side-chains revert: symmetry clash outliers start: 10 outliers final: 3 residues processed: 129 average time/residue: 0.2099 time to fit residues: 39.0393 Evaluate side-chains 119 residues out of total 1004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 116 time to evaluate : 1.163 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0922 time to fit residues: 2.0689 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 63 optimal weight: 0.5980 chunk 31 optimal weight: 0.0000 chunk 20 optimal weight: 0.0970 chunk 67 optimal weight: 1.9990 chunk 72 optimal weight: 0.0470 chunk 52 optimal weight: 0.0670 chunk 9 optimal weight: 1.9990 chunk 83 optimal weight: 0.6980 chunk 96 optimal weight: 0.6980 chunk 101 optimal weight: 3.9990 chunk 92 optimal weight: 0.0070 overall best weight: 0.0436 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 558 HIS ** C 659 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8288 moved from start: 0.3297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.029 9300 Z= 0.125 Angle : 0.503 7.363 12542 Z= 0.257 Chirality : 0.038 0.213 1405 Planarity : 0.003 0.058 1576 Dihedral : 3.758 14.622 1208 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer Outliers : 0.80 % 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: -0.68 (0.27), residues: 1073 helix: 0.07 (0.20), residues: 741 sheet: -1.95 (0.94), residues: 22 loop : -1.36 (0.37), residues: 310 *********************** 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 138 residues out of total 1004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 130 time to evaluate : 1.115 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 5 residues processed: 135 average time/residue: 0.2031 time to fit residues: 39.2350 Evaluate side-chains 127 residues out of total 1004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 122 time to evaluate : 1.196 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0947 time to fit residues: 2.6290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 98 optimal weight: 3.9990 chunk 101 optimal weight: 1.9990 chunk 59 optimal weight: 0.7980 chunk 43 optimal weight: 1.9990 chunk 77 optimal weight: 0.0570 chunk 30 optimal weight: 0.9990 chunk 89 optimal weight: 1.9990 chunk 93 optimal weight: 0.3980 chunk 64 optimal weight: 0.6980 chunk 104 optimal weight: 3.9990 chunk 63 optimal weight: 0.6980 overall best weight: 0.5298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 486 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 659 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8334 moved from start: 0.3256 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= 0.186 Angle : 0.542 8.995 12542 Z= 0.274 Chirality : 0.041 0.221 1405 Planarity : 0.003 0.059 1576 Dihedral : 3.833 14.007 1208 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.08 % Favored : 96.83 % Rotamer Outliers : 0.70 % 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: -0.56 (0.27), residues: 1073 helix: 0.17 (0.20), residues: 741 sheet: -1.88 (0.95), residues: 22 loop : -1.35 (0.37), residues: 310 *********************** 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 129 residues out of total 1004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 122 time to evaluate : 1.050 Fit side-chains revert: symmetry clash outliers start: 7 outliers final: 4 residues processed: 126 average time/residue: 0.2073 time to fit residues: 37.9014 Evaluate side-chains 122 residues out of total 1004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 118 time to evaluate : 1.110 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0837 time to fit residues: 2.1376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 49 optimal weight: 0.9990 chunk 72 optimal weight: 1.9990 chunk 109 optimal weight: 0.9990 chunk 100 optimal weight: 0.5980 chunk 87 optimal weight: 0.9980 chunk 9 optimal weight: 2.9990 chunk 67 optimal weight: 0.7980 chunk 53 optimal weight: 1.9990 chunk 69 optimal weight: 0.9990 chunk 92 optimal weight: 0.9990 chunk 26 optimal weight: 0.9980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 486 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 659 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8372 moved from start: 0.3175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.036 9300 Z= 0.264 Angle : 0.586 7.955 12542 Z= 0.292 Chirality : 0.042 0.213 1405 Planarity : 0.004 0.060 1576 Dihedral : 4.052 18.365 1208 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.73 % Favored : 96.18 % Rotamer Outliers : 0.10 % 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: -0.62 (0.27), residues: 1073 helix: 0.13 (0.20), residues: 741 sheet: -1.71 (0.99), residues: 22 loop : -1.40 (0.37), residues: 310 ********************** 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 119 residues out of total 1004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 118 time to evaluate : 1.076 Fit side-chains revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 119 average time/residue: 0.1996 time to fit residues: 34.4633 Evaluate side-chains 116 residues out of total 1004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 116 time to evaluate : 1.030 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.6663 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 80 optimal weight: 1.9990 chunk 12 optimal weight: 0.9990 chunk 24 optimal weight: 0.0050 chunk 87 optimal weight: 0.5980 chunk 36 optimal weight: 0.8980 chunk 89 optimal weight: 0.5980 chunk 11 optimal weight: 0.9980 chunk 16 optimal weight: 0.2980 chunk 76 optimal weight: 1.9990 chunk 4 optimal weight: 0.6980 chunk 63 optimal weight: 0.7980 overall best weight: 0.4394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 486 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 659 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.123422 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.097564 restraints weight = 14829.066| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.097641 restraints weight = 11021.708| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.098597 restraints weight = 9024.129| |-----------------------------------------------------------------------------| r_work (final): 0.3135 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8329 moved from start: 0.3305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.030 9300 Z= 0.170 Angle : 0.542 8.174 12542 Z= 0.272 Chirality : 0.040 0.209 1405 Planarity : 0.003 0.061 1576 Dihedral : 3.937 17.471 1208 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.36 % Favored : 96.55 % Rotamer Outliers : 0.30 % 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: -0.42 (0.27), residues: 1073 helix: 0.27 (0.20), residues: 741 sheet: -1.60 (0.98), residues: 22 loop : -1.30 (0.37), residues: 310 =============================================================================== Job complete usr+sys time: 1802.60 seconds wall clock time: 34 minutes 11.04 seconds (2051.04 seconds total)