Starting phenix.real_space_refine on Sun Sep 29 09:41:12 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8apl_15574/09_2024/8apl_15574.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8apl_15574/09_2024/8apl_15574.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8apl_15574/09_2024/8apl_15574.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8apl_15574/09_2024/8apl_15574.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8apl_15574/09_2024/8apl_15574.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8apl_15574/09_2024/8apl_15574.cif" } resolution = 4.1 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 108 5.16 5 C 14082 2.51 5 N 3648 2.21 5 O 4050 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 30 residue(s): 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 21888 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 3648 Number of conformers: 1 Conformer: "" Number of residues, atoms: 449, 3648 Classifications: {'peptide': 449} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 429} Chain breaks: 1 Restraints were copied for chains: C, B, E, D, F Time building chain proxies: 8.95, per 1000 atoms: 0.41 Number of scatterers: 21888 At special positions: 0 Unit cell: (129.47, 122.21, 107.69, 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 108 16.00 O 4050 8.00 N 3648 7.00 C 14082 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 6.27 Conformation dependent library (CDL) restraints added in 2.7 seconds 5340 Ramachandran restraints generated. 2670 Oldfield, 0 Emsley, 2670 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5148 Finding SS restraints... Secondary structure from input PDB file: 132 helices and 42 sheets defined 47.2% alpha, 11.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.09 Creating SS restraints... Processing helix chain 'A' and resid 324 through 336 removed outlier: 3.975A pdb=" N ASN A 328 " --> pdb=" O ASN A 324 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N THR A 336 " --> pdb=" O ARG A 332 " (cutoff:3.500A) Processing helix chain 'A' and resid 363 through 372 Processing helix chain 'A' and resid 373 through 375 No H-bonds generated for 'chain 'A' and resid 373 through 375' Processing helix chain 'A' and resid 376 through 384 removed outlier: 3.683A pdb=" N SER A 381 " --> pdb=" O LYS A 377 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N GLU A 382 " --> pdb=" O GLU A 378 " (cutoff:3.500A) Processing helix chain 'A' and resid 385 through 400 Processing helix chain 'A' and resid 430 through 435 Processing helix chain 'A' and resid 455 through 469 Processing helix chain 'A' and resid 475 through 489 Processing helix chain 'A' and resid 508 through 521 Processing helix chain 'A' and resid 529 through 534 Processing helix chain 'A' and resid 541 through 548 Processing helix chain 'A' and resid 570 through 577 Processing helix chain 'A' and resid 614 through 620 Processing helix chain 'A' and resid 654 through 661 removed outlier: 3.837A pdb=" N LYS A 658 " --> pdb=" O GLY A 654 " (cutoff:3.500A) Processing helix chain 'A' and resid 664 through 680 Processing helix chain 'A' and resid 689 through 692 Processing helix chain 'A' and resid 693 through 706 Processing helix chain 'A' and resid 713 through 715 No H-bonds generated for 'chain 'A' and resid 713 through 715' Processing helix chain 'A' and resid 716 through 721 Processing helix chain 'A' and resid 736 through 747 removed outlier: 3.971A pdb=" N LYS A 745 " --> pdb=" O GLN A 741 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N TYR A 746 " --> pdb=" O LYS A 742 " (cutoff:3.500A) Processing helix chain 'A' and resid 752 through 764 Processing helix chain 'A' and resid 778 through 782 Processing helix chain 'B' and resid 324 through 336 removed outlier: 3.975A pdb=" N ASN B 328 " --> pdb=" O ASN B 324 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N THR B 336 " --> pdb=" O ARG B 332 " (cutoff:3.500A) Processing helix chain 'B' and resid 363 through 372 Processing helix chain 'B' and resid 373 through 375 No H-bonds generated for 'chain 'B' and resid 373 through 375' Processing helix chain 'B' and resid 376 through 384 removed outlier: 3.683A pdb=" N SER B 381 " --> pdb=" O LYS B 377 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N GLU B 382 " --> pdb=" O GLU B 378 " (cutoff:3.500A) Processing helix chain 'B' and resid 385 through 400 Processing helix chain 'B' and resid 430 through 435 Processing helix chain 'B' and resid 455 through 469 Processing helix chain 'B' and resid 475 through 489 Processing helix chain 'B' and resid 508 through 521 Processing helix chain 'B' and resid 529 through 534 Processing helix chain 'B' and resid 541 through 548 Processing helix chain 'B' and resid 570 through 577 Processing helix chain 'B' and resid 614 through 620 Processing helix chain 'B' and resid 654 through 661 removed outlier: 3.838A pdb=" N LYS B 658 " --> pdb=" O GLY B 654 " (cutoff:3.500A) Processing helix chain 'B' and resid 664 through 680 Processing helix chain 'B' and resid 689 through 692 Processing helix chain 'B' and resid 693 through 706 Processing helix chain 'B' and resid 713 through 715 No H-bonds generated for 'chain 'B' and resid 713 through 715' Processing helix chain 'B' and resid 716 through 721 Processing helix chain 'B' and resid 736 through 747 removed outlier: 3.972A pdb=" N LYS B 745 " --> pdb=" O GLN B 741 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N TYR B 746 " --> pdb=" O LYS B 742 " (cutoff:3.500A) Processing helix chain 'B' and resid 752 through 764 Processing helix chain 'B' and resid 778 through 782 Processing helix chain 'C' and resid 324 through 336 removed outlier: 3.975A pdb=" N ASN C 328 " --> pdb=" O ASN C 324 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N THR C 336 " --> pdb=" O ARG C 332 " (cutoff:3.500A) Processing helix chain 'C' and resid 363 through 372 Processing helix chain 'C' and resid 373 through 375 No H-bonds generated for 'chain 'C' and resid 373 through 375' Processing helix chain 'C' and resid 376 through 384 removed outlier: 3.683A pdb=" N SER C 381 " --> pdb=" O LYS C 377 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N GLU C 382 " --> pdb=" O GLU C 378 " (cutoff:3.500A) Processing helix chain 'C' and resid 385 through 400 Processing helix chain 'C' and resid 430 through 435 Processing helix chain 'C' and resid 455 through 469 Processing helix chain 'C' and resid 475 through 489 Processing helix chain 'C' and resid 508 through 521 Processing helix chain 'C' and resid 529 through 534 Processing helix chain 'C' and resid 541 through 548 Processing helix chain 'C' and resid 570 through 577 Processing helix chain 'C' and resid 614 through 620 Processing helix chain 'C' and resid 654 through 661 removed outlier: 3.837A pdb=" N LYS C 658 " --> pdb=" O GLY C 654 " (cutoff:3.500A) Processing helix chain 'C' and resid 664 through 680 Processing helix chain 'C' and resid 689 through 692 Processing helix chain 'C' and resid 693 through 706 Processing helix chain 'C' and resid 713 through 715 No H-bonds generated for 'chain 'C' and resid 713 through 715' Processing helix chain 'C' and resid 716 through 721 Processing helix chain 'C' and resid 736 through 747 removed outlier: 3.972A pdb=" N LYS C 745 " --> pdb=" O GLN C 741 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N TYR C 746 " --> pdb=" O LYS C 742 " (cutoff:3.500A) Processing helix chain 'C' and resid 752 through 764 Processing helix chain 'C' and resid 778 through 782 Processing helix chain 'D' and resid 324 through 336 removed outlier: 3.976A pdb=" N ASN D 328 " --> pdb=" O ASN D 324 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N THR D 336 " --> pdb=" O ARG D 332 " (cutoff:3.500A) Processing helix chain 'D' and resid 363 through 372 Processing helix chain 'D' and resid 373 through 375 No H-bonds generated for 'chain 'D' and resid 373 through 375' Processing helix chain 'D' and resid 376 through 384 removed outlier: 3.684A pdb=" N SER D 381 " --> pdb=" O LYS D 377 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N GLU D 382 " --> pdb=" O GLU D 378 " (cutoff:3.500A) Processing helix chain 'D' and resid 385 through 400 Processing helix chain 'D' and resid 430 through 435 Processing helix chain 'D' and resid 455 through 469 Processing helix chain 'D' and resid 475 through 489 Processing helix chain 'D' and resid 508 through 521 Processing helix chain 'D' and resid 529 through 534 Processing helix chain 'D' and resid 541 through 548 Processing helix chain 'D' and resid 570 through 577 Processing helix chain 'D' and resid 614 through 620 Processing helix chain 'D' and resid 654 through 661 removed outlier: 3.838A pdb=" N LYS D 658 " --> pdb=" O GLY D 654 " (cutoff:3.500A) Processing helix chain 'D' and resid 664 through 680 Processing helix chain 'D' and resid 689 through 692 Processing helix chain 'D' and resid 693 through 706 Processing helix chain 'D' and resid 713 through 715 No H-bonds generated for 'chain 'D' and resid 713 through 715' Processing helix chain 'D' and resid 716 through 721 Processing helix chain 'D' and resid 736 through 747 removed outlier: 3.972A pdb=" N LYS D 745 " --> pdb=" O GLN D 741 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N TYR D 746 " --> pdb=" O LYS D 742 " (cutoff:3.500A) Processing helix chain 'D' and resid 752 through 764 Processing helix chain 'D' and resid 778 through 782 Processing helix chain 'E' and resid 324 through 336 removed outlier: 3.975A pdb=" N ASN E 328 " --> pdb=" O ASN E 324 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N THR E 336 " --> pdb=" O ARG E 332 " (cutoff:3.500A) Processing helix chain 'E' and resid 363 through 372 Processing helix chain 'E' and resid 373 through 375 No H-bonds generated for 'chain 'E' and resid 373 through 375' Processing helix chain 'E' and resid 376 through 384 removed outlier: 3.683A pdb=" N SER E 381 " --> pdb=" O LYS E 377 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N GLU E 382 " --> pdb=" O GLU E 378 " (cutoff:3.500A) Processing helix chain 'E' and resid 385 through 400 Processing helix chain 'E' and resid 430 through 435 Processing helix chain 'E' and resid 455 through 469 Processing helix chain 'E' and resid 475 through 489 Processing helix chain 'E' and resid 508 through 521 Processing helix chain 'E' and resid 529 through 534 Processing helix chain 'E' and resid 541 through 548 Processing helix chain 'E' and resid 570 through 577 Processing helix chain 'E' and resid 614 through 620 Processing helix chain 'E' and resid 654 through 661 removed outlier: 3.838A pdb=" N LYS E 658 " --> pdb=" O GLY E 654 " (cutoff:3.500A) Processing helix chain 'E' and resid 664 through 680 Processing helix chain 'E' and resid 689 through 692 Processing helix chain 'E' and resid 693 through 706 Processing helix chain 'E' and resid 713 through 715 No H-bonds generated for 'chain 'E' and resid 713 through 715' Processing helix chain 'E' and resid 716 through 721 Processing helix chain 'E' and resid 736 through 747 removed outlier: 3.972A pdb=" N LYS E 745 " --> pdb=" O GLN E 741 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N TYR E 746 " --> pdb=" O LYS E 742 " (cutoff:3.500A) Processing helix chain 'E' and resid 752 through 764 Processing helix chain 'E' and resid 778 through 782 Processing helix chain 'F' and resid 324 through 336 removed outlier: 3.975A pdb=" N ASN F 328 " --> pdb=" O ASN F 324 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N THR F 336 " --> pdb=" O ARG F 332 " (cutoff:3.500A) Processing helix chain 'F' and resid 363 through 372 Processing helix chain 'F' and resid 373 through 375 No H-bonds generated for 'chain 'F' and resid 373 through 375' Processing helix chain 'F' and resid 376 through 384 removed outlier: 3.683A pdb=" N SER F 381 " --> pdb=" O LYS F 377 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N GLU F 382 " --> pdb=" O GLU F 378 " (cutoff:3.500A) Processing helix chain 'F' and resid 385 through 400 Processing helix chain 'F' and resid 430 through 435 Processing helix chain 'F' and resid 455 through 469 Processing helix chain 'F' and resid 475 through 489 Processing helix chain 'F' and resid 508 through 521 Processing helix chain 'F' and resid 529 through 534 Processing helix chain 'F' and resid 541 through 548 Processing helix chain 'F' and resid 570 through 577 Processing helix chain 'F' and resid 614 through 620 Processing helix chain 'F' and resid 654 through 661 removed outlier: 3.837A pdb=" N LYS F 658 " --> pdb=" O GLY F 654 " (cutoff:3.500A) Processing helix chain 'F' and resid 664 through 680 Processing helix chain 'F' and resid 689 through 692 Processing helix chain 'F' and resid 693 through 706 Processing helix chain 'F' and resid 713 through 715 No H-bonds generated for 'chain 'F' and resid 713 through 715' Processing helix chain 'F' and resid 716 through 721 Processing helix chain 'F' and resid 736 through 747 removed outlier: 3.972A pdb=" N LYS F 745 " --> pdb=" O GLN F 741 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N TYR F 746 " --> pdb=" O LYS F 742 " (cutoff:3.500A) Processing helix chain 'F' and resid 752 through 764 Processing helix chain 'F' and resid 778 through 782 Processing sheet with id=AA1, first strand: chain 'A' and resid 339 through 341 Processing sheet with id=AA2, first strand: chain 'A' and resid 412 through 414 Processing sheet with id=AA3, first strand: chain 'A' and resid 524 through 527 removed outlier: 5.926A pdb=" N VAL A 553 " --> pdb=" O ILE A 601 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N ASP A 603 " --> pdb=" O VAL A 553 " (cutoff:3.500A) removed outlier: 5.959A pdb=" N CYS A 555 " --> pdb=" O ASP A 603 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N THR A 499 " --> pdb=" O ILE A 600 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N LEU A 498 " --> pdb=" O ALA A 622 " (cutoff:3.500A) removed outlier: 7.483A pdb=" N VAL A 624 " --> pdb=" O LEU A 498 " (cutoff:3.500A) removed outlier: 6.049A pdb=" N PHE A 500 " --> pdb=" O VAL A 624 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 581 through 582 Processing sheet with id=AA5, first strand: chain 'A' and resid 628 through 631 Processing sheet with id=AA6, first strand: chain 'A' and resid 707 through 708 Processing sheet with id=AA7, first strand: chain 'A' and resid 726 through 728 Processing sheet with id=AA8, first strand: chain 'B' and resid 339 through 341 Processing sheet with id=AA9, first strand: chain 'B' and resid 412 through 414 Processing sheet with id=AB1, first strand: chain 'B' and resid 524 through 527 removed outlier: 5.926A pdb=" N VAL B 553 " --> pdb=" O ILE B 601 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N ASP B 603 " --> pdb=" O VAL B 553 " (cutoff:3.500A) removed outlier: 5.960A pdb=" N CYS B 555 " --> pdb=" O ASP B 603 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N THR B 499 " --> pdb=" O ILE B 600 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N LEU B 498 " --> pdb=" O ALA B 622 " (cutoff:3.500A) removed outlier: 7.482A pdb=" N VAL B 624 " --> pdb=" O LEU B 498 " (cutoff:3.500A) removed outlier: 6.050A pdb=" N PHE B 500 " --> pdb=" O VAL B 624 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 581 through 582 Processing sheet with id=AB3, first strand: chain 'B' and resid 628 through 631 Processing sheet with id=AB4, first strand: chain 'B' and resid 707 through 708 Processing sheet with id=AB5, first strand: chain 'B' and resid 726 through 728 Processing sheet with id=AB6, first strand: chain 'C' and resid 339 through 341 Processing sheet with id=AB7, first strand: chain 'C' and resid 412 through 414 Processing sheet with id=AB8, first strand: chain 'C' and resid 524 through 527 removed outlier: 5.927A pdb=" N VAL C 553 " --> pdb=" O ILE C 601 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N ASP C 603 " --> pdb=" O VAL C 553 " (cutoff:3.500A) removed outlier: 5.960A pdb=" N CYS C 555 " --> pdb=" O ASP C 603 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N THR C 499 " --> pdb=" O ILE C 600 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N LEU C 498 " --> pdb=" O ALA C 622 " (cutoff:3.500A) removed outlier: 7.483A pdb=" N VAL C 624 " --> pdb=" O LEU C 498 " (cutoff:3.500A) removed outlier: 6.049A pdb=" N PHE C 500 " --> pdb=" O VAL C 624 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 581 through 582 Processing sheet with id=AC1, first strand: chain 'C' and resid 628 through 631 Processing sheet with id=AC2, first strand: chain 'C' and resid 707 through 708 Processing sheet with id=AC3, first strand: chain 'C' and resid 726 through 728 Processing sheet with id=AC4, first strand: chain 'D' and resid 339 through 341 Processing sheet with id=AC5, first strand: chain 'D' and resid 412 through 414 Processing sheet with id=AC6, first strand: chain 'D' and resid 524 through 527 removed outlier: 5.927A pdb=" N VAL D 553 " --> pdb=" O ILE D 601 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N ASP D 603 " --> pdb=" O VAL D 553 " (cutoff:3.500A) removed outlier: 5.960A pdb=" N CYS D 555 " --> pdb=" O ASP D 603 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N THR D 499 " --> pdb=" O ILE D 600 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N LEU D 498 " --> pdb=" O ALA D 622 " (cutoff:3.500A) removed outlier: 7.482A pdb=" N VAL D 624 " --> pdb=" O LEU D 498 " (cutoff:3.500A) removed outlier: 6.049A pdb=" N PHE D 500 " --> pdb=" O VAL D 624 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'D' and resid 581 through 582 Processing sheet with id=AC8, first strand: chain 'D' and resid 628 through 631 Processing sheet with id=AC9, first strand: chain 'D' and resid 707 through 708 Processing sheet with id=AD1, first strand: chain 'D' and resid 726 through 728 Processing sheet with id=AD2, first strand: chain 'E' and resid 339 through 341 Processing sheet with id=AD3, first strand: chain 'E' and resid 412 through 414 Processing sheet with id=AD4, first strand: chain 'E' and resid 524 through 527 removed outlier: 5.927A pdb=" N VAL E 553 " --> pdb=" O ILE E 601 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N ASP E 603 " --> pdb=" O VAL E 553 " (cutoff:3.500A) removed outlier: 5.959A pdb=" N CYS E 555 " --> pdb=" O ASP E 603 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N THR E 499 " --> pdb=" O ILE E 600 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N LEU E 498 " --> pdb=" O ALA E 622 " (cutoff:3.500A) removed outlier: 7.483A pdb=" N VAL E 624 " --> pdb=" O LEU E 498 " (cutoff:3.500A) removed outlier: 6.049A pdb=" N PHE E 500 " --> pdb=" O VAL E 624 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'E' and resid 581 through 582 Processing sheet with id=AD6, first strand: chain 'E' and resid 628 through 631 Processing sheet with id=AD7, first strand: chain 'E' and resid 707 through 708 Processing sheet with id=AD8, first strand: chain 'E' and resid 726 through 728 Processing sheet with id=AD9, first strand: chain 'F' and resid 339 through 341 Processing sheet with id=AE1, first strand: chain 'F' and resid 412 through 414 Processing sheet with id=AE2, first strand: chain 'F' and resid 524 through 527 removed outlier: 5.926A pdb=" N VAL F 553 " --> pdb=" O ILE F 601 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N ASP F 603 " --> pdb=" O VAL F 553 " (cutoff:3.500A) removed outlier: 5.960A pdb=" N CYS F 555 " --> pdb=" O ASP F 603 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N THR F 499 " --> pdb=" O ILE F 600 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N LEU F 498 " --> pdb=" O ALA F 622 " (cutoff:3.500A) removed outlier: 7.483A pdb=" N VAL F 624 " --> pdb=" O LEU F 498 " (cutoff:3.500A) removed outlier: 6.048A pdb=" N PHE F 500 " --> pdb=" O VAL F 624 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'F' and resid 581 through 582 Processing sheet with id=AE4, first strand: chain 'F' and resid 628 through 631 Processing sheet with id=AE5, first strand: chain 'F' and resid 707 through 708 Processing sheet with id=AE6, first strand: chain 'F' and resid 726 through 728 894 hydrogen bonds defined for protein. 2538 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: 7.92 Time building geometry restraints manager: 7.13 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 6942 1.34 - 1.46: 4818 1.46 - 1.58: 10434 1.58 - 1.69: 0 1.69 - 1.81: 162 Bond restraints: 22356 Sorted by residual: bond pdb=" C ILE F 714 " pdb=" N PRO F 715 " ideal model delta sigma weight residual 1.336 1.344 -0.008 1.08e-02 8.57e+03 5.21e-01 bond pdb=" C ILE D 714 " pdb=" N PRO D 715 " ideal model delta sigma weight residual 1.336 1.343 -0.008 1.08e-02 8.57e+03 4.85e-01 bond pdb=" N GLY C 503 " pdb=" CA GLY C 503 " ideal model delta sigma weight residual 1.455 1.448 0.007 1.05e-02 9.07e+03 4.70e-01 bond pdb=" C ILE C 714 " pdb=" N PRO C 715 " ideal model delta sigma weight residual 1.336 1.343 -0.007 1.08e-02 8.57e+03 4.35e-01 bond pdb=" N GLY D 503 " pdb=" CA GLY D 503 " ideal model delta sigma weight residual 1.455 1.448 0.007 1.05e-02 9.07e+03 4.34e-01 ... (remaining 22351 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.85: 29883 1.85 - 3.70: 267 3.70 - 5.56: 18 5.56 - 7.41: 6 7.41 - 9.26: 6 Bond angle restraints: 30180 Sorted by residual: angle pdb=" C THR F 408 " pdb=" N TYR F 409 " pdb=" CA TYR F 409 " ideal model delta sigma weight residual 120.39 127.34 -6.95 1.39e+00 5.18e-01 2.50e+01 angle pdb=" C THR C 408 " pdb=" N TYR C 409 " pdb=" CA TYR C 409 " ideal model delta sigma weight residual 120.39 127.34 -6.95 1.39e+00 5.18e-01 2.50e+01 angle pdb=" C THR D 408 " pdb=" N TYR D 409 " pdb=" CA TYR D 409 " ideal model delta sigma weight residual 120.39 127.32 -6.93 1.39e+00 5.18e-01 2.49e+01 angle pdb=" C THR B 408 " pdb=" N TYR B 409 " pdb=" CA TYR B 409 " ideal model delta sigma weight residual 120.39 127.32 -6.93 1.39e+00 5.18e-01 2.48e+01 angle pdb=" C THR E 408 " pdb=" N TYR E 409 " pdb=" CA TYR E 409 " ideal model delta sigma weight residual 120.39 127.31 -6.92 1.39e+00 5.18e-01 2.48e+01 ... (remaining 30175 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.34: 12774 13.34 - 26.67: 636 26.67 - 40.01: 132 40.01 - 53.35: 30 53.35 - 66.68: 24 Dihedral angle restraints: 13596 sinusoidal: 5652 harmonic: 7944 Sorted by residual: dihedral pdb=" N LEU D 334 " pdb=" CA LEU D 334 " pdb=" CB LEU D 334 " pdb=" CG LEU D 334 " ideal model delta sinusoidal sigma weight residual -60.00 -118.89 58.89 3 1.50e+01 4.44e-03 9.47e+00 dihedral pdb=" N LEU F 334 " pdb=" CA LEU F 334 " pdb=" CB LEU F 334 " pdb=" CG LEU F 334 " ideal model delta sinusoidal sigma weight residual -60.00 -118.87 58.87 3 1.50e+01 4.44e-03 9.47e+00 dihedral pdb=" N LEU C 334 " pdb=" CA LEU C 334 " pdb=" CB LEU C 334 " pdb=" CG LEU C 334 " ideal model delta sinusoidal sigma weight residual -60.00 -118.86 58.86 3 1.50e+01 4.44e-03 9.47e+00 ... (remaining 13593 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 2030 0.027 - 0.055: 907 0.055 - 0.082: 263 0.082 - 0.110: 144 0.110 - 0.137: 46 Chirality restraints: 3390 Sorted by residual: chirality pdb=" CA ILE A 693 " pdb=" N ILE A 693 " pdb=" C ILE A 693 " pdb=" CB ILE A 693 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.69e-01 chirality pdb=" CA ILE E 693 " pdb=" N ILE E 693 " pdb=" C ILE E 693 " pdb=" CB ILE E 693 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.69e-01 chirality pdb=" CA ILE B 693 " pdb=" N ILE B 693 " pdb=" C ILE B 693 " pdb=" CB ILE B 693 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.52e-01 ... (remaining 3387 not shown) Planarity restraints: 3816 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR A 409 " 0.028 5.00e-02 4.00e+02 4.20e-02 2.82e+00 pdb=" N PRO A 410 " -0.073 5.00e-02 4.00e+02 pdb=" CA PRO A 410 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 410 " 0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR F 409 " 0.028 5.00e-02 4.00e+02 4.18e-02 2.80e+00 pdb=" N PRO F 410 " -0.072 5.00e-02 4.00e+02 pdb=" CA PRO F 410 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO F 410 " 0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR D 409 " -0.028 5.00e-02 4.00e+02 4.18e-02 2.79e+00 pdb=" N PRO D 410 " 0.072 5.00e-02 4.00e+02 pdb=" CA PRO D 410 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO D 410 " -0.023 5.00e-02 4.00e+02 ... (remaining 3813 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 2241 2.75 - 3.29: 22063 3.29 - 3.83: 37655 3.83 - 4.36: 45804 4.36 - 4.90: 75976 Nonbonded interactions: 183739 Sorted by model distance: nonbonded pdb=" OG1 THR E 406 " pdb=" O THR E 437 " model vdw 2.213 3.040 nonbonded pdb=" OG1 THR F 406 " pdb=" O THR F 437 " model vdw 2.213 3.040 nonbonded pdb=" OG1 THR B 406 " pdb=" O THR B 437 " model vdw 2.213 3.040 nonbonded pdb=" OG1 THR A 406 " pdb=" O THR A 437 " model vdw 2.213 3.040 nonbonded pdb=" OG1 THR D 406 " pdb=" O THR D 437 " model vdw 2.213 3.040 ... (remaining 183734 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } 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: 1.530 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: 0.050 Extract box with map and model: 0.820 Check model and map are aligned: 0.170 Set scattering table: 0.210 Process input model: 47.270 Find NCS groups from input model: 0.900 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 54.210 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7405 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 : 0.002 0.017 22356 Z= 0.104 Angle : 0.477 9.262 30180 Z= 0.273 Chirality : 0.038 0.137 3390 Planarity : 0.003 0.042 3816 Dihedral : 9.134 66.684 8448 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 10.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 1.93 % Allowed : 4.11 % Favored : 93.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: 0.14 (0.17), residues: 2670 helix: 1.14 (0.17), residues: 1098 sheet: -0.76 (0.29), residues: 318 loop : -0.55 (0.17), residues: 1254 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP A 350 HIS 0.002 0.001 HIS E 763 PHE 0.006 0.001 PHE C 444 TYR 0.013 0.001 TYR F 409 ARG 0.002 0.000 ARG D 372 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5340 Ramachandran restraints generated. 2670 Oldfield, 0 Emsley, 2670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5340 Ramachandran restraints generated. 2670 Oldfield, 0 Emsley, 2670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 739 residues out of total 2484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 691 time to evaluate : 2.975 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 353 ASN cc_start: 0.8030 (m-40) cc_final: 0.7728 (m110) REVERT: A 363 LEU cc_start: 0.9105 (mt) cc_final: 0.8870 (mt) REVERT: A 390 LYS cc_start: 0.9034 (tttt) cc_final: 0.8758 (tppt) REVERT: A 428 TYR cc_start: 0.8444 (m-80) cc_final: 0.7985 (m-10) REVERT: A 437 THR cc_start: 0.9184 (p) cc_final: 0.7854 (p) REVERT: A 486 LEU cc_start: 0.9096 (mt) cc_final: 0.8821 (mm) REVERT: A 516 LEU cc_start: 0.9461 (tp) cc_final: 0.9053 (tp) REVERT: A 544 ILE cc_start: 0.9159 (mm) cc_final: 0.8911 (mt) REVERT: A 671 LEU cc_start: 0.9109 (tp) cc_final: 0.8476 (tp) REVERT: A 675 TRP cc_start: 0.8161 (m-10) cc_final: 0.7954 (m-10) REVERT: A 759 PHE cc_start: 0.6243 (t80) cc_final: 0.5615 (t80) REVERT: B 353 ASN cc_start: 0.8113 (m-40) cc_final: 0.7811 (m110) REVERT: B 369 LEU cc_start: 0.9372 (OUTLIER) cc_final: 0.9015 (tm) REVERT: B 387 ARG cc_start: 0.7334 (ttt180) cc_final: 0.6823 (tmm-80) REVERT: B 390 LYS cc_start: 0.9076 (tttt) cc_final: 0.8743 (tppt) REVERT: B 437 THR cc_start: 0.9122 (p) cc_final: 0.7598 (p) REVERT: B 463 ASN cc_start: 0.8099 (m-40) cc_final: 0.7766 (t0) REVERT: B 486 LEU cc_start: 0.8975 (mt) cc_final: 0.8736 (mm) REVERT: B 516 LEU cc_start: 0.9463 (tp) cc_final: 0.9140 (tp) REVERT: B 538 LYS cc_start: 0.6665 (tptp) cc_final: 0.6458 (mtmm) REVERT: B 544 ILE cc_start: 0.9101 (mm) cc_final: 0.8812 (mt) REVERT: B 671 LEU cc_start: 0.9203 (tp) cc_final: 0.7919 (tp) REVERT: B 675 TRP cc_start: 0.8202 (m-10) cc_final: 0.7836 (m-10) REVERT: B 759 PHE cc_start: 0.6143 (t80) cc_final: 0.5515 (t80) REVERT: C 406 THR cc_start: 0.8402 (OUTLIER) cc_final: 0.8042 (t) REVERT: C 428 TYR cc_start: 0.8372 (m-80) cc_final: 0.7961 (m-10) REVERT: C 437 THR cc_start: 0.8963 (p) cc_final: 0.7463 (p) REVERT: C 516 LEU cc_start: 0.9461 (tp) cc_final: 0.9055 (tp) REVERT: C 544 ILE cc_start: 0.9111 (mm) cc_final: 0.8909 (mt) REVERT: C 759 PHE cc_start: 0.5787 (t80) cc_final: 0.5335 (t80) REVERT: D 353 ASN cc_start: 0.8111 (m-40) cc_final: 0.7773 (m110) REVERT: D 428 TYR cc_start: 0.8469 (m-80) cc_final: 0.8015 (m-10) REVERT: D 437 THR cc_start: 0.9191 (p) cc_final: 0.7861 (p) REVERT: D 516 LEU cc_start: 0.9420 (tp) cc_final: 0.8940 (tp) REVERT: D 538 LYS cc_start: 0.6946 (tptp) cc_final: 0.6720 (mttt) REVERT: D 544 ILE cc_start: 0.9157 (mm) cc_final: 0.8915 (mt) REVERT: D 671 LEU cc_start: 0.9111 (tp) cc_final: 0.8431 (tp) REVERT: D 759 PHE cc_start: 0.6341 (t80) cc_final: 0.5780 (t80) REVERT: E 353 ASN cc_start: 0.8278 (m-40) cc_final: 0.7958 (m110) REVERT: E 365 THR cc_start: 0.9142 (OUTLIER) cc_final: 0.8863 (p) REVERT: E 369 LEU cc_start: 0.9482 (OUTLIER) cc_final: 0.9094 (tm) REVERT: E 437 THR cc_start: 0.9113 (p) cc_final: 0.7498 (p) REVERT: E 486 LEU cc_start: 0.8976 (mt) cc_final: 0.8724 (mm) REVERT: E 516 LEU cc_start: 0.9441 (tp) cc_final: 0.9056 (tp) REVERT: E 533 THR cc_start: 0.7736 (p) cc_final: 0.7535 (p) REVERT: E 544 ILE cc_start: 0.9075 (mm) cc_final: 0.8764 (mt) REVERT: E 555 CYS cc_start: 0.8245 (m) cc_final: 0.7888 (m) REVERT: E 629 HIS cc_start: 0.9300 (t70) cc_final: 0.9032 (t70) REVERT: E 630 PHE cc_start: 0.7971 (m-80) cc_final: 0.7007 (m-80) REVERT: E 671 LEU cc_start: 0.9204 (tp) cc_final: 0.8049 (tp) REVERT: E 675 TRP cc_start: 0.8146 (m-10) cc_final: 0.7823 (m-10) REVERT: E 759 PHE cc_start: 0.6372 (t80) cc_final: 0.5890 (t80) REVERT: F 333 ILE cc_start: 0.9596 (mt) cc_final: 0.9385 (mm) REVERT: F 353 ASN cc_start: 0.8165 (m-40) cc_final: 0.7761 (m110) REVERT: F 384 LEU cc_start: 0.9441 (mt) cc_final: 0.9141 (mt) REVERT: F 437 THR cc_start: 0.8952 (p) cc_final: 0.7672 (p) REVERT: F 516 LEU cc_start: 0.9481 (tp) cc_final: 0.9010 (tp) REVERT: F 534 ASP cc_start: 0.8095 (m-30) cc_final: 0.7795 (m-30) REVERT: F 538 LYS cc_start: 0.6837 (tptp) cc_final: 0.6572 (mtmt) REVERT: F 544 ILE cc_start: 0.9074 (mm) cc_final: 0.8833 (mt) REVERT: F 555 CYS cc_start: 0.8044 (m) cc_final: 0.7707 (m) REVERT: F 577 LEU cc_start: 0.8929 (OUTLIER) cc_final: 0.8711 (mp) REVERT: F 759 PHE cc_start: 0.6410 (t80) cc_final: 0.6165 (t80) outliers start: 48 outliers final: 13 residues processed: 727 average time/residue: 0.3737 time to fit residues: 400.9401 Evaluate side-chains 427 residues out of total 2484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 409 time to evaluate : 2.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 222 optimal weight: 0.9980 chunk 200 optimal weight: 6.9990 chunk 111 optimal weight: 6.9990 chunk 68 optimal weight: 9.9990 chunk 134 optimal weight: 1.9990 chunk 106 optimal weight: 10.0000 chunk 206 optimal weight: 6.9990 chunk 80 optimal weight: 6.9990 chunk 125 optimal weight: 9.9990 chunk 154 optimal weight: 0.9980 chunk 239 optimal weight: 0.8980 overall best weight: 2.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 324 ASN A 763 HIS A 775 GLN B 324 ASN ** B 573 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 763 HIS B 775 GLN C 324 ASN ** C 573 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 775 GLN D 324 ASN ** D 573 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 763 HIS D 775 GLN E 324 ASN ** E 573 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 763 HIS E 775 GLN F 324 ASN F 463 ASN ** F 573 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 775 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7553 moved from start: 0.3164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 22356 Z= 0.309 Angle : 0.655 7.889 30180 Z= 0.336 Chirality : 0.044 0.310 3390 Planarity : 0.005 0.073 3816 Dihedral : 4.152 18.032 2922 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 16.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: -0.60 (0.16), residues: 2670 helix: 0.41 (0.15), residues: 1104 sheet: -1.24 (0.29), residues: 288 loop : -0.83 (0.17), residues: 1278 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP C 675 HIS 0.005 0.001 HIS D 763 PHE 0.031 0.002 PHE E 554 TYR 0.020 0.002 TYR C 606 ARG 0.005 0.001 ARG F 625 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5340 Ramachandran restraints generated. 2670 Oldfield, 0 Emsley, 2670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5340 Ramachandran restraints generated. 2670 Oldfield, 0 Emsley, 2670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 501 residues out of total 2484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 501 time to evaluate : 2.403 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 467 ASP cc_start: 0.8728 (t0) cc_final: 0.8486 (t0) REVERT: A 491 CYS cc_start: 0.8496 (t) cc_final: 0.8161 (p) REVERT: A 501 PHE cc_start: 0.9007 (m-10) cc_final: 0.8675 (m-80) REVERT: A 597 HIS cc_start: 0.6743 (m170) cc_final: 0.6378 (m170) REVERT: A 625 ARG cc_start: 0.8197 (tpt170) cc_final: 0.7938 (tpt170) REVERT: A 671 LEU cc_start: 0.9137 (tp) cc_final: 0.8134 (tp) REVERT: A 675 TRP cc_start: 0.8312 (m-10) cc_final: 0.8107 (m-10) REVERT: B 371 ILE cc_start: 0.9482 (pt) cc_final: 0.9184 (pt) REVERT: B 384 LEU cc_start: 0.9426 (mt) cc_final: 0.9115 (mt) REVERT: B 390 LYS cc_start: 0.9098 (tttt) cc_final: 0.8876 (tppt) REVERT: B 491 CYS cc_start: 0.8384 (t) cc_final: 0.7999 (p) REVERT: B 495 LYS cc_start: 0.7563 (pptt) cc_final: 0.7249 (pptt) REVERT: B 501 PHE cc_start: 0.9041 (m-10) cc_final: 0.8703 (m-10) REVERT: B 531 ILE cc_start: 0.8073 (mt) cc_final: 0.7706 (mm) REVERT: B 538 LYS cc_start: 0.6728 (tptp) cc_final: 0.6473 (mtmm) REVERT: B 544 ILE cc_start: 0.9053 (mm) cc_final: 0.8842 (mt) REVERT: B 577 LEU cc_start: 0.9206 (mp) cc_final: 0.8948 (mp) REVERT: B 618 MET cc_start: 0.7852 (tmm) cc_final: 0.7611 (tmm) REVERT: B 671 LEU cc_start: 0.9204 (tp) cc_final: 0.7831 (tp) REVERT: B 675 TRP cc_start: 0.8174 (m-10) cc_final: 0.7819 (m-10) REVERT: B 759 PHE cc_start: 0.6189 (t80) cc_final: 0.5923 (t80) REVERT: C 384 LEU cc_start: 0.9376 (mt) cc_final: 0.9101 (mt) REVERT: C 428 TYR cc_start: 0.8160 (m-80) cc_final: 0.7931 (m-10) REVERT: C 467 ASP cc_start: 0.8695 (t0) cc_final: 0.8434 (t0) REVERT: C 491 CYS cc_start: 0.8639 (t) cc_final: 0.8303 (p) REVERT: C 567 LYS cc_start: 0.7754 (mttt) cc_final: 0.7364 (mtpt) REVERT: C 618 MET cc_start: 0.7956 (tmm) cc_final: 0.7713 (tmm) REVERT: C 671 LEU cc_start: 0.9267 (tp) cc_final: 0.9063 (tp) REVERT: C 759 PHE cc_start: 0.5701 (t80) cc_final: 0.5450 (t80) REVERT: D 351 ILE cc_start: 0.9346 (pt) cc_final: 0.8968 (pt) REVERT: D 491 CYS cc_start: 0.8539 (t) cc_final: 0.7953 (p) REVERT: D 501 PHE cc_start: 0.9261 (m-10) cc_final: 0.8971 (m-10) REVERT: D 597 HIS cc_start: 0.6710 (m170) cc_final: 0.6263 (m170) REVERT: D 671 LEU cc_start: 0.9150 (tp) cc_final: 0.7820 (tp) REVERT: D 675 TRP cc_start: 0.8328 (m-10) cc_final: 0.8042 (m-10) REVERT: E 387 ARG cc_start: 0.7436 (ttt180) cc_final: 0.7107 (ttt180) REVERT: E 486 LEU cc_start: 0.8847 (mt) cc_final: 0.8647 (mm) REVERT: E 491 CYS cc_start: 0.8494 (t) cc_final: 0.8134 (p) REVERT: E 495 LYS cc_start: 0.7415 (pptt) cc_final: 0.7170 (pptt) REVERT: E 618 MET cc_start: 0.7768 (tmm) cc_final: 0.7511 (tmm) REVERT: E 671 LEU cc_start: 0.9222 (tp) cc_final: 0.7806 (tp) REVERT: E 675 TRP cc_start: 0.8142 (m-10) cc_final: 0.7820 (m-10) REVERT: F 384 LEU cc_start: 0.9439 (mt) cc_final: 0.9026 (mt) REVERT: F 467 ASP cc_start: 0.8603 (t0) cc_final: 0.8308 (t0) REVERT: F 491 CYS cc_start: 0.8585 (t) cc_final: 0.8265 (p) REVERT: F 500 PHE cc_start: 0.8683 (m-10) cc_final: 0.8420 (m-80) REVERT: F 501 PHE cc_start: 0.9184 (m-10) cc_final: 0.8951 (m-10) REVERT: F 517 LYS cc_start: 0.9379 (tptm) cc_final: 0.9134 (tptt) REVERT: F 675 TRP cc_start: 0.8239 (m-10) cc_final: 0.7942 (m-10) outliers start: 0 outliers final: 0 residues processed: 501 average time/residue: 0.3369 time to fit residues: 256.8846 Evaluate side-chains 344 residues out of total 2484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 344 time to evaluate : 2.632 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 133 optimal weight: 1.9990 chunk 74 optimal weight: 0.7980 chunk 199 optimal weight: 6.9990 chunk 163 optimal weight: 0.7980 chunk 66 optimal weight: 3.9990 chunk 240 optimal weight: 0.8980 chunk 259 optimal weight: 0.2980 chunk 213 optimal weight: 20.0000 chunk 238 optimal weight: 0.0980 chunk 81 optimal weight: 0.1980 chunk 192 optimal weight: 1.9990 overall best weight: 0.4380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 593 ASN ** B 573 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 763 HIS ** C 573 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 597 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 593 ASN ** E 573 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 629 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 763 HIS F 593 ASN ** F 597 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7494 moved from start: 0.3573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 22356 Z= 0.188 Angle : 0.552 6.041 30180 Z= 0.290 Chirality : 0.042 0.217 3390 Planarity : 0.004 0.053 3816 Dihedral : 4.136 19.062 2922 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 14.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 0.16 % Allowed : 2.74 % Favored : 97.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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 (0.16), residues: 2670 helix: 0.41 (0.16), residues: 1122 sheet: -2.09 (0.27), residues: 342 loop : -0.54 (0.18), residues: 1206 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 675 HIS 0.006 0.001 HIS C 597 PHE 0.035 0.002 PHE F 502 TYR 0.017 0.001 TYR B 606 ARG 0.006 0.000 ARG D 514 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5340 Ramachandran restraints generated. 2670 Oldfield, 0 Emsley, 2670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5340 Ramachandran restraints generated. 2670 Oldfield, 0 Emsley, 2670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 491 residues out of total 2484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 487 time to evaluate : 2.521 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 393 GLU cc_start: 0.8792 (tm-30) cc_final: 0.8584 (tm-30) REVERT: A 491 CYS cc_start: 0.8482 (t) cc_final: 0.8059 (p) REVERT: A 531 ILE cc_start: 0.8062 (mm) cc_final: 0.7776 (mm) REVERT: A 548 HIS cc_start: 0.8423 (p-80) cc_final: 0.7992 (p-80) REVERT: A 597 HIS cc_start: 0.6724 (m170) cc_final: 0.6329 (m170) REVERT: A 671 LEU cc_start: 0.9121 (tp) cc_final: 0.8174 (tp) REVERT: B 384 LEU cc_start: 0.9311 (mt) cc_final: 0.9013 (mt) REVERT: B 387 ARG cc_start: 0.7482 (ttt180) cc_final: 0.7232 (ttt180) REVERT: B 390 LYS cc_start: 0.9042 (tttt) cc_final: 0.8795 (tppt) REVERT: B 486 LEU cc_start: 0.9050 (mm) cc_final: 0.8816 (mm) REVERT: B 491 CYS cc_start: 0.8489 (t) cc_final: 0.8080 (p) REVERT: B 495 LYS cc_start: 0.7495 (pptt) cc_final: 0.7000 (pptt) REVERT: B 499 THR cc_start: 0.7722 (t) cc_final: 0.7398 (t) REVERT: B 531 ILE cc_start: 0.8064 (mt) cc_final: 0.7858 (mm) REVERT: B 538 LYS cc_start: 0.6759 (tptp) cc_final: 0.6433 (mtmm) REVERT: B 577 LEU cc_start: 0.9157 (mp) cc_final: 0.8883 (mt) REVERT: B 629 HIS cc_start: 0.8558 (t-90) cc_final: 0.8227 (t-90) REVERT: B 671 LEU cc_start: 0.9163 (tp) cc_final: 0.7846 (tp) REVERT: B 675 TRP cc_start: 0.8235 (m-10) cc_final: 0.7861 (m-10) REVERT: B 759 PHE cc_start: 0.6075 (t80) cc_final: 0.5759 (t80) REVERT: C 349 VAL cc_start: 0.9383 (t) cc_final: 0.9085 (p) REVERT: C 371 ILE cc_start: 0.9407 (pt) cc_final: 0.9180 (pt) REVERT: C 384 LEU cc_start: 0.9258 (mt) cc_final: 0.9039 (mt) REVERT: C 428 TYR cc_start: 0.8218 (m-80) cc_final: 0.7963 (m-80) REVERT: C 458 MET cc_start: 0.7563 (ttm) cc_final: 0.7240 (ttm) REVERT: C 463 ASN cc_start: 0.8513 (m-40) cc_final: 0.8148 (m-40) REVERT: C 491 CYS cc_start: 0.8556 (t) cc_final: 0.8144 (p) REVERT: C 531 ILE cc_start: 0.8255 (mm) cc_final: 0.7950 (mm) REVERT: C 567 LYS cc_start: 0.7619 (mttt) cc_final: 0.7338 (mtpt) REVERT: C 603 ASP cc_start: 0.5827 (m-30) cc_final: 0.5232 (m-30) REVERT: C 671 LEU cc_start: 0.9258 (tp) cc_final: 0.9046 (tp) REVERT: C 759 PHE cc_start: 0.5726 (t80) cc_final: 0.5443 (t80) REVERT: D 481 LEU cc_start: 0.8923 (mt) cc_final: 0.8561 (mt) REVERT: D 484 LYS cc_start: 0.9057 (mtmt) cc_final: 0.8722 (mtmt) REVERT: D 486 LEU cc_start: 0.9368 (mm) cc_final: 0.8943 (mm) REVERT: D 501 PHE cc_start: 0.9198 (m-10) cc_final: 0.8851 (m-80) REVERT: D 516 LEU cc_start: 0.9334 (tp) cc_final: 0.9014 (tp) REVERT: D 531 ILE cc_start: 0.8004 (mm) cc_final: 0.7709 (mm) REVERT: D 548 HIS cc_start: 0.8417 (p-80) cc_final: 0.7900 (p-80) REVERT: D 597 HIS cc_start: 0.6764 (m170) cc_final: 0.6407 (m170) REVERT: D 626 PHE cc_start: 0.5682 (m-80) cc_final: 0.5255 (m-80) REVERT: D 671 LEU cc_start: 0.9103 (tp) cc_final: 0.7702 (tp) REVERT: E 371 ILE cc_start: 0.9317 (pt) cc_final: 0.9011 (pt) REVERT: E 393 GLU cc_start: 0.8482 (tm-30) cc_final: 0.8247 (tm-30) REVERT: E 458 MET cc_start: 0.7917 (ttm) cc_final: 0.7529 (ttm) REVERT: E 486 LEU cc_start: 0.8838 (mt) cc_final: 0.8435 (mt) REVERT: E 491 CYS cc_start: 0.8496 (t) cc_final: 0.8070 (p) REVERT: E 495 LYS cc_start: 0.7421 (pptt) cc_final: 0.7103 (pptt) REVERT: E 499 THR cc_start: 0.7603 (t) cc_final: 0.7273 (t) REVERT: E 500 PHE cc_start: 0.8332 (m-10) cc_final: 0.8117 (m-80) REVERT: E 501 PHE cc_start: 0.9171 (m-10) cc_final: 0.8927 (m-80) REVERT: E 531 ILE cc_start: 0.7906 (mt) cc_final: 0.7505 (tt) REVERT: E 577 LEU cc_start: 0.9112 (mp) cc_final: 0.8884 (mt) REVERT: E 625 ARG cc_start: 0.8273 (tpt90) cc_final: 0.7999 (tpt170) REVERT: E 629 HIS cc_start: 0.8691 (t-90) cc_final: 0.8334 (t-90) REVERT: F 371 ILE cc_start: 0.9295 (pt) cc_final: 0.8965 (pt) REVERT: F 384 LEU cc_start: 0.9354 (mt) cc_final: 0.8994 (mt) REVERT: F 491 CYS cc_start: 0.8616 (t) cc_final: 0.8124 (p) REVERT: F 499 THR cc_start: 0.7609 (t) cc_final: 0.7273 (t) REVERT: F 500 PHE cc_start: 0.8628 (m-10) cc_final: 0.8407 (m-80) REVERT: F 517 LYS cc_start: 0.9307 (tptm) cc_final: 0.9029 (tptp) REVERT: F 538 LYS cc_start: 0.6566 (tptp) cc_final: 0.6308 (mtmt) REVERT: F 597 HIS cc_start: 0.6999 (m90) cc_final: 0.6457 (m170) REVERT: F 671 LEU cc_start: 0.9256 (tp) cc_final: 0.7921 (tp) REVERT: F 675 TRP cc_start: 0.8199 (m-10) cc_final: 0.7880 (m-10) outliers start: 4 outliers final: 0 residues processed: 491 average time/residue: 0.3308 time to fit residues: 250.6572 Evaluate side-chains 350 residues out of total 2484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 350 time to evaluate : 2.601 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 237 optimal weight: 10.0000 chunk 180 optimal weight: 0.8980 chunk 124 optimal weight: 3.9990 chunk 26 optimal weight: 8.9990 chunk 114 optimal weight: 8.9990 chunk 161 optimal weight: 0.8980 chunk 241 optimal weight: 8.9990 chunk 255 optimal weight: 7.9990 chunk 125 optimal weight: 4.9990 chunk 228 optimal weight: 0.6980 chunk 68 optimal weight: 0.8980 overall best weight: 1.4782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 417 ASN A 593 ASN ** B 573 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 763 HIS ** C 573 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 597 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 353 ASN D 593 ASN ** D 629 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 573 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 629 HIS E 763 HIS F 593 ASN ** F 597 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 629 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7534 moved from start: 0.3872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 22356 Z= 0.231 Angle : 0.575 7.536 30180 Z= 0.295 Chirality : 0.042 0.150 3390 Planarity : 0.004 0.042 3816 Dihedral : 4.237 19.049 2922 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 14.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 0.12 % Allowed : 2.25 % Favored : 97.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: -0.70 (0.16), residues: 2670 helix: 0.28 (0.15), residues: 1122 sheet: -2.10 (0.27), residues: 342 loop : -0.53 (0.17), residues: 1206 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 355 HIS 0.006 0.001 HIS C 548 PHE 0.027 0.002 PHE E 554 TYR 0.016 0.001 TYR C 699 ARG 0.008 0.000 ARG E 387 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5340 Ramachandran restraints generated. 2670 Oldfield, 0 Emsley, 2670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5340 Ramachandran restraints generated. 2670 Oldfield, 0 Emsley, 2670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 443 residues out of total 2484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 440 time to evaluate : 2.321 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 393 GLU cc_start: 0.8840 (tm-30) cc_final: 0.8632 (tm-30) REVERT: A 486 LEU cc_start: 0.9358 (mm) cc_final: 0.8920 (mm) REVERT: A 491 CYS cc_start: 0.8368 (t) cc_final: 0.8045 (p) REVERT: A 516 LEU cc_start: 0.9386 (tp) cc_final: 0.9000 (tp) REVERT: A 597 HIS cc_start: 0.6717 (m170) cc_final: 0.6315 (m170) REVERT: A 671 LEU cc_start: 0.9143 (tp) cc_final: 0.7967 (tp) REVERT: A 675 TRP cc_start: 0.8266 (m-10) cc_final: 0.8034 (m-10) REVERT: A 759 PHE cc_start: 0.6337 (t80) cc_final: 0.6020 (t80) REVERT: B 384 LEU cc_start: 0.9342 (mt) cc_final: 0.8969 (mt) REVERT: B 398 ASP cc_start: 0.8564 (m-30) cc_final: 0.8347 (m-30) REVERT: B 486 LEU cc_start: 0.9134 (mm) cc_final: 0.8905 (mm) REVERT: B 491 CYS cc_start: 0.8372 (t) cc_final: 0.7927 (p) REVERT: B 495 LYS cc_start: 0.7261 (pptt) cc_final: 0.6795 (pptt) REVERT: B 499 THR cc_start: 0.7660 (t) cc_final: 0.7275 (t) REVERT: B 501 PHE cc_start: 0.9165 (m-10) cc_final: 0.8920 (m-80) REVERT: B 577 LEU cc_start: 0.9151 (mp) cc_final: 0.8940 (mt) REVERT: B 629 HIS cc_start: 0.8489 (t-90) cc_final: 0.8186 (t-90) REVERT: B 671 LEU cc_start: 0.9175 (tp) cc_final: 0.7835 (tp) REVERT: B 675 TRP cc_start: 0.8209 (m-10) cc_final: 0.7830 (m-10) REVERT: B 759 PHE cc_start: 0.6188 (t80) cc_final: 0.5916 (t80) REVERT: C 349 VAL cc_start: 0.9485 (t) cc_final: 0.9117 (p) REVERT: C 428 TYR cc_start: 0.8176 (m-80) cc_final: 0.7938 (m-80) REVERT: C 439 THR cc_start: 0.8522 (p) cc_final: 0.8319 (t) REVERT: C 486 LEU cc_start: 0.9085 (mm) cc_final: 0.8628 (mm) REVERT: C 491 CYS cc_start: 0.8559 (t) cc_final: 0.8087 (p) REVERT: C 499 THR cc_start: 0.7326 (t) cc_final: 0.7113 (t) REVERT: C 567 LYS cc_start: 0.7654 (mttt) cc_final: 0.7356 (mtpt) REVERT: C 759 PHE cc_start: 0.5932 (t80) cc_final: 0.5607 (t80) REVERT: D 486 LEU cc_start: 0.9223 (mm) cc_final: 0.8891 (mm) REVERT: D 500 PHE cc_start: 0.8449 (m-10) cc_final: 0.8196 (m-80) REVERT: D 671 LEU cc_start: 0.9166 (tp) cc_final: 0.7859 (tp) REVERT: D 675 TRP cc_start: 0.8289 (m-10) cc_final: 0.7982 (m-10) REVERT: D 759 PHE cc_start: 0.6361 (t80) cc_final: 0.6088 (t80) REVERT: E 491 CYS cc_start: 0.8635 (t) cc_final: 0.8199 (p) REVERT: E 495 LYS cc_start: 0.7228 (pptt) cc_final: 0.6779 (pptt) REVERT: E 499 THR cc_start: 0.7551 (t) cc_final: 0.7329 (t) REVERT: E 500 PHE cc_start: 0.8276 (m-10) cc_final: 0.8039 (m-80) REVERT: E 531 ILE cc_start: 0.7989 (mt) cc_final: 0.7641 (tt) REVERT: E 577 LEU cc_start: 0.9133 (mp) cc_final: 0.8881 (mt) REVERT: E 625 ARG cc_start: 0.8212 (tpt90) cc_final: 0.7975 (tpt170) REVERT: E 629 HIS cc_start: 0.8495 (t70) cc_final: 0.8244 (t-90) REVERT: E 671 LEU cc_start: 0.9152 (tp) cc_final: 0.7730 (tp) REVERT: E 675 TRP cc_start: 0.8182 (m-10) cc_final: 0.7799 (m-10) REVERT: E 759 PHE cc_start: 0.6223 (t80) cc_final: 0.5972 (t80) REVERT: F 343 GLU cc_start: 0.7857 (mp0) cc_final: 0.7510 (pm20) REVERT: F 384 LEU cc_start: 0.9366 (mt) cc_final: 0.8989 (mt) REVERT: F 491 CYS cc_start: 0.8603 (t) cc_final: 0.8087 (p) REVERT: F 500 PHE cc_start: 0.8786 (m-10) cc_final: 0.8553 (m-80) REVERT: F 517 LYS cc_start: 0.9329 (tptm) cc_final: 0.9095 (tptt) REVERT: F 548 HIS cc_start: 0.8395 (p-80) cc_final: 0.8115 (p90) REVERT: F 597 HIS cc_start: 0.7191 (m90) cc_final: 0.6608 (m170) REVERT: F 601 ILE cc_start: 0.8382 (mt) cc_final: 0.8165 (tp) REVERT: F 629 HIS cc_start: 0.8639 (t-90) cc_final: 0.8245 (t-90) REVERT: F 671 LEU cc_start: 0.9263 (tp) cc_final: 0.7947 (tp) REVERT: F 675 TRP cc_start: 0.8251 (m-10) cc_final: 0.7841 (m-10) outliers start: 3 outliers final: 0 residues processed: 443 average time/residue: 0.3443 time to fit residues: 233.4251 Evaluate side-chains 332 residues out of total 2484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 332 time to evaluate : 2.626 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 212 optimal weight: 4.9990 chunk 144 optimal weight: 0.9990 chunk 3 optimal weight: 0.1980 chunk 190 optimal weight: 9.9990 chunk 105 optimal weight: 5.9990 chunk 217 optimal weight: 10.0000 chunk 176 optimal weight: 0.9980 chunk 0 optimal weight: 4.9990 chunk 130 optimal weight: 6.9990 chunk 229 optimal weight: 2.9990 chunk 64 optimal weight: 8.9990 overall best weight: 2.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 593 ASN ** B 573 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 597 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 763 HIS ** C 573 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 593 ASN ** C 597 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 593 ASN D 629 HIS E 763 HIS F 593 ASN ** F 597 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7570 moved from start: 0.4239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 22356 Z= 0.267 Angle : 0.622 9.713 30180 Z= 0.313 Chirality : 0.043 0.158 3390 Planarity : 0.004 0.042 3816 Dihedral : 4.420 17.580 2922 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 16.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 0.16 % Allowed : 2.09 % Favored : 97.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: -0.76 (0.16), residues: 2670 helix: 0.15 (0.15), residues: 1122 sheet: -1.98 (0.28), residues: 342 loop : -0.53 (0.18), residues: 1206 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP D 675 HIS 0.007 0.001 HIS B 597 PHE 0.031 0.002 PHE E 554 TYR 0.017 0.001 TYR B 606 ARG 0.004 0.001 ARG E 570 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5340 Ramachandran restraints generated. 2670 Oldfield, 0 Emsley, 2670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5340 Ramachandran restraints generated. 2670 Oldfield, 0 Emsley, 2670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 420 residues out of total 2484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 416 time to evaluate : 2.332 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 486 LEU cc_start: 0.9144 (mm) cc_final: 0.8879 (mm) REVERT: A 491 CYS cc_start: 0.8117 (t) cc_final: 0.7732 (p) REVERT: A 597 HIS cc_start: 0.6785 (m170) cc_final: 0.6500 (m170) REVERT: A 626 PHE cc_start: 0.6347 (m-10) cc_final: 0.6120 (m-10) REVERT: A 671 LEU cc_start: 0.9094 (tp) cc_final: 0.7702 (tp) REVERT: A 759 PHE cc_start: 0.6346 (t80) cc_final: 0.5999 (t80) REVERT: B 384 LEU cc_start: 0.9387 (mt) cc_final: 0.9119 (mt) REVERT: B 458 MET cc_start: 0.8236 (ttt) cc_final: 0.7989 (ttt) REVERT: B 486 LEU cc_start: 0.9260 (mm) cc_final: 0.9026 (mm) REVERT: B 491 CYS cc_start: 0.8153 (t) cc_final: 0.7876 (p) REVERT: B 548 HIS cc_start: 0.8480 (p-80) cc_final: 0.8222 (p-80) REVERT: B 629 HIS cc_start: 0.8845 (t-90) cc_final: 0.8473 (t-90) REVERT: B 671 LEU cc_start: 0.9209 (tp) cc_final: 0.7876 (tp) REVERT: B 675 TRP cc_start: 0.8237 (m-10) cc_final: 0.8034 (m-10) REVERT: C 349 VAL cc_start: 0.9470 (t) cc_final: 0.9147 (p) REVERT: C 384 LEU cc_start: 0.9351 (mt) cc_final: 0.9144 (mt) REVERT: C 428 TYR cc_start: 0.8162 (m-80) cc_final: 0.7862 (m-80) REVERT: C 491 CYS cc_start: 0.8546 (t) cc_final: 0.7912 (p) REVERT: C 499 THR cc_start: 0.7368 (t) cc_final: 0.7162 (t) REVERT: C 531 ILE cc_start: 0.8212 (mm) cc_final: 0.7960 (mm) REVERT: C 567 LYS cc_start: 0.7550 (mttt) cc_final: 0.7235 (mtpt) REVERT: C 629 HIS cc_start: 0.8792 (t70) cc_final: 0.8134 (t70) REVERT: C 759 PHE cc_start: 0.5863 (t80) cc_final: 0.5565 (t80) REVERT: D 398 ASP cc_start: 0.8689 (m-30) cc_final: 0.8410 (m-30) REVERT: D 486 LEU cc_start: 0.9286 (mm) cc_final: 0.8997 (mm) REVERT: D 500 PHE cc_start: 0.8625 (m-10) cc_final: 0.8338 (m-80) REVERT: D 531 ILE cc_start: 0.7906 (mm) cc_final: 0.7518 (tt) REVERT: D 671 LEU cc_start: 0.9210 (tp) cc_final: 0.7952 (tp) REVERT: D 675 TRP cc_start: 0.8279 (m-10) cc_final: 0.7842 (m-10) REVERT: D 759 PHE cc_start: 0.6407 (t80) cc_final: 0.6186 (t80) REVERT: E 439 THR cc_start: 0.8485 (p) cc_final: 0.8283 (t) REVERT: E 486 LEU cc_start: 0.9015 (mm) cc_final: 0.8792 (mm) REVERT: E 491 CYS cc_start: 0.8615 (t) cc_final: 0.8127 (p) REVERT: E 495 LYS cc_start: 0.7111 (pptt) cc_final: 0.6478 (pptt) REVERT: E 499 THR cc_start: 0.7909 (t) cc_final: 0.7670 (t) REVERT: E 500 PHE cc_start: 0.8426 (m-10) cc_final: 0.8192 (m-80) REVERT: E 548 HIS cc_start: 0.8451 (p-80) cc_final: 0.8211 (p-80) REVERT: E 577 LEU cc_start: 0.9152 (mp) cc_final: 0.8855 (mt) REVERT: E 629 HIS cc_start: 0.8687 (t70) cc_final: 0.8359 (t-90) REVERT: E 671 LEU cc_start: 0.9130 (tp) cc_final: 0.7765 (tp) REVERT: E 675 TRP cc_start: 0.8221 (m-10) cc_final: 0.7816 (m-10) REVERT: E 759 PHE cc_start: 0.6209 (t80) cc_final: 0.5996 (t80) REVERT: F 384 LEU cc_start: 0.9375 (mt) cc_final: 0.8960 (mt) REVERT: F 486 LEU cc_start: 0.9248 (mm) cc_final: 0.8975 (mm) REVERT: F 491 CYS cc_start: 0.7779 (t) cc_final: 0.7332 (p) REVERT: F 500 PHE cc_start: 0.8723 (m-10) cc_final: 0.8296 (m-80) REVERT: F 516 LEU cc_start: 0.9401 (tp) cc_final: 0.9009 (tp) REVERT: F 533 THR cc_start: 0.8496 (p) cc_final: 0.8225 (p) REVERT: F 567 LYS cc_start: 0.7564 (mtpt) cc_final: 0.7092 (mtpt) REVERT: F 597 HIS cc_start: 0.7170 (m90) cc_final: 0.6604 (m170) REVERT: F 629 HIS cc_start: 0.8572 (t-90) cc_final: 0.8154 (t-90) REVERT: F 671 LEU cc_start: 0.9281 (tp) cc_final: 0.8002 (tp) REVERT: F 675 TRP cc_start: 0.8259 (m-10) cc_final: 0.7843 (m-10) REVERT: F 759 PHE cc_start: 0.6400 (t80) cc_final: 0.6184 (t80) outliers start: 4 outliers final: 0 residues processed: 420 average time/residue: 0.3270 time to fit residues: 214.2887 Evaluate side-chains 308 residues out of total 2484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 308 time to evaluate : 2.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 85 optimal weight: 0.1980 chunk 229 optimal weight: 0.9990 chunk 50 optimal weight: 0.7980 chunk 149 optimal weight: 3.9990 chunk 62 optimal weight: 3.9990 chunk 255 optimal weight: 0.8980 chunk 212 optimal weight: 0.9980 chunk 118 optimal weight: 4.9990 chunk 21 optimal weight: 4.9990 chunk 84 optimal weight: 8.9990 chunk 134 optimal weight: 1.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 593 ASN ** B 573 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 597 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 763 HIS ** C 573 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 593 ASN ** C 597 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 548 HIS D 593 ASN D 629 HIS E 763 HIS F 593 ASN ** F 597 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7507 moved from start: 0.4436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 22356 Z= 0.176 Angle : 0.561 8.027 30180 Z= 0.286 Chirality : 0.042 0.170 3390 Planarity : 0.004 0.038 3816 Dihedral : 4.297 17.532 2922 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 14.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 0.16 % Allowed : 1.57 % Favored : 98.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: -0.63 (0.16), residues: 2670 helix: 0.28 (0.15), residues: 1122 sheet: -1.88 (0.28), residues: 342 loop : -0.47 (0.18), residues: 1206 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP E 355 HIS 0.005 0.001 HIS D 548 PHE 0.028 0.002 PHE C 554 TYR 0.022 0.001 TYR A 482 ARG 0.007 0.000 ARG C 625 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5340 Ramachandran restraints generated. 2670 Oldfield, 0 Emsley, 2670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5340 Ramachandran restraints generated. 2670 Oldfield, 0 Emsley, 2670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 450 residues out of total 2484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 446 time to evaluate : 2.324 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 343 GLU cc_start: 0.7360 (pm20) cc_final: 0.7115 (mp0) REVERT: A 393 GLU cc_start: 0.8763 (tm-30) cc_final: 0.8551 (tm-30) REVERT: A 481 LEU cc_start: 0.8828 (mt) cc_final: 0.8271 (mt) REVERT: A 484 LYS cc_start: 0.8936 (mtmt) cc_final: 0.8541 (mtmt) REVERT: A 486 LEU cc_start: 0.9065 (mm) cc_final: 0.8456 (mm) REVERT: A 491 CYS cc_start: 0.7873 (t) cc_final: 0.7587 (p) REVERT: A 525 VAL cc_start: 0.9177 (p) cc_final: 0.8858 (m) REVERT: A 597 HIS cc_start: 0.6741 (m170) cc_final: 0.6423 (m170) REVERT: A 671 LEU cc_start: 0.9140 (tp) cc_final: 0.8026 (tp) REVERT: B 384 LEU cc_start: 0.9358 (mt) cc_final: 0.8937 (mt) REVERT: B 398 ASP cc_start: 0.8555 (m-30) cc_final: 0.8347 (m-30) REVERT: B 458 MET cc_start: 0.8077 (ttt) cc_final: 0.7853 (ttt) REVERT: B 486 LEU cc_start: 0.9137 (mm) cc_final: 0.8875 (mm) REVERT: B 491 CYS cc_start: 0.7990 (t) cc_final: 0.7734 (p) REVERT: B 495 LYS cc_start: 0.7157 (pptt) cc_final: 0.6503 (pptt) REVERT: B 524 PHE cc_start: 0.8051 (t80) cc_final: 0.7602 (t80) REVERT: B 548 HIS cc_start: 0.8426 (p-80) cc_final: 0.8174 (p-80) REVERT: B 671 LEU cc_start: 0.9204 (tp) cc_final: 0.7847 (tp) REVERT: B 675 TRP cc_start: 0.8225 (m-10) cc_final: 0.7935 (m-10) REVERT: C 322 MET cc_start: 0.6126 (mpp) cc_final: 0.5789 (mtt) REVERT: C 349 VAL cc_start: 0.9449 (t) cc_final: 0.9219 (p) REVERT: C 353 ASN cc_start: 0.7979 (m-40) cc_final: 0.7101 (m-40) REVERT: C 384 LEU cc_start: 0.9319 (mt) cc_final: 0.9092 (mt) REVERT: C 428 TYR cc_start: 0.8061 (m-80) cc_final: 0.7799 (m-80) REVERT: C 499 THR cc_start: 0.7549 (t) cc_final: 0.7204 (t) REVERT: C 567 LYS cc_start: 0.7620 (mttt) cc_final: 0.7321 (mtpt) REVERT: C 618 MET cc_start: 0.7975 (tmm) cc_final: 0.7671 (tmm) REVERT: C 629 HIS cc_start: 0.8727 (t70) cc_final: 0.8200 (t70) REVERT: C 759 PHE cc_start: 0.5833 (t80) cc_final: 0.5555 (t80) REVERT: D 398 ASP cc_start: 0.8481 (m-30) cc_final: 0.8201 (m-30) REVERT: D 486 LEU cc_start: 0.9116 (mm) cc_final: 0.8728 (mm) REVERT: D 499 THR cc_start: 0.7709 (t) cc_final: 0.7475 (t) REVERT: D 500 PHE cc_start: 0.8576 (m-10) cc_final: 0.8275 (m-80) REVERT: D 671 LEU cc_start: 0.9174 (tp) cc_final: 0.7921 (tp) REVERT: D 675 TRP cc_start: 0.8218 (m-10) cc_final: 0.7798 (m-10) REVERT: E 439 THR cc_start: 0.8418 (p) cc_final: 0.8191 (t) REVERT: E 486 LEU cc_start: 0.8994 (mm) cc_final: 0.8731 (mm) REVERT: E 491 CYS cc_start: 0.8149 (t) cc_final: 0.7774 (p) REVERT: E 495 LYS cc_start: 0.7122 (pptt) cc_final: 0.6570 (pptt) REVERT: E 500 PHE cc_start: 0.8366 (m-10) cc_final: 0.8109 (m-80) REVERT: E 531 ILE cc_start: 0.8016 (mt) cc_final: 0.7703 (tt) REVERT: E 548 HIS cc_start: 0.8424 (p-80) cc_final: 0.8194 (p-80) REVERT: E 601 ILE cc_start: 0.8558 (mt) cc_final: 0.8318 (tp) REVERT: E 629 HIS cc_start: 0.8697 (t70) cc_final: 0.8477 (t-90) REVERT: F 384 LEU cc_start: 0.9364 (mt) cc_final: 0.9123 (mt) REVERT: F 491 CYS cc_start: 0.7990 (t) cc_final: 0.7623 (p) REVERT: F 500 PHE cc_start: 0.8734 (m-10) cc_final: 0.8374 (m-80) REVERT: F 533 THR cc_start: 0.8482 (p) cc_final: 0.8143 (p) REVERT: F 567 LYS cc_start: 0.7417 (mtpt) cc_final: 0.6913 (mtpt) REVERT: F 597 HIS cc_start: 0.7216 (m90) cc_final: 0.6664 (m170) REVERT: F 671 LEU cc_start: 0.9233 (tp) cc_final: 0.7893 (tp) REVERT: F 675 TRP cc_start: 0.8194 (m-10) cc_final: 0.7793 (m-10) outliers start: 4 outliers final: 0 residues processed: 450 average time/residue: 0.3280 time to fit residues: 227.9467 Evaluate side-chains 337 residues out of total 2484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 337 time to evaluate : 2.592 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 246 optimal weight: 1.9990 chunk 28 optimal weight: 6.9990 chunk 145 optimal weight: 3.9990 chunk 186 optimal weight: 0.9980 chunk 144 optimal weight: 2.9990 chunk 215 optimal weight: 0.0010 chunk 142 optimal weight: 0.9990 chunk 254 optimal weight: 4.9990 chunk 159 optimal weight: 1.9990 chunk 155 optimal weight: 1.9990 chunk 117 optimal weight: 0.8980 overall best weight: 0.9790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 548 HIS A 593 ASN ** B 573 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 597 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 763 HIS C 548 HIS ** C 573 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 593 ASN ** C 597 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 593 ASN F 548 HIS F 593 ASN ** F 597 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7515 moved from start: 0.4613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 22356 Z= 0.189 Angle : 0.563 8.120 30180 Z= 0.287 Chirality : 0.042 0.208 3390 Planarity : 0.004 0.035 3816 Dihedral : 4.313 19.173 2922 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 14.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 0.16 % Allowed : 0.89 % Favored : 98.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: -0.57 (0.16), residues: 2670 helix: 0.24 (0.15), residues: 1122 sheet: -1.15 (0.32), residues: 288 loop : -0.65 (0.17), residues: 1260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 355 HIS 0.006 0.001 HIS F 548 PHE 0.045 0.002 PHE F 554 TYR 0.020 0.001 TYR C 482 ARG 0.004 0.000 ARG E 625 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5340 Ramachandran restraints generated. 2670 Oldfield, 0 Emsley, 2670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5340 Ramachandran restraints generated. 2670 Oldfield, 0 Emsley, 2670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 440 residues out of total 2484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 436 time to evaluate : 2.712 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 327 PHE cc_start: 0.8733 (t80) cc_final: 0.8352 (t80) REVERT: A 343 GLU cc_start: 0.7376 (pm20) cc_final: 0.7117 (mp0) REVERT: A 481 LEU cc_start: 0.8825 (mt) cc_final: 0.8226 (mt) REVERT: A 484 LYS cc_start: 0.8933 (mtmt) cc_final: 0.8535 (mtmt) REVERT: A 486 LEU cc_start: 0.9025 (mm) cc_final: 0.8577 (mm) REVERT: A 491 CYS cc_start: 0.8039 (t) cc_final: 0.7625 (p) REVERT: A 501 PHE cc_start: 0.9019 (m-80) cc_final: 0.8385 (m-80) REVERT: A 525 VAL cc_start: 0.9200 (p) cc_final: 0.8886 (m) REVERT: A 597 HIS cc_start: 0.6773 (m170) cc_final: 0.6446 (m170) REVERT: A 625 ARG cc_start: 0.7937 (tpt90) cc_final: 0.7627 (tpt170) REVERT: A 671 LEU cc_start: 0.9121 (tp) cc_final: 0.8048 (tp) REVERT: A 759 PHE cc_start: 0.6261 (t80) cc_final: 0.6010 (t80) REVERT: B 398 ASP cc_start: 0.8596 (m-30) cc_final: 0.8350 (m-30) REVERT: B 486 LEU cc_start: 0.8953 (mm) cc_final: 0.8712 (mm) REVERT: B 501 PHE cc_start: 0.9069 (m-10) cc_final: 0.8798 (m-10) REVERT: B 548 HIS cc_start: 0.8443 (p-80) cc_final: 0.8201 (p-80) REVERT: B 671 LEU cc_start: 0.9217 (tp) cc_final: 0.7858 (tp) REVERT: B 675 TRP cc_start: 0.8256 (m-10) cc_final: 0.7912 (m-10) REVERT: C 322 MET cc_start: 0.6112 (mpp) cc_final: 0.5881 (mtt) REVERT: C 353 ASN cc_start: 0.7960 (m-40) cc_final: 0.7030 (m-40) REVERT: C 367 LEU cc_start: 0.9750 (tt) cc_final: 0.9494 (tp) REVERT: C 384 LEU cc_start: 0.9319 (mt) cc_final: 0.9025 (mt) REVERT: C 428 TYR cc_start: 0.8053 (m-80) cc_final: 0.7811 (m-80) REVERT: C 458 MET cc_start: 0.7451 (ptm) cc_final: 0.7150 (ppp) REVERT: C 531 ILE cc_start: 0.8162 (mm) cc_final: 0.7947 (mm) REVERT: C 567 LYS cc_start: 0.7608 (mttt) cc_final: 0.7301 (mtpt) REVERT: C 618 MET cc_start: 0.7975 (tmm) cc_final: 0.7690 (tmm) REVERT: C 629 HIS cc_start: 0.8693 (t70) cc_final: 0.8217 (t70) REVERT: D 398 ASP cc_start: 0.8539 (m-30) cc_final: 0.8332 (m-30) REVERT: D 486 LEU cc_start: 0.9126 (mm) cc_final: 0.8823 (mm) REVERT: D 500 PHE cc_start: 0.8535 (m-10) cc_final: 0.8321 (m-80) REVERT: D 671 LEU cc_start: 0.9180 (tp) cc_final: 0.7914 (tp) REVERT: D 675 TRP cc_start: 0.8231 (m-10) cc_final: 0.7796 (m-10) REVERT: D 759 PHE cc_start: 0.6346 (t80) cc_final: 0.6129 (t80) REVERT: E 439 THR cc_start: 0.8413 (p) cc_final: 0.8192 (t) REVERT: E 458 MET cc_start: 0.7450 (ptm) cc_final: 0.7040 (ppp) REVERT: E 486 LEU cc_start: 0.9004 (mm) cc_final: 0.8703 (mm) REVERT: E 491 CYS cc_start: 0.8202 (t) cc_final: 0.7905 (p) REVERT: E 500 PHE cc_start: 0.8383 (m-10) cc_final: 0.7978 (m-80) REVERT: E 548 HIS cc_start: 0.8438 (p-80) cc_final: 0.8217 (p-80) REVERT: E 602 ILE cc_start: 0.8620 (mt) cc_final: 0.8401 (mm) REVERT: E 625 ARG cc_start: 0.8214 (tpt90) cc_final: 0.7972 (tpt170) REVERT: F 384 LEU cc_start: 0.9379 (mt) cc_final: 0.8993 (mt) REVERT: F 491 CYS cc_start: 0.7990 (t) cc_final: 0.7537 (p) REVERT: F 499 THR cc_start: 0.7622 (t) cc_final: 0.7277 (t) REVERT: F 500 PHE cc_start: 0.8717 (m-10) cc_final: 0.8289 (m-80) REVERT: F 517 LYS cc_start: 0.9406 (tppt) cc_final: 0.9130 (tptp) REVERT: F 533 THR cc_start: 0.8461 (p) cc_final: 0.8088 (p) REVERT: F 567 LYS cc_start: 0.7450 (mtpt) cc_final: 0.6959 (mtpt) REVERT: F 597 HIS cc_start: 0.7349 (m90) cc_final: 0.6895 (m170) REVERT: F 671 LEU cc_start: 0.9214 (tp) cc_final: 0.7881 (tp) REVERT: F 675 TRP cc_start: 0.8216 (m-10) cc_final: 0.7786 (m-10) outliers start: 4 outliers final: 0 residues processed: 440 average time/residue: 0.3237 time to fit residues: 221.9949 Evaluate side-chains 325 residues out of total 2484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 325 time to evaluate : 2.482 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 157 optimal weight: 0.5980 chunk 101 optimal weight: 5.9990 chunk 151 optimal weight: 0.8980 chunk 76 optimal weight: 0.9980 chunk 49 optimal weight: 0.5980 chunk 161 optimal weight: 10.0000 chunk 173 optimal weight: 8.9990 chunk 125 optimal weight: 3.9990 chunk 23 optimal weight: 2.9990 chunk 200 optimal weight: 6.9990 chunk 231 optimal weight: 4.9990 overall best weight: 1.2182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 593 ASN ** B 573 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 597 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 573 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 593 ASN ** C 597 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 593 ASN D 629 HIS F 593 ASN ** F 597 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7530 moved from start: 0.4770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 22356 Z= 0.206 Angle : 0.578 8.860 30180 Z= 0.294 Chirality : 0.042 0.205 3390 Planarity : 0.004 0.043 3816 Dihedral : 4.350 18.888 2922 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 15.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 0.16 % Allowed : 0.60 % Favored : 99.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: -0.57 (0.16), residues: 2670 helix: 0.22 (0.15), residues: 1122 sheet: -1.16 (0.32), residues: 288 loop : -0.61 (0.18), residues: 1260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 675 HIS 0.005 0.001 HIS C 548 PHE 0.037 0.002 PHE D 626 TYR 0.020 0.001 TYR B 482 ARG 0.007 0.000 ARG B 625 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5340 Ramachandran restraints generated. 2670 Oldfield, 0 Emsley, 2670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5340 Ramachandran restraints generated. 2670 Oldfield, 0 Emsley, 2670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 433 residues out of total 2484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 429 time to evaluate : 2.465 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 343 GLU cc_start: 0.7412 (pm20) cc_final: 0.7159 (mp0) REVERT: A 481 LEU cc_start: 0.8755 (mt) cc_final: 0.8108 (mt) REVERT: A 484 LYS cc_start: 0.8896 (mtmt) cc_final: 0.8539 (mtmt) REVERT: A 491 CYS cc_start: 0.8079 (t) cc_final: 0.7627 (p) REVERT: A 501 PHE cc_start: 0.9048 (m-10) cc_final: 0.8613 (m-80) REVERT: A 525 VAL cc_start: 0.9203 (p) cc_final: 0.8900 (m) REVERT: A 597 HIS cc_start: 0.6708 (m170) cc_final: 0.6410 (m170) REVERT: A 625 ARG cc_start: 0.8024 (tpt90) cc_final: 0.7706 (tpt170) REVERT: A 671 LEU cc_start: 0.9125 (tp) cc_final: 0.7758 (tp) REVERT: A 675 TRP cc_start: 0.8174 (m-10) cc_final: 0.7955 (m-10) REVERT: A 759 PHE cc_start: 0.6215 (t80) cc_final: 0.5896 (t80) REVERT: B 384 LEU cc_start: 0.9306 (mt) cc_final: 0.8920 (mt) REVERT: B 398 ASP cc_start: 0.8574 (m-30) cc_final: 0.8358 (m-30) REVERT: B 486 LEU cc_start: 0.8922 (mm) cc_final: 0.8594 (mm) REVERT: B 618 MET cc_start: 0.7705 (tmm) cc_final: 0.7235 (mtp) REVERT: B 671 LEU cc_start: 0.9204 (tp) cc_final: 0.7822 (tp) REVERT: B 675 TRP cc_start: 0.8266 (m-10) cc_final: 0.8014 (m-10) REVERT: C 322 MET cc_start: 0.6112 (mpp) cc_final: 0.5828 (mtt) REVERT: C 384 LEU cc_start: 0.9323 (mt) cc_final: 0.9011 (mt) REVERT: C 399 MET cc_start: 0.8600 (mtp) cc_final: 0.8251 (mtm) REVERT: C 428 TYR cc_start: 0.8037 (m-80) cc_final: 0.7760 (m-80) REVERT: C 458 MET cc_start: 0.7285 (ptm) cc_final: 0.6969 (ppp) REVERT: C 462 MET cc_start: 0.7872 (tmm) cc_final: 0.7629 (tmm) REVERT: C 491 CYS cc_start: 0.7993 (t) cc_final: 0.7741 (p) REVERT: C 495 LYS cc_start: 0.7307 (pptt) cc_final: 0.6760 (pptt) REVERT: C 567 LYS cc_start: 0.7641 (mttt) cc_final: 0.7338 (mtpt) REVERT: C 618 MET cc_start: 0.8014 (tmm) cc_final: 0.7699 (tmm) REVERT: C 629 HIS cc_start: 0.8668 (t70) cc_final: 0.8265 (t70) REVERT: D 486 LEU cc_start: 0.9194 (mm) cc_final: 0.8911 (mm) REVERT: D 671 LEU cc_start: 0.9133 (tp) cc_final: 0.7747 (tp) REVERT: D 675 TRP cc_start: 0.8328 (m-10) cc_final: 0.8051 (m-10) REVERT: D 759 PHE cc_start: 0.6365 (t80) cc_final: 0.6104 (t80) REVERT: E 384 LEU cc_start: 0.9179 (mt) cc_final: 0.8919 (mt) REVERT: E 458 MET cc_start: 0.7427 (ptm) cc_final: 0.7013 (ppp) REVERT: E 486 LEU cc_start: 0.8967 (mm) cc_final: 0.8725 (mm) REVERT: E 491 CYS cc_start: 0.8342 (t) cc_final: 0.7880 (p) REVERT: E 500 PHE cc_start: 0.8330 (m-10) cc_final: 0.8009 (m-80) REVERT: F 327 PHE cc_start: 0.8505 (t80) cc_final: 0.8160 (t80) REVERT: F 384 LEU cc_start: 0.9398 (mt) cc_final: 0.9084 (mt) REVERT: F 499 THR cc_start: 0.7717 (t) cc_final: 0.7453 (t) REVERT: F 500 PHE cc_start: 0.8684 (m-10) cc_final: 0.8318 (m-80) REVERT: F 517 LYS cc_start: 0.9374 (tppt) cc_final: 0.9163 (tptp) REVERT: F 533 THR cc_start: 0.8500 (p) cc_final: 0.8091 (p) REVERT: F 567 LYS cc_start: 0.7451 (mtpt) cc_final: 0.6941 (mtpt) REVERT: F 597 HIS cc_start: 0.7339 (m90) cc_final: 0.6914 (m170) REVERT: F 601 ILE cc_start: 0.8679 (mp) cc_final: 0.8291 (mp) REVERT: F 671 LEU cc_start: 0.9223 (tp) cc_final: 0.7909 (tp) REVERT: F 675 TRP cc_start: 0.8260 (m-10) cc_final: 0.7815 (m-10) outliers start: 4 outliers final: 0 residues processed: 433 average time/residue: 0.3156 time to fit residues: 212.8659 Evaluate side-chains 321 residues out of total 2484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 321 time to evaluate : 2.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 243 optimal weight: 1.9990 chunk 222 optimal weight: 3.9990 chunk 237 optimal weight: 8.9990 chunk 142 optimal weight: 0.0570 chunk 103 optimal weight: 0.1980 chunk 186 optimal weight: 5.9990 chunk 72 optimal weight: 0.0670 chunk 214 optimal weight: 0.3980 chunk 224 optimal weight: 0.9980 chunk 236 optimal weight: 0.8980 chunk 155 optimal weight: 1.9990 overall best weight: 0.3236 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 593 ASN ** B 573 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 597 HIS ** C 573 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 593 ASN C 597 HIS D 593 ASN E 775 GLN F 593 ASN F 597 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7478 moved from start: 0.4920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 22356 Z= 0.159 Angle : 0.561 7.606 30180 Z= 0.288 Chirality : 0.043 0.387 3390 Planarity : 0.004 0.053 3816 Dihedral : 4.259 19.087 2922 Min Nonbonded Distance : 2.303 Molprobity Statistics. All-atom Clashscore : 13.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 0.16 % Allowed : 0.48 % Favored : 99.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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 (0.16), residues: 2670 helix: 0.38 (0.16), residues: 1122 sheet: -1.75 (0.29), residues: 336 loop : -0.30 (0.18), residues: 1212 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 350 HIS 0.007 0.001 HIS B 548 PHE 0.045 0.002 PHE D 500 TYR 0.022 0.001 TYR C 482 ARG 0.012 0.000 ARG F 551 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5340 Ramachandran restraints generated. 2670 Oldfield, 0 Emsley, 2670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5340 Ramachandran restraints generated. 2670 Oldfield, 0 Emsley, 2670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 453 residues out of total 2484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 449 time to evaluate : 2.621 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 327 PHE cc_start: 0.8599 (t80) cc_final: 0.8160 (t80) REVERT: A 343 GLU cc_start: 0.7335 (pm20) cc_final: 0.7084 (mp0) REVERT: A 481 LEU cc_start: 0.8825 (mt) cc_final: 0.8172 (mt) REVERT: A 484 LYS cc_start: 0.8846 (mtmt) cc_final: 0.8460 (mtmt) REVERT: A 491 CYS cc_start: 0.8066 (t) cc_final: 0.7601 (p) REVERT: A 501 PHE cc_start: 0.8989 (m-10) cc_final: 0.8687 (m-80) REVERT: A 525 VAL cc_start: 0.9123 (p) cc_final: 0.8889 (m) REVERT: A 597 HIS cc_start: 0.6757 (m170) cc_final: 0.6466 (m170) REVERT: A 618 MET cc_start: 0.7470 (tmm) cc_final: 0.6904 (mtp) REVERT: A 671 LEU cc_start: 0.9156 (tp) cc_final: 0.8142 (tp) REVERT: A 759 PHE cc_start: 0.6241 (t80) cc_final: 0.5992 (t80) REVERT: B 384 LEU cc_start: 0.9285 (mt) cc_final: 0.8940 (mt) REVERT: B 398 ASP cc_start: 0.8572 (m-30) cc_final: 0.8318 (m-30) REVERT: B 486 LEU cc_start: 0.8850 (mm) cc_final: 0.8572 (mm) REVERT: B 513 LYS cc_start: 0.9332 (ttpt) cc_final: 0.8652 (ttmt) REVERT: B 671 LEU cc_start: 0.9190 (tp) cc_final: 0.7807 (tp) REVERT: B 675 TRP cc_start: 0.8212 (m-10) cc_final: 0.7825 (m-10) REVERT: C 349 VAL cc_start: 0.9416 (t) cc_final: 0.9022 (p) REVERT: C 353 ASN cc_start: 0.7935 (m-40) cc_final: 0.7044 (m-40) REVERT: C 384 LEU cc_start: 0.9257 (mt) cc_final: 0.8987 (mt) REVERT: C 398 ASP cc_start: 0.8495 (m-30) cc_final: 0.8291 (m-30) REVERT: C 428 TYR cc_start: 0.7954 (m-80) cc_final: 0.7726 (m-80) REVERT: C 458 MET cc_start: 0.7236 (ptm) cc_final: 0.6702 (ppp) REVERT: C 495 LYS cc_start: 0.7183 (pptt) cc_final: 0.6849 (pptt) REVERT: C 525 VAL cc_start: 0.9071 (p) cc_final: 0.8663 (m) REVERT: C 531 ILE cc_start: 0.8127 (mm) cc_final: 0.7879 (tt) REVERT: C 567 LYS cc_start: 0.7675 (mttt) cc_final: 0.7389 (mtpt) REVERT: C 629 HIS cc_start: 0.8642 (t70) cc_final: 0.8362 (t70) REVERT: D 343 GLU cc_start: 0.7119 (mp0) cc_final: 0.6756 (pm20) REVERT: D 398 ASP cc_start: 0.8498 (m-30) cc_final: 0.8218 (m-30) REVERT: D 486 LEU cc_start: 0.9123 (mm) cc_final: 0.8854 (mm) REVERT: D 500 PHE cc_start: 0.7968 (m-80) cc_final: 0.7755 (m-80) REVERT: D 525 VAL cc_start: 0.8976 (p) cc_final: 0.8616 (m) REVERT: D 671 LEU cc_start: 0.9107 (tp) cc_final: 0.8172 (tp) REVERT: D 675 TRP cc_start: 0.8244 (m-10) cc_final: 0.7913 (m-10) REVERT: D 759 PHE cc_start: 0.6293 (t80) cc_final: 0.6078 (t80) REVERT: E 384 LEU cc_start: 0.9070 (mt) cc_final: 0.8793 (mt) REVERT: E 393 GLU cc_start: 0.8560 (tm-30) cc_final: 0.8287 (tm-30) REVERT: E 458 MET cc_start: 0.7318 (ptm) cc_final: 0.6950 (ppp) REVERT: E 491 CYS cc_start: 0.8300 (t) cc_final: 0.7898 (p) REVERT: E 500 PHE cc_start: 0.8444 (m-10) cc_final: 0.8105 (m-80) REVERT: E 615 ASN cc_start: 0.8131 (t0) cc_final: 0.7818 (t0) REVERT: F 327 PHE cc_start: 0.8409 (t80) cc_final: 0.8145 (t80) REVERT: F 384 LEU cc_start: 0.9289 (mt) cc_final: 0.8741 (mt) REVERT: F 499 THR cc_start: 0.7744 (t) cc_final: 0.7544 (t) REVERT: F 500 PHE cc_start: 0.8698 (m-10) cc_final: 0.8246 (m-80) REVERT: F 517 LYS cc_start: 0.9325 (tppt) cc_final: 0.9102 (tptp) REVERT: F 533 THR cc_start: 0.8522 (p) cc_final: 0.8119 (p) REVERT: F 567 LYS cc_start: 0.7427 (mtpt) cc_final: 0.6906 (mtpt) REVERT: F 671 LEU cc_start: 0.9187 (tp) cc_final: 0.7825 (tp) REVERT: F 675 TRP cc_start: 0.8174 (m-10) cc_final: 0.7790 (m-10) outliers start: 4 outliers final: 0 residues processed: 453 average time/residue: 0.3229 time to fit residues: 225.5746 Evaluate side-chains 339 residues out of total 2484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 339 time to evaluate : 2.471 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 250 optimal weight: 5.9990 chunk 153 optimal weight: 0.7980 chunk 118 optimal weight: 0.9990 chunk 174 optimal weight: 10.0000 chunk 263 optimal weight: 7.9990 chunk 242 optimal weight: 8.9990 chunk 209 optimal weight: 4.9990 chunk 21 optimal weight: 4.9990 chunk 161 optimal weight: 0.9990 chunk 128 optimal weight: 8.9990 chunk 166 optimal weight: 3.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 593 ASN ** B 573 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 597 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 573 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 593 ASN D 593 ASN E 775 GLN F 593 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7595 moved from start: 0.5083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 22356 Z= 0.310 Angle : 0.693 11.128 30180 Z= 0.344 Chirality : 0.045 0.343 3390 Planarity : 0.004 0.052 3816 Dihedral : 4.630 19.529 2922 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 18.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.21 % Favored : 94.79 % Rotamer: Outliers : 0.16 % Allowed : 0.24 % Favored : 99.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: -0.73 (0.16), residues: 2670 helix: 0.08 (0.15), residues: 1122 sheet: -1.89 (0.29), residues: 336 loop : -0.43 (0.18), residues: 1212 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C 675 HIS 0.006 0.002 HIS E 548 PHE 0.038 0.002 PHE E 554 TYR 0.021 0.002 TYR A 670 ARG 0.011 0.001 ARG C 625 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5340 Ramachandran restraints generated. 2670 Oldfield, 0 Emsley, 2670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5340 Ramachandran restraints generated. 2670 Oldfield, 0 Emsley, 2670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 398 residues out of total 2484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 394 time to evaluate : 2.555 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 491 CYS cc_start: 0.8250 (t) cc_final: 0.7744 (p) REVERT: A 554 PHE cc_start: 0.8382 (m-80) cc_final: 0.8151 (m-80) REVERT: A 597 HIS cc_start: 0.6766 (m170) cc_final: 0.6468 (m170) REVERT: A 618 MET cc_start: 0.7150 (tmm) cc_final: 0.6700 (mtp) REVERT: A 671 LEU cc_start: 0.9187 (tp) cc_final: 0.7870 (tp) REVERT: A 675 TRP cc_start: 0.8236 (m-10) cc_final: 0.8013 (m-10) REVERT: A 759 PHE cc_start: 0.6270 (t80) cc_final: 0.5938 (t80) REVERT: B 343 GLU cc_start: 0.7178 (mp0) cc_final: 0.6819 (pm20) REVERT: B 384 LEU cc_start: 0.9312 (mt) cc_final: 0.8928 (mt) REVERT: B 398 ASP cc_start: 0.8580 (m-30) cc_final: 0.8354 (m-30) REVERT: B 458 MET cc_start: 0.7998 (ttt) cc_final: 0.7785 (ttt) REVERT: B 481 LEU cc_start: 0.8748 (mt) cc_final: 0.8531 (mt) REVERT: B 484 LYS cc_start: 0.8879 (mtmt) cc_final: 0.8586 (mtmp) REVERT: B 486 LEU cc_start: 0.8862 (mm) cc_final: 0.8566 (mm) REVERT: B 500 PHE cc_start: 0.8335 (m-10) cc_final: 0.8115 (m-80) REVERT: B 625 ARG cc_start: 0.8105 (tpt90) cc_final: 0.7884 (tpt170) REVERT: B 671 LEU cc_start: 0.9148 (tp) cc_final: 0.8177 (tp) REVERT: B 675 TRP cc_start: 0.8329 (m-10) cc_final: 0.7998 (m-10) REVERT: C 349 VAL cc_start: 0.9495 (t) cc_final: 0.9282 (p) REVERT: C 384 LEU cc_start: 0.9385 (mt) cc_final: 0.9050 (mt) REVERT: C 428 TYR cc_start: 0.8022 (m-80) cc_final: 0.7686 (m-80) REVERT: C 458 MET cc_start: 0.7303 (ptm) cc_final: 0.7082 (ptm) REVERT: C 491 CYS cc_start: 0.8103 (t) cc_final: 0.7648 (p) REVERT: C 500 PHE cc_start: 0.8198 (m-80) cc_final: 0.7940 (m-80) REVERT: C 567 LYS cc_start: 0.7650 (mttt) cc_final: 0.7357 (mtpt) REVERT: C 618 MET cc_start: 0.7998 (tmm) cc_final: 0.7471 (mtp) REVERT: C 629 HIS cc_start: 0.8744 (t70) cc_final: 0.8439 (t70) REVERT: D 343 GLU cc_start: 0.7159 (mp0) cc_final: 0.6819 (pm20) REVERT: D 398 ASP cc_start: 0.8526 (m-30) cc_final: 0.8274 (m-30) REVERT: D 500 PHE cc_start: 0.8140 (m-80) cc_final: 0.7913 (m-80) REVERT: D 517 LYS cc_start: 0.9470 (tptt) cc_final: 0.9236 (tptp) REVERT: D 601 ILE cc_start: 0.8574 (mt) cc_final: 0.8336 (tp) REVERT: D 759 PHE cc_start: 0.6349 (t80) cc_final: 0.6053 (t80) REVERT: E 343 GLU cc_start: 0.7172 (mp0) cc_final: 0.6758 (pm20) REVERT: E 491 CYS cc_start: 0.8311 (t) cc_final: 0.7939 (p) REVERT: E 500 PHE cc_start: 0.8484 (m-10) cc_final: 0.8042 (m-80) REVERT: E 625 ARG cc_start: 0.8023 (tpt90) cc_final: 0.7810 (tpt170) REVERT: F 384 LEU cc_start: 0.9442 (mt) cc_final: 0.9029 (mt) REVERT: F 500 PHE cc_start: 0.8699 (m-10) cc_final: 0.8405 (m-80) REVERT: F 533 THR cc_start: 0.8537 (p) cc_final: 0.8084 (p) REVERT: F 567 LYS cc_start: 0.7534 (mtpt) cc_final: 0.7030 (mtpt) REVERT: F 671 LEU cc_start: 0.9220 (tp) cc_final: 0.7905 (tp) REVERT: F 675 TRP cc_start: 0.8362 (m-10) cc_final: 0.7888 (m-10) outliers start: 4 outliers final: 0 residues processed: 398 average time/residue: 0.3358 time to fit residues: 207.3371 Evaluate side-chains 301 residues out of total 2484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 301 time to evaluate : 2.722 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 223 optimal weight: 0.8980 chunk 64 optimal weight: 1.9990 chunk 193 optimal weight: 0.1980 chunk 30 optimal weight: 0.7980 chunk 58 optimal weight: 6.9990 chunk 209 optimal weight: 0.8980 chunk 87 optimal weight: 0.0970 chunk 215 optimal weight: 9.9990 chunk 26 optimal weight: 4.9990 chunk 38 optimal weight: 9.9990 chunk 184 optimal weight: 5.9990 overall best weight: 0.5778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 593 ASN ** B 573 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 597 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 573 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 593 ASN D 593 ASN F 548 HIS F 629 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4332 r_free = 0.4332 target = 0.145729 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.103512 restraints weight = 63231.542| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.106006 restraints weight = 37859.849| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.107594 restraints weight = 27186.812| |-----------------------------------------------------------------------------| r_work (final): 0.3714 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7383 moved from start: 0.5186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 22356 Z= 0.173 Angle : 0.589 8.581 30180 Z= 0.301 Chirality : 0.044 0.437 3390 Planarity : 0.004 0.034 3816 Dihedral : 4.431 18.910 2922 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 14.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 0.12 % Allowed : 0.32 % Favored : 99.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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 (0.16), residues: 2670 helix: 0.22 (0.15), residues: 1122 sheet: -1.80 (0.29), residues: 336 loop : -0.33 (0.18), residues: 1212 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 355 HIS 0.008 0.001 HIS E 548 PHE 0.040 0.002 PHE E 554 TYR 0.020 0.001 TYR C 482 ARG 0.009 0.001 ARG C 619 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5070.97 seconds wall clock time: 91 minutes 50.41 seconds (5510.41 seconds total)