Starting phenix.real_space_refine on Sun Aug 24 18:29:38 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8apl_15574/08_2025/8apl_15574.cif Found real_map, /net/cci-nas-00/data/ceres_data/8apl_15574/08_2025/8apl_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/cci-nas-00/data/ceres_data/8apl_15574/08_2025/8apl_15574.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8apl_15574/08_2025/8apl_15574.map" model { file = "/net/cci-nas-00/data/ceres_data/8apl_15574/08_2025/8apl_15574.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8apl_15574/08_2025/8apl_15574.cif" } resolution = 4.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: B, C, D, E, F Time building chain proxies: 3.74, per 1000 atoms: 0.17 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: 1.91 Conformation dependent library (CDL) restraints added in 942.8 milliseconds Enol-peptide restraints added in 1.2 microseconds 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: 1.02 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: 4.73 Time building geometry restraints manager: 2.51 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: 0.08 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: 1.710 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.300 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 20.150 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.560 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.100 ------------------------------------------------------------------------------- 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= 0.089 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.002 0.000 ARG D 372 TYR 0.013 0.001 TYR F 409 PHE 0.006 0.001 PHE C 444 TRP 0.002 0.000 TRP A 350 HIS 0.002 0.001 HIS E 763 Details of bonding type rmsd covalent geometry : bond 0.00162 (22356) covalent geometry : angle 0.47671 (30180) hydrogen bonds : bond 0.16131 ( 894) hydrogen bonds : angle 6.00980 ( 2538) *********************** 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 to be fit. rotamer outliers: 48 poor density : 691 time to evaluate : 0.907 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: 0.1849 time to fit residues: 200.4038 Evaluate side-chains 427 residues out of total 2484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 409 time to evaluate : 0.977 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 197 optimal weight: 3.9990 chunk 215 optimal weight: 4.9990 chunk 20 optimal weight: 0.9980 chunk 132 optimal weight: 3.9990 chunk 261 optimal weight: 0.8980 chunk 248 optimal weight: 5.9990 chunk 207 optimal weight: 9.9990 chunk 155 optimal weight: 4.9990 chunk 244 optimal weight: 3.9990 chunk 183 optimal weight: 3.9990 chunk 111 optimal weight: 6.9990 overall best weight: 2.7786 ------------------------------------------------------------------------------- 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 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 573 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 775 GLN D 324 ASN D 763 HIS D 775 GLN E 324 ASN E 763 HIS E 775 GLN F 324 ASN F 463 ASN F 573 ASN F 775 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4290 r_free = 0.4290 target = 0.142493 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.100441 restraints weight = 64986.533| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.102873 restraints weight = 38447.550| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.104409 restraints weight = 27710.350| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.105172 restraints weight = 22758.032| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.105874 restraints weight = 20411.830| |-----------------------------------------------------------------------------| r_work (final): 0.3678 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7426 moved from start: 0.3372 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= 0.249 Angle : 0.705 9.108 30180 Z= 0.356 Chirality : 0.045 0.301 3390 Planarity : 0.005 0.072 3816 Dihedral : 4.343 19.289 2922 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 17.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer: Outliers : 0.08 % Allowed : 4.15 % Favored : 95.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.77 (0.16), residues: 2670 helix: 0.24 (0.15), residues: 1104 sheet: -2.02 (0.27), residues: 342 loop : -0.62 (0.17), residues: 1224 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 570 TYR 0.021 0.002 TYR C 606 PHE 0.031 0.002 PHE D 502 TRP 0.015 0.002 TRP C 675 HIS 0.004 0.001 HIS A 763 Details of bonding type rmsd covalent geometry : bond 0.00536 (22356) covalent geometry : angle 0.70457 (30180) hydrogen bonds : bond 0.04400 ( 894) hydrogen bonds : angle 5.34576 ( 2538) *********************** 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 481 residues out of total 2484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 479 time to evaluate : 1.044 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: A 467 ASP cc_start: 0.8722 (t0) cc_final: 0.8508 (t0) REVERT: A 491 CYS cc_start: 0.8341 (t) cc_final: 0.7833 (p) REVERT: A 501 PHE cc_start: 0.8950 (m-10) cc_final: 0.8659 (m-80) REVERT: A 514 ARG cc_start: 0.8295 (mtm180) cc_final: 0.7919 (ptp90) REVERT: A 597 HIS cc_start: 0.6739 (m170) cc_final: 0.6116 (m170) REVERT: A 671 LEU cc_start: 0.9109 (tp) cc_final: 0.8051 (tp) REVERT: B 384 LEU cc_start: 0.9402 (mt) cc_final: 0.9136 (mt) REVERT: B 387 ARG cc_start: 0.7635 (ttt180) cc_final: 0.7422 (ttt180) REVERT: B 491 CYS cc_start: 0.8164 (t) cc_final: 0.7846 (p) REVERT: B 495 LYS cc_start: 0.7333 (pptt) cc_final: 0.6843 (pptt) REVERT: B 501 PHE cc_start: 0.8924 (m-10) cc_final: 0.8615 (m-10) REVERT: B 531 ILE cc_start: 0.8086 (mt) cc_final: 0.7727 (mm) REVERT: B 544 ILE cc_start: 0.9069 (mm) cc_final: 0.8854 (mt) REVERT: B 577 LEU cc_start: 0.9143 (mp) cc_final: 0.8922 (mt) REVERT: B 671 LEU cc_start: 0.9133 (tp) cc_final: 0.8187 (tp) REVERT: B 675 TRP cc_start: 0.8068 (m-10) cc_final: 0.7752 (m-10) REVERT: B 759 PHE cc_start: 0.6096 (t80) cc_final: 0.5811 (t80) REVERT: C 384 LEU cc_start: 0.9285 (mt) cc_final: 0.9050 (mt) REVERT: C 467 ASP cc_start: 0.8620 (t0) cc_final: 0.8377 (t0) REVERT: C 491 CYS cc_start: 0.8470 (t) cc_final: 0.8134 (p) REVERT: C 544 ILE cc_start: 0.9087 (mm) cc_final: 0.8808 (mt) REVERT: C 548 HIS cc_start: 0.8290 (p-80) cc_final: 0.8030 (p-80) REVERT: C 567 LYS cc_start: 0.7725 (mttt) cc_final: 0.7308 (mtpt) REVERT: C 603 ASP cc_start: 0.5993 (m-30) cc_final: 0.5691 (m-30) REVERT: C 759 PHE cc_start: 0.5705 (t80) cc_final: 0.5477 (t80) REVERT: D 371 ILE cc_start: 0.9373 (pt) cc_final: 0.9168 (pt) REVERT: D 491 CYS cc_start: 0.8365 (t) cc_final: 0.7875 (p) REVERT: D 597 HIS cc_start: 0.6624 (m170) cc_final: 0.6103 (m170) REVERT: D 630 PHE cc_start: 0.7176 (OUTLIER) cc_final: 0.6535 (m-80) REVERT: D 671 LEU cc_start: 0.9118 (tp) cc_final: 0.7782 (tp) REVERT: E 384 LEU cc_start: 0.9388 (mt) cc_final: 0.9175 (mt) REVERT: E 387 ARG cc_start: 0.7386 (ttt180) cc_final: 0.7056 (ttt180) REVERT: E 491 CYS cc_start: 0.8230 (t) cc_final: 0.7930 (p) REVERT: E 495 LYS cc_start: 0.7348 (pptt) cc_final: 0.7004 (pptt) REVERT: F 371 ILE cc_start: 0.9482 (pt) cc_final: 0.9183 (pt) REVERT: F 384 LEU cc_start: 0.9369 (mt) cc_final: 0.8984 (mt) REVERT: F 467 ASP cc_start: 0.8580 (t0) cc_final: 0.8305 (t0) REVERT: F 491 CYS cc_start: 0.8442 (t) cc_final: 0.8165 (p) REVERT: F 500 PHE cc_start: 0.8530 (m-10) cc_final: 0.8271 (m-80) REVERT: F 501 PHE cc_start: 0.9158 (m-10) cc_final: 0.8950 (m-10) REVERT: F 572 ASP cc_start: 0.8933 (m-30) cc_final: 0.8660 (p0) REVERT: F 603 ASP cc_start: 0.6076 (m-30) cc_final: 0.5610 (m-30) REVERT: F 675 TRP cc_start: 0.8081 (m-10) cc_final: 0.7799 (m-10) outliers start: 2 outliers final: 1 residues processed: 481 average time/residue: 0.1715 time to fit residues: 126.2908 Evaluate side-chains 340 residues out of total 2484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 338 time to evaluate : 0.738 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 192 optimal weight: 0.8980 chunk 27 optimal weight: 10.0000 chunk 200 optimal weight: 0.0870 chunk 20 optimal weight: 0.8980 chunk 235 optimal weight: 3.9990 chunk 36 optimal weight: 8.9990 chunk 218 optimal weight: 7.9990 chunk 21 optimal weight: 2.9990 chunk 10 optimal weight: 5.9990 chunk 131 optimal weight: 8.9990 chunk 56 optimal weight: 0.8980 overall best weight: 1.1560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 353 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 E 763 HIS F 573 ASN F 593 ASN ** F 597 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4324 r_free = 0.4324 target = 0.145588 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.102610 restraints weight = 63470.243| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.105709 restraints weight = 42210.065| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.106454 restraints weight = 27678.401| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.107380 restraints weight = 23090.751| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.107289 restraints weight = 24145.517| |-----------------------------------------------------------------------------| r_work (final): 0.3685 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7427 moved from start: 0.3690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 22356 Z= 0.148 Angle : 0.570 7.707 30180 Z= 0.295 Chirality : 0.042 0.182 3390 Planarity : 0.004 0.051 3816 Dihedral : 4.231 18.243 2922 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 14.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 0.20 % Allowed : 3.14 % Favored : 96.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.77 (0.16), residues: 2670 helix: 0.25 (0.15), residues: 1116 sheet: -2.14 (0.27), residues: 342 loop : -0.59 (0.17), residues: 1212 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 514 TYR 0.018 0.002 TYR A 606 PHE 0.036 0.002 PHE D 501 TRP 0.007 0.001 TRP C 675 HIS 0.007 0.001 HIS F 597 Details of bonding type rmsd covalent geometry : bond 0.00333 (22356) covalent geometry : angle 0.56975 (30180) hydrogen bonds : bond 0.03720 ( 894) hydrogen bonds : angle 4.98822 ( 2538) *********************** 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 470 residues out of total 2484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 465 time to evaluate : 0.911 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 393 GLU cc_start: 0.8590 (tm-30) cc_final: 0.8374 (tm-30) REVERT: A 486 LEU cc_start: 0.9337 (mm) cc_final: 0.8945 (mm) REVERT: A 516 LEU cc_start: 0.9225 (tp) cc_final: 0.8973 (tp) REVERT: A 531 ILE cc_start: 0.8060 (mm) cc_final: 0.7746 (mm) REVERT: A 671 LEU cc_start: 0.9086 (tp) cc_final: 0.7843 (tp) REVERT: B 384 LEU cc_start: 0.9333 (mt) cc_final: 0.9045 (mt) REVERT: B 486 LEU cc_start: 0.9053 (mm) cc_final: 0.8821 (mm) REVERT: B 491 CYS cc_start: 0.8358 (t) cc_final: 0.7939 (p) REVERT: B 495 LYS cc_start: 0.7446 (pptt) cc_final: 0.6755 (pptt) REVERT: B 499 THR cc_start: 0.7461 (t) cc_final: 0.7255 (t) REVERT: B 500 PHE cc_start: 0.8109 (m-10) cc_final: 0.7774 (m-80) REVERT: B 577 LEU cc_start: 0.9101 (mp) cc_final: 0.8847 (mt) REVERT: B 629 HIS cc_start: 0.8721 (t-90) cc_final: 0.8387 (t-90) REVERT: B 671 LEU cc_start: 0.9135 (tp) cc_final: 0.7808 (tp) REVERT: B 675 TRP cc_start: 0.8130 (m-10) cc_final: 0.7675 (m-10) REVERT: C 349 VAL cc_start: 0.9350 (t) cc_final: 0.9030 (p) REVERT: C 384 LEU cc_start: 0.9231 (mt) cc_final: 0.9030 (mt) REVERT: C 491 CYS cc_start: 0.8433 (t) cc_final: 0.8051 (p) REVERT: C 495 LYS cc_start: 0.7227 (pptt) cc_final: 0.6950 (pptt) REVERT: C 567 LYS cc_start: 0.7594 (mttt) cc_final: 0.7305 (mtpt) REVERT: C 603 ASP cc_start: 0.6167 (m-30) cc_final: 0.5686 (m-30) REVERT: C 759 PHE cc_start: 0.5726 (t80) cc_final: 0.5499 (t80) REVERT: D 486 LEU cc_start: 0.9250 (mm) cc_final: 0.9036 (mm) REVERT: D 495 LYS cc_start: 0.6780 (mmtt) cc_final: 0.5843 (mmtm) REVERT: D 499 THR cc_start: 0.7278 (t) cc_final: 0.7005 (t) REVERT: D 500 PHE cc_start: 0.8285 (m-10) cc_final: 0.8081 (m-80) REVERT: D 531 ILE cc_start: 0.7914 (mm) cc_final: 0.7608 (mm) REVERT: D 597 HIS cc_start: 0.6638 (m170) cc_final: 0.6298 (m170) REVERT: D 601 ILE cc_start: 0.8519 (mt) cc_final: 0.8119 (mp) REVERT: D 671 LEU cc_start: 0.9073 (tp) cc_final: 0.7813 (tp) REVERT: D 759 PHE cc_start: 0.6153 (t80) cc_final: 0.5826 (t80) REVERT: E 384 LEU cc_start: 0.9339 (mt) cc_final: 0.9122 (mt) REVERT: E 458 MET cc_start: 0.7987 (ttm) cc_final: 0.7696 (ttp) REVERT: E 486 LEU cc_start: 0.9076 (mm) cc_final: 0.8813 (mm) REVERT: E 491 CYS cc_start: 0.8299 (t) cc_final: 0.7880 (p) REVERT: E 495 LYS cc_start: 0.7406 (pptt) cc_final: 0.6877 (pptt) REVERT: E 500 PHE cc_start: 0.8174 (m-10) cc_final: 0.7918 (m-80) REVERT: E 577 LEU cc_start: 0.9103 (mp) cc_final: 0.8856 (mt) REVERT: E 625 ARG cc_start: 0.8233 (tpt90) cc_final: 0.8028 (tpt170) REVERT: E 629 HIS cc_start: 0.8751 (t-90) cc_final: 0.8419 (t-90) REVERT: F 384 LEU cc_start: 0.9347 (mt) cc_final: 0.8981 (mt) REVERT: F 491 CYS cc_start: 0.8481 (t) cc_final: 0.7999 (p) REVERT: F 499 THR cc_start: 0.7532 (t) cc_final: 0.7229 (t) REVERT: F 500 PHE cc_start: 0.8611 (m-10) cc_final: 0.8245 (m-80) REVERT: F 572 ASP cc_start: 0.8861 (m-30) cc_final: 0.8603 (p0) REVERT: F 597 HIS cc_start: 0.7294 (m90) cc_final: 0.6666 (m170) REVERT: F 671 LEU cc_start: 0.9214 (tp) cc_final: 0.7825 (tp) REVERT: F 675 TRP cc_start: 0.8059 (m-10) cc_final: 0.7725 (m-10) outliers start: 5 outliers final: 0 residues processed: 470 average time/residue: 0.1670 time to fit residues: 121.5263 Evaluate side-chains 341 residues out of total 2484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 341 time to evaluate : 0.860 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 125 optimal weight: 8.9990 chunk 82 optimal weight: 0.0050 chunk 184 optimal weight: 1.9990 chunk 24 optimal weight: 9.9990 chunk 78 optimal weight: 0.6980 chunk 11 optimal weight: 3.9990 chunk 27 optimal weight: 6.9990 chunk 30 optimal weight: 6.9990 chunk 60 optimal weight: 0.8980 chunk 194 optimal weight: 6.9990 chunk 231 optimal weight: 3.9990 overall best weight: 1.5198 ------------------------------------------------------------------------------- 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 593 ASN ** C 597 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 593 ASN ** E 629 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4324 r_free = 0.4324 target = 0.145564 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.102517 restraints weight = 62658.601| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.105073 restraints weight = 36789.086| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.106679 restraints weight = 26456.314| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.107581 restraints weight = 21484.355| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.107929 restraints weight = 19089.789| |-----------------------------------------------------------------------------| r_work (final): 0.3714 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7389 moved from start: 0.4044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 22356 Z= 0.166 Angle : 0.596 8.566 30180 Z= 0.303 Chirality : 0.042 0.148 3390 Planarity : 0.004 0.043 3816 Dihedral : 4.340 19.295 2922 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 15.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.72 (0.16), residues: 2670 helix: 0.21 (0.15), residues: 1122 sheet: -2.03 (0.27), residues: 342 loop : -0.51 (0.17), residues: 1206 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 387 TYR 0.018 0.001 TYR B 606 PHE 0.028 0.002 PHE E 554 TRP 0.006 0.001 TRP C 675 HIS 0.005 0.001 HIS C 597 Details of bonding type rmsd covalent geometry : bond 0.00374 (22356) covalent geometry : angle 0.59588 (30180) hydrogen bonds : bond 0.03603 ( 894) hydrogen bonds : angle 4.94659 ( 2538) *********************** 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 439 residues out of total 2484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 435 time to evaluate : 0.924 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: A 514 ARG cc_start: 0.8365 (mtm110) cc_final: 0.8088 (mtm110) REVERT: A 625 ARG cc_start: 0.8027 (tpt170) cc_final: 0.7809 (tpt170) REVERT: A 671 LEU cc_start: 0.9089 (tp) cc_final: 0.7842 (tp) REVERT: A 675 TRP cc_start: 0.8106 (m-10) cc_final: 0.7859 (m-10) REVERT: A 759 PHE cc_start: 0.6279 (t80) cc_final: 0.5980 (t80) REVERT: B 384 LEU cc_start: 0.9397 (mt) cc_final: 0.9122 (mt) REVERT: B 398 ASP cc_start: 0.8349 (m-30) cc_final: 0.8118 (m-30) REVERT: B 486 LEU cc_start: 0.9121 (mm) cc_final: 0.8889 (mm) REVERT: B 491 CYS cc_start: 0.8313 (t) cc_final: 0.7874 (p) REVERT: B 500 PHE cc_start: 0.7996 (m-10) cc_final: 0.7749 (m-80) REVERT: B 531 ILE cc_start: 0.7960 (mm) cc_final: 0.7759 (mm) REVERT: B 629 HIS cc_start: 0.8348 (t-90) cc_final: 0.7970 (t-90) REVERT: B 671 LEU cc_start: 0.9131 (tp) cc_final: 0.7675 (tp) REVERT: B 675 TRP cc_start: 0.8097 (m-10) cc_final: 0.7815 (m-10) REVERT: B 759 PHE cc_start: 0.6093 (t80) cc_final: 0.5842 (t80) REVERT: C 349 VAL cc_start: 0.9397 (t) cc_final: 0.9055 (p) REVERT: C 458 MET cc_start: 0.7546 (ttm) cc_final: 0.7111 (ttm) REVERT: C 491 CYS cc_start: 0.8413 (t) cc_final: 0.7923 (p) REVERT: C 495 LYS cc_start: 0.7037 (pptt) cc_final: 0.6655 (pptt) REVERT: C 531 ILE cc_start: 0.8162 (mm) cc_final: 0.7911 (mm) REVERT: C 567 LYS cc_start: 0.7690 (mttt) cc_final: 0.7389 (mtpt) REVERT: C 759 PHE cc_start: 0.5861 (t80) cc_final: 0.5589 (t80) REVERT: D 486 LEU cc_start: 0.9385 (mm) cc_final: 0.9012 (mm) REVERT: D 495 LYS cc_start: 0.6896 (mmtt) cc_final: 0.5916 (mmtm) REVERT: D 499 THR cc_start: 0.7295 (t) cc_final: 0.7094 (t) REVERT: D 500 PHE cc_start: 0.8165 (m-10) cc_final: 0.7955 (m-80) REVERT: D 501 PHE cc_start: 0.9151 (m-10) cc_final: 0.8783 (m-80) REVERT: D 516 LEU cc_start: 0.9208 (tp) cc_final: 0.8909 (tp) REVERT: D 517 LYS cc_start: 0.9351 (tptt) cc_final: 0.9034 (tptp) REVERT: D 597 HIS cc_start: 0.6542 (m170) cc_final: 0.6102 (m170) REVERT: D 603 ASP cc_start: 0.5825 (m-30) cc_final: 0.5534 (m-30) REVERT: D 671 LEU cc_start: 0.9130 (tp) cc_final: 0.7912 (tp) REVERT: D 759 PHE cc_start: 0.6203 (t80) cc_final: 0.5817 (t80) REVERT: E 384 LEU cc_start: 0.9406 (mt) cc_final: 0.9158 (mt) REVERT: E 458 MET cc_start: 0.7814 (ttm) cc_final: 0.7411 (ttm) REVERT: E 486 LEU cc_start: 0.9117 (mm) cc_final: 0.8862 (mm) REVERT: E 491 CYS cc_start: 0.8253 (t) cc_final: 0.7799 (p) REVERT: E 495 LYS cc_start: 0.7246 (pptt) cc_final: 0.6639 (pptt) REVERT: E 531 ILE cc_start: 0.7993 (mm) cc_final: 0.7770 (mm) REVERT: E 548 HIS cc_start: 0.8348 (p-80) cc_final: 0.7988 (p-80) REVERT: E 577 LEU cc_start: 0.9111 (mp) cc_final: 0.8861 (mt) REVERT: E 629 HIS cc_start: 0.8590 (t-90) cc_final: 0.8368 (t-90) REVERT: F 343 GLU cc_start: 0.7738 (mp0) cc_final: 0.7444 (pm20) REVERT: F 384 LEU cc_start: 0.9356 (mt) cc_final: 0.8996 (mt) REVERT: F 499 THR cc_start: 0.7470 (t) cc_final: 0.7220 (t) REVERT: F 500 PHE cc_start: 0.8412 (m-10) cc_final: 0.8138 (m-80) REVERT: F 548 HIS cc_start: 0.8138 (p-80) cc_final: 0.7890 (p90) REVERT: F 572 ASP cc_start: 0.8945 (m-30) cc_final: 0.8653 (p0) REVERT: F 597 HIS cc_start: 0.7065 (m90) cc_final: 0.6485 (m170) REVERT: F 629 HIS cc_start: 0.8595 (t-90) cc_final: 0.8163 (t-90) REVERT: F 671 LEU cc_start: 0.9203 (tp) cc_final: 0.7810 (tp) REVERT: F 675 TRP cc_start: 0.8039 (m-10) cc_final: 0.7657 (m-10) REVERT: F 759 PHE cc_start: 0.6372 (t80) cc_final: 0.6147 (t80) outliers start: 4 outliers final: 0 residues processed: 439 average time/residue: 0.1637 time to fit residues: 111.5844 Evaluate side-chains 323 residues out of total 2484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 323 time to evaluate : 0.865 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 169 optimal weight: 9.9990 chunk 8 optimal weight: 1.9990 chunk 118 optimal weight: 6.9990 chunk 13 optimal weight: 0.8980 chunk 102 optimal weight: 6.9990 chunk 103 optimal weight: 4.9990 chunk 210 optimal weight: 4.9990 chunk 241 optimal weight: 5.9990 chunk 183 optimal weight: 0.6980 chunk 76 optimal weight: 0.9980 chunk 164 optimal weight: 0.0670 overall best weight: 0.9320 ------------------------------------------------------------------------------- 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 593 ASN ** C 597 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 593 ASN E 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4325 r_free = 0.4325 target = 0.145528 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.102608 restraints weight = 63014.636| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.105106 restraints weight = 37303.552| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.106643 restraints weight = 26640.520| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.107321 restraints weight = 21889.561| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.108006 restraints weight = 19733.609| |-----------------------------------------------------------------------------| r_work (final): 0.3721 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7359 moved from start: 0.4237 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= 0.127 Angle : 0.551 7.857 30180 Z= 0.280 Chirality : 0.041 0.154 3390 Planarity : 0.004 0.040 3816 Dihedral : 4.240 19.071 2922 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 14.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.61 (0.16), residues: 2670 helix: 0.27 (0.15), residues: 1128 sheet: -1.96 (0.28), residues: 342 loop : -0.42 (0.18), residues: 1200 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 625 TYR 0.015 0.001 TYR C 606 PHE 0.026 0.002 PHE C 554 TRP 0.006 0.001 TRP C 675 HIS 0.005 0.001 HIS F 597 Details of bonding type rmsd covalent geometry : bond 0.00291 (22356) covalent geometry : angle 0.55129 (30180) hydrogen bonds : bond 0.03338 ( 894) hydrogen bonds : angle 4.80721 ( 2538) *********************** 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 455 residues out of total 2484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 451 time to evaluate : 0.951 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 327 PHE cc_start: 0.8587 (t80) cc_final: 0.8245 (t80) REVERT: A 481 LEU cc_start: 0.8763 (mt) cc_final: 0.8142 (mt) REVERT: A 484 LYS cc_start: 0.8965 (mtmt) cc_final: 0.8556 (mtmt) REVERT: A 486 LEU cc_start: 0.9327 (mm) cc_final: 0.8916 (mm) REVERT: A 499 THR cc_start: 0.7508 (t) cc_final: 0.7187 (t) REVERT: A 500 PHE cc_start: 0.8236 (m-10) cc_final: 0.7961 (m-80) REVERT: A 618 MET cc_start: 0.7258 (tmm) cc_final: 0.6797 (mtp) REVERT: A 671 LEU cc_start: 0.9046 (tp) cc_final: 0.7632 (tp) REVERT: B 384 LEU cc_start: 0.9347 (mt) cc_final: 0.9008 (mt) REVERT: B 393 GLU cc_start: 0.8468 (tm-30) cc_final: 0.8193 (tm-30) REVERT: B 398 ASP cc_start: 0.8298 (m-30) cc_final: 0.8067 (m-30) REVERT: B 458 MET cc_start: 0.8125 (ttt) cc_final: 0.7876 (ttt) REVERT: B 486 LEU cc_start: 0.9123 (mm) cc_final: 0.8904 (mm) REVERT: B 491 CYS cc_start: 0.7867 (t) cc_final: 0.7510 (p) REVERT: B 495 LYS cc_start: 0.7074 (pptt) cc_final: 0.6424 (pptt) REVERT: B 500 PHE cc_start: 0.7963 (m-10) cc_final: 0.7648 (m-80) REVERT: B 629 HIS cc_start: 0.8559 (t-90) cc_final: 0.8181 (t-90) REVERT: B 671 LEU cc_start: 0.9124 (tp) cc_final: 0.7677 (tp) REVERT: B 675 TRP cc_start: 0.7987 (m-10) cc_final: 0.7719 (m-10) REVERT: C 353 ASN cc_start: 0.7728 (m110) cc_final: 0.6987 (m-40) REVERT: C 359 SER cc_start: 0.8725 (p) cc_final: 0.8503 (p) REVERT: C 495 LYS cc_start: 0.7197 (pptt) cc_final: 0.6677 (pptt) REVERT: C 567 LYS cc_start: 0.7730 (mttt) cc_final: 0.7440 (mtpt) REVERT: C 618 MET cc_start: 0.7297 (tmm) cc_final: 0.6965 (tmm) REVERT: C 759 PHE cc_start: 0.5837 (t80) cc_final: 0.5587 (t80) REVERT: D 486 LEU cc_start: 0.9229 (mm) cc_final: 0.8969 (mm) REVERT: D 495 LYS cc_start: 0.6989 (mmtt) cc_final: 0.6002 (mmtm) REVERT: D 500 PHE cc_start: 0.7906 (m-10) cc_final: 0.7684 (m-80) REVERT: D 501 PHE cc_start: 0.9229 (m-10) cc_final: 0.8969 (m-80) REVERT: D 531 ILE cc_start: 0.7913 (mm) cc_final: 0.7484 (tt) REVERT: D 597 HIS cc_start: 0.6480 (m170) cc_final: 0.6072 (m170) REVERT: D 603 ASP cc_start: 0.5581 (m-30) cc_final: 0.5298 (m-30) REVERT: D 671 LEU cc_start: 0.9098 (tp) cc_final: 0.7915 (tp) REVERT: D 759 PHE cc_start: 0.6317 (t80) cc_final: 0.6006 (t80) REVERT: E 371 ILE cc_start: 0.9281 (pt) cc_final: 0.8942 (pt) REVERT: E 439 THR cc_start: 0.8678 (p) cc_final: 0.8297 (t) REVERT: E 486 LEU cc_start: 0.9132 (mm) cc_final: 0.8887 (mm) REVERT: E 491 CYS cc_start: 0.7943 (t) cc_final: 0.7611 (p) REVERT: E 495 LYS cc_start: 0.7371 (pptt) cc_final: 0.6623 (pptt) REVERT: E 548 HIS cc_start: 0.8247 (p-80) cc_final: 0.7964 (p-80) REVERT: E 577 LEU cc_start: 0.9107 (mp) cc_final: 0.8840 (mt) REVERT: E 759 PHE cc_start: 0.6693 (t80) cc_final: 0.6256 (t80) REVERT: F 343 GLU cc_start: 0.7720 (mp0) cc_final: 0.7433 (pm20) REVERT: F 384 LEU cc_start: 0.9343 (mt) cc_final: 0.8927 (mt) REVERT: F 499 THR cc_start: 0.7455 (t) cc_final: 0.7109 (t) REVERT: F 500 PHE cc_start: 0.8444 (m-10) cc_final: 0.8109 (m-80) REVERT: F 517 LYS cc_start: 0.9268 (tppt) cc_final: 0.9056 (tptt) REVERT: F 572 ASP cc_start: 0.8935 (m-30) cc_final: 0.8638 (p0) REVERT: F 671 LEU cc_start: 0.9172 (tp) cc_final: 0.7746 (tp) REVERT: F 675 TRP cc_start: 0.8027 (m-10) cc_final: 0.7632 (m-10) outliers start: 4 outliers final: 0 residues processed: 455 average time/residue: 0.1652 time to fit residues: 115.9573 Evaluate side-chains 328 residues out of total 2484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 328 time to evaluate : 0.891 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 92 optimal weight: 0.9980 chunk 58 optimal weight: 9.9990 chunk 122 optimal weight: 4.9990 chunk 163 optimal weight: 10.0000 chunk 230 optimal weight: 5.9990 chunk 147 optimal weight: 0.0870 chunk 138 optimal weight: 0.0870 chunk 107 optimal weight: 1.9990 chunk 131 optimal weight: 5.9990 chunk 105 optimal weight: 2.9990 chunk 240 optimal weight: 0.2980 overall best weight: 0.6938 ------------------------------------------------------------------------------- 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 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** C 629 HIS D 593 ASN D 629 HIS E 763 HIS ** F 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 593 ASN ** F 597 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4331 r_free = 0.4331 target = 0.146016 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.103357 restraints weight = 62898.044| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.105818 restraints weight = 37491.859| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.107394 restraints weight = 26823.780| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.108104 restraints weight = 21949.702| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.108793 restraints weight = 19788.543| |-----------------------------------------------------------------------------| r_work (final): 0.3736 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7336 moved from start: 0.4391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 22356 Z= 0.120 Angle : 0.556 7.415 30180 Z= 0.283 Chirality : 0.042 0.276 3390 Planarity : 0.004 0.057 3816 Dihedral : 4.204 21.430 2922 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 14.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 0.16 % Allowed : 1.17 % Favored : 98.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.53 (0.16), residues: 2670 helix: 0.34 (0.15), residues: 1128 sheet: -1.90 (0.28), residues: 342 loop : -0.38 (0.18), residues: 1200 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 625 TYR 0.019 0.001 TYR C 482 PHE 0.030 0.002 PHE E 554 TRP 0.005 0.001 TRP C 675 HIS 0.005 0.001 HIS C 548 Details of bonding type rmsd covalent geometry : bond 0.00279 (22356) covalent geometry : angle 0.55622 (30180) hydrogen bonds : bond 0.03287 ( 894) hydrogen bonds : angle 4.80525 ( 2538) *********************** 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 446 residues out of total 2484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 442 time to evaluate : 0.981 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: symmetry clash REVERT: A 327 PHE cc_start: 0.8460 (t80) cc_final: 0.8096 (t80) REVERT: A 486 LEU cc_start: 0.9358 (mm) cc_final: 0.9030 (mm) REVERT: A 499 THR cc_start: 0.7475 (t) cc_final: 0.7205 (t) REVERT: A 500 PHE cc_start: 0.8198 (m-10) cc_final: 0.7930 (m-80) REVERT: A 548 HIS cc_start: 0.8191 (p90) cc_final: 0.7942 (p-80) REVERT: A 626 PHE cc_start: 0.5984 (m-80) cc_final: 0.5458 (m-80) REVERT: A 671 LEU cc_start: 0.9047 (tp) cc_final: 0.7829 (tp) REVERT: A 759 PHE cc_start: 0.6270 (t80) cc_final: 0.6058 (t80) REVERT: B 384 LEU cc_start: 0.9314 (mt) cc_final: 0.8947 (mt) REVERT: B 398 ASP cc_start: 0.8290 (m-30) cc_final: 0.8059 (m-30) REVERT: B 458 MET cc_start: 0.8045 (ttt) cc_final: 0.7790 (ttt) REVERT: B 486 LEU cc_start: 0.9122 (mm) cc_final: 0.8890 (mm) REVERT: B 491 CYS cc_start: 0.7920 (t) cc_final: 0.7661 (p) REVERT: B 499 THR cc_start: 0.7333 (t) cc_final: 0.7121 (t) REVERT: B 500 PHE cc_start: 0.7925 (m-10) cc_final: 0.7646 (m-80) REVERT: B 671 LEU cc_start: 0.9129 (tp) cc_final: 0.7631 (tp) REVERT: B 675 TRP cc_start: 0.7945 (m-10) cc_final: 0.7689 (m-10) REVERT: C 353 ASN cc_start: 0.7698 (m110) cc_final: 0.6958 (m-40) REVERT: C 384 LEU cc_start: 0.9280 (mt) cc_final: 0.9031 (mt) REVERT: C 495 LYS cc_start: 0.7132 (pptt) cc_final: 0.6712 (pptt) REVERT: C 525 VAL cc_start: 0.9193 (p) cc_final: 0.8914 (m) REVERT: C 531 ILE cc_start: 0.8038 (mm) cc_final: 0.7736 (tt) REVERT: C 567 LYS cc_start: 0.7778 (mttt) cc_final: 0.7487 (mtpt) REVERT: C 759 PHE cc_start: 0.5809 (t80) cc_final: 0.5534 (t80) REVERT: D 486 LEU cc_start: 0.9218 (mm) cc_final: 0.8997 (mm) REVERT: D 495 LYS cc_start: 0.7052 (mmtt) cc_final: 0.6134 (mmtm) REVERT: D 501 PHE cc_start: 0.9268 (m-10) cc_final: 0.9029 (m-80) REVERT: D 531 ILE cc_start: 0.7889 (mm) cc_final: 0.7559 (tt) REVERT: D 597 HIS cc_start: 0.6478 (m170) cc_final: 0.6098 (m170) REVERT: D 671 LEU cc_start: 0.9086 (tp) cc_final: 0.7895 (tp) REVERT: D 759 PHE cc_start: 0.6219 (t80) cc_final: 0.5907 (t80) REVERT: E 439 THR cc_start: 0.8548 (p) cc_final: 0.8243 (t) REVERT: E 486 LEU cc_start: 0.9115 (mm) cc_final: 0.8900 (mm) REVERT: E 491 CYS cc_start: 0.8047 (t) cc_final: 0.7799 (p) REVERT: E 495 LYS cc_start: 0.7359 (pptt) cc_final: 0.6659 (pptt) REVERT: E 548 HIS cc_start: 0.8121 (p-80) cc_final: 0.7881 (p-80) REVERT: E 577 LEU cc_start: 0.9087 (mp) cc_final: 0.8841 (mt) REVERT: E 625 ARG cc_start: 0.8128 (tpt90) cc_final: 0.7913 (tpt170) REVERT: E 759 PHE cc_start: 0.6637 (t80) cc_final: 0.6382 (t80) REVERT: F 384 LEU cc_start: 0.9335 (mt) cc_final: 0.8926 (mt) REVERT: F 500 PHE cc_start: 0.8470 (m-10) cc_final: 0.8170 (m-80) REVERT: F 517 LYS cc_start: 0.9283 (tppt) cc_final: 0.9072 (tptt) REVERT: F 572 ASP cc_start: 0.9014 (m-30) cc_final: 0.8685 (p0) REVERT: F 597 HIS cc_start: 0.7383 (m90) cc_final: 0.6787 (m170) REVERT: F 671 LEU cc_start: 0.9147 (tp) cc_final: 0.7708 (tp) REVERT: F 675 TRP cc_start: 0.8023 (m-10) cc_final: 0.7627 (m-10) outliers start: 4 outliers final: 0 residues processed: 446 average time/residue: 0.1645 time to fit residues: 113.5860 Evaluate side-chains 327 residues out of total 2484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 327 time to evaluate : 0.849 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 163 optimal weight: 6.9990 chunk 214 optimal weight: 0.7980 chunk 216 optimal weight: 9.9990 chunk 193 optimal weight: 6.9990 chunk 112 optimal weight: 9.9990 chunk 249 optimal weight: 0.9990 chunk 127 optimal weight: 9.9990 chunk 148 optimal weight: 0.3980 chunk 39 optimal weight: 0.0070 chunk 191 optimal weight: 0.0270 chunk 186 optimal weight: 0.4980 overall best weight: 0.3456 ------------------------------------------------------------------------------- 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 B 763 HIS ** C 573 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 593 ASN ** C 597 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 629 HIS D 593 ASN D 615 ASN D 629 HIS F 548 HIS F 593 ASN ** F 597 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4342 r_free = 0.4342 target = 0.147105 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.105369 restraints weight = 62807.830| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.107947 restraints weight = 42740.392| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.108390 restraints weight = 29449.893| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.108491 restraints weight = 27885.569| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.108701 restraints weight = 26998.249| |-----------------------------------------------------------------------------| r_work (final): 0.3713 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7388 moved from start: 0.4571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 22356 Z= 0.105 Angle : 0.542 9.327 30180 Z= 0.277 Chirality : 0.041 0.197 3390 Planarity : 0.004 0.041 3816 Dihedral : 4.145 20.381 2922 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 13.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 0.16 % Allowed : 1.05 % Favored : 98.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.40 (0.16), residues: 2670 helix: 0.44 (0.16), residues: 1128 sheet: -1.75 (0.29), residues: 336 loop : -0.33 (0.18), residues: 1206 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 663 TYR 0.017 0.001 TYR A 664 PHE 0.021 0.001 PHE E 554 TRP 0.005 0.001 TRP C 350 HIS 0.008 0.001 HIS F 548 Details of bonding type rmsd covalent geometry : bond 0.00241 (22356) covalent geometry : angle 0.54187 (30180) hydrogen bonds : bond 0.03210 ( 894) hydrogen bonds : angle 4.77137 ( 2538) *********************** 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 448 residues out of total 2484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 444 time to evaluate : 0.866 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: symmetry clash REVERT: A 327 PHE cc_start: 0.8474 (t80) cc_final: 0.8036 (t80) REVERT: A 499 THR cc_start: 0.7663 (t) cc_final: 0.7387 (t) REVERT: A 500 PHE cc_start: 0.8351 (m-10) cc_final: 0.7989 (m-80) REVERT: A 626 PHE cc_start: 0.6161 (m-80) cc_final: 0.5579 (m-80) REVERT: A 671 LEU cc_start: 0.9026 (tp) cc_final: 0.7849 (tp) REVERT: A 759 PHE cc_start: 0.6187 (t80) cc_final: 0.5955 (t80) REVERT: B 384 LEU cc_start: 0.9212 (mt) cc_final: 0.8834 (mt) REVERT: B 458 MET cc_start: 0.8049 (ttt) cc_final: 0.7814 (ttt) REVERT: B 486 LEU cc_start: 0.8883 (mm) cc_final: 0.8667 (mm) REVERT: B 499 THR cc_start: 0.7483 (t) cc_final: 0.7253 (t) REVERT: B 500 PHE cc_start: 0.8129 (m-10) cc_final: 0.7751 (m-80) REVERT: B 671 LEU cc_start: 0.9146 (tp) cc_final: 0.7640 (tp) REVERT: B 675 TRP cc_start: 0.8001 (m-10) cc_final: 0.7710 (m-10) REVERT: C 353 ASN cc_start: 0.7595 (m110) cc_final: 0.6857 (m-40) REVERT: C 384 LEU cc_start: 0.9208 (mt) cc_final: 0.8967 (mt) REVERT: C 458 MET cc_start: 0.7681 (ptt) cc_final: 0.6777 (ptm) REVERT: C 495 LYS cc_start: 0.7271 (pptt) cc_final: 0.6761 (pptt) REVERT: C 567 LYS cc_start: 0.7611 (mttt) cc_final: 0.7330 (mtpt) REVERT: C 759 PHE cc_start: 0.5816 (t80) cc_final: 0.5611 (t80) REVERT: D 486 LEU cc_start: 0.9020 (mm) cc_final: 0.8761 (mm) REVERT: D 495 LYS cc_start: 0.6963 (mmtt) cc_final: 0.6512 (mmtm) REVERT: D 500 PHE cc_start: 0.8204 (m-10) cc_final: 0.7965 (m-80) REVERT: D 531 ILE cc_start: 0.7902 (mm) cc_final: 0.7583 (tt) REVERT: D 548 HIS cc_start: 0.8245 (p-80) cc_final: 0.7808 (p-80) REVERT: D 567 LYS cc_start: 0.7251 (mttt) cc_final: 0.7014 (mtpt) REVERT: D 597 HIS cc_start: 0.6504 (m170) cc_final: 0.6194 (m-70) REVERT: D 671 LEU cc_start: 0.9071 (tp) cc_final: 0.7671 (tp) REVERT: D 675 TRP cc_start: 0.8016 (m-10) cc_final: 0.7703 (m-10) REVERT: D 759 PHE cc_start: 0.6272 (t80) cc_final: 0.5962 (t80) REVERT: E 439 THR cc_start: 0.8460 (p) cc_final: 0.8155 (t) REVERT: E 486 LEU cc_start: 0.8993 (mm) cc_final: 0.8749 (mm) REVERT: E 491 CYS cc_start: 0.8159 (t) cc_final: 0.7811 (p) REVERT: E 495 LYS cc_start: 0.7519 (pptt) cc_final: 0.6797 (pptt) REVERT: E 500 PHE cc_start: 0.8268 (m-80) cc_final: 0.7918 (m-80) REVERT: E 577 LEU cc_start: 0.9107 (mp) cc_final: 0.8866 (mt) REVERT: E 625 ARG cc_start: 0.8013 (tpt90) cc_final: 0.7810 (tpt170) REVERT: E 759 PHE cc_start: 0.6458 (t80) cc_final: 0.6079 (t80) REVERT: F 384 LEU cc_start: 0.9239 (mt) cc_final: 0.8749 (mt) REVERT: F 500 PHE cc_start: 0.8579 (m-10) cc_final: 0.8195 (m-80) REVERT: F 525 VAL cc_start: 0.9121 (p) cc_final: 0.8686 (m) REVERT: F 572 ASP cc_start: 0.8881 (m-30) cc_final: 0.8610 (p0) REVERT: F 597 HIS cc_start: 0.7413 (m90) cc_final: 0.6919 (m170) REVERT: F 615 ASN cc_start: 0.7544 (t0) cc_final: 0.7291 (t0) REVERT: F 671 LEU cc_start: 0.9114 (tp) cc_final: 0.7650 (tp) REVERT: F 675 TRP cc_start: 0.8024 (m-10) cc_final: 0.7675 (m-10) outliers start: 4 outliers final: 0 residues processed: 448 average time/residue: 0.1693 time to fit residues: 117.2697 Evaluate side-chains 326 residues out of total 2484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 326 time to evaluate : 0.888 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 64 optimal weight: 4.9990 chunk 238 optimal weight: 3.9990 chunk 202 optimal weight: 0.2980 chunk 125 optimal weight: 5.9990 chunk 127 optimal weight: 7.9990 chunk 213 optimal weight: 0.7980 chunk 40 optimal weight: 7.9990 chunk 130 optimal weight: 3.9990 chunk 262 optimal weight: 6.9990 chunk 55 optimal weight: 5.9990 chunk 76 optimal weight: 0.0770 overall best weight: 1.8342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 593 ASN 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 F 548 HIS F 593 ASN ** F 597 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4305 r_free = 0.4305 target = 0.144043 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.101314 restraints weight = 63548.198| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.103709 restraints weight = 38275.341| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.105263 restraints weight = 27597.544| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.106244 restraints weight = 22548.409| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.106564 restraints weight = 20130.481| |-----------------------------------------------------------------------------| r_work (final): 0.3695 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7407 moved from start: 0.4747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 22356 Z= 0.177 Angle : 0.613 10.244 30180 Z= 0.308 Chirality : 0.042 0.192 3390 Planarity : 0.004 0.037 3816 Dihedral : 4.365 19.601 2922 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 16.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 0.16 % Allowed : 0.81 % Favored : 99.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.52 (0.16), residues: 2670 helix: 0.26 (0.15), residues: 1128 sheet: -1.65 (0.30), residues: 330 loop : -0.37 (0.18), residues: 1212 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 551 TYR 0.025 0.001 TYR C 482 PHE 0.033 0.002 PHE E 554 TRP 0.010 0.002 TRP A 675 HIS 0.009 0.001 HIS D 548 Details of bonding type rmsd covalent geometry : bond 0.00399 (22356) covalent geometry : angle 0.61305 (30180) hydrogen bonds : bond 0.03290 ( 894) hydrogen bonds : angle 4.87487 ( 2538) *********************** 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 416 residues out of total 2484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 412 time to evaluate : 0.936 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: A 343 GLU cc_start: 0.7087 (mp0) cc_final: 0.6741 (pm20) REVERT: A 486 LEU cc_start: 0.9368 (mm) cc_final: 0.8866 (mm) REVERT: A 499 THR cc_start: 0.7393 (t) cc_final: 0.7152 (t) REVERT: A 500 PHE cc_start: 0.8164 (m-10) cc_final: 0.7856 (m-80) REVERT: A 525 VAL cc_start: 0.9142 (p) cc_final: 0.8854 (m) REVERT: A 671 LEU cc_start: 0.9068 (tp) cc_final: 0.7553 (tp) REVERT: A 675 TRP cc_start: 0.8019 (m-10) cc_final: 0.7800 (m-10) REVERT: A 759 PHE cc_start: 0.6239 (t80) cc_final: 0.5961 (t80) REVERT: B 384 LEU cc_start: 0.9336 (mt) cc_final: 0.8895 (mt) REVERT: B 387 ARG cc_start: 0.7347 (ttt180) cc_final: 0.6736 (tmm-80) REVERT: B 393 GLU cc_start: 0.8497 (tm-30) cc_final: 0.8174 (tm-30) REVERT: B 398 ASP cc_start: 0.8370 (m-30) cc_final: 0.8121 (m-30) REVERT: B 458 MET cc_start: 0.7999 (ttt) cc_final: 0.7765 (ttt) REVERT: B 486 LEU cc_start: 0.8884 (mm) cc_final: 0.8567 (mm) REVERT: B 499 THR cc_start: 0.7290 (t) cc_final: 0.7040 (t) REVERT: B 500 PHE cc_start: 0.8023 (m-10) cc_final: 0.7715 (m-80) REVERT: B 671 LEU cc_start: 0.9138 (tp) cc_final: 0.7583 (tp) REVERT: B 675 TRP cc_start: 0.7982 (m-10) cc_final: 0.7749 (m-10) REVERT: C 349 VAL cc_start: 0.9439 (t) cc_final: 0.9076 (p) REVERT: C 384 LEU cc_start: 0.9301 (mt) cc_final: 0.8993 (mt) REVERT: C 567 LYS cc_start: 0.7668 (mttt) cc_final: 0.7345 (mtpt) REVERT: C 618 MET cc_start: 0.8202 (tmm) cc_final: 0.7898 (tmm) REVERT: C 759 PHE cc_start: 0.5831 (t80) cc_final: 0.5594 (t80) REVERT: D 398 ASP cc_start: 0.8269 (m-30) cc_final: 0.8044 (m-30) REVERT: D 486 LEU cc_start: 0.9110 (mm) cc_final: 0.8814 (mm) REVERT: D 495 LYS cc_start: 0.7045 (mmtt) cc_final: 0.6799 (mmtm) REVERT: D 597 HIS cc_start: 0.6411 (m170) cc_final: 0.6090 (m-70) REVERT: D 671 LEU cc_start: 0.9072 (tp) cc_final: 0.7511 (tp) REVERT: D 675 TRP cc_start: 0.8117 (m-10) cc_final: 0.7905 (m-10) REVERT: D 759 PHE cc_start: 0.6296 (t80) cc_final: 0.5945 (t80) REVERT: E 439 THR cc_start: 0.8608 (p) cc_final: 0.8323 (t) REVERT: E 491 CYS cc_start: 0.8075 (t) cc_final: 0.7765 (p) REVERT: E 495 LYS cc_start: 0.7183 (pptt) cc_final: 0.6401 (pptt) REVERT: E 671 LEU cc_start: 0.9119 (tp) cc_final: 0.8170 (tp) REVERT: E 675 TRP cc_start: 0.8038 (m-10) cc_final: 0.7600 (m-10) REVERT: F 349 VAL cc_start: 0.9400 (t) cc_final: 0.9094 (p) REVERT: F 384 LEU cc_start: 0.9361 (mt) cc_final: 0.9018 (mt) REVERT: F 525 VAL cc_start: 0.9153 (p) cc_final: 0.8861 (m) REVERT: F 533 THR cc_start: 0.8514 (p) cc_final: 0.7829 (p) REVERT: F 548 HIS cc_start: 0.8149 (p90) cc_final: 0.7858 (p-80) REVERT: F 567 LYS cc_start: 0.7535 (mtpt) cc_final: 0.6944 (ttpt) REVERT: F 572 ASP cc_start: 0.8946 (m-30) cc_final: 0.8655 (p0) REVERT: F 597 HIS cc_start: 0.7301 (m90) cc_final: 0.6761 (m170) REVERT: F 625 ARG cc_start: 0.7793 (tpt90) cc_final: 0.7449 (tpt170) REVERT: F 671 LEU cc_start: 0.9151 (tp) cc_final: 0.7741 (tp) REVERT: F 675 TRP cc_start: 0.8088 (m-10) cc_final: 0.7683 (m-10) outliers start: 4 outliers final: 0 residues processed: 416 average time/residue: 0.1653 time to fit residues: 107.3933 Evaluate side-chains 314 residues out of total 2484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 314 time to evaluate : 0.800 ------------------------------------------------------------------------------- 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: 0.4980 chunk 12 optimal weight: 3.9990 chunk 216 optimal weight: 5.9990 chunk 68 optimal weight: 7.9990 chunk 159 optimal weight: 0.6980 chunk 179 optimal weight: 0.0570 chunk 93 optimal weight: 2.9990 chunk 45 optimal weight: 2.9990 chunk 194 optimal weight: 1.9990 chunk 146 optimal weight: 3.9990 chunk 47 optimal weight: 1.9990 overall best weight: 1.0502 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 593 ASN ** 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4318 r_free = 0.4318 target = 0.145340 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.102712 restraints weight = 63022.223| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.105254 restraints weight = 39012.310| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.106785 restraints weight = 27493.686| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.107806 restraints weight = 22203.542| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.108211 restraints weight = 19593.912| |-----------------------------------------------------------------------------| r_work (final): 0.3723 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7369 moved from start: 0.4855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 22356 Z= 0.128 Angle : 0.567 8.564 30180 Z= 0.287 Chirality : 0.042 0.190 3390 Planarity : 0.004 0.038 3816 Dihedral : 4.305 18.816 2922 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 14.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 0.16 % Allowed : 0.52 % Favored : 99.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.43 (0.16), residues: 2670 helix: 0.30 (0.15), residues: 1128 sheet: -0.91 (0.32), residues: 276 loop : -0.55 (0.18), residues: 1266 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 625 TYR 0.020 0.001 TYR B 482 PHE 0.032 0.002 PHE E 501 TRP 0.006 0.001 TRP A 675 HIS 0.005 0.001 HIS B 548 Details of bonding type rmsd covalent geometry : bond 0.00298 (22356) covalent geometry : angle 0.56680 (30180) hydrogen bonds : bond 0.03136 ( 894) hydrogen bonds : angle 4.78454 ( 2538) *********************** 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 425 residues out of total 2484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 421 time to evaluate : 0.731 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: A 327 PHE cc_start: 0.8501 (t80) cc_final: 0.8062 (t80) REVERT: A 384 LEU cc_start: 0.9344 (mt) cc_final: 0.9080 (tp) REVERT: A 501 PHE cc_start: 0.9058 (m-80) cc_final: 0.8370 (m-80) REVERT: A 516 LEU cc_start: 0.9135 (tp) cc_final: 0.8881 (tp) REVERT: A 525 VAL cc_start: 0.9114 (p) cc_final: 0.8797 (m) REVERT: A 671 LEU cc_start: 0.9052 (tp) cc_final: 0.7460 (tp) REVERT: A 675 TRP cc_start: 0.8053 (m-10) cc_final: 0.7789 (m-10) REVERT: A 759 PHE cc_start: 0.6256 (t80) cc_final: 0.5963 (t80) REVERT: B 343 GLU cc_start: 0.7123 (mp0) cc_final: 0.6662 (pm20) REVERT: B 384 LEU cc_start: 0.9300 (mt) cc_final: 0.8971 (mt) REVERT: B 393 GLU cc_start: 0.8422 (tm-30) cc_final: 0.8113 (tm-30) REVERT: B 398 ASP cc_start: 0.8346 (m-30) cc_final: 0.8077 (m-30) REVERT: B 486 LEU cc_start: 0.8836 (mm) cc_final: 0.8476 (mm) REVERT: B 491 CYS cc_start: 0.8065 (t) cc_final: 0.7812 (p) REVERT: B 500 PHE cc_start: 0.8018 (m-10) cc_final: 0.7717 (m-80) REVERT: B 671 LEU cc_start: 0.9117 (tp) cc_final: 0.7563 (tp) REVERT: B 675 TRP cc_start: 0.7985 (m-10) cc_final: 0.7736 (m-10) REVERT: C 353 ASN cc_start: 0.7892 (m110) cc_final: 0.7059 (t0) REVERT: C 384 LEU cc_start: 0.9283 (mt) cc_final: 0.8972 (mt) REVERT: C 458 MET cc_start: 0.7255 (ptt) cc_final: 0.6903 (ptp) REVERT: C 513 LYS cc_start: 0.9232 (ttpt) cc_final: 0.9001 (ptmm) REVERT: C 567 LYS cc_start: 0.7705 (mttt) cc_final: 0.7410 (mtpt) REVERT: C 618 MET cc_start: 0.8215 (tmm) cc_final: 0.7956 (tmm) REVERT: C 629 HIS cc_start: 0.8509 (t-90) cc_final: 0.8217 (t-90) REVERT: C 759 PHE cc_start: 0.5811 (t80) cc_final: 0.5587 (t80) REVERT: D 398 ASP cc_start: 0.8186 (m-30) cc_final: 0.7962 (m-30) REVERT: D 486 LEU cc_start: 0.9034 (mm) cc_final: 0.8667 (mm) REVERT: D 495 LYS cc_start: 0.6889 (mmtt) cc_final: 0.6336 (mmtm) REVERT: D 500 PHE cc_start: 0.8209 (m-80) cc_final: 0.7963 (m-80) REVERT: D 597 HIS cc_start: 0.6314 (m170) cc_final: 0.6102 (m-70) REVERT: D 671 LEU cc_start: 0.9003 (tp) cc_final: 0.7381 (tp) REVERT: D 675 TRP cc_start: 0.8101 (m-10) cc_final: 0.7864 (m-10) REVERT: D 759 PHE cc_start: 0.6293 (t80) cc_final: 0.5942 (t80) REVERT: E 439 THR cc_start: 0.8369 (p) cc_final: 0.8138 (t) REVERT: E 491 CYS cc_start: 0.8091 (t) cc_final: 0.7766 (p) REVERT: E 495 LYS cc_start: 0.7109 (pptt) cc_final: 0.6183 (pptt) REVERT: E 517 LYS cc_start: 0.9327 (tptt) cc_final: 0.9079 (tptp) REVERT: E 618 MET cc_start: 0.7406 (tmm) cc_final: 0.7103 (tmm) REVERT: E 625 ARG cc_start: 0.7730 (tpt90) cc_final: 0.7495 (tpt170) REVERT: E 759 PHE cc_start: 0.6210 (t80) cc_final: 0.6000 (t80) REVERT: F 349 VAL cc_start: 0.9343 (t) cc_final: 0.9028 (p) REVERT: F 384 LEU cc_start: 0.9344 (mt) cc_final: 0.8829 (mt) REVERT: F 525 VAL cc_start: 0.9152 (p) cc_final: 0.8842 (m) REVERT: F 533 THR cc_start: 0.8525 (p) cc_final: 0.7848 (p) REVERT: F 567 LYS cc_start: 0.7408 (mtpt) cc_final: 0.6796 (ttpt) REVERT: F 572 ASP cc_start: 0.8943 (m-30) cc_final: 0.8709 (p0) REVERT: F 597 HIS cc_start: 0.7271 (m90) cc_final: 0.6777 (m170) REVERT: F 671 LEU cc_start: 0.9152 (tp) cc_final: 0.7778 (tp) REVERT: F 675 TRP cc_start: 0.8087 (m-10) cc_final: 0.7713 (m-10) REVERT: F 759 PHE cc_start: 0.6306 (t80) cc_final: 0.6089 (t80) outliers start: 4 outliers final: 0 residues processed: 425 average time/residue: 0.1484 time to fit residues: 98.4837 Evaluate side-chains 319 residues out of total 2484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 319 time to evaluate : 0.790 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 52 optimal weight: 4.9990 chunk 136 optimal weight: 1.9990 chunk 0 optimal weight: 4.9990 chunk 137 optimal weight: 2.9990 chunk 168 optimal weight: 0.0270 chunk 106 optimal weight: 5.9990 chunk 236 optimal weight: 0.8980 chunk 23 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 chunk 55 optimal weight: 6.9990 chunk 92 optimal weight: 0.7980 overall best weight: 1.1442 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 593 ASN ** C 573 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 593 ASN ** C 597 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 629 HIS D 629 HIS ** E 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 593 ASN ** F 597 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4319 r_free = 0.4319 target = 0.145042 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.102356 restraints weight = 63344.864| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.104798 restraints weight = 37662.702| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.106341 restraints weight = 27180.691| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.107011 restraints weight = 22145.969| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.107683 restraints weight = 20009.061| |-----------------------------------------------------------------------------| r_work (final): 0.3717 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7382 moved from start: 0.4968 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= 0.135 Angle : 0.586 10.134 30180 Z= 0.295 Chirality : 0.042 0.198 3390 Planarity : 0.004 0.053 3816 Dihedral : 4.336 18.725 2922 Min Nonbonded Distance : 2.333 Molprobity Statistics. All-atom Clashscore : 14.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 0.12 % Allowed : 0.48 % Favored : 99.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.40 (0.16), residues: 2670 helix: 0.33 (0.15), residues: 1128 sheet: -1.10 (0.32), residues: 282 loop : -0.50 (0.18), residues: 1260 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG E 619 TYR 0.027 0.001 TYR E 482 PHE 0.030 0.002 PHE B 327 TRP 0.007 0.001 TRP A 675 HIS 0.005 0.001 HIS A 548 Details of bonding type rmsd covalent geometry : bond 0.00311 (22356) covalent geometry : angle 0.58578 (30180) hydrogen bonds : bond 0.03146 ( 894) hydrogen bonds : angle 4.77813 ( 2538) ********************** 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 408 residues out of total 2484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 405 time to evaluate : 0.908 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 327 PHE cc_start: 0.8493 (t80) cc_final: 0.8060 (t80) REVERT: A 343 GLU cc_start: 0.7027 (mp0) cc_final: 0.6642 (pm20) REVERT: A 384 LEU cc_start: 0.9328 (mt) cc_final: 0.8945 (mt) REVERT: A 501 PHE cc_start: 0.9109 (m-80) cc_final: 0.8354 (m-80) REVERT: A 525 VAL cc_start: 0.9105 (p) cc_final: 0.8790 (m) REVERT: A 671 LEU cc_start: 0.9053 (tp) cc_final: 0.7458 (tp) REVERT: A 675 TRP cc_start: 0.8091 (m-10) cc_final: 0.7799 (m-10) REVERT: A 759 PHE cc_start: 0.6273 (t80) cc_final: 0.5995 (t80) REVERT: B 327 PHE cc_start: 0.8358 (t80) cc_final: 0.8087 (t80) REVERT: B 343 GLU cc_start: 0.7031 (mp0) cc_final: 0.6580 (pm20) REVERT: B 393 GLU cc_start: 0.8386 (tm-30) cc_final: 0.8129 (tm-30) REVERT: B 398 ASP cc_start: 0.8308 (m-30) cc_final: 0.8073 (m-30) REVERT: B 484 LYS cc_start: 0.8854 (mtmt) cc_final: 0.8595 (mtmp) REVERT: B 491 CYS cc_start: 0.8059 (t) cc_final: 0.7811 (p) REVERT: B 500 PHE cc_start: 0.7993 (m-10) cc_final: 0.7717 (m-80) REVERT: B 513 LYS cc_start: 0.9292 (ttpt) cc_final: 0.9074 (ttpt) REVERT: B 671 LEU cc_start: 0.9132 (tp) cc_final: 0.7582 (tp) REVERT: B 675 TRP cc_start: 0.8006 (m-10) cc_final: 0.7713 (m-10) REVERT: C 384 LEU cc_start: 0.9300 (mt) cc_final: 0.8955 (mt) REVERT: C 458 MET cc_start: 0.7210 (ptt) cc_final: 0.6887 (ptt) REVERT: C 500 PHE cc_start: 0.8464 (m-10) cc_final: 0.8263 (m-80) REVERT: C 567 LYS cc_start: 0.7734 (mttt) cc_final: 0.7430 (mtpt) REVERT: C 601 ILE cc_start: 0.7905 (mt) cc_final: 0.7634 (mp) REVERT: C 618 MET cc_start: 0.8123 (tmm) cc_final: 0.7819 (tmm) REVERT: D 398 ASP cc_start: 0.8276 (m-30) cc_final: 0.8028 (m-30) REVERT: D 481 LEU cc_start: 0.8752 (mt) cc_final: 0.7979 (mt) REVERT: D 484 LYS cc_start: 0.8839 (mtmt) cc_final: 0.8391 (mtmt) REVERT: D 500 PHE cc_start: 0.8172 (m-80) cc_final: 0.7952 (m-80) REVERT: D 517 LYS cc_start: 0.9303 (tptt) cc_final: 0.9081 (tptp) REVERT: D 597 HIS cc_start: 0.6366 (m170) cc_final: 0.6164 (m-70) REVERT: D 671 LEU cc_start: 0.9034 (tp) cc_final: 0.7413 (tp) REVERT: D 675 TRP cc_start: 0.8117 (m-10) cc_final: 0.7853 (m-10) REVERT: D 759 PHE cc_start: 0.6344 (t80) cc_final: 0.5998 (t80) REVERT: E 491 CYS cc_start: 0.8069 (t) cc_final: 0.7757 (p) REVERT: E 517 LYS cc_start: 0.9308 (tptt) cc_final: 0.9086 (tptp) REVERT: E 531 ILE cc_start: 0.8217 (mm) cc_final: 0.7843 (tt) REVERT: E 615 ASN cc_start: 0.8296 (t0) cc_final: 0.7887 (t0) REVERT: E 618 MET cc_start: 0.8207 (tmm) cc_final: 0.7993 (ptt) REVERT: F 349 VAL cc_start: 0.9356 (t) cc_final: 0.9037 (p) REVERT: F 384 LEU cc_start: 0.9348 (mt) cc_final: 0.8829 (mt) REVERT: F 525 VAL cc_start: 0.9155 (p) cc_final: 0.8804 (m) REVERT: F 533 THR cc_start: 0.8552 (p) cc_final: 0.7866 (p) REVERT: F 567 LYS cc_start: 0.7399 (mtpt) cc_final: 0.6810 (ttpt) REVERT: F 572 ASP cc_start: 0.8932 (m-30) cc_final: 0.8714 (p0) REVERT: F 597 HIS cc_start: 0.7255 (m90) cc_final: 0.6778 (m170) REVERT: F 671 LEU cc_start: 0.9170 (tp) cc_final: 0.7810 (tp) REVERT: F 675 TRP cc_start: 0.8128 (m-10) cc_final: 0.7699 (m-10) REVERT: F 759 PHE cc_start: 0.6313 (t80) cc_final: 0.6097 (t80) outliers start: 3 outliers final: 0 residues processed: 408 average time/residue: 0.1617 time to fit residues: 103.8649 Evaluate side-chains 314 residues out of total 2484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 314 time to evaluate : 0.962 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 246 optimal weight: 3.9990 chunk 237 optimal weight: 4.9990 chunk 194 optimal weight: 1.9990 chunk 220 optimal weight: 0.9990 chunk 26 optimal weight: 0.9980 chunk 28 optimal weight: 0.8980 chunk 69 optimal weight: 2.9990 chunk 186 optimal weight: 0.7980 chunk 206 optimal weight: 1.9990 chunk 64 optimal weight: 0.7980 chunk 209 optimal weight: 4.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 593 ASN ** C 573 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 597 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 548 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 597 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4328 r_free = 0.4328 target = 0.146076 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.103372 restraints weight = 62295.378| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.105808 restraints weight = 37583.631| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.107368 restraints weight = 27303.843| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.108067 restraints weight = 22354.532| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.108225 restraints weight = 20198.203| |-----------------------------------------------------------------------------| r_work (final): 0.3723 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7367 moved from start: 0.5093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 22356 Z= 0.121 Angle : 0.567 8.153 30180 Z= 0.288 Chirality : 0.042 0.195 3390 Planarity : 0.004 0.055 3816 Dihedral : 4.304 18.468 2922 Min Nonbonded Distance : 2.303 Molprobity Statistics. All-atom Clashscore : 14.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 0.04 % Allowed : 0.24 % Favored : 99.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.40 (0.16), residues: 2670 helix: 0.35 (0.16), residues: 1128 sheet: -1.72 (0.29), residues: 336 loop : -0.24 (0.18), residues: 1206 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG E 619 TYR 0.021 0.001 TYR B 482 PHE 0.039 0.002 PHE A 554 TRP 0.006 0.001 TRP D 350 HIS 0.008 0.001 HIS B 548 Details of bonding type rmsd covalent geometry : bond 0.00281 (22356) covalent geometry : angle 0.56719 (30180) hydrogen bonds : bond 0.03116 ( 894) hydrogen bonds : angle 4.78318 ( 2538) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4402.49 seconds wall clock time: 77 minutes 10.12 seconds (4630.12 seconds total)