Starting phenix.real_space_refine on Thu Jun 19 03:58:10 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8apl_15574/06_2025/8apl_15574.cif Found real_map, /net/cci-nas-00/data/ceres_data/8apl_15574/06_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_15574/06_2025/8apl_15574.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8apl_15574/06_2025/8apl_15574.map" model { file = "/net/cci-nas-00/data/ceres_data/8apl_15574/06_2025/8apl_15574.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8apl_15574/06_2025/8apl_15574.cif" } resolution = 4.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 108 5.16 5 C 14082 2.51 5 N 3648 2.21 5 O 4050 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 30 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 21888 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 3648 Number of conformers: 1 Conformer: "" Number of residues, atoms: 449, 3648 Classifications: {'peptide': 449} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 429} Chain breaks: 1 Restraints were copied for chains: C, B, E, D, F Time building chain proxies: 8.29, per 1000 atoms: 0.38 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: 4.84 Conformation dependent library (CDL) restraints added in 2.6 seconds 5340 Ramachandran restraints generated. 2670 Oldfield, 0 Emsley, 2670 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5148 Finding SS restraints... Secondary structure from input PDB file: 132 helices and 42 sheets defined 47.2% alpha, 11.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.13 Creating SS restraints... Processing helix chain 'A' and resid 324 through 336 removed outlier: 3.975A pdb=" N ASN A 328 " --> pdb=" O ASN A 324 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N THR A 336 " --> pdb=" O ARG A 332 " (cutoff:3.500A) Processing helix chain 'A' and resid 363 through 372 Processing helix chain 'A' and resid 373 through 375 No H-bonds generated for 'chain 'A' and resid 373 through 375' Processing helix chain 'A' and resid 376 through 384 removed outlier: 3.683A pdb=" N SER A 381 " --> pdb=" O LYS A 377 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N GLU A 382 " --> pdb=" O GLU A 378 " (cutoff:3.500A) Processing helix chain 'A' and resid 385 through 400 Processing helix chain 'A' and resid 430 through 435 Processing helix chain 'A' and resid 455 through 469 Processing helix chain 'A' and resid 475 through 489 Processing helix chain 'A' and resid 508 through 521 Processing helix chain 'A' and resid 529 through 534 Processing helix chain 'A' and resid 541 through 548 Processing helix chain 'A' and resid 570 through 577 Processing helix chain 'A' and resid 614 through 620 Processing helix chain 'A' and resid 654 through 661 removed outlier: 3.837A pdb=" N LYS A 658 " --> pdb=" O GLY A 654 " (cutoff:3.500A) Processing helix chain 'A' and resid 664 through 680 Processing helix chain 'A' and resid 689 through 692 Processing helix chain 'A' and resid 693 through 706 Processing helix chain 'A' and resid 713 through 715 No H-bonds generated for 'chain 'A' and resid 713 through 715' Processing helix chain 'A' and resid 716 through 721 Processing helix chain 'A' and resid 736 through 747 removed outlier: 3.971A pdb=" N LYS A 745 " --> pdb=" O GLN A 741 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N TYR A 746 " --> pdb=" O LYS A 742 " (cutoff:3.500A) Processing helix chain 'A' and resid 752 through 764 Processing helix chain 'A' and resid 778 through 782 Processing helix chain 'B' and resid 324 through 336 removed outlier: 3.975A pdb=" N ASN B 328 " --> pdb=" O ASN B 324 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N THR B 336 " --> pdb=" O ARG B 332 " (cutoff:3.500A) Processing helix chain 'B' and resid 363 through 372 Processing helix chain 'B' and resid 373 through 375 No H-bonds generated for 'chain 'B' and resid 373 through 375' Processing helix chain 'B' and resid 376 through 384 removed outlier: 3.683A pdb=" N SER B 381 " --> pdb=" O LYS B 377 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N GLU B 382 " --> pdb=" O GLU B 378 " (cutoff:3.500A) Processing helix chain 'B' and resid 385 through 400 Processing helix chain 'B' and resid 430 through 435 Processing helix chain 'B' and resid 455 through 469 Processing helix chain 'B' and resid 475 through 489 Processing helix chain 'B' and resid 508 through 521 Processing helix chain 'B' and resid 529 through 534 Processing helix chain 'B' and resid 541 through 548 Processing helix chain 'B' and resid 570 through 577 Processing helix chain 'B' and resid 614 through 620 Processing helix chain 'B' and resid 654 through 661 removed outlier: 3.838A pdb=" N LYS B 658 " --> pdb=" O GLY B 654 " (cutoff:3.500A) Processing helix chain 'B' and resid 664 through 680 Processing helix chain 'B' and resid 689 through 692 Processing helix chain 'B' and resid 693 through 706 Processing helix chain 'B' and resid 713 through 715 No H-bonds generated for 'chain 'B' and resid 713 through 715' Processing helix chain 'B' and resid 716 through 721 Processing helix chain 'B' and resid 736 through 747 removed outlier: 3.972A pdb=" N LYS B 745 " --> pdb=" O GLN B 741 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N TYR B 746 " --> pdb=" O LYS B 742 " (cutoff:3.500A) Processing helix chain 'B' and resid 752 through 764 Processing helix chain 'B' and resid 778 through 782 Processing helix chain 'C' and resid 324 through 336 removed outlier: 3.975A pdb=" N ASN C 328 " --> pdb=" O ASN C 324 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N THR C 336 " --> pdb=" O ARG C 332 " (cutoff:3.500A) Processing helix chain 'C' and resid 363 through 372 Processing helix chain 'C' and resid 373 through 375 No H-bonds generated for 'chain 'C' and resid 373 through 375' Processing helix chain 'C' and resid 376 through 384 removed outlier: 3.683A pdb=" N SER C 381 " --> pdb=" O LYS C 377 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N GLU C 382 " --> pdb=" O GLU C 378 " (cutoff:3.500A) Processing helix chain 'C' and resid 385 through 400 Processing helix chain 'C' and resid 430 through 435 Processing helix chain 'C' and resid 455 through 469 Processing helix chain 'C' and resid 475 through 489 Processing helix chain 'C' and resid 508 through 521 Processing helix chain 'C' and resid 529 through 534 Processing helix chain 'C' and resid 541 through 548 Processing helix chain 'C' and resid 570 through 577 Processing helix chain 'C' and resid 614 through 620 Processing helix chain 'C' and resid 654 through 661 removed outlier: 3.837A pdb=" N LYS C 658 " --> pdb=" O GLY C 654 " (cutoff:3.500A) Processing helix chain 'C' and resid 664 through 680 Processing helix chain 'C' and resid 689 through 692 Processing helix chain 'C' and resid 693 through 706 Processing helix chain 'C' and resid 713 through 715 No H-bonds generated for 'chain 'C' and resid 713 through 715' Processing helix chain 'C' and resid 716 through 721 Processing helix chain 'C' and resid 736 through 747 removed outlier: 3.972A pdb=" N LYS C 745 " --> pdb=" O GLN C 741 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N TYR C 746 " --> pdb=" O LYS C 742 " (cutoff:3.500A) Processing helix chain 'C' and resid 752 through 764 Processing helix chain 'C' and resid 778 through 782 Processing helix chain 'D' and resid 324 through 336 removed outlier: 3.976A pdb=" N ASN D 328 " --> pdb=" O ASN D 324 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N THR D 336 " --> pdb=" O ARG D 332 " (cutoff:3.500A) Processing helix chain 'D' and resid 363 through 372 Processing helix chain 'D' and resid 373 through 375 No H-bonds generated for 'chain 'D' and resid 373 through 375' Processing helix chain 'D' and resid 376 through 384 removed outlier: 3.684A pdb=" N SER D 381 " --> pdb=" O LYS D 377 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N GLU D 382 " --> pdb=" O GLU D 378 " (cutoff:3.500A) Processing helix chain 'D' and resid 385 through 400 Processing helix chain 'D' and resid 430 through 435 Processing helix chain 'D' and resid 455 through 469 Processing helix chain 'D' and resid 475 through 489 Processing helix chain 'D' and resid 508 through 521 Processing helix chain 'D' and resid 529 through 534 Processing helix chain 'D' and resid 541 through 548 Processing helix chain 'D' and resid 570 through 577 Processing helix chain 'D' and resid 614 through 620 Processing helix chain 'D' and resid 654 through 661 removed outlier: 3.838A pdb=" N LYS D 658 " --> pdb=" O GLY D 654 " (cutoff:3.500A) Processing helix chain 'D' and resid 664 through 680 Processing helix chain 'D' and resid 689 through 692 Processing helix chain 'D' and resid 693 through 706 Processing helix chain 'D' and resid 713 through 715 No H-bonds generated for 'chain 'D' and resid 713 through 715' Processing helix chain 'D' and resid 716 through 721 Processing helix chain 'D' and resid 736 through 747 removed outlier: 3.972A pdb=" N LYS D 745 " --> pdb=" O GLN D 741 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N TYR D 746 " --> pdb=" O LYS D 742 " (cutoff:3.500A) Processing helix chain 'D' and resid 752 through 764 Processing helix chain 'D' and resid 778 through 782 Processing helix chain 'E' and resid 324 through 336 removed outlier: 3.975A pdb=" N ASN E 328 " --> pdb=" O ASN E 324 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N THR E 336 " --> pdb=" O ARG E 332 " (cutoff:3.500A) Processing helix chain 'E' and resid 363 through 372 Processing helix chain 'E' and resid 373 through 375 No H-bonds generated for 'chain 'E' and resid 373 through 375' Processing helix chain 'E' and resid 376 through 384 removed outlier: 3.683A pdb=" N SER E 381 " --> pdb=" O LYS E 377 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N GLU E 382 " --> pdb=" O GLU E 378 " (cutoff:3.500A) Processing helix chain 'E' and resid 385 through 400 Processing helix chain 'E' and resid 430 through 435 Processing helix chain 'E' and resid 455 through 469 Processing helix chain 'E' and resid 475 through 489 Processing helix chain 'E' and resid 508 through 521 Processing helix chain 'E' and resid 529 through 534 Processing helix chain 'E' and resid 541 through 548 Processing helix chain 'E' and resid 570 through 577 Processing helix chain 'E' and resid 614 through 620 Processing helix chain 'E' and resid 654 through 661 removed outlier: 3.838A pdb=" N LYS E 658 " --> pdb=" O GLY E 654 " (cutoff:3.500A) Processing helix chain 'E' and resid 664 through 680 Processing helix chain 'E' and resid 689 through 692 Processing helix chain 'E' and resid 693 through 706 Processing helix chain 'E' and resid 713 through 715 No H-bonds generated for 'chain 'E' and resid 713 through 715' Processing helix chain 'E' and resid 716 through 721 Processing helix chain 'E' and resid 736 through 747 removed outlier: 3.972A pdb=" N LYS E 745 " --> pdb=" O GLN E 741 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N TYR E 746 " --> pdb=" O LYS E 742 " (cutoff:3.500A) Processing helix chain 'E' and resid 752 through 764 Processing helix chain 'E' and resid 778 through 782 Processing helix chain 'F' and resid 324 through 336 removed outlier: 3.975A pdb=" N ASN F 328 " --> pdb=" O ASN F 324 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N THR F 336 " --> pdb=" O ARG F 332 " (cutoff:3.500A) Processing helix chain 'F' and resid 363 through 372 Processing helix chain 'F' and resid 373 through 375 No H-bonds generated for 'chain 'F' and resid 373 through 375' Processing helix chain 'F' and resid 376 through 384 removed outlier: 3.683A pdb=" N SER F 381 " --> pdb=" O LYS F 377 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N GLU F 382 " --> pdb=" O GLU F 378 " (cutoff:3.500A) Processing helix chain 'F' and resid 385 through 400 Processing helix chain 'F' and resid 430 through 435 Processing helix chain 'F' and resid 455 through 469 Processing helix chain 'F' and resid 475 through 489 Processing helix chain 'F' and resid 508 through 521 Processing helix chain 'F' and resid 529 through 534 Processing helix chain 'F' and resid 541 through 548 Processing helix chain 'F' and resid 570 through 577 Processing helix chain 'F' and resid 614 through 620 Processing helix chain 'F' and resid 654 through 661 removed outlier: 3.837A pdb=" N LYS F 658 " --> pdb=" O GLY F 654 " (cutoff:3.500A) Processing helix chain 'F' and resid 664 through 680 Processing helix chain 'F' and resid 689 through 692 Processing helix chain 'F' and resid 693 through 706 Processing helix chain 'F' and resid 713 through 715 No H-bonds generated for 'chain 'F' and resid 713 through 715' Processing helix chain 'F' and resid 716 through 721 Processing helix chain 'F' and resid 736 through 747 removed outlier: 3.972A pdb=" N LYS F 745 " --> pdb=" O GLN F 741 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N TYR F 746 " --> pdb=" O LYS F 742 " (cutoff:3.500A) Processing helix chain 'F' and resid 752 through 764 Processing helix chain 'F' and resid 778 through 782 Processing sheet with id=AA1, first strand: chain 'A' and resid 339 through 341 Processing sheet with id=AA2, first strand: chain 'A' and resid 412 through 414 Processing sheet with id=AA3, first strand: chain 'A' and resid 524 through 527 removed outlier: 5.926A pdb=" N VAL A 553 " --> pdb=" O ILE A 601 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N ASP A 603 " --> pdb=" O VAL A 553 " (cutoff:3.500A) removed outlier: 5.959A pdb=" N CYS A 555 " --> pdb=" O ASP A 603 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N THR A 499 " --> pdb=" O ILE A 600 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N LEU A 498 " --> pdb=" O ALA A 622 " (cutoff:3.500A) removed outlier: 7.483A pdb=" N VAL A 624 " --> pdb=" O LEU A 498 " (cutoff:3.500A) removed outlier: 6.049A pdb=" N PHE A 500 " --> pdb=" O VAL A 624 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 581 through 582 Processing sheet with id=AA5, first strand: chain 'A' and resid 628 through 631 Processing sheet with id=AA6, first strand: chain 'A' and resid 707 through 708 Processing sheet with id=AA7, first strand: chain 'A' and resid 726 through 728 Processing sheet with id=AA8, first strand: chain 'B' and resid 339 through 341 Processing sheet with id=AA9, first strand: chain 'B' and resid 412 through 414 Processing sheet with id=AB1, first strand: chain 'B' and resid 524 through 527 removed outlier: 5.926A pdb=" N VAL B 553 " --> pdb=" O ILE B 601 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N ASP B 603 " --> pdb=" O VAL B 553 " (cutoff:3.500A) removed outlier: 5.960A pdb=" N CYS B 555 " --> pdb=" O ASP B 603 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N THR B 499 " --> pdb=" O ILE B 600 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N LEU B 498 " --> pdb=" O ALA B 622 " (cutoff:3.500A) removed outlier: 7.482A pdb=" N VAL B 624 " --> pdb=" O LEU B 498 " (cutoff:3.500A) removed outlier: 6.050A pdb=" N PHE B 500 " --> pdb=" O VAL B 624 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 581 through 582 Processing sheet with id=AB3, first strand: chain 'B' and resid 628 through 631 Processing sheet with id=AB4, first strand: chain 'B' and resid 707 through 708 Processing sheet with id=AB5, first strand: chain 'B' and resid 726 through 728 Processing sheet with id=AB6, first strand: chain 'C' and resid 339 through 341 Processing sheet with id=AB7, first strand: chain 'C' and resid 412 through 414 Processing sheet with id=AB8, first strand: chain 'C' and resid 524 through 527 removed outlier: 5.927A pdb=" N VAL C 553 " --> pdb=" O ILE C 601 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N ASP C 603 " --> pdb=" O VAL C 553 " (cutoff:3.500A) removed outlier: 5.960A pdb=" N CYS C 555 " --> pdb=" O ASP C 603 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N THR C 499 " --> pdb=" O ILE C 600 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N LEU C 498 " --> pdb=" O ALA C 622 " (cutoff:3.500A) removed outlier: 7.483A pdb=" N VAL C 624 " --> pdb=" O LEU C 498 " (cutoff:3.500A) removed outlier: 6.049A pdb=" N PHE C 500 " --> pdb=" O VAL C 624 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 581 through 582 Processing sheet with id=AC1, first strand: chain 'C' and resid 628 through 631 Processing sheet with id=AC2, first strand: chain 'C' and resid 707 through 708 Processing sheet with id=AC3, first strand: chain 'C' and resid 726 through 728 Processing sheet with id=AC4, first strand: chain 'D' and resid 339 through 341 Processing sheet with id=AC5, first strand: chain 'D' and resid 412 through 414 Processing sheet with id=AC6, first strand: chain 'D' and resid 524 through 527 removed outlier: 5.927A pdb=" N VAL D 553 " --> pdb=" O ILE D 601 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N ASP D 603 " --> pdb=" O VAL D 553 " (cutoff:3.500A) removed outlier: 5.960A pdb=" N CYS D 555 " --> pdb=" O ASP D 603 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N THR D 499 " --> pdb=" O ILE D 600 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N LEU D 498 " --> pdb=" O ALA D 622 " (cutoff:3.500A) removed outlier: 7.482A pdb=" N VAL D 624 " --> pdb=" O LEU D 498 " (cutoff:3.500A) removed outlier: 6.049A pdb=" N PHE D 500 " --> pdb=" O VAL D 624 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'D' and resid 581 through 582 Processing sheet with id=AC8, first strand: chain 'D' and resid 628 through 631 Processing sheet with id=AC9, first strand: chain 'D' and resid 707 through 708 Processing sheet with id=AD1, first strand: chain 'D' and resid 726 through 728 Processing sheet with id=AD2, first strand: chain 'E' and resid 339 through 341 Processing sheet with id=AD3, first strand: chain 'E' and resid 412 through 414 Processing sheet with id=AD4, first strand: chain 'E' and resid 524 through 527 removed outlier: 5.927A pdb=" N VAL E 553 " --> pdb=" O ILE E 601 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N ASP E 603 " --> pdb=" O VAL E 553 " (cutoff:3.500A) removed outlier: 5.959A pdb=" N CYS E 555 " --> pdb=" O ASP E 603 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N THR E 499 " --> pdb=" O ILE E 600 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N LEU E 498 " --> pdb=" O ALA E 622 " (cutoff:3.500A) removed outlier: 7.483A pdb=" N VAL E 624 " --> pdb=" O LEU E 498 " (cutoff:3.500A) removed outlier: 6.049A pdb=" N PHE E 500 " --> pdb=" O VAL E 624 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'E' and resid 581 through 582 Processing sheet with id=AD6, first strand: chain 'E' and resid 628 through 631 Processing sheet with id=AD7, first strand: chain 'E' and resid 707 through 708 Processing sheet with id=AD8, first strand: chain 'E' and resid 726 through 728 Processing sheet with id=AD9, first strand: chain 'F' and resid 339 through 341 Processing sheet with id=AE1, first strand: chain 'F' and resid 412 through 414 Processing sheet with id=AE2, first strand: chain 'F' and resid 524 through 527 removed outlier: 5.926A pdb=" N VAL F 553 " --> pdb=" O ILE F 601 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N ASP F 603 " --> pdb=" O VAL F 553 " (cutoff:3.500A) removed outlier: 5.960A pdb=" N CYS F 555 " --> pdb=" O ASP F 603 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N THR F 499 " --> pdb=" O ILE F 600 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N LEU F 498 " --> pdb=" O ALA F 622 " (cutoff:3.500A) removed outlier: 7.483A pdb=" N VAL F 624 " --> pdb=" O LEU F 498 " (cutoff:3.500A) removed outlier: 6.048A pdb=" N PHE F 500 " --> pdb=" O VAL F 624 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'F' and resid 581 through 582 Processing sheet with id=AE4, first strand: chain 'F' and resid 628 through 631 Processing sheet with id=AE5, first strand: chain 'F' and resid 707 through 708 Processing sheet with id=AE6, first strand: chain 'F' and resid 726 through 728 894 hydrogen bonds defined for protein. 2538 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 7.93 Time building geometry restraints manager: 5.82 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: 0.18 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'E' selection = chain 'D' 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: 1.170 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: 0.030 Extract box with map and model: 0.760 Check model and map are aligned: 0.140 Set scattering table: 0.200 Process input model: 44.420 Find NCS groups from input model: 0.480 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.190 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.14 (0.17), residues: 2670 helix: 1.14 (0.17), residues: 1098 sheet: -0.76 (0.29), residues: 318 loop : -0.55 (0.17), residues: 1254 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP A 350 HIS 0.002 0.001 HIS E 763 PHE 0.006 0.001 PHE C 444 TYR 0.013 0.001 TYR F 409 ARG 0.002 0.000 ARG D 372 Details of bonding type rmsd hydrogen bonds : bond 0.16131 ( 894) hydrogen bonds : angle 6.00980 ( 2538) covalent geometry : bond 0.00162 (22356) covalent geometry : angle 0.47671 (30180) *********************** 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 : 2.357 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: 0.3889 time to fit residues: 419.5196 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 : 2.874 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 222 optimal weight: 0.9980 chunk 200 optimal weight: 6.9990 chunk 111 optimal weight: 6.9990 chunk 68 optimal weight: 9.9990 chunk 134 optimal weight: 1.9990 chunk 106 optimal weight: 10.0000 chunk 206 optimal weight: 6.9990 chunk 80 optimal weight: 6.9990 chunk 125 optimal weight: 9.9990 chunk 154 optimal weight: 0.9980 chunk 239 optimal weight: 0.8980 overall best weight: 2.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 324 ASN A 763 HIS A 775 GLN B 324 ASN ** B 573 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 763 HIS B 775 GLN C 324 ASN ** C 573 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 775 GLN D 324 ASN ** D 573 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 763 HIS D 775 GLN E 324 ASN ** E 573 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 763 HIS E 775 GLN F 324 ASN F 463 ASN ** F 573 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 775 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4307 r_free = 0.4307 target = 0.143685 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.101538 restraints weight = 64238.323| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.104051 restraints weight = 38264.065| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.105557 restraints weight = 27466.912| |-----------------------------------------------------------------------------| r_work (final): 0.3670 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7423 moved from start: 0.3164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 22356 Z= 0.227 Angle : 0.655 7.889 30180 Z= 0.336 Chirality : 0.044 0.310 3390 Planarity : 0.005 0.073 3816 Dihedral : 4.152 18.032 2922 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 16.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.60 (0.16), residues: 2670 helix: 0.41 (0.15), residues: 1104 sheet: -1.24 (0.29), residues: 288 loop : -0.83 (0.17), residues: 1278 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP C 675 HIS 0.005 0.001 HIS D 763 PHE 0.031 0.002 PHE E 554 TYR 0.020 0.002 TYR C 606 ARG 0.005 0.001 ARG F 625 Details of bonding type rmsd hydrogen bonds : bond 0.04219 ( 894) hydrogen bonds : angle 5.28499 ( 2538) covalent geometry : bond 0.00488 (22356) covalent geometry : angle 0.65475 (30180) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5340 Ramachandran restraints generated. 2670 Oldfield, 0 Emsley, 2670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5340 Ramachandran restraints generated. 2670 Oldfield, 0 Emsley, 2670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 501 residues out of total 2484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 501 time to evaluate : 2.206 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 467 ASP cc_start: 0.8719 (t0) cc_final: 0.8478 (t0) REVERT: A 491 CYS cc_start: 0.8316 (t) cc_final: 0.8031 (p) REVERT: A 501 PHE cc_start: 0.8927 (m-10) cc_final: 0.8614 (m-80) REVERT: A 597 HIS cc_start: 0.6660 (m170) cc_final: 0.6275 (m170) REVERT: A 625 ARG cc_start: 0.8113 (tpt170) cc_final: 0.7886 (tpt170) REVERT: A 671 LEU cc_start: 0.9075 (tp) cc_final: 0.7997 (tp) REVERT: B 371 ILE cc_start: 0.9496 (pt) cc_final: 0.9158 (pt) REVERT: B 384 LEU cc_start: 0.9417 (mt) cc_final: 0.9134 (mt) REVERT: B 491 CYS cc_start: 0.8122 (t) cc_final: 0.7846 (p) REVERT: B 495 LYS cc_start: 0.7465 (pptt) cc_final: 0.7233 (pptt) REVERT: B 501 PHE cc_start: 0.8893 (m-10) cc_final: 0.8576 (m-10) REVERT: B 531 ILE cc_start: 0.8058 (mt) cc_final: 0.7687 (mm) REVERT: B 577 LEU cc_start: 0.9127 (mp) cc_final: 0.8900 (mp) REVERT: B 618 MET cc_start: 0.7902 (tmm) cc_final: 0.7674 (tmm) REVERT: B 671 LEU cc_start: 0.9128 (tp) cc_final: 0.7710 (tp) REVERT: B 675 TRP cc_start: 0.8039 (m-10) cc_final: 0.7715 (m-10) REVERT: B 759 PHE cc_start: 0.6112 (t80) cc_final: 0.5827 (t80) REVERT: C 384 LEU cc_start: 0.9323 (mt) cc_final: 0.9065 (mt) REVERT: C 467 ASP cc_start: 0.8629 (t0) cc_final: 0.8367 (t0) REVERT: C 491 CYS cc_start: 0.8481 (t) cc_final: 0.8251 (p) REVERT: C 567 LYS cc_start: 0.7809 (mttt) cc_final: 0.7402 (mtpt) REVERT: C 618 MET cc_start: 0.8003 (tmm) cc_final: 0.7787 (tmm) REVERT: C 759 PHE cc_start: 0.5691 (t80) cc_final: 0.5421 (t80) REVERT: D 351 ILE cc_start: 0.9264 (pt) cc_final: 0.8904 (pt) REVERT: D 491 CYS cc_start: 0.8331 (t) cc_final: 0.7857 (p) REVERT: D 501 PHE cc_start: 0.9172 (m-10) cc_final: 0.8920 (m-10) REVERT: D 597 HIS cc_start: 0.6598 (m170) cc_final: 0.6164 (m170) REVERT: D 671 LEU cc_start: 0.9094 (tp) cc_final: 0.7639 (tp) REVERT: D 675 TRP cc_start: 0.8128 (m-10) cc_final: 0.7896 (m-10) REVERT: E 387 ARG cc_start: 0.7406 (ttt180) cc_final: 0.7081 (ttt180) REVERT: E 491 CYS cc_start: 0.8173 (t) cc_final: 0.7942 (p) REVERT: E 618 MET cc_start: 0.7818 (tmm) cc_final: 0.7581 (tmm) REVERT: E 671 LEU cc_start: 0.9136 (tp) cc_final: 0.7656 (tp) REVERT: E 675 TRP cc_start: 0.7956 (m-10) cc_final: 0.7679 (m-10) REVERT: F 384 LEU cc_start: 0.9378 (mt) cc_final: 0.8979 (mt) REVERT: F 467 ASP cc_start: 0.8571 (t0) cc_final: 0.8280 (t0) REVERT: F 491 CYS cc_start: 0.8394 (t) cc_final: 0.8179 (p) REVERT: F 501 PHE cc_start: 0.9139 (m-10) cc_final: 0.8914 (m-10) REVERT: F 572 ASP cc_start: 0.8951 (m-30) cc_final: 0.8719 (p0) REVERT: F 675 TRP cc_start: 0.8027 (m-10) cc_final: 0.7781 (m-10) outliers start: 0 outliers final: 0 residues processed: 501 average time/residue: 0.3742 time to fit residues: 287.0226 Evaluate side-chains 340 residues out of total 2484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 340 time to evaluate : 2.723 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 146 optimal weight: 3.9990 chunk 220 optimal weight: 2.9990 chunk 260 optimal weight: 1.9990 chunk 109 optimal weight: 8.9990 chunk 237 optimal weight: 0.3980 chunk 59 optimal weight: 0.8980 chunk 124 optimal weight: 3.9990 chunk 166 optimal weight: 0.9990 chunk 60 optimal weight: 0.8980 chunk 20 optimal weight: 8.9990 chunk 10 optimal weight: 5.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 593 ASN ** B 573 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 763 HIS ** C 573 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 597 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 593 ASN ** E 573 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 629 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 763 HIS F 593 ASN ** F 597 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4333 r_free = 0.4333 target = 0.145914 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.103083 restraints weight = 62818.359| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.105628 restraints weight = 37252.215| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.106847 restraints weight = 26821.640| |-----------------------------------------------------------------------------| r_work (final): 0.3695 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7401 moved from start: 0.3609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 22356 Z= 0.144 Angle : 0.564 7.018 30180 Z= 0.295 Chirality : 0.042 0.210 3390 Planarity : 0.004 0.052 3816 Dihedral : 4.219 19.812 2922 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 15.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 0.20 % Allowed : 3.10 % Favored : 96.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.72 (0.16), residues: 2670 helix: 0.33 (0.15), residues: 1116 sheet: -2.10 (0.27), residues: 342 loop : -0.62 (0.17), residues: 1212 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 675 HIS 0.006 0.001 HIS F 597 PHE 0.035 0.002 PHE F 502 TYR 0.019 0.001 TYR B 606 ARG 0.005 0.001 ARG D 514 Details of bonding type rmsd hydrogen bonds : bond 0.03719 ( 894) hydrogen bonds : angle 4.97363 ( 2538) covalent geometry : bond 0.00333 (22356) covalent geometry : angle 0.56442 (30180) *********************** 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 473 residues out of total 2484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 468 time to evaluate : 2.517 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: A 393 GLU cc_start: 0.8545 (tm-30) cc_final: 0.8333 (tm-30) REVERT: A 486 LEU cc_start: 0.9333 (mm) cc_final: 0.9090 (mm) REVERT: A 491 CYS cc_start: 0.8256 (t) cc_final: 0.7889 (p) REVERT: A 531 ILE cc_start: 0.8032 (mm) cc_final: 0.7729 (mm) REVERT: A 597 HIS cc_start: 0.6548 (m170) cc_final: 0.6174 (m170) REVERT: A 671 LEU cc_start: 0.9056 (tp) cc_final: 0.7756 (tp) REVERT: B 384 LEU cc_start: 0.9329 (mt) cc_final: 0.9077 (mt) REVERT: B 387 ARG cc_start: 0.7560 (ttt180) cc_final: 0.7331 (ttt180) REVERT: B 486 LEU cc_start: 0.9024 (mm) cc_final: 0.8811 (mm) REVERT: B 491 CYS cc_start: 0.8092 (t) cc_final: 0.7783 (p) REVERT: B 495 LYS cc_start: 0.7427 (pptt) cc_final: 0.6973 (pptt) REVERT: B 577 LEU cc_start: 0.9055 (mp) cc_final: 0.8805 (mt) REVERT: B 629 HIS cc_start: 0.8528 (t-90) cc_final: 0.8179 (t-90) REVERT: B 671 LEU cc_start: 0.9062 (tp) cc_final: 0.7669 (tp) REVERT: B 675 TRP cc_start: 0.8034 (m-10) cc_final: 0.7640 (m-10) REVERT: B 759 PHE cc_start: 0.6021 (t80) cc_final: 0.5739 (t80) REVERT: C 349 VAL cc_start: 0.9360 (t) cc_final: 0.9090 (p) REVERT: C 384 LEU cc_start: 0.9220 (mt) cc_final: 0.8996 (mt) REVERT: C 458 MET cc_start: 0.7568 (ttm) cc_final: 0.7111 (ttm) REVERT: C 491 CYS cc_start: 0.8351 (t) cc_final: 0.8042 (p) REVERT: C 531 ILE cc_start: 0.8198 (mm) cc_final: 0.7935 (mm) REVERT: C 567 LYS cc_start: 0.7628 (mttt) cc_final: 0.7355 (mtpt) REVERT: C 759 PHE cc_start: 0.5753 (t80) cc_final: 0.5474 (t80) REVERT: D 348 ILE cc_start: 0.9419 (mp) cc_final: 0.9175 (mt) REVERT: D 486 LEU cc_start: 0.9367 (mm) cc_final: 0.8941 (mm) REVERT: D 501 PHE cc_start: 0.9140 (m-10) cc_final: 0.8876 (m-80) REVERT: D 516 LEU cc_start: 0.9092 (tp) cc_final: 0.8838 (tp) REVERT: D 531 ILE cc_start: 0.7979 (mm) cc_final: 0.7691 (mm) REVERT: D 597 HIS cc_start: 0.6675 (m170) cc_final: 0.6287 (m170) REVERT: D 625 ARG cc_start: 0.8035 (tpt170) cc_final: 0.7756 (tpt170) REVERT: D 671 LEU cc_start: 0.9037 (tp) cc_final: 0.7520 (tp) REVERT: E 387 ARG cc_start: 0.7226 (ttt180) cc_final: 0.6434 (tmm-80) REVERT: E 458 MET cc_start: 0.7894 (ttm) cc_final: 0.7635 (ttp) REVERT: E 486 LEU cc_start: 0.9172 (mm) cc_final: 0.8912 (mm) REVERT: E 491 CYS cc_start: 0.8126 (t) cc_final: 0.7846 (p) REVERT: E 531 ILE cc_start: 0.7946 (mt) cc_final: 0.7588 (tt) REVERT: E 603 ASP cc_start: 0.5593 (m-30) cc_final: 0.5143 (m-30) REVERT: E 629 HIS cc_start: 0.8804 (t-90) cc_final: 0.8432 (t-90) REVERT: F 371 ILE cc_start: 0.9382 (pt) cc_final: 0.9027 (pt) REVERT: F 384 LEU cc_start: 0.9286 (mt) cc_final: 0.8929 (mt) REVERT: F 491 CYS cc_start: 0.8384 (t) cc_final: 0.8013 (p) REVERT: F 499 THR cc_start: 0.7267 (t) cc_final: 0.6960 (t) REVERT: F 572 ASP cc_start: 0.8927 (m-30) cc_final: 0.8648 (p0) REVERT: F 597 HIS cc_start: 0.7070 (m90) cc_final: 0.6453 (m170) REVERT: F 671 LEU cc_start: 0.9155 (tp) cc_final: 0.7707 (tp) REVERT: F 675 TRP cc_start: 0.7978 (m-10) cc_final: 0.7697 (m-10) outliers start: 5 outliers final: 0 residues processed: 473 average time/residue: 0.3281 time to fit residues: 240.6029 Evaluate side-chains 337 residues out of total 2484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 337 time to evaluate : 2.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 231 optimal weight: 4.9990 chunk 223 optimal weight: 0.4980 chunk 134 optimal weight: 2.9990 chunk 42 optimal weight: 9.9990 chunk 28 optimal weight: 0.9980 chunk 182 optimal weight: 0.9990 chunk 260 optimal weight: 0.9980 chunk 22 optimal weight: 5.9990 chunk 79 optimal weight: 0.8980 chunk 44 optimal weight: 1.9990 chunk 0 optimal weight: 4.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- 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 763 HIS ** C 573 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 593 ASN ** C 597 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 353 ASN D 593 ASN ** E 573 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 629 HIS E 763 HIS F 593 ASN ** F 597 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 629 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4334 r_free = 0.4334 target = 0.145873 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.103125 restraints weight = 63332.033| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.105531 restraints weight = 37942.404| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.107088 restraints weight = 27433.186| |-----------------------------------------------------------------------------| r_work (final): 0.3711 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7378 moved from start: 0.3878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 22356 Z= 0.134 Angle : 0.551 6.780 30180 Z= 0.286 Chirality : 0.041 0.150 3390 Planarity : 0.004 0.042 3816 Dihedral : 4.177 17.958 2922 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 13.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 0.16 % Allowed : 1.85 % Favored : 97.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.62 (0.16), residues: 2670 helix: 0.37 (0.15), residues: 1116 sheet: -2.06 (0.28), residues: 342 loop : -0.51 (0.17), residues: 1212 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 355 HIS 0.005 0.001 HIS C 597 PHE 0.030 0.002 PHE E 554 TYR 0.016 0.001 TYR B 606 ARG 0.004 0.000 ARG E 625 Details of bonding type rmsd hydrogen bonds : bond 0.03416 ( 894) hydrogen bonds : angle 4.88839 ( 2538) covalent geometry : bond 0.00306 (22356) covalent geometry : angle 0.55069 (30180) *********************** 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 467 residues out of total 2484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 463 time to evaluate : 2.309 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 486 LEU cc_start: 0.9354 (mm) cc_final: 0.8960 (mm) REVERT: A 491 CYS cc_start: 0.8319 (t) cc_final: 0.7909 (p) REVERT: A 516 LEU cc_start: 0.9207 (tp) cc_final: 0.8850 (tp) REVERT: A 597 HIS cc_start: 0.6587 (m170) cc_final: 0.6253 (m170) REVERT: A 671 LEU cc_start: 0.9069 (tp) cc_final: 0.7798 (tp) REVERT: A 759 PHE cc_start: 0.6299 (t80) cc_final: 0.5969 (t80) REVERT: B 384 LEU cc_start: 0.9249 (mt) cc_final: 0.8987 (mt) REVERT: B 398 ASP cc_start: 0.8287 (m-30) cc_final: 0.8062 (m-30) REVERT: B 458 MET cc_start: 0.7984 (ttm) cc_final: 0.7411 (ttt) REVERT: B 486 LEU cc_start: 0.9088 (mm) cc_final: 0.8868 (mm) REVERT: B 491 CYS cc_start: 0.8293 (t) cc_final: 0.7900 (p) REVERT: B 495 LYS cc_start: 0.7332 (pptt) cc_final: 0.6881 (pptt) REVERT: B 629 HIS cc_start: 0.8418 (t-90) cc_final: 0.8144 (t-90) REVERT: B 671 LEU cc_start: 0.9099 (tp) cc_final: 0.7662 (tp) REVERT: B 675 TRP cc_start: 0.8022 (m-10) cc_final: 0.7700 (m-10) REVERT: B 759 PHE cc_start: 0.6002 (t80) cc_final: 0.5782 (t80) REVERT: C 349 VAL cc_start: 0.9341 (t) cc_final: 0.9021 (p) REVERT: C 353 ASN cc_start: 0.7509 (m-40) cc_final: 0.7091 (m-40) REVERT: C 486 LEU cc_start: 0.9236 (mm) cc_final: 0.8895 (mm) REVERT: C 491 CYS cc_start: 0.8381 (t) cc_final: 0.7881 (p) REVERT: C 516 LEU cc_start: 0.9158 (tp) cc_final: 0.8882 (tp) REVERT: C 567 LYS cc_start: 0.7650 (mttt) cc_final: 0.7348 (mtpt) REVERT: C 629 HIS cc_start: 0.8625 (t70) cc_final: 0.8173 (t70) REVERT: C 759 PHE cc_start: 0.5875 (t80) cc_final: 0.5566 (t80) REVERT: D 348 ILE cc_start: 0.9382 (mp) cc_final: 0.9143 (mt) REVERT: D 486 LEU cc_start: 0.9193 (mm) cc_final: 0.8934 (mm) REVERT: D 671 LEU cc_start: 0.9080 (tp) cc_final: 0.7608 (tp) REVERT: D 675 TRP cc_start: 0.8059 (m-10) cc_final: 0.7799 (m-10) REVERT: E 371 ILE cc_start: 0.9355 (pt) cc_final: 0.9027 (pt) REVERT: E 458 MET cc_start: 0.7771 (ttm) cc_final: 0.7339 (ttm) REVERT: E 486 LEU cc_start: 0.9190 (mm) cc_final: 0.8943 (mm) REVERT: E 491 CYS cc_start: 0.8183 (t) cc_final: 0.7834 (p) REVERT: E 629 HIS cc_start: 0.8516 (t70) cc_final: 0.8262 (t-90) REVERT: F 343 GLU cc_start: 0.7703 (mp0) cc_final: 0.7361 (pm20) REVERT: F 384 LEU cc_start: 0.9266 (mt) cc_final: 0.8918 (mt) REVERT: F 490 LEU cc_start: 0.8961 (mt) cc_final: 0.8741 (mt) REVERT: F 548 HIS cc_start: 0.8231 (p-80) cc_final: 0.7926 (p90) REVERT: F 572 ASP cc_start: 0.8983 (m-30) cc_final: 0.8682 (p0) REVERT: F 597 HIS cc_start: 0.6949 (m90) cc_final: 0.6463 (m170) REVERT: F 629 HIS cc_start: 0.8488 (t-90) cc_final: 0.8109 (t-90) REVERT: F 671 LEU cc_start: 0.9158 (tp) cc_final: 0.7728 (tp) REVERT: F 675 TRP cc_start: 0.8052 (m-10) cc_final: 0.7692 (m-10) outliers start: 4 outliers final: 0 residues processed: 467 average time/residue: 0.3437 time to fit residues: 245.0847 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 : 2.569 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 89 optimal weight: 2.9990 chunk 191 optimal weight: 0.9980 chunk 236 optimal weight: 0.9990 chunk 230 optimal weight: 5.9990 chunk 24 optimal weight: 7.9990 chunk 14 optimal weight: 4.9990 chunk 76 optimal weight: 0.0060 chunk 53 optimal weight: 1.9990 chunk 252 optimal weight: 7.9990 chunk 171 optimal weight: 0.5980 chunk 208 optimal weight: 0.9990 overall best weight: 0.7200 ------------------------------------------------------------------------------- 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 D 629 HIS E 763 HIS F 593 ASN ** F 597 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4339 r_free = 0.4339 target = 0.146330 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.103386 restraints weight = 63726.135| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.105746 restraints weight = 38405.848| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.107306 restraints weight = 27661.569| |-----------------------------------------------------------------------------| r_work (final): 0.3704 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7367 moved from start: 0.4156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 22356 Z= 0.118 Angle : 0.545 9.171 30180 Z= 0.281 Chirality : 0.041 0.148 3390 Planarity : 0.004 0.063 3816 Dihedral : 4.174 16.533 2922 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 13.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 0.16 % Allowed : 1.89 % Favored : 97.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.58 (0.16), residues: 2670 helix: 0.33 (0.15), residues: 1128 sheet: -1.97 (0.28), residues: 342 loop : -0.42 (0.18), residues: 1200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 675 HIS 0.004 0.001 HIS A 548 PHE 0.024 0.002 PHE E 554 TYR 0.021 0.001 TYR F 699 ARG 0.010 0.000 ARG A 663 Details of bonding type rmsd hydrogen bonds : bond 0.03335 ( 894) hydrogen bonds : angle 4.75314 ( 2538) covalent geometry : bond 0.00271 (22356) covalent geometry : angle 0.54477 (30180) *********************** 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 460 residues out of total 2484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 456 time to evaluate : 2.714 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 327 PHE cc_start: 0.8536 (t80) cc_final: 0.8218 (t80) REVERT: A 486 LEU cc_start: 0.9107 (mm) cc_final: 0.8854 (mm) REVERT: A 491 CYS cc_start: 0.8158 (t) cc_final: 0.7826 (p) REVERT: A 597 HIS cc_start: 0.6631 (m170) cc_final: 0.6294 (m170) REVERT: A 671 LEU cc_start: 0.9069 (tp) cc_final: 0.7826 (tp) REVERT: A 759 PHE cc_start: 0.6390 (t80) cc_final: 0.6091 (t80) REVERT: B 384 LEU cc_start: 0.9257 (mt) cc_final: 0.8974 (mt) REVERT: B 398 ASP cc_start: 0.8256 (m-30) cc_final: 0.8045 (m-30) REVERT: B 458 MET cc_start: 0.8000 (ttm) cc_final: 0.7426 (ttt) REVERT: B 486 LEU cc_start: 0.9088 (mm) cc_final: 0.8878 (mm) REVERT: B 491 CYS cc_start: 0.8278 (t) cc_final: 0.7867 (p) REVERT: B 495 LYS cc_start: 0.7259 (pptt) cc_final: 0.6836 (pptt) REVERT: B 499 THR cc_start: 0.7317 (t) cc_final: 0.7016 (t) REVERT: B 548 HIS cc_start: 0.8297 (p-80) cc_final: 0.8064 (p-80) REVERT: B 629 HIS cc_start: 0.8636 (t-90) cc_final: 0.8305 (t-90) REVERT: B 671 LEU cc_start: 0.9111 (tp) cc_final: 0.7669 (tp) REVERT: B 675 TRP cc_start: 0.8037 (m-10) cc_final: 0.7711 (m-10) REVERT: C 349 VAL cc_start: 0.9327 (t) cc_final: 0.9014 (p) REVERT: C 353 ASN cc_start: 0.7496 (m-40) cc_final: 0.6893 (m-40) REVERT: C 359 SER cc_start: 0.8740 (p) cc_final: 0.8531 (p) REVERT: C 482 TYR cc_start: 0.8654 (t80) cc_final: 0.8381 (t80) REVERT: C 486 LEU cc_start: 0.9047 (mm) cc_final: 0.8496 (mm) REVERT: C 499 THR cc_start: 0.7002 (t) cc_final: 0.6758 (t) REVERT: C 567 LYS cc_start: 0.7650 (mttt) cc_final: 0.7338 (mtpt) REVERT: C 618 MET cc_start: 0.7939 (tmm) cc_final: 0.7619 (tmm) REVERT: C 629 HIS cc_start: 0.8701 (t70) cc_final: 0.8139 (t70) REVERT: C 759 PHE cc_start: 0.5831 (t80) cc_final: 0.5589 (t80) REVERT: D 348 ILE cc_start: 0.9355 (mp) cc_final: 0.9100 (mt) REVERT: D 398 ASP cc_start: 0.8268 (m-30) cc_final: 0.8007 (m-30) REVERT: D 486 LEU cc_start: 0.9325 (mm) cc_final: 0.9024 (mm) REVERT: D 500 PHE cc_start: 0.8381 (m-80) cc_final: 0.8127 (m-80) REVERT: D 531 ILE cc_start: 0.7918 (mm) cc_final: 0.7446 (tt) REVERT: D 671 LEU cc_start: 0.9128 (tp) cc_final: 0.7633 (tp) REVERT: D 675 TRP cc_start: 0.8005 (m-10) cc_final: 0.7732 (m-10) REVERT: D 759 PHE cc_start: 0.6313 (t80) cc_final: 0.6032 (t80) REVERT: E 486 LEU cc_start: 0.9171 (mm) cc_final: 0.8653 (mm) REVERT: E 491 CYS cc_start: 0.8329 (t) cc_final: 0.7955 (p) REVERT: E 501 PHE cc_start: 0.9073 (m-10) cc_final: 0.8784 (m-80) REVERT: E 629 HIS cc_start: 0.8575 (t70) cc_final: 0.8343 (t-90) REVERT: E 759 PHE cc_start: 0.6685 (t80) cc_final: 0.6368 (t80) REVERT: F 343 GLU cc_start: 0.7739 (mp0) cc_final: 0.7477 (pm20) REVERT: F 384 LEU cc_start: 0.9274 (mt) cc_final: 0.8893 (mt) REVERT: F 572 ASP cc_start: 0.8966 (m-30) cc_final: 0.8686 (p0) REVERT: F 597 HIS cc_start: 0.6911 (m90) cc_final: 0.6532 (m170) REVERT: F 629 HIS cc_start: 0.8498 (t-90) cc_final: 0.8100 (t-90) REVERT: F 671 LEU cc_start: 0.9149 (tp) cc_final: 0.7740 (tp) REVERT: F 675 TRP cc_start: 0.8078 (m-10) cc_final: 0.7713 (m-10) outliers start: 4 outliers final: 0 residues processed: 460 average time/residue: 0.3583 time to fit residues: 252.9972 Evaluate side-chains 334 residues out of total 2484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 334 time to evaluate : 2.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 72 optimal weight: 8.9990 chunk 82 optimal weight: 10.0000 chunk 22 optimal weight: 0.9980 chunk 253 optimal weight: 6.9990 chunk 12 optimal weight: 4.9990 chunk 95 optimal weight: 0.5980 chunk 182 optimal weight: 0.7980 chunk 256 optimal weight: 0.9980 chunk 11 optimal weight: 0.5980 chunk 249 optimal weight: 2.9990 chunk 130 optimal weight: 10.0000 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 D 629 HIS E 763 HIS F 593 ASN ** F 597 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4336 r_free = 0.4336 target = 0.146316 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.103387 restraints weight = 62661.008| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.105796 restraints weight = 37811.449| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.107340 restraints weight = 27438.705| |-----------------------------------------------------------------------------| r_work (final): 0.3705 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7367 moved from start: 0.4352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 22356 Z= 0.120 Angle : 0.560 9.120 30180 Z= 0.285 Chirality : 0.042 0.168 3390 Planarity : 0.004 0.050 3816 Dihedral : 4.160 17.170 2922 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 13.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 0.16 % Allowed : 1.13 % Favored : 98.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.48 (0.16), residues: 2670 helix: 0.39 (0.15), residues: 1128 sheet: -1.84 (0.28), residues: 342 loop : -0.38 (0.18), residues: 1200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 355 HIS 0.005 0.001 HIS E 548 PHE 0.030 0.002 PHE B 554 TYR 0.018 0.001 TYR F 606 ARG 0.005 0.000 ARG E 625 Details of bonding type rmsd hydrogen bonds : bond 0.03306 ( 894) hydrogen bonds : angle 4.80231 ( 2538) covalent geometry : bond 0.00276 (22356) covalent geometry : angle 0.55998 (30180) *********************** 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 : 2.324 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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: 0.8499 (t80) cc_final: 0.8187 (t80) REVERT: A 486 LEU cc_start: 0.9062 (mm) cc_final: 0.8718 (mm) REVERT: A 491 CYS cc_start: 0.8152 (t) cc_final: 0.7798 (p) REVERT: A 597 HIS cc_start: 0.6606 (m170) cc_final: 0.6314 (m-70) REVERT: A 618 MET cc_start: 0.7075 (tmm) cc_final: 0.6617 (mtp) REVERT: A 671 LEU cc_start: 0.9070 (tp) cc_final: 0.7848 (tp) REVERT: A 759 PHE cc_start: 0.6358 (t80) cc_final: 0.6068 (t80) REVERT: B 384 LEU cc_start: 0.9259 (mt) cc_final: 0.8881 (mt) REVERT: B 458 MET cc_start: 0.7959 (ttm) cc_final: 0.7458 (ttt) REVERT: B 486 LEU cc_start: 0.9124 (mm) cc_final: 0.8877 (mm) REVERT: B 495 LYS cc_start: 0.7276 (pptt) cc_final: 0.6738 (pptt) REVERT: B 671 LEU cc_start: 0.9103 (tp) cc_final: 0.7671 (tp) REVERT: B 675 TRP cc_start: 0.8034 (m-10) cc_final: 0.7720 (m-10) REVERT: C 359 SER cc_start: 0.8689 (p) cc_final: 0.8451 (p) REVERT: C 371 ILE cc_start: 0.9235 (pt) cc_final: 0.8953 (pt) REVERT: C 482 TYR cc_start: 0.8613 (t80) cc_final: 0.8324 (t80) REVERT: C 486 LEU cc_start: 0.9079 (mm) cc_final: 0.8527 (mm) REVERT: C 531 ILE cc_start: 0.8124 (mm) cc_final: 0.7861 (mm) REVERT: C 548 HIS cc_start: 0.8137 (p-80) cc_final: 0.7915 (p-80) REVERT: C 567 LYS cc_start: 0.7646 (mttt) cc_final: 0.7363 (mtpt) REVERT: C 618 MET cc_start: 0.7999 (tmm) cc_final: 0.7634 (tmm) REVERT: C 629 HIS cc_start: 0.8711 (t70) cc_final: 0.8267 (t70) REVERT: C 759 PHE cc_start: 0.5805 (t80) cc_final: 0.5596 (t80) REVERT: D 348 ILE cc_start: 0.9262 (mp) cc_final: 0.9058 (mp) REVERT: D 398 ASP cc_start: 0.8283 (m-30) cc_final: 0.8072 (m-30) REVERT: D 486 LEU cc_start: 0.9300 (mm) cc_final: 0.9003 (mm) REVERT: D 500 PHE cc_start: 0.8387 (m-80) cc_final: 0.8177 (m-80) REVERT: D 531 ILE cc_start: 0.7813 (mm) cc_final: 0.7402 (tt) REVERT: D 548 HIS cc_start: 0.8174 (p-80) cc_final: 0.7721 (p-80) REVERT: D 597 HIS cc_start: 0.6509 (m170) cc_final: 0.6162 (m170) REVERT: D 671 LEU cc_start: 0.9129 (tp) cc_final: 0.7768 (tp) REVERT: D 675 TRP cc_start: 0.8022 (m-10) cc_final: 0.7581 (m-10) REVERT: D 759 PHE cc_start: 0.6299 (t80) cc_final: 0.6025 (t80) REVERT: E 393 GLU cc_start: 0.8402 (tm-30) cc_final: 0.8127 (tm-30) REVERT: E 501 PHE cc_start: 0.9036 (m-10) cc_final: 0.8814 (m-80) REVERT: E 625 ARG cc_start: 0.8192 (tpt90) cc_final: 0.7927 (tpt170) REVERT: E 759 PHE cc_start: 0.6625 (t80) cc_final: 0.6387 (t80) REVERT: F 343 GLU cc_start: 0.7675 (mp0) cc_final: 0.7448 (pm20) REVERT: F 384 LEU cc_start: 0.9281 (mt) cc_final: 0.8881 (mt) REVERT: F 499 THR cc_start: 0.7306 (t) cc_final: 0.6971 (t) REVERT: F 572 ASP cc_start: 0.8974 (m-30) cc_final: 0.8693 (p0) REVERT: F 597 HIS cc_start: 0.6823 (m90) cc_final: 0.6436 (m170) REVERT: F 615 ASN cc_start: 0.7512 (t0) cc_final: 0.7286 (t0) REVERT: F 671 LEU cc_start: 0.9104 (tp) cc_final: 0.7667 (tp) REVERT: F 675 TRP cc_start: 0.8055 (m-10) cc_final: 0.7682 (m-10) outliers start: 4 outliers final: 0 residues processed: 446 average time/residue: 0.3297 time to fit residues: 226.2350 Evaluate side-chains 334 residues out of total 2484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 334 time to evaluate : 2.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 32 optimal weight: 4.9990 chunk 179 optimal weight: 0.0020 chunk 260 optimal weight: 10.0000 chunk 160 optimal weight: 3.9990 chunk 218 optimal weight: 10.0000 chunk 34 optimal weight: 0.9990 chunk 39 optimal weight: 10.0000 chunk 82 optimal weight: 10.0000 chunk 48 optimal weight: 0.9990 chunk 262 optimal weight: 8.9990 chunk 214 optimal weight: 0.8980 overall best weight: 1.3794 ------------------------------------------------------------------------------- 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** ** 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 = 0.4319 r_free = 0.4319 target = 0.145088 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.101863 restraints weight = 63737.160| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.104269 restraints weight = 38030.119| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.105835 restraints weight = 27616.624| |-----------------------------------------------------------------------------| r_work (final): 0.3678 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7414 moved from start: 0.4516 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= 0.145 Angle : 0.573 8.935 30180 Z= 0.290 Chirality : 0.042 0.192 3390 Planarity : 0.004 0.034 3816 Dihedral : 4.252 19.019 2922 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 14.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 0.16 % Allowed : 0.76 % Favored : 99.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.49 (0.16), residues: 2670 helix: 0.32 (0.15), residues: 1128 sheet: -1.73 (0.29), residues: 342 loop : -0.35 (0.18), residues: 1200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 675 HIS 0.005 0.001 HIS A 548 PHE 0.043 0.002 PHE F 554 TYR 0.018 0.001 TYR F 606 ARG 0.003 0.000 ARG B 344 Details of bonding type rmsd hydrogen bonds : bond 0.03251 ( 894) hydrogen bonds : angle 4.82487 ( 2538) covalent geometry : bond 0.00329 (22356) covalent geometry : angle 0.57313 (30180) *********************** 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 429 residues out of total 2484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 425 time to evaluate : 2.706 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 327 PHE cc_start: 0.8538 (t80) cc_final: 0.8188 (t80) REVERT: A 491 CYS cc_start: 0.8200 (t) cc_final: 0.7773 (p) REVERT: A 501 PHE cc_start: 0.9022 (m-80) cc_final: 0.8457 (m-80) REVERT: A 597 HIS cc_start: 0.6611 (m170) cc_final: 0.6318 (m-70) REVERT: A 618 MET cc_start: 0.7436 (tmm) cc_final: 0.6855 (mtp) REVERT: A 671 LEU cc_start: 0.9131 (tp) cc_final: 0.7960 (tp) REVERT: A 759 PHE cc_start: 0.6327 (t80) cc_final: 0.6044 (t80) REVERT: B 384 LEU cc_start: 0.9316 (mt) cc_final: 0.9015 (mt) REVERT: B 398 ASP cc_start: 0.8213 (m-30) cc_final: 0.7963 (m-30) REVERT: B 486 LEU cc_start: 0.8907 (mm) cc_final: 0.8679 (mm) REVERT: B 499 THR cc_start: 0.7282 (t) cc_final: 0.6957 (t) REVERT: B 671 LEU cc_start: 0.9133 (tp) cc_final: 0.8188 (tp) REVERT: B 675 TRP cc_start: 0.8079 (m-10) cc_final: 0.7769 (m-10) REVERT: C 371 ILE cc_start: 0.9244 (pt) cc_final: 0.8756 (pt) REVERT: C 482 TYR cc_start: 0.8685 (t80) cc_final: 0.8480 (t80) REVERT: C 501 PHE cc_start: 0.9158 (m-10) cc_final: 0.8913 (m-10) REVERT: C 525 VAL cc_start: 0.8994 (p) cc_final: 0.8664 (m) REVERT: C 567 LYS cc_start: 0.7601 (mttt) cc_final: 0.7287 (mtpt) REVERT: C 618 MET cc_start: 0.7996 (tmm) cc_final: 0.7670 (tmm) REVERT: C 629 HIS cc_start: 0.8752 (t70) cc_final: 0.8322 (t70) REVERT: C 759 PHE cc_start: 0.5810 (t80) cc_final: 0.5535 (t80) REVERT: D 398 ASP cc_start: 0.8250 (m-30) cc_final: 0.8033 (m-30) REVERT: D 486 LEU cc_start: 0.9327 (mm) cc_final: 0.8957 (mm) REVERT: D 500 PHE cc_start: 0.8348 (m-80) cc_final: 0.8125 (m-80) REVERT: D 671 LEU cc_start: 0.9110 (tp) cc_final: 0.7753 (tp) REVERT: D 675 TRP cc_start: 0.8063 (m-10) cc_final: 0.7580 (m-10) REVERT: D 759 PHE cc_start: 0.6305 (t80) cc_final: 0.6059 (t80) REVERT: E 393 GLU cc_start: 0.8430 (tm-30) cc_final: 0.8044 (tm-30) REVERT: E 759 PHE cc_start: 0.6476 (t80) cc_final: 0.6113 (t80) REVERT: F 384 LEU cc_start: 0.9324 (mt) cc_final: 0.8929 (mt) REVERT: F 499 THR cc_start: 0.7286 (t) cc_final: 0.6946 (t) REVERT: F 517 LYS cc_start: 0.9097 (tptm) cc_final: 0.8820 (tptp) REVERT: F 551 ARG cc_start: 0.7290 (tpp-160) cc_final: 0.7038 (mmt180) REVERT: F 572 ASP cc_start: 0.8980 (m-30) cc_final: 0.8722 (p0) REVERT: F 597 HIS cc_start: 0.6878 (m90) cc_final: 0.6444 (m170) REVERT: F 615 ASN cc_start: 0.7577 (t0) cc_final: 0.7255 (t0) REVERT: F 671 LEU cc_start: 0.9167 (tp) cc_final: 0.7827 (tp) REVERT: F 675 TRP cc_start: 0.8128 (m-10) cc_final: 0.7733 (m-10) outliers start: 4 outliers final: 0 residues processed: 429 average time/residue: 0.3264 time to fit residues: 217.5405 Evaluate side-chains 325 residues out of total 2484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 325 time to evaluate : 2.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 6 optimal weight: 0.7980 chunk 101 optimal weight: 2.9990 chunk 176 optimal weight: 0.6980 chunk 98 optimal weight: 4.9990 chunk 259 optimal weight: 0.9990 chunk 183 optimal weight: 0.5980 chunk 203 optimal weight: 0.9980 chunk 50 optimal weight: 0.8980 chunk 115 optimal weight: 5.9990 chunk 196 optimal weight: 4.9990 chunk 182 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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** ** C 573 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 593 ASN ** C 597 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 593 ASN F 593 ASN ** F 597 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4325 r_free = 0.4325 target = 0.145645 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.102968 restraints weight = 63470.533| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.105438 restraints weight = 37638.487| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.107024 restraints weight = 27230.472| |-----------------------------------------------------------------------------| r_work (final): 0.3701 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7381 moved from start: 0.4653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 22356 Z= 0.119 Angle : 0.563 9.672 30180 Z= 0.285 Chirality : 0.042 0.181 3390 Planarity : 0.004 0.036 3816 Dihedral : 4.194 20.635 2922 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 13.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 0.16 % Allowed : 0.72 % Favored : 99.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.39 (0.16), residues: 2670 helix: 0.35 (0.15), residues: 1128 sheet: -0.99 (0.32), residues: 288 loop : -0.52 (0.17), residues: 1254 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 675 HIS 0.005 0.001 HIS F 548 PHE 0.034 0.002 PHE E 501 TYR 0.020 0.001 TYR B 482 ARG 0.007 0.000 ARG E 625 Details of bonding type rmsd hydrogen bonds : bond 0.03190 ( 894) hydrogen bonds : angle 4.75790 ( 2538) covalent geometry : bond 0.00279 (22356) covalent geometry : angle 0.56277 (30180) *********************** 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 444 residues out of total 2484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 440 time to evaluate : 2.657 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: A 327 PHE cc_start: 0.8478 (t80) cc_final: 0.8062 (t80) REVERT: A 484 LYS cc_start: 0.8889 (mtmt) cc_final: 0.8634 (mttp) REVERT: A 491 CYS cc_start: 0.8204 (t) cc_final: 0.7772 (p) REVERT: A 597 HIS cc_start: 0.6667 (m170) cc_final: 0.6372 (m-70) REVERT: A 618 MET cc_start: 0.7482 (tmm) cc_final: 0.6825 (mtp) REVERT: A 671 LEU cc_start: 0.9103 (tp) cc_final: 0.7768 (tp) REVERT: A 675 TRP cc_start: 0.8022 (m-10) cc_final: 0.7662 (m-10) REVERT: A 759 PHE cc_start: 0.6314 (t80) cc_final: 0.6030 (t80) REVERT: B 384 LEU cc_start: 0.9310 (mt) cc_final: 0.8983 (mt) REVERT: B 398 ASP cc_start: 0.8288 (m-30) cc_final: 0.7988 (m-30) REVERT: B 486 LEU cc_start: 0.8829 (mm) cc_final: 0.8536 (mm) REVERT: B 615 ASN cc_start: 0.8059 (t0) cc_final: 0.7817 (t0) REVERT: B 618 MET cc_start: 0.7724 (tmm) cc_final: 0.7332 (mtp) REVERT: B 626 PHE cc_start: 0.4682 (m-80) cc_final: 0.4402 (m-80) REVERT: B 671 LEU cc_start: 0.9185 (tp) cc_final: 0.8280 (tp) REVERT: B 675 TRP cc_start: 0.8081 (m-10) cc_final: 0.7791 (m-10) REVERT: C 458 MET cc_start: 0.7638 (ptt) cc_final: 0.6579 (ptt) REVERT: C 501 PHE cc_start: 0.9128 (m-10) cc_final: 0.8909 (m-10) REVERT: C 567 LYS cc_start: 0.7683 (mttt) cc_final: 0.7386 (mtpt) REVERT: C 618 MET cc_start: 0.8065 (tmm) cc_final: 0.7701 (tmm) REVERT: C 629 HIS cc_start: 0.8700 (t70) cc_final: 0.8355 (t70) REVERT: C 759 PHE cc_start: 0.5783 (t80) cc_final: 0.5577 (t80) REVERT: D 398 ASP cc_start: 0.8254 (m-30) cc_final: 0.8052 (m-30) REVERT: D 486 LEU cc_start: 0.9426 (mm) cc_final: 0.9192 (mm) REVERT: D 500 PHE cc_start: 0.8300 (m-80) cc_final: 0.8097 (m-80) REVERT: D 597 HIS cc_start: 0.6433 (m170) cc_final: 0.6079 (m170) REVERT: D 671 LEU cc_start: 0.9083 (tp) cc_final: 0.7713 (tp) REVERT: D 675 TRP cc_start: 0.8046 (m-10) cc_final: 0.7548 (m-10) REVERT: D 759 PHE cc_start: 0.6273 (t80) cc_final: 0.6009 (t80) REVERT: E 393 GLU cc_start: 0.8407 (tm-30) cc_final: 0.8164 (tm-30) REVERT: E 491 CYS cc_start: 0.8180 (t) cc_final: 0.7886 (p) REVERT: E 548 HIS cc_start: 0.8008 (p90) cc_final: 0.7550 (p-80) REVERT: E 618 MET cc_start: 0.7824 (tmm) cc_final: 0.7296 (mtp) REVERT: E 625 ARG cc_start: 0.7952 (tpt90) cc_final: 0.7649 (tpt170) REVERT: E 759 PHE cc_start: 0.6224 (t80) cc_final: 0.6003 (t80) REVERT: F 384 LEU cc_start: 0.9281 (mt) cc_final: 0.8783 (mt) REVERT: F 572 ASP cc_start: 0.8954 (m-30) cc_final: 0.8705 (p0) REVERT: F 597 HIS cc_start: 0.6941 (m90) cc_final: 0.6473 (m170) REVERT: F 615 ASN cc_start: 0.7526 (t0) cc_final: 0.7185 (t0) REVERT: F 671 LEU cc_start: 0.9115 (tp) cc_final: 0.7728 (tp) REVERT: F 675 TRP cc_start: 0.8113 (m-10) cc_final: 0.7723 (m-10) outliers start: 4 outliers final: 0 residues processed: 444 average time/residue: 0.3324 time to fit residues: 229.7450 Evaluate side-chains 339 residues out of total 2484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 339 time to evaluate : 2.542 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 26 optimal weight: 3.9990 chunk 21 optimal weight: 0.9990 chunk 199 optimal weight: 10.0000 chunk 71 optimal weight: 0.8980 chunk 253 optimal weight: 5.9990 chunk 230 optimal weight: 4.9990 chunk 158 optimal weight: 2.9990 chunk 63 optimal weight: 1.9990 chunk 191 optimal weight: 0.8980 chunk 86 optimal weight: 8.9990 chunk 130 optimal weight: 2.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- 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** C 548 HIS ** C 573 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 593 ASN ** C 597 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 593 ASN F 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 = 0.4311 r_free = 0.4311 target = 0.144212 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.101122 restraints weight = 63854.784| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.103522 restraints weight = 38016.438| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.105048 restraints weight = 27427.780| |-----------------------------------------------------------------------------| r_work (final): 0.3668 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7430 moved from start: 0.4788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 22356 Z= 0.160 Angle : 0.608 9.155 30180 Z= 0.305 Chirality : 0.042 0.201 3390 Planarity : 0.004 0.031 3816 Dihedral : 4.309 19.907 2922 Min Nonbonded Distance : 2.309 Molprobity Statistics. All-atom Clashscore : 15.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 0.16 % Allowed : 0.48 % Favored : 99.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.48 (0.16), residues: 2670 helix: 0.31 (0.15), residues: 1122 sheet: -1.69 (0.29), residues: 342 loop : -0.33 (0.18), residues: 1206 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 355 HIS 0.006 0.001 HIS D 548 PHE 0.039 0.002 PHE E 501 TYR 0.040 0.001 TYR A 670 ARG 0.005 0.000 ARG E 625 Details of bonding type rmsd hydrogen bonds : bond 0.03282 ( 894) hydrogen bonds : angle 4.83592 ( 2538) covalent geometry : bond 0.00364 (22356) covalent geometry : angle 0.60814 (30180) *********************** 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 421 residues out of total 2484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 417 time to evaluate : 2.662 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 327 PHE cc_start: 0.8460 (t80) cc_final: 0.8028 (t80) REVERT: A 343 GLU cc_start: 0.6925 (mp0) cc_final: 0.6520 (pm20) REVERT: A 481 LEU cc_start: 0.8732 (mt) cc_final: 0.8124 (mt) REVERT: A 484 LYS cc_start: 0.8890 (mtmt) cc_final: 0.8457 (mtmt) REVERT: A 491 CYS cc_start: 0.8182 (t) cc_final: 0.7834 (p) REVERT: A 597 HIS cc_start: 0.6651 (m170) cc_final: 0.6364 (m-70) REVERT: A 618 MET cc_start: 0.7482 (tmm) cc_final: 0.6883 (mtp) REVERT: A 671 LEU cc_start: 0.9097 (tp) cc_final: 0.7755 (tp) REVERT: A 675 TRP cc_start: 0.7997 (m-10) cc_final: 0.7717 (m-10) REVERT: A 759 PHE cc_start: 0.6349 (t80) cc_final: 0.5986 (t80) REVERT: B 384 LEU cc_start: 0.9351 (mt) cc_final: 0.9029 (mt) REVERT: B 398 ASP cc_start: 0.8304 (m-30) cc_final: 0.8085 (m-30) REVERT: B 484 LYS cc_start: 0.8848 (mtmt) cc_final: 0.8642 (mtmm) REVERT: B 615 ASN cc_start: 0.8116 (t0) cc_final: 0.7838 (t0) REVERT: B 618 MET cc_start: 0.7757 (tmm) cc_final: 0.7342 (mtp) REVERT: B 671 LEU cc_start: 0.9185 (tp) cc_final: 0.8254 (tp) REVERT: B 675 TRP cc_start: 0.8134 (m-10) cc_final: 0.7902 (m-10) REVERT: C 458 MET cc_start: 0.7190 (ptt) cc_final: 0.6742 (ptt) REVERT: C 567 LYS cc_start: 0.7702 (mttt) cc_final: 0.7383 (mtpt) REVERT: C 618 MET cc_start: 0.8027 (tmm) cc_final: 0.7683 (tmm) REVERT: C 629 HIS cc_start: 0.8801 (t70) cc_final: 0.8443 (t70) REVERT: C 759 PHE cc_start: 0.5791 (t80) cc_final: 0.5566 (t80) REVERT: D 486 LEU cc_start: 0.9380 (mm) cc_final: 0.9066 (mm) REVERT: D 671 LEU cc_start: 0.9047 (tp) cc_final: 0.7554 (tp) REVERT: D 675 TRP cc_start: 0.8107 (m-10) cc_final: 0.7804 (m-10) REVERT: D 759 PHE cc_start: 0.6340 (t80) cc_final: 0.6051 (t80) REVERT: E 393 GLU cc_start: 0.8421 (tm-30) cc_final: 0.8099 (tm-30) REVERT: E 491 CYS cc_start: 0.8186 (t) cc_final: 0.7886 (p) REVERT: E 548 HIS cc_start: 0.8140 (p90) cc_final: 0.7720 (p-80) REVERT: E 625 ARG cc_start: 0.7841 (tpt90) cc_final: 0.7638 (tpt170) REVERT: F 384 LEU cc_start: 0.9350 (mt) cc_final: 0.8863 (mt) REVERT: F 517 LYS cc_start: 0.9115 (tptm) cc_final: 0.8833 (tptp) REVERT: F 533 THR cc_start: 0.8528 (p) cc_final: 0.7842 (p) REVERT: F 567 LYS cc_start: 0.7456 (mtpt) cc_final: 0.6838 (ttpt) REVERT: F 572 ASP cc_start: 0.8969 (m-30) cc_final: 0.8703 (p0) REVERT: F 597 HIS cc_start: 0.7023 (m90) cc_final: 0.6491 (m170) REVERT: F 615 ASN cc_start: 0.7545 (t0) cc_final: 0.7163 (t0) REVERT: F 671 LEU cc_start: 0.9165 (tp) cc_final: 0.7789 (tp) REVERT: F 675 TRP cc_start: 0.8119 (m-10) cc_final: 0.7711 (m-10) outliers start: 4 outliers final: 0 residues processed: 421 average time/residue: 0.3496 time to fit residues: 230.0284 Evaluate side-chains 325 residues out of total 2484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 325 time to evaluate : 3.238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 245 optimal weight: 7.9990 chunk 232 optimal weight: 5.9990 chunk 111 optimal weight: 0.9980 chunk 79 optimal weight: 20.0000 chunk 102 optimal weight: 5.9990 chunk 238 optimal weight: 2.9990 chunk 25 optimal weight: 0.7980 chunk 2 optimal weight: 0.9980 chunk 100 optimal weight: 4.9990 chunk 249 optimal weight: 2.9990 chunk 226 optimal weight: 0.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- 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 = 0.4312 r_free = 0.4312 target = 0.144474 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.101647 restraints weight = 63763.992| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.104091 restraints weight = 37967.436| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.105667 restraints weight = 27337.312| |-----------------------------------------------------------------------------| r_work (final): 0.3677 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7418 moved from start: 0.4915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 22356 Z= 0.148 Angle : 0.597 8.983 30180 Z= 0.299 Chirality : 0.043 0.209 3390 Planarity : 0.004 0.038 3816 Dihedral : 4.318 19.091 2922 Min Nonbonded Distance : 2.296 Molprobity Statistics. All-atom Clashscore : 15.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 0.16 % Allowed : 0.24 % Favored : 99.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.51 (0.16), residues: 2670 helix: 0.27 (0.15), residues: 1122 sheet: -1.66 (0.29), residues: 336 loop : -0.35 (0.18), residues: 1212 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 675 HIS 0.006 0.001 HIS D 548 PHE 0.035 0.002 PHE B 554 TYR 0.025 0.001 TYR A 670 ARG 0.004 0.000 ARG D 612 Details of bonding type rmsd hydrogen bonds : bond 0.03235 ( 894) hydrogen bonds : angle 4.83347 ( 2538) covalent geometry : bond 0.00339 (22356) covalent geometry : angle 0.59718 (30180) ********************** 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 419 residues out of total 2484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 415 time to evaluate : 2.636 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: 0.8482 (t80) cc_final: 0.8053 (t80) REVERT: A 343 GLU cc_start: 0.6902 (mp0) cc_final: 0.6513 (pm20) REVERT: A 384 LEU cc_start: 0.9296 (mt) cc_final: 0.9047 (tp) REVERT: A 481 LEU cc_start: 0.8701 (mt) cc_final: 0.8067 (mt) REVERT: A 484 LYS cc_start: 0.8877 (mtmt) cc_final: 0.8465 (mtmt) REVERT: A 491 CYS cc_start: 0.7810 (t) cc_final: 0.7539 (p) REVERT: A 495 LYS cc_start: 0.7289 (pptt) cc_final: 0.7028 (pptt) REVERT: A 525 VAL cc_start: 0.9125 (p) cc_final: 0.8826 (m) REVERT: A 597 HIS cc_start: 0.6605 (m170) cc_final: 0.6362 (m-70) REVERT: A 618 MET cc_start: 0.7455 (tmm) cc_final: 0.6899 (mtp) REVERT: A 671 LEU cc_start: 0.9041 (tp) cc_final: 0.7596 (tp) REVERT: A 675 TRP cc_start: 0.8037 (m-10) cc_final: 0.7780 (m-10) REVERT: A 759 PHE cc_start: 0.6369 (t80) cc_final: 0.6147 (t80) REVERT: B 384 LEU cc_start: 0.9353 (mt) cc_final: 0.9026 (mt) REVERT: B 398 ASP cc_start: 0.8243 (m-30) cc_final: 0.7980 (m-30) REVERT: B 491 CYS cc_start: 0.8093 (t) cc_final: 0.7752 (p) REVERT: B 615 ASN cc_start: 0.8064 (t0) cc_final: 0.7826 (t0) REVERT: B 618 MET cc_start: 0.7833 (tmm) cc_final: 0.7415 (mtp) REVERT: B 671 LEU cc_start: 0.9177 (tp) cc_final: 0.8266 (tp) REVERT: B 675 TRP cc_start: 0.8163 (m-10) cc_final: 0.7900 (m-10) REVERT: C 567 LYS cc_start: 0.7682 (mttt) cc_final: 0.7432 (mtpt) REVERT: C 618 MET cc_start: 0.7986 (tmm) cc_final: 0.7680 (tmm) REVERT: C 629 HIS cc_start: 0.8747 (t70) cc_final: 0.8483 (t70) REVERT: D 398 ASP cc_start: 0.8210 (m-30) cc_final: 0.7968 (m-30) REVERT: D 486 LEU cc_start: 0.9268 (mm) cc_final: 0.8818 (mm) REVERT: D 597 HIS cc_start: 0.6420 (m170) cc_final: 0.6033 (m170) REVERT: D 618 MET cc_start: 0.7111 (tmm) cc_final: 0.6691 (mtp) REVERT: D 671 LEU cc_start: 0.9032 (tp) cc_final: 0.7547 (tp) REVERT: D 675 TRP cc_start: 0.8162 (m-10) cc_final: 0.7817 (m-10) REVERT: D 759 PHE cc_start: 0.6345 (t80) cc_final: 0.6024 (t80) REVERT: E 384 LEU cc_start: 0.9150 (mt) cc_final: 0.8866 (tp) REVERT: E 393 GLU cc_start: 0.8451 (tm-30) cc_final: 0.8081 (tm-30) REVERT: E 491 CYS cc_start: 0.8179 (t) cc_final: 0.7852 (p) REVERT: E 548 HIS cc_start: 0.8194 (p90) cc_final: 0.7754 (p-80) REVERT: F 384 LEU cc_start: 0.9352 (mt) cc_final: 0.8842 (mt) REVERT: F 517 LYS cc_start: 0.9128 (tptm) cc_final: 0.8798 (tptp) REVERT: F 533 THR cc_start: 0.8554 (p) cc_final: 0.7887 (p) REVERT: F 567 LYS cc_start: 0.7394 (mtpt) cc_final: 0.6783 (ttpt) REVERT: F 572 ASP cc_start: 0.8969 (m-30) cc_final: 0.8712 (p0) REVERT: F 597 HIS cc_start: 0.7228 (m90) cc_final: 0.6671 (m170) REVERT: F 615 ASN cc_start: 0.7611 (t0) cc_final: 0.7207 (t0) REVERT: F 671 LEU cc_start: 0.9152 (tp) cc_final: 0.7784 (tp) REVERT: F 675 TRP cc_start: 0.8103 (m-10) cc_final: 0.7687 (m-10) outliers start: 4 outliers final: 0 residues processed: 419 average time/residue: 0.3368 time to fit residues: 221.1187 Evaluate side-chains 331 residues out of total 2484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 331 time to evaluate : 3.140 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 7 optimal weight: 0.6980 chunk 246 optimal weight: 0.5980 chunk 173 optimal weight: 0.0980 chunk 176 optimal weight: 3.9990 chunk 231 optimal weight: 3.9990 chunk 54 optimal weight: 0.0770 chunk 118 optimal weight: 1.9990 chunk 228 optimal weight: 2.9990 chunk 217 optimal weight: 8.9990 chunk 110 optimal weight: 2.9990 chunk 205 optimal weight: 0.8980 overall best weight: 0.4738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 593 ASN A 775 GLN ** C 573 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 597 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 593 ASN D 629 HIS E 775 GLN F 597 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4335 r_free = 0.4335 target = 0.146294 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.103978 restraints weight = 62775.784| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.107005 restraints weight = 40716.061| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.108342 restraints weight = 26987.875| |-----------------------------------------------------------------------------| r_work (final): 0.3716 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7374 moved from start: 0.5039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 22356 Z= 0.111 Angle : 0.569 7.792 30180 Z= 0.288 Chirality : 0.043 0.311 3390 Planarity : 0.004 0.036 3816 Dihedral : 4.207 19.638 2922 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 13.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 0.08 % Allowed : 0.28 % Favored : 99.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.36 (0.16), residues: 2670 helix: 0.34 (0.15), residues: 1128 sheet: -1.63 (0.29), residues: 342 loop : -0.19 (0.18), residues: 1200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 355 HIS 0.009 0.001 HIS B 548 PHE 0.032 0.002 PHE B 554 TYR 0.021 0.001 TYR A 670 ARG 0.012 0.000 ARG D 387 Details of bonding type rmsd hydrogen bonds : bond 0.03136 ( 894) hydrogen bonds : angle 4.80066 ( 2538) covalent geometry : bond 0.00262 (22356) covalent geometry : angle 0.56853 (30180) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8068.15 seconds wall clock time: 142 minutes 10.77 seconds (8530.77 seconds total)