Starting phenix.real_space_refine on Thu Mar 5 08:42:33 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7f5u_31467/03_2026/7f5u_31467.cif Found real_map, /net/cci-nas-00/data/ceres_data/7f5u_31467/03_2026/7f5u_31467.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/7f5u_31467/03_2026/7f5u_31467.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7f5u_31467/03_2026/7f5u_31467.map" model { file = "/net/cci-nas-00/data/ceres_data/7f5u_31467/03_2026/7f5u_31467.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7f5u_31467/03_2026/7f5u_31467.cif" } resolution = 4.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 112 5.16 5 C 12992 2.51 5 N 3668 2.21 5 O 3972 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 104 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 20744 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 5186 Number of conformers: 1 Conformer: "" Number of residues, atoms: 685, 5186 Classifications: {'peptide': 685} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 24, 'TRANS': 660} Chain breaks: 3 Restraints were copied for chains: B, C, D Time building chain proxies: 5.11, per 1000 atoms: 0.25 Number of scatterers: 20744 At special positions: 0 Unit cell: (196.1, 96.46, 92.22, 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 112 16.00 O 3972 8.00 N 3668 7.00 C 12992 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.74 Conformation dependent library (CDL) restraints added in 1.0 seconds 5416 Ramachandran restraints generated. 2708 Oldfield, 0 Emsley, 2708 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5104 Finding SS restraints... Secondary structure from input PDB file: 116 helices and 36 sheets defined 49.9% alpha, 8.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.81 Creating SS restraints... Processing helix chain 'A' and resid 51 through 56 Processing helix chain 'A' and resid 64 through 69 removed outlier: 3.612A pdb=" N ILE A 68 " --> pdb=" O GLY A 64 " (cutoff:3.500A) Processing helix chain 'A' and resid 77 through 94 Processing helix chain 'A' and resid 104 through 119 removed outlier: 3.678A pdb=" N PHE A 108 " --> pdb=" O GLY A 104 " (cutoff:3.500A) Processing helix chain 'A' and resid 124 through 128 removed outlier: 3.717A pdb=" N ASN A 128 " --> pdb=" O GLU A 125 " (cutoff:3.500A) Processing helix chain 'A' and resid 142 through 163 Processing helix chain 'A' and resid 175 through 179 Processing helix chain 'A' and resid 180 through 197 Processing helix chain 'A' and resid 232 through 245 removed outlier: 3.630A pdb=" N LEU A 236 " --> pdb=" O ASP A 232 " (cutoff:3.500A) Processing helix chain 'A' and resid 297 through 307 Processing helix chain 'A' and resid 321 through 328 Processing helix chain 'A' and resid 348 through 364 removed outlier: 3.902A pdb=" N ALA A 352 " --> pdb=" O VAL A 348 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N ALA A 364 " --> pdb=" O ARG A 360 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 384 Processing helix chain 'A' and resid 384 through 403 removed outlier: 3.522A pdb=" N LYS A 401 " --> pdb=" O ALA A 397 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N SER A 402 " --> pdb=" O GLU A 398 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 412 Processing helix chain 'A' and resid 415 through 433 Processing helix chain 'A' and resid 471 through 484 removed outlier: 4.223A pdb=" N GLN A 475 " --> pdb=" O ASP A 471 " (cutoff:3.500A) Processing helix chain 'A' and resid 495 through 513 removed outlier: 4.199A pdb=" N VAL A 513 " --> pdb=" O ALA A 509 " (cutoff:3.500A) Processing helix chain 'A' and resid 527 through 534 removed outlier: 3.508A pdb=" N LEU A 531 " --> pdb=" O GLU A 527 " (cutoff:3.500A) Processing helix chain 'A' and resid 546 through 557 Processing helix chain 'A' and resid 579 through 592 removed outlier: 3.549A pdb=" N ALA A 583 " --> pdb=" O ASP A 579 " (cutoff:3.500A) Processing helix chain 'A' and resid 609 through 613 removed outlier: 3.966A pdb=" N SER A 612 " --> pdb=" O ASP A 609 " (cutoff:3.500A) Processing helix chain 'A' and resid 614 through 626 Processing helix chain 'A' and resid 633 through 640 Processing helix chain 'A' and resid 666 through 678 Processing helix chain 'A' and resid 689 through 700 removed outlier: 3.506A pdb=" N ALA A 693 " --> pdb=" O ASN A 689 " (cutoff:3.500A) Processing helix chain 'A' and resid 710 through 714 Processing helix chain 'A' and resid 740 through 742 No H-bonds generated for 'chain 'A' and resid 740 through 742' Processing helix chain 'A' and resid 756 through 761 removed outlier: 3.604A pdb=" N ALA A 761 " --> pdb=" O ALA A 757 " (cutoff:3.500A) Processing helix chain 'B' and resid 51 through 56 Processing helix chain 'B' and resid 64 through 69 removed outlier: 3.612A pdb=" N ILE B 68 " --> pdb=" O GLY B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 77 through 94 Processing helix chain 'B' and resid 104 through 119 removed outlier: 3.678A pdb=" N PHE B 108 " --> pdb=" O GLY B 104 " (cutoff:3.500A) Processing helix chain 'B' and resid 124 through 128 removed outlier: 3.717A pdb=" N ASN B 128 " --> pdb=" O GLU B 125 " (cutoff:3.500A) Processing helix chain 'B' and resid 142 through 163 Processing helix chain 'B' and resid 175 through 179 Processing helix chain 'B' and resid 180 through 197 Processing helix chain 'B' and resid 232 through 245 removed outlier: 3.630A pdb=" N LEU B 236 " --> pdb=" O ASP B 232 " (cutoff:3.500A) Processing helix chain 'B' and resid 297 through 307 Processing helix chain 'B' and resid 321 through 328 Processing helix chain 'B' and resid 348 through 364 removed outlier: 3.902A pdb=" N ALA B 352 " --> pdb=" O VAL B 348 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N ALA B 364 " --> pdb=" O ARG B 360 " (cutoff:3.500A) Processing helix chain 'B' and resid 368 through 384 Processing helix chain 'B' and resid 384 through 403 removed outlier: 3.522A pdb=" N LYS B 401 " --> pdb=" O ALA B 397 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N SER B 402 " --> pdb=" O GLU B 398 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 412 Processing helix chain 'B' and resid 415 through 433 Processing helix chain 'B' and resid 471 through 484 removed outlier: 4.223A pdb=" N GLN B 475 " --> pdb=" O ASP B 471 " (cutoff:3.500A) Processing helix chain 'B' and resid 495 through 513 removed outlier: 4.199A pdb=" N VAL B 513 " --> pdb=" O ALA B 509 " (cutoff:3.500A) Processing helix chain 'B' and resid 527 through 534 removed outlier: 3.508A pdb=" N LEU B 531 " --> pdb=" O GLU B 527 " (cutoff:3.500A) Processing helix chain 'B' and resid 546 through 557 Processing helix chain 'B' and resid 579 through 592 removed outlier: 3.549A pdb=" N ALA B 583 " --> pdb=" O ASP B 579 " (cutoff:3.500A) Processing helix chain 'B' and resid 609 through 613 removed outlier: 3.966A pdb=" N SER B 612 " --> pdb=" O ASP B 609 " (cutoff:3.500A) Processing helix chain 'B' and resid 614 through 626 Processing helix chain 'B' and resid 633 through 640 Processing helix chain 'B' and resid 666 through 678 Processing helix chain 'B' and resid 689 through 700 removed outlier: 3.506A pdb=" N ALA B 693 " --> pdb=" O ASN B 689 " (cutoff:3.500A) Processing helix chain 'B' and resid 710 through 714 Processing helix chain 'B' and resid 740 through 742 No H-bonds generated for 'chain 'B' and resid 740 through 742' Processing helix chain 'B' and resid 756 through 761 removed outlier: 3.604A pdb=" N ALA B 761 " --> pdb=" O ALA B 757 " (cutoff:3.500A) Processing helix chain 'C' and resid 51 through 56 Processing helix chain 'C' and resid 64 through 69 removed outlier: 3.612A pdb=" N ILE C 68 " --> pdb=" O GLY C 64 " (cutoff:3.500A) Processing helix chain 'C' and resid 77 through 94 Processing helix chain 'C' and resid 104 through 119 removed outlier: 3.678A pdb=" N PHE C 108 " --> pdb=" O GLY C 104 " (cutoff:3.500A) Processing helix chain 'C' and resid 124 through 128 removed outlier: 3.717A pdb=" N ASN C 128 " --> pdb=" O GLU C 125 " (cutoff:3.500A) Processing helix chain 'C' and resid 142 through 163 Processing helix chain 'C' and resid 175 through 179 Processing helix chain 'C' and resid 180 through 197 Processing helix chain 'C' and resid 232 through 245 removed outlier: 3.630A pdb=" N LEU C 236 " --> pdb=" O ASP C 232 " (cutoff:3.500A) Processing helix chain 'C' and resid 297 through 307 Processing helix chain 'C' and resid 321 through 328 Processing helix chain 'C' and resid 348 through 364 removed outlier: 3.902A pdb=" N ALA C 352 " --> pdb=" O VAL C 348 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N ALA C 364 " --> pdb=" O ARG C 360 " (cutoff:3.500A) Processing helix chain 'C' and resid 368 through 384 Processing helix chain 'C' and resid 384 through 403 removed outlier: 3.522A pdb=" N LYS C 401 " --> pdb=" O ALA C 397 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N SER C 402 " --> pdb=" O GLU C 398 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 412 Processing helix chain 'C' and resid 415 through 433 Processing helix chain 'C' and resid 471 through 484 removed outlier: 4.223A pdb=" N GLN C 475 " --> pdb=" O ASP C 471 " (cutoff:3.500A) Processing helix chain 'C' and resid 495 through 513 removed outlier: 4.199A pdb=" N VAL C 513 " --> pdb=" O ALA C 509 " (cutoff:3.500A) Processing helix chain 'C' and resid 527 through 534 removed outlier: 3.508A pdb=" N LEU C 531 " --> pdb=" O GLU C 527 " (cutoff:3.500A) Processing helix chain 'C' and resid 546 through 557 Processing helix chain 'C' and resid 579 through 592 removed outlier: 3.549A pdb=" N ALA C 583 " --> pdb=" O ASP C 579 " (cutoff:3.500A) Processing helix chain 'C' and resid 609 through 613 removed outlier: 3.966A pdb=" N SER C 612 " --> pdb=" O ASP C 609 " (cutoff:3.500A) Processing helix chain 'C' and resid 614 through 626 Processing helix chain 'C' and resid 633 through 640 Processing helix chain 'C' and resid 666 through 678 Processing helix chain 'C' and resid 689 through 700 removed outlier: 3.506A pdb=" N ALA C 693 " --> pdb=" O ASN C 689 " (cutoff:3.500A) Processing helix chain 'C' and resid 710 through 714 Processing helix chain 'C' and resid 740 through 742 No H-bonds generated for 'chain 'C' and resid 740 through 742' Processing helix chain 'C' and resid 756 through 761 removed outlier: 3.604A pdb=" N ALA C 761 " --> pdb=" O ALA C 757 " (cutoff:3.500A) Processing helix chain 'D' and resid 51 through 56 Processing helix chain 'D' and resid 64 through 69 removed outlier: 3.612A pdb=" N ILE D 68 " --> pdb=" O GLY D 64 " (cutoff:3.500A) Processing helix chain 'D' and resid 77 through 94 Processing helix chain 'D' and resid 104 through 119 removed outlier: 3.678A pdb=" N PHE D 108 " --> pdb=" O GLY D 104 " (cutoff:3.500A) Processing helix chain 'D' and resid 124 through 128 removed outlier: 3.717A pdb=" N ASN D 128 " --> pdb=" O GLU D 125 " (cutoff:3.500A) Processing helix chain 'D' and resid 142 through 163 Processing helix chain 'D' and resid 175 through 179 Processing helix chain 'D' and resid 180 through 197 Processing helix chain 'D' and resid 232 through 245 removed outlier: 3.630A pdb=" N LEU D 236 " --> pdb=" O ASP D 232 " (cutoff:3.500A) Processing helix chain 'D' and resid 297 through 307 Processing helix chain 'D' and resid 321 through 328 Processing helix chain 'D' and resid 348 through 364 removed outlier: 3.902A pdb=" N ALA D 352 " --> pdb=" O VAL D 348 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N ALA D 364 " --> pdb=" O ARG D 360 " (cutoff:3.500A) Processing helix chain 'D' and resid 368 through 384 Processing helix chain 'D' and resid 384 through 403 removed outlier: 3.522A pdb=" N LYS D 401 " --> pdb=" O ALA D 397 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N SER D 402 " --> pdb=" O GLU D 398 " (cutoff:3.500A) Processing helix chain 'D' and resid 405 through 412 Processing helix chain 'D' and resid 415 through 433 Processing helix chain 'D' and resid 471 through 484 removed outlier: 4.223A pdb=" N GLN D 475 " --> pdb=" O ASP D 471 " (cutoff:3.500A) Processing helix chain 'D' and resid 495 through 513 removed outlier: 4.199A pdb=" N VAL D 513 " --> pdb=" O ALA D 509 " (cutoff:3.500A) Processing helix chain 'D' and resid 527 through 534 removed outlier: 3.508A pdb=" N LEU D 531 " --> pdb=" O GLU D 527 " (cutoff:3.500A) Processing helix chain 'D' and resid 546 through 557 Processing helix chain 'D' and resid 579 through 592 removed outlier: 3.549A pdb=" N ALA D 583 " --> pdb=" O ASP D 579 " (cutoff:3.500A) Processing helix chain 'D' and resid 609 through 613 removed outlier: 3.966A pdb=" N SER D 612 " --> pdb=" O ASP D 609 " (cutoff:3.500A) Processing helix chain 'D' and resid 614 through 626 Processing helix chain 'D' and resid 633 through 640 Processing helix chain 'D' and resid 666 through 678 Processing helix chain 'D' and resid 689 through 700 removed outlier: 3.506A pdb=" N ALA D 693 " --> pdb=" O ASN D 689 " (cutoff:3.500A) Processing helix chain 'D' and resid 710 through 714 Processing helix chain 'D' and resid 740 through 742 No H-bonds generated for 'chain 'D' and resid 740 through 742' Processing helix chain 'D' and resid 756 through 761 removed outlier: 3.604A pdb=" N ALA D 761 " --> pdb=" O ALA D 757 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 58 through 59 Processing sheet with id=AA2, first strand: chain 'A' and resid 171 through 173 Processing sheet with id=AA3, first strand: chain 'A' and resid 248 through 250 removed outlier: 6.490A pdb=" N LEU A 249 " --> pdb=" O VAL A 313 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 273 through 274 Processing sheet with id=AA5, first strand: chain 'A' and resid 744 through 751 removed outlier: 3.515A pdb=" N GLU A 751 " --> pdb=" O GLU A 451 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N GLU A 451 " --> pdb=" O GLU A 751 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N LEU A 450 " --> pdb=" O LEU A 446 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N THR A 444 " --> pdb=" O LEU A 452 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 520 through 521 removed outlier: 5.949A pdb=" N LEU A 462 " --> pdb=" O LEU A 488 " (cutoff:3.500A) removed outlier: 7.291A pdb=" N LYS A 490 " --> pdb=" O LEU A 462 " (cutoff:3.500A) removed outlier: 6.125A pdb=" N VAL A 464 " --> pdb=" O LYS A 490 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 662 through 664 removed outlier: 5.556A pdb=" N ILE A 606 " --> pdb=" O VAL A 664 " (cutoff:3.500A) removed outlier: 5.862A pdb=" N VAL A 572 " --> pdb=" O LEU A 605 " (cutoff:3.500A) removed outlier: 7.596A pdb=" N HIS A 607 " --> pdb=" O VAL A 572 " (cutoff:3.500A) removed outlier: 7.574A pdb=" N ILE A 574 " --> pdb=" O HIS A 607 " (cutoff:3.500A) removed outlier: 7.007A pdb=" N TYR A 573 " --> pdb=" O VAL A 686 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'A' and resid 629 through 630 removed outlier: 7.014A pdb=" N LYS A 629 " --> pdb=" O CYS A 659 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'A' and resid 726 through 728 removed outlier: 4.128A pdb=" N GLY A 726 " --> pdb=" O VAL A 738 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N VAL A 738 " --> pdb=" O GLY A 726 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 58 through 59 Processing sheet with id=AB2, first strand: chain 'B' and resid 171 through 173 Processing sheet with id=AB3, first strand: chain 'B' and resid 248 through 250 removed outlier: 6.490A pdb=" N LEU B 249 " --> pdb=" O VAL B 313 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'B' and resid 273 through 274 Processing sheet with id=AB5, first strand: chain 'B' and resid 744 through 751 removed outlier: 3.515A pdb=" N GLU B 751 " --> pdb=" O GLU B 451 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N GLU B 451 " --> pdb=" O GLU B 751 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N LEU B 450 " --> pdb=" O LEU B 446 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N THR B 444 " --> pdb=" O LEU B 452 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 520 through 521 removed outlier: 5.949A pdb=" N LEU B 462 " --> pdb=" O LEU B 488 " (cutoff:3.500A) removed outlier: 7.291A pdb=" N LYS B 490 " --> pdb=" O LEU B 462 " (cutoff:3.500A) removed outlier: 6.125A pdb=" N VAL B 464 " --> pdb=" O LYS B 490 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 662 through 664 removed outlier: 5.556A pdb=" N ILE B 606 " --> pdb=" O VAL B 664 " (cutoff:3.500A) removed outlier: 5.862A pdb=" N VAL B 572 " --> pdb=" O LEU B 605 " (cutoff:3.500A) removed outlier: 7.596A pdb=" N HIS B 607 " --> pdb=" O VAL B 572 " (cutoff:3.500A) removed outlier: 7.574A pdb=" N ILE B 574 " --> pdb=" O HIS B 607 " (cutoff:3.500A) removed outlier: 7.007A pdb=" N TYR B 573 " --> pdb=" O VAL B 686 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'B' and resid 629 through 630 removed outlier: 7.014A pdb=" N LYS B 629 " --> pdb=" O CYS B 659 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'B' and resid 726 through 728 removed outlier: 4.128A pdb=" N GLY B 726 " --> pdb=" O VAL B 738 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N VAL B 738 " --> pdb=" O GLY B 726 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 58 through 59 Processing sheet with id=AC2, first strand: chain 'C' and resid 171 through 173 Processing sheet with id=AC3, first strand: chain 'C' and resid 248 through 250 removed outlier: 6.490A pdb=" N LEU C 249 " --> pdb=" O VAL C 313 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC3 Processing sheet with id=AC4, first strand: chain 'C' and resid 273 through 274 Processing sheet with id=AC5, first strand: chain 'C' and resid 744 through 751 removed outlier: 3.515A pdb=" N GLU C 751 " --> pdb=" O GLU C 451 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N GLU C 451 " --> pdb=" O GLU C 751 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N LEU C 450 " --> pdb=" O LEU C 446 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N THR C 444 " --> pdb=" O LEU C 452 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 520 through 521 removed outlier: 5.949A pdb=" N LEU C 462 " --> pdb=" O LEU C 488 " (cutoff:3.500A) removed outlier: 7.291A pdb=" N LYS C 490 " --> pdb=" O LEU C 462 " (cutoff:3.500A) removed outlier: 6.125A pdb=" N VAL C 464 " --> pdb=" O LYS C 490 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 662 through 664 removed outlier: 5.556A pdb=" N ILE C 606 " --> pdb=" O VAL C 664 " (cutoff:3.500A) removed outlier: 5.862A pdb=" N VAL C 572 " --> pdb=" O LEU C 605 " (cutoff:3.500A) removed outlier: 7.596A pdb=" N HIS C 607 " --> pdb=" O VAL C 572 " (cutoff:3.500A) removed outlier: 7.574A pdb=" N ILE C 574 " --> pdb=" O HIS C 607 " (cutoff:3.500A) removed outlier: 7.007A pdb=" N TYR C 573 " --> pdb=" O VAL C 686 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, first strand: chain 'C' and resid 629 through 630 removed outlier: 7.014A pdb=" N LYS C 629 " --> pdb=" O CYS C 659 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC8 Processing sheet with id=AC9, first strand: chain 'C' and resid 726 through 728 removed outlier: 4.128A pdb=" N GLY C 726 " --> pdb=" O VAL C 738 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N VAL C 738 " --> pdb=" O GLY C 726 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'D' and resid 58 through 59 Processing sheet with id=AD2, first strand: chain 'D' and resid 171 through 173 Processing sheet with id=AD3, first strand: chain 'D' and resid 248 through 250 removed outlier: 6.490A pdb=" N LEU D 249 " --> pdb=" O VAL D 313 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD3 Processing sheet with id=AD4, first strand: chain 'D' and resid 273 through 274 Processing sheet with id=AD5, first strand: chain 'D' and resid 744 through 751 removed outlier: 3.515A pdb=" N GLU D 751 " --> pdb=" O GLU D 451 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N GLU D 451 " --> pdb=" O GLU D 751 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N LEU D 450 " --> pdb=" O LEU D 446 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N THR D 444 " --> pdb=" O LEU D 452 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'D' and resid 520 through 521 removed outlier: 5.949A pdb=" N LEU D 462 " --> pdb=" O LEU D 488 " (cutoff:3.500A) removed outlier: 7.291A pdb=" N LYS D 490 " --> pdb=" O LEU D 462 " (cutoff:3.500A) removed outlier: 6.125A pdb=" N VAL D 464 " --> pdb=" O LYS D 490 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'D' and resid 662 through 664 removed outlier: 5.556A pdb=" N ILE D 606 " --> pdb=" O VAL D 664 " (cutoff:3.500A) removed outlier: 5.862A pdb=" N VAL D 572 " --> pdb=" O LEU D 605 " (cutoff:3.500A) removed outlier: 7.596A pdb=" N HIS D 607 " --> pdb=" O VAL D 572 " (cutoff:3.500A) removed outlier: 7.574A pdb=" N ILE D 574 " --> pdb=" O HIS D 607 " (cutoff:3.500A) removed outlier: 7.007A pdb=" N TYR D 573 " --> pdb=" O VAL D 686 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD7 Processing sheet with id=AD8, first strand: chain 'D' and resid 629 through 630 removed outlier: 7.014A pdb=" N LYS D 629 " --> pdb=" O CYS D 659 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD8 Processing sheet with id=AD9, first strand: chain 'D' and resid 726 through 728 removed outlier: 4.128A pdb=" N GLY D 726 " --> pdb=" O VAL D 738 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N VAL D 738 " --> pdb=" O GLY D 726 " (cutoff:3.500A) 952 hydrogen bonds defined for protein. 2712 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: 3.74 Time building geometry restraints manager: 2.35 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 7100 1.34 - 1.46: 3804 1.46 - 1.57: 9960 1.57 - 1.69: 0 1.69 - 1.81: 184 Bond restraints: 21048 Sorted by residual: bond pdb=" CA SER B 679 " pdb=" C SER B 679 " ideal model delta sigma weight residual 1.524 1.489 0.036 1.66e-02 3.63e+03 4.64e+00 bond pdb=" CA SER A 679 " pdb=" C SER A 679 " ideal model delta sigma weight residual 1.524 1.489 0.036 1.66e-02 3.63e+03 4.64e+00 bond pdb=" CA SER D 679 " pdb=" C SER D 679 " ideal model delta sigma weight residual 1.524 1.489 0.036 1.66e-02 3.63e+03 4.64e+00 bond pdb=" CA SER C 679 " pdb=" C SER C 679 " ideal model delta sigma weight residual 1.524 1.489 0.036 1.66e-02 3.63e+03 4.64e+00 bond pdb=" C VAL A 200 " pdb=" N PRO A 201 " ideal model delta sigma weight residual 1.334 1.295 0.039 2.34e-02 1.83e+03 2.83e+00 ... (remaining 21043 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.86: 27524 1.86 - 3.73: 844 3.73 - 5.59: 92 5.59 - 7.45: 20 7.45 - 9.31: 4 Bond angle restraints: 28484 Sorted by residual: angle pdb=" N VAL B 209 " pdb=" CA VAL B 209 " pdb=" C VAL B 209 " ideal model delta sigma weight residual 113.53 108.48 5.05 9.80e-01 1.04e+00 2.66e+01 angle pdb=" N VAL D 209 " pdb=" CA VAL D 209 " pdb=" C VAL D 209 " ideal model delta sigma weight residual 113.53 108.48 5.05 9.80e-01 1.04e+00 2.66e+01 angle pdb=" N VAL A 209 " pdb=" CA VAL A 209 " pdb=" C VAL A 209 " ideal model delta sigma weight residual 113.53 108.48 5.05 9.80e-01 1.04e+00 2.66e+01 angle pdb=" N VAL C 209 " pdb=" CA VAL C 209 " pdb=" C VAL C 209 " ideal model delta sigma weight residual 113.53 108.48 5.05 9.80e-01 1.04e+00 2.66e+01 angle pdb=" C VAL C 209 " pdb=" N SER C 210 " pdb=" CA SER C 210 " ideal model delta sigma weight residual 122.74 118.98 3.76 1.06e+00 8.90e-01 1.26e+01 ... (remaining 28479 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.68: 11540 17.68 - 35.35: 1060 35.35 - 53.03: 240 53.03 - 70.71: 32 70.71 - 88.38: 20 Dihedral angle restraints: 12892 sinusoidal: 5020 harmonic: 7872 Sorted by residual: dihedral pdb=" CA VAL B 348 " pdb=" C VAL B 348 " pdb=" N GLU B 349 " pdb=" CA GLU B 349 " ideal model delta harmonic sigma weight residual -180.00 -151.07 -28.93 0 5.00e+00 4.00e-02 3.35e+01 dihedral pdb=" CA VAL D 348 " pdb=" C VAL D 348 " pdb=" N GLU D 349 " pdb=" CA GLU D 349 " ideal model delta harmonic sigma weight residual 180.00 -151.07 -28.93 0 5.00e+00 4.00e-02 3.35e+01 dihedral pdb=" CA VAL C 348 " pdb=" C VAL C 348 " pdb=" N GLU C 349 " pdb=" CA GLU C 349 " ideal model delta harmonic sigma weight residual 180.00 -151.07 -28.93 0 5.00e+00 4.00e-02 3.35e+01 ... (remaining 12889 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 1852 0.029 - 0.058: 988 0.058 - 0.086: 304 0.086 - 0.115: 184 0.115 - 0.144: 32 Chirality restraints: 3360 Sorted by residual: chirality pdb=" CA VAL B 313 " pdb=" N VAL B 313 " pdb=" C VAL B 313 " pdb=" CB VAL B 313 " both_signs ideal model delta sigma weight residual False 2.44 2.59 -0.14 2.00e-01 2.50e+01 5.18e-01 chirality pdb=" CA VAL D 313 " pdb=" N VAL D 313 " pdb=" C VAL D 313 " pdb=" CB VAL D 313 " both_signs ideal model delta sigma weight residual False 2.44 2.59 -0.14 2.00e-01 2.50e+01 5.18e-01 chirality pdb=" CA VAL C 313 " pdb=" N VAL C 313 " pdb=" C VAL C 313 " pdb=" CB VAL C 313 " both_signs ideal model delta sigma weight residual False 2.44 2.59 -0.14 2.00e-01 2.50e+01 5.18e-01 ... (remaining 3357 not shown) Planarity restraints: 3696 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR C 524 " 0.008 2.00e-02 2.50e+03 1.66e-02 2.75e+00 pdb=" C THR C 524 " -0.029 2.00e-02 2.50e+03 pdb=" O THR C 524 " 0.011 2.00e-02 2.50e+03 pdb=" N ARG C 525 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR A 524 " 0.008 2.00e-02 2.50e+03 1.66e-02 2.75e+00 pdb=" C THR A 524 " -0.029 2.00e-02 2.50e+03 pdb=" O THR A 524 " 0.011 2.00e-02 2.50e+03 pdb=" N ARG A 525 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR D 524 " -0.008 2.00e-02 2.50e+03 1.66e-02 2.75e+00 pdb=" C THR D 524 " 0.029 2.00e-02 2.50e+03 pdb=" O THR D 524 " -0.011 2.00e-02 2.50e+03 pdb=" N ARG D 525 " -0.009 2.00e-02 2.50e+03 ... (remaining 3693 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 780 2.66 - 3.22: 23964 3.22 - 3.78: 33516 3.78 - 4.34: 44046 4.34 - 4.90: 68032 Nonbonded interactions: 170338 Sorted by model distance: nonbonded pdb=" O ALA C 509 " pdb=" OG1 THR C 512 " model vdw 2.101 3.040 nonbonded pdb=" O ALA A 509 " pdb=" OG1 THR A 512 " model vdw 2.101 3.040 nonbonded pdb=" O ALA B 509 " pdb=" OG1 THR B 512 " model vdw 2.101 3.040 nonbonded pdb=" O ALA D 509 " pdb=" OG1 THR D 512 " model vdw 2.101 3.040 nonbonded pdb=" O ASN D 672 " pdb=" OG1 THR D 676 " model vdw 2.159 3.040 ... (remaining 170333 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: 0.05 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } 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: 1.830 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.370 Check model and map are aligned: 0.040 Set scattering table: 0.070 Process input model: 19.960 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.550 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8388 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 : 0.007 0.048 21048 Z= 0.342 Angle : 0.797 9.314 28484 Z= 0.461 Chirality : 0.043 0.144 3360 Planarity : 0.004 0.039 3696 Dihedral : 14.712 88.382 7788 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 24.28 Ramachandran Plot: Outliers : 0.15 % Allowed : 12.26 % Favored : 87.59 % Rotamer: Outliers : 0.00 % Allowed : 9.53 % Favored : 90.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.58 (0.14), residues: 2708 helix: -2.22 (0.13), residues: 1196 sheet: -4.34 (0.17), residues: 452 loop : -3.19 (0.18), residues: 1060 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 308 TYR 0.013 0.002 TYR D 55 PHE 0.012 0.002 PHE B 760 TRP 0.009 0.002 TRP A 768 HIS 0.008 0.001 HIS D 517 Details of bonding type rmsd covalent geometry : bond 0.00670 (21048) covalent geometry : angle 0.79658 (28484) hydrogen bonds : bond 0.15318 ( 952) hydrogen bonds : angle 6.62559 ( 2712) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5416 Ramachandran restraints generated. 2708 Oldfield, 0 Emsley, 2708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5416 Ramachandran restraints generated. 2708 Oldfield, 0 Emsley, 2708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 2224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 260 time to evaluate : 0.797 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: A 193 GLU cc_start: 0.8807 (tm-30) cc_final: 0.8585 (tm-30) REVERT: A 271 MET cc_start: 0.7778 (tpp) cc_final: 0.6504 (mmt) REVERT: A 318 MET cc_start: 0.7948 (mpp) cc_final: 0.7611 (mpp) REVERT: A 605 LEU cc_start: 0.9445 (tp) cc_final: 0.9073 (mp) REVERT: A 677 TYR cc_start: 0.9325 (m-80) cc_final: 0.9075 (m-80) REVERT: B 193 GLU cc_start: 0.8802 (tm-30) cc_final: 0.8584 (tm-30) REVERT: B 271 MET cc_start: 0.7789 (tpp) cc_final: 0.6514 (mmt) REVERT: B 318 MET cc_start: 0.7948 (mpp) cc_final: 0.7605 (mpp) REVERT: B 605 LEU cc_start: 0.9456 (tp) cc_final: 0.9089 (mp) REVERT: B 677 TYR cc_start: 0.9335 (m-80) cc_final: 0.9080 (m-80) REVERT: C 193 GLU cc_start: 0.8823 (tm-30) cc_final: 0.8597 (tm-30) REVERT: C 271 MET cc_start: 0.7778 (tpp) cc_final: 0.6509 (mmt) REVERT: C 318 MET cc_start: 0.7944 (mpp) cc_final: 0.7614 (mpp) REVERT: C 605 LEU cc_start: 0.9438 (tp) cc_final: 0.9060 (mp) REVERT: C 677 TYR cc_start: 0.9314 (m-80) cc_final: 0.9074 (m-80) REVERT: D 193 GLU cc_start: 0.8804 (tm-30) cc_final: 0.8586 (tm-30) REVERT: D 271 MET cc_start: 0.7781 (tpp) cc_final: 0.6507 (mmt) REVERT: D 318 MET cc_start: 0.7944 (mpp) cc_final: 0.7611 (mpp) REVERT: D 605 LEU cc_start: 0.9439 (tp) cc_final: 0.9062 (mp) REVERT: D 677 TYR cc_start: 0.9308 (m-80) cc_final: 0.9065 (m-80) outliers start: 0 outliers final: 0 residues processed: 260 average time/residue: 0.1821 time to fit residues: 68.7143 Evaluate side-chains 196 residues out of total 2224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 196 time to evaluate : 0.831 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 197 optimal weight: 9.9990 chunk 215 optimal weight: 1.9990 chunk 20 optimal weight: 4.9990 chunk 132 optimal weight: 9.9990 chunk 261 optimal weight: 10.0000 chunk 248 optimal weight: 1.9990 chunk 207 optimal weight: 0.9980 chunk 155 optimal weight: 0.0570 chunk 244 optimal weight: 6.9990 chunk 183 optimal weight: 5.9990 chunk 111 optimal weight: 8.9990 overall best weight: 2.0104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 92 HIS A 170 GLN A 354 ASN A 369 GLN A 375 ASN A 436 ASN A 565 HIS A 599 ASN A 675 HIS B 92 HIS B 170 GLN B 354 ASN B 369 GLN B 375 ASN B 436 ASN B 565 HIS B 599 ASN B 675 HIS C 92 HIS C 170 GLN C 354 ASN C 369 GLN C 375 ASN C 436 ASN C 565 HIS C 599 ASN C 675 HIS D 92 HIS D 170 GLN D 354 ASN D 369 GLN D 375 ASN D 436 ASN D 565 HIS D 599 ASN D 675 HIS Total number of N/Q/H flips: 36 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.085633 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.061679 restraints weight = 77664.087| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.063500 restraints weight = 49500.302| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.064784 restraints weight = 37320.096| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.065647 restraints weight = 31002.763| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.065971 restraints weight = 27395.933| |-----------------------------------------------------------------------------| r_work (final): 0.3213 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8266 moved from start: 0.2249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 21048 Z= 0.142 Angle : 0.634 8.297 28484 Z= 0.321 Chirality : 0.042 0.139 3360 Planarity : 0.004 0.038 3696 Dihedral : 4.987 24.814 2912 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 10.58 Ramachandran Plot: Outliers : 0.15 % Allowed : 8.12 % Favored : 91.73 % Rotamer: Outliers : 0.00 % Allowed : 7.55 % Favored : 92.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.94 (0.16), residues: 2708 helix: -0.61 (0.14), residues: 1268 sheet: -3.79 (0.19), residues: 456 loop : -2.66 (0.20), residues: 984 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 50 TYR 0.007 0.001 TYR B 157 PHE 0.016 0.001 PHE B 760 TRP 0.006 0.001 TRP A 748 HIS 0.003 0.001 HIS B 272 Details of bonding type rmsd covalent geometry : bond 0.00300 (21048) covalent geometry : angle 0.63379 (28484) hydrogen bonds : bond 0.03917 ( 952) hydrogen bonds : angle 4.46760 ( 2712) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5416 Ramachandran restraints generated. 2708 Oldfield, 0 Emsley, 2708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5416 Ramachandran restraints generated. 2708 Oldfield, 0 Emsley, 2708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 2224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 300 time to evaluate : 0.816 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 90 GLU cc_start: 0.8115 (mm-30) cc_final: 0.7828 (mm-30) REVERT: A 207 ASP cc_start: 0.8804 (p0) cc_final: 0.8565 (p0) REVERT: A 318 MET cc_start: 0.8099 (mpp) cc_final: 0.7883 (mpp) REVERT: A 570 CYS cc_start: 0.8769 (m) cc_final: 0.8251 (m) REVERT: A 601 MET cc_start: 0.8129 (tmm) cc_final: 0.7661 (tmm) REVERT: A 605 LEU cc_start: 0.9360 (tp) cc_final: 0.8990 (mp) REVERT: A 653 GLU cc_start: 0.8800 (pm20) cc_final: 0.8577 (mp0) REVERT: A 696 PHE cc_start: 0.9019 (t80) cc_final: 0.8780 (t80) REVERT: B 90 GLU cc_start: 0.8117 (mm-30) cc_final: 0.7835 (mm-30) REVERT: B 207 ASP cc_start: 0.8790 (p0) cc_final: 0.8552 (p0) REVERT: B 318 MET cc_start: 0.8084 (mpp) cc_final: 0.7873 (mpp) REVERT: B 570 CYS cc_start: 0.8766 (m) cc_final: 0.8240 (m) REVERT: B 601 MET cc_start: 0.8130 (tmm) cc_final: 0.7662 (tmm) REVERT: B 605 LEU cc_start: 0.9358 (tp) cc_final: 0.8988 (mp) REVERT: B 653 GLU cc_start: 0.8790 (pm20) cc_final: 0.8571 (mp0) REVERT: B 696 PHE cc_start: 0.9016 (t80) cc_final: 0.8773 (t80) REVERT: C 90 GLU cc_start: 0.8122 (mm-30) cc_final: 0.7835 (mm-30) REVERT: C 207 ASP cc_start: 0.8790 (p0) cc_final: 0.8550 (p0) REVERT: C 318 MET cc_start: 0.8098 (mpp) cc_final: 0.7881 (mpp) REVERT: C 570 CYS cc_start: 0.8771 (m) cc_final: 0.8245 (m) REVERT: C 601 MET cc_start: 0.8126 (tmm) cc_final: 0.7656 (tmm) REVERT: C 605 LEU cc_start: 0.9370 (tp) cc_final: 0.9003 (mp) REVERT: C 653 GLU cc_start: 0.8804 (pm20) cc_final: 0.8578 (mp0) REVERT: C 696 PHE cc_start: 0.9027 (t80) cc_final: 0.8782 (t80) REVERT: D 90 GLU cc_start: 0.8106 (mm-30) cc_final: 0.7820 (mm-30) REVERT: D 207 ASP cc_start: 0.8804 (p0) cc_final: 0.8565 (p0) REVERT: D 318 MET cc_start: 0.8091 (mpp) cc_final: 0.7876 (mpp) REVERT: D 570 CYS cc_start: 0.8775 (m) cc_final: 0.8249 (m) REVERT: D 601 MET cc_start: 0.8131 (tmm) cc_final: 0.7663 (tmm) REVERT: D 605 LEU cc_start: 0.9368 (tp) cc_final: 0.8999 (mp) REVERT: D 653 GLU cc_start: 0.8783 (pm20) cc_final: 0.8566 (mp0) REVERT: D 696 PHE cc_start: 0.9020 (t80) cc_final: 0.8777 (t80) outliers start: 0 outliers final: 0 residues processed: 300 average time/residue: 0.1657 time to fit residues: 74.9286 Evaluate side-chains 220 residues out of total 2224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 220 time to evaluate : 0.809 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 150 optimal weight: 3.9990 chunk 108 optimal weight: 20.0000 chunk 62 optimal weight: 10.0000 chunk 55 optimal weight: 20.0000 chunk 211 optimal weight: 5.9990 chunk 260 optimal weight: 20.0000 chunk 14 optimal weight: 0.9990 chunk 92 optimal weight: 9.9990 chunk 246 optimal weight: 20.0000 chunk 143 optimal weight: 6.9990 chunk 169 optimal weight: 20.0000 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 392 ASN ** A 517 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 571 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 770 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 392 ASN ** B 517 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 770 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 392 ASN ** C 517 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 571 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 770 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 392 ASN ** D 517 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 770 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 = 0.3614 r_free = 0.3614 target = 0.081922 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.058671 restraints weight = 79243.916| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.060091 restraints weight = 52279.774| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.060611 restraints weight = 38722.764| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.060985 restraints weight = 36761.101| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.061125 restraints weight = 33510.292| |-----------------------------------------------------------------------------| r_work (final): 0.3104 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8372 moved from start: 0.2592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 21048 Z= 0.290 Angle : 0.717 7.588 28484 Z= 0.370 Chirality : 0.044 0.134 3360 Planarity : 0.005 0.046 3696 Dihedral : 5.378 26.703 2912 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 13.10 Ramachandran Plot: Outliers : 0.15 % Allowed : 10.34 % Favored : 89.51 % Rotamer: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.65 (0.16), residues: 2708 helix: -0.41 (0.14), residues: 1288 sheet: -3.60 (0.19), residues: 456 loop : -2.51 (0.20), residues: 964 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 588 TYR 0.011 0.001 TYR B 677 PHE 0.007 0.002 PHE B 760 TRP 0.007 0.002 TRP B 304 HIS 0.006 0.001 HIS A 517 Details of bonding type rmsd covalent geometry : bond 0.00612 (21048) covalent geometry : angle 0.71651 (28484) hydrogen bonds : bond 0.04752 ( 952) hydrogen bonds : angle 4.65002 ( 2712) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5416 Ramachandran restraints generated. 2708 Oldfield, 0 Emsley, 2708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5416 Ramachandran restraints generated. 2708 Oldfield, 0 Emsley, 2708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 2224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 220 time to evaluate : 0.597 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 90 GLU cc_start: 0.8157 (mm-30) cc_final: 0.7914 (mm-30) REVERT: A 118 LEU cc_start: 0.9147 (mm) cc_final: 0.8807 (tp) REVERT: A 193 GLU cc_start: 0.8815 (tm-30) cc_final: 0.8442 (tm-30) REVERT: A 207 ASP cc_start: 0.8890 (p0) cc_final: 0.8661 (p0) REVERT: A 318 MET cc_start: 0.8167 (mpp) cc_final: 0.7689 (mpp) REVERT: A 570 CYS cc_start: 0.8811 (m) cc_final: 0.8306 (m) REVERT: A 601 MET cc_start: 0.8115 (tmm) cc_final: 0.7706 (tmm) REVERT: A 605 LEU cc_start: 0.9432 (tp) cc_final: 0.9040 (mp) REVERT: A 653 GLU cc_start: 0.9005 (pm20) cc_final: 0.8726 (mp0) REVERT: B 90 GLU cc_start: 0.8143 (mm-30) cc_final: 0.7905 (mm-30) REVERT: B 118 LEU cc_start: 0.9147 (mm) cc_final: 0.8807 (tp) REVERT: B 193 GLU cc_start: 0.8796 (tm-30) cc_final: 0.8423 (tm-30) REVERT: B 207 ASP cc_start: 0.8890 (p0) cc_final: 0.8659 (p0) REVERT: B 318 MET cc_start: 0.8159 (mpp) cc_final: 0.7675 (mpp) REVERT: B 570 CYS cc_start: 0.8802 (m) cc_final: 0.8301 (m) REVERT: B 601 MET cc_start: 0.8111 (tmm) cc_final: 0.7706 (tmm) REVERT: B 605 LEU cc_start: 0.9427 (tp) cc_final: 0.9035 (mp) REVERT: B 653 GLU cc_start: 0.8992 (pm20) cc_final: 0.8720 (mp0) REVERT: C 90 GLU cc_start: 0.8152 (mm-30) cc_final: 0.7907 (mm-30) REVERT: C 118 LEU cc_start: 0.9151 (mm) cc_final: 0.8812 (tp) REVERT: C 193 GLU cc_start: 0.8802 (tm-30) cc_final: 0.8430 (tm-30) REVERT: C 207 ASP cc_start: 0.8880 (p0) cc_final: 0.8649 (p0) REVERT: C 318 MET cc_start: 0.8173 (mpp) cc_final: 0.7694 (mpp) REVERT: C 570 CYS cc_start: 0.8822 (m) cc_final: 0.8314 (m) REVERT: C 601 MET cc_start: 0.8112 (tmm) cc_final: 0.7706 (tmm) REVERT: C 605 LEU cc_start: 0.9441 (tp) cc_final: 0.9054 (mp) REVERT: C 653 GLU cc_start: 0.9004 (pm20) cc_final: 0.8731 (mp0) REVERT: D 90 GLU cc_start: 0.8125 (mm-30) cc_final: 0.7890 (mm-30) REVERT: D 118 LEU cc_start: 0.9149 (mm) cc_final: 0.8810 (tp) REVERT: D 193 GLU cc_start: 0.8798 (tm-30) cc_final: 0.8430 (tm-30) REVERT: D 207 ASP cc_start: 0.8906 (p0) cc_final: 0.8679 (p0) REVERT: D 318 MET cc_start: 0.8145 (mpp) cc_final: 0.7672 (mpp) REVERT: D 570 CYS cc_start: 0.8810 (m) cc_final: 0.8308 (m) REVERT: D 601 MET cc_start: 0.8114 (tmm) cc_final: 0.7707 (tmm) REVERT: D 605 LEU cc_start: 0.9435 (tp) cc_final: 0.9046 (mp) REVERT: D 653 GLU cc_start: 0.9000 (pm20) cc_final: 0.8729 (mp0) outliers start: 0 outliers final: 0 residues processed: 220 average time/residue: 0.1486 time to fit residues: 51.4980 Evaluate side-chains 184 residues out of total 2224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 184 time to evaluate : 1.098 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 46 optimal weight: 7.9990 chunk 166 optimal weight: 20.0000 chunk 90 optimal weight: 2.9990 chunk 168 optimal weight: 7.9990 chunk 238 optimal weight: 10.0000 chunk 176 optimal weight: 4.9990 chunk 251 optimal weight: 2.9990 chunk 95 optimal weight: 0.1980 chunk 223 optimal weight: 0.9990 chunk 267 optimal weight: 1.9990 chunk 14 optimal weight: 3.9990 overall best weight: 1.8388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 571 HIS ** A 770 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 517 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 571 HIS ** C 770 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 517 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 770 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.084577 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.060451 restraints weight = 78209.625| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.062308 restraints weight = 49642.810| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.063578 restraints weight = 37376.237| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.064411 restraints weight = 31114.229| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.064965 restraints weight = 27631.248| |-----------------------------------------------------------------------------| r_work (final): 0.3201 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8267 moved from start: 0.3144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 21048 Z= 0.131 Angle : 0.616 8.210 28484 Z= 0.311 Chirality : 0.042 0.146 3360 Planarity : 0.004 0.039 3696 Dihedral : 4.854 24.576 2912 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 10.58 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.83 % Favored : 94.02 % Rotamer: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.11 (0.16), residues: 2708 helix: 0.08 (0.15), residues: 1292 sheet: -3.34 (0.20), residues: 464 loop : -2.31 (0.20), residues: 952 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 544 TYR 0.008 0.001 TYR B 157 PHE 0.006 0.001 PHE B 760 TRP 0.010 0.001 TRP A 304 HIS 0.004 0.001 HIS B 673 Details of bonding type rmsd covalent geometry : bond 0.00284 (21048) covalent geometry : angle 0.61552 (28484) hydrogen bonds : bond 0.03708 ( 952) hydrogen bonds : angle 4.29306 ( 2712) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5416 Ramachandran restraints generated. 2708 Oldfield, 0 Emsley, 2708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5416 Ramachandran restraints generated. 2708 Oldfield, 0 Emsley, 2708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 2224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 260 time to evaluate : 0.781 Fit side-chains REVERT: A 90 GLU cc_start: 0.8123 (mm-30) cc_final: 0.7871 (mm-30) REVERT: A 118 LEU cc_start: 0.9108 (mm) cc_final: 0.8776 (tp) REVERT: A 119 MET cc_start: 0.8164 (tmm) cc_final: 0.7947 (tmm) REVERT: A 193 GLU cc_start: 0.8642 (tm-30) cc_final: 0.8374 (tm-30) REVERT: A 207 ASP cc_start: 0.8714 (p0) cc_final: 0.8446 (p0) REVERT: A 271 MET cc_start: 0.7345 (tpp) cc_final: 0.7035 (tpp) REVERT: A 318 MET cc_start: 0.8195 (mpp) cc_final: 0.7790 (mpp) REVERT: A 570 CYS cc_start: 0.8663 (m) cc_final: 0.8160 (m) REVERT: A 601 MET cc_start: 0.8131 (tmm) cc_final: 0.7752 (tmm) REVERT: A 605 LEU cc_start: 0.9447 (tp) cc_final: 0.9247 (mm) REVERT: A 653 GLU cc_start: 0.8823 (pm20) cc_final: 0.8586 (mp0) REVERT: A 677 TYR cc_start: 0.9016 (m-80) cc_final: 0.8778 (m-80) REVERT: B 90 GLU cc_start: 0.8109 (mm-30) cc_final: 0.7854 (mm-30) REVERT: B 118 LEU cc_start: 0.9109 (mm) cc_final: 0.8775 (tp) REVERT: B 119 MET cc_start: 0.8167 (tmm) cc_final: 0.7951 (tmm) REVERT: B 193 GLU cc_start: 0.8623 (tm-30) cc_final: 0.8358 (tm-30) REVERT: B 207 ASP cc_start: 0.8713 (p0) cc_final: 0.8443 (p0) REVERT: B 271 MET cc_start: 0.7349 (tpp) cc_final: 0.7046 (tpp) REVERT: B 318 MET cc_start: 0.8186 (mpp) cc_final: 0.7780 (mpp) REVERT: B 570 CYS cc_start: 0.8722 (m) cc_final: 0.8238 (m) REVERT: B 601 MET cc_start: 0.8127 (tmm) cc_final: 0.7746 (tmm) REVERT: B 653 GLU cc_start: 0.8823 (pm20) cc_final: 0.8585 (mp0) REVERT: B 677 TYR cc_start: 0.9008 (m-80) cc_final: 0.8774 (m-80) REVERT: C 90 GLU cc_start: 0.8129 (mm-30) cc_final: 0.7868 (mm-30) REVERT: C 118 LEU cc_start: 0.9109 (mm) cc_final: 0.8778 (tp) REVERT: C 119 MET cc_start: 0.8166 (tmm) cc_final: 0.7950 (tmm) REVERT: C 193 GLU cc_start: 0.8629 (tm-30) cc_final: 0.8364 (tm-30) REVERT: C 207 ASP cc_start: 0.8721 (p0) cc_final: 0.8451 (p0) REVERT: C 271 MET cc_start: 0.7354 (tpp) cc_final: 0.7044 (tpp) REVERT: C 318 MET cc_start: 0.8196 (mpp) cc_final: 0.7786 (mpp) REVERT: C 570 CYS cc_start: 0.8659 (m) cc_final: 0.8154 (m) REVERT: C 601 MET cc_start: 0.8131 (tmm) cc_final: 0.7750 (tmm) REVERT: C 605 LEU cc_start: 0.9450 (tp) cc_final: 0.9246 (mm) REVERT: C 653 GLU cc_start: 0.8831 (pm20) cc_final: 0.8593 (mp0) REVERT: C 677 TYR cc_start: 0.9006 (m-80) cc_final: 0.8770 (m-80) REVERT: D 90 GLU cc_start: 0.8116 (mm-30) cc_final: 0.7863 (mm-30) REVERT: D 118 LEU cc_start: 0.9111 (mm) cc_final: 0.8780 (tp) REVERT: D 119 MET cc_start: 0.8161 (tmm) cc_final: 0.7943 (tmm) REVERT: D 193 GLU cc_start: 0.8633 (tm-30) cc_final: 0.8369 (tm-30) REVERT: D 207 ASP cc_start: 0.8727 (p0) cc_final: 0.8456 (p0) REVERT: D 271 MET cc_start: 0.7347 (tpp) cc_final: 0.7044 (tpp) REVERT: D 318 MET cc_start: 0.8182 (mpp) cc_final: 0.7779 (mpp) REVERT: D 570 CYS cc_start: 0.8731 (m) cc_final: 0.8248 (m) REVERT: D 601 MET cc_start: 0.8133 (tmm) cc_final: 0.7754 (tmm) REVERT: D 605 LEU cc_start: 0.9452 (tp) cc_final: 0.9249 (mm) REVERT: D 653 GLU cc_start: 0.8825 (pm20) cc_final: 0.8591 (mp0) REVERT: D 677 TYR cc_start: 0.9004 (m-80) cc_final: 0.8772 (m-80) outliers start: 0 outliers final: 0 residues processed: 260 average time/residue: 0.1602 time to fit residues: 64.6436 Evaluate side-chains 203 residues out of total 2224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 203 time to evaluate : 0.792 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 65 optimal weight: 9.9990 chunk 203 optimal weight: 0.9980 chunk 265 optimal weight: 6.9990 chunk 256 optimal weight: 3.9990 chunk 136 optimal weight: 10.0000 chunk 132 optimal weight: 0.9980 chunk 79 optimal weight: 4.9990 chunk 186 optimal weight: 20.0000 chunk 96 optimal weight: 3.9990 chunk 95 optimal weight: 2.9990 chunk 11 optimal weight: 4.9990 overall best weight: 2.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 369 GLN A 517 HIS ** A 708 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 369 GLN B 517 HIS ** B 708 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 770 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 369 GLN C 517 HIS ** C 708 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 770 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 369 GLN D 517 HIS ** D 708 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 770 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.084460 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.060311 restraints weight = 77633.976| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.062166 restraints weight = 49041.806| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.063403 restraints weight = 37031.527| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.064185 restraints weight = 30871.001| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.064767 restraints weight = 27509.078| |-----------------------------------------------------------------------------| r_work (final): 0.3194 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8276 moved from start: 0.3385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 21048 Z= 0.156 Angle : 0.623 7.379 28484 Z= 0.314 Chirality : 0.043 0.191 3360 Planarity : 0.004 0.038 3696 Dihedral : 4.782 25.374 2912 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 10.65 Ramachandran Plot: Outliers : 0.15 % Allowed : 7.39 % Favored : 92.47 % Rotamer: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.81 (0.17), residues: 2708 helix: 0.29 (0.15), residues: 1292 sheet: -3.16 (0.21), residues: 464 loop : -2.11 (0.21), residues: 952 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 80 TYR 0.010 0.001 TYR C 157 PHE 0.011 0.001 PHE B 696 TRP 0.009 0.001 TRP C 304 HIS 0.003 0.001 HIS A 517 Details of bonding type rmsd covalent geometry : bond 0.00334 (21048) covalent geometry : angle 0.62328 (28484) hydrogen bonds : bond 0.03726 ( 952) hydrogen bonds : angle 4.26912 ( 2712) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5416 Ramachandran restraints generated. 2708 Oldfield, 0 Emsley, 2708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5416 Ramachandran restraints generated. 2708 Oldfield, 0 Emsley, 2708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 2224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 251 time to evaluate : 0.823 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: A 90 GLU cc_start: 0.8157 (mm-30) cc_final: 0.7869 (mm-30) REVERT: A 118 LEU cc_start: 0.8990 (mm) cc_final: 0.8758 (tp) REVERT: A 193 GLU cc_start: 0.8698 (tm-30) cc_final: 0.8475 (tm-30) REVERT: A 207 ASP cc_start: 0.8661 (p0) cc_final: 0.8431 (p0) REVERT: A 234 ASP cc_start: 0.9067 (m-30) cc_final: 0.8817 (m-30) REVERT: A 318 MET cc_start: 0.8218 (mpp) cc_final: 0.7726 (mpp) REVERT: A 570 CYS cc_start: 0.8685 (m) cc_final: 0.8223 (m) REVERT: A 601 MET cc_start: 0.8119 (tmm) cc_final: 0.7723 (tmm) REVERT: A 605 LEU cc_start: 0.9420 (tp) cc_final: 0.9095 (tp) REVERT: A 677 TYR cc_start: 0.9023 (m-80) cc_final: 0.8732 (m-80) REVERT: B 90 GLU cc_start: 0.8138 (mm-30) cc_final: 0.7852 (mm-30) REVERT: B 118 LEU cc_start: 0.8995 (mm) cc_final: 0.8762 (tp) REVERT: B 193 GLU cc_start: 0.8670 (tm-30) cc_final: 0.8457 (tm-30) REVERT: B 207 ASP cc_start: 0.8650 (p0) cc_final: 0.8414 (p0) REVERT: B 234 ASP cc_start: 0.9058 (m-30) cc_final: 0.8810 (m-30) REVERT: B 318 MET cc_start: 0.8212 (mpp) cc_final: 0.7715 (mpp) REVERT: B 570 CYS cc_start: 0.8702 (m) cc_final: 0.8254 (m) REVERT: B 601 MET cc_start: 0.8125 (tmm) cc_final: 0.7733 (tmm) REVERT: B 677 TYR cc_start: 0.9025 (m-80) cc_final: 0.8733 (m-80) REVERT: C 90 GLU cc_start: 0.8155 (mm-30) cc_final: 0.7865 (mm-30) REVERT: C 118 LEU cc_start: 0.8992 (mm) cc_final: 0.8759 (tp) REVERT: C 193 GLU cc_start: 0.8684 (tm-30) cc_final: 0.8467 (tm-30) REVERT: C 207 ASP cc_start: 0.8664 (p0) cc_final: 0.8431 (p0) REVERT: C 234 ASP cc_start: 0.9067 (m-30) cc_final: 0.8818 (m-30) REVERT: C 318 MET cc_start: 0.8217 (mpp) cc_final: 0.7722 (mpp) REVERT: C 570 CYS cc_start: 0.8681 (m) cc_final: 0.8223 (m) REVERT: C 601 MET cc_start: 0.8119 (tmm) cc_final: 0.7725 (tmm) REVERT: C 605 LEU cc_start: 0.9421 (tp) cc_final: 0.9096 (tp) REVERT: C 677 TYR cc_start: 0.9014 (m-80) cc_final: 0.8725 (m-80) REVERT: D 90 GLU cc_start: 0.8146 (mm-30) cc_final: 0.7857 (mm-30) REVERT: D 118 LEU cc_start: 0.8996 (mm) cc_final: 0.8764 (tp) REVERT: D 193 GLU cc_start: 0.8678 (tm-30) cc_final: 0.8466 (tm-30) REVERT: D 207 ASP cc_start: 0.8669 (p0) cc_final: 0.8433 (p0) REVERT: D 234 ASP cc_start: 0.9064 (m-30) cc_final: 0.8812 (m-30) REVERT: D 318 MET cc_start: 0.8201 (mpp) cc_final: 0.7709 (mpp) REVERT: D 570 CYS cc_start: 0.8710 (m) cc_final: 0.8262 (m) REVERT: D 601 MET cc_start: 0.8114 (tmm) cc_final: 0.7722 (tmm) REVERT: D 605 LEU cc_start: 0.9424 (tp) cc_final: 0.9100 (tp) REVERT: D 677 TYR cc_start: 0.9022 (m-80) cc_final: 0.8728 (m-80) outliers start: 0 outliers final: 0 residues processed: 251 average time/residue: 0.1506 time to fit residues: 58.9120 Evaluate side-chains 187 residues out of total 2224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 187 time to evaluate : 0.815 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 209 optimal weight: 6.9990 chunk 242 optimal weight: 0.9990 chunk 21 optimal weight: 6.9990 chunk 15 optimal weight: 9.9990 chunk 72 optimal weight: 3.9990 chunk 24 optimal weight: 10.0000 chunk 259 optimal weight: 9.9990 chunk 53 optimal weight: 5.9990 chunk 71 optimal weight: 1.9990 chunk 220 optimal weight: 6.9990 chunk 41 optimal weight: 8.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 770 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 571 HIS ** B 770 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 770 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 571 HIS ** D 770 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.083747 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.059797 restraints weight = 77554.995| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.061533 restraints weight = 49609.346| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.062710 restraints weight = 37529.313| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.063497 restraints weight = 31431.602| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.064031 restraints weight = 27931.852| |-----------------------------------------------------------------------------| r_work (final): 0.3171 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8304 moved from start: 0.3431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 21048 Z= 0.211 Angle : 0.645 6.766 28484 Z= 0.327 Chirality : 0.043 0.147 3360 Planarity : 0.005 0.040 3696 Dihedral : 4.978 24.601 2912 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 11.11 Ramachandran Plot: Outliers : 0.15 % Allowed : 8.16 % Favored : 91.69 % Rotamer: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.72 (0.17), residues: 2708 helix: 0.37 (0.15), residues: 1300 sheet: -3.15 (0.21), residues: 464 loop : -2.09 (0.21), residues: 944 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 308 TYR 0.012 0.001 TYR A 157 PHE 0.009 0.001 PHE B 696 TRP 0.013 0.002 TRP C 304 HIS 0.003 0.001 HIS B 517 Details of bonding type rmsd covalent geometry : bond 0.00448 (21048) covalent geometry : angle 0.64456 (28484) hydrogen bonds : bond 0.04011 ( 952) hydrogen bonds : angle 4.26725 ( 2712) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5416 Ramachandran restraints generated. 2708 Oldfield, 0 Emsley, 2708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5416 Ramachandran restraints generated. 2708 Oldfield, 0 Emsley, 2708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 2224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 227 time to evaluate : 0.835 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: A 90 GLU cc_start: 0.8129 (mm-30) cc_final: 0.7784 (mm-30) REVERT: A 118 LEU cc_start: 0.9159 (mm) cc_final: 0.8868 (tp) REVERT: A 207 ASP cc_start: 0.8699 (p0) cc_final: 0.8470 (p0) REVERT: A 318 MET cc_start: 0.8263 (mpp) cc_final: 0.7690 (mpp) REVERT: A 570 CYS cc_start: 0.8658 (m) cc_final: 0.8220 (m) REVERT: A 601 MET cc_start: 0.8051 (tmm) cc_final: 0.7636 (tmm) REVERT: A 605 LEU cc_start: 0.9440 (tp) cc_final: 0.9121 (tp) REVERT: A 677 TYR cc_start: 0.9098 (m-80) cc_final: 0.8762 (m-80) REVERT: B 90 GLU cc_start: 0.8123 (mm-30) cc_final: 0.7780 (mm-30) REVERT: B 118 LEU cc_start: 0.9157 (mm) cc_final: 0.8863 (tp) REVERT: B 207 ASP cc_start: 0.8690 (p0) cc_final: 0.8458 (p0) REVERT: B 318 MET cc_start: 0.8254 (mpp) cc_final: 0.7674 (mpp) REVERT: B 570 CYS cc_start: 0.8603 (m) cc_final: 0.8172 (m) REVERT: B 601 MET cc_start: 0.8127 (tmm) cc_final: 0.7739 (tmm) REVERT: B 677 TYR cc_start: 0.9119 (m-80) cc_final: 0.8781 (m-80) REVERT: C 90 GLU cc_start: 0.8134 (mm-30) cc_final: 0.7785 (mm-30) REVERT: C 118 LEU cc_start: 0.9159 (mm) cc_final: 0.8868 (tp) REVERT: C 207 ASP cc_start: 0.8699 (p0) cc_final: 0.8468 (p0) REVERT: C 318 MET cc_start: 0.8256 (mpp) cc_final: 0.7680 (mpp) REVERT: C 570 CYS cc_start: 0.8655 (m) cc_final: 0.8216 (m) REVERT: C 601 MET cc_start: 0.8041 (tmm) cc_final: 0.7627 (tmm) REVERT: C 605 LEU cc_start: 0.9445 (tp) cc_final: 0.9128 (tp) REVERT: C 677 TYR cc_start: 0.9095 (m-80) cc_final: 0.8760 (m-80) REVERT: D 90 GLU cc_start: 0.8122 (mm-30) cc_final: 0.7779 (mm-30) REVERT: D 118 LEU cc_start: 0.9159 (mm) cc_final: 0.8867 (tp) REVERT: D 207 ASP cc_start: 0.8704 (p0) cc_final: 0.8469 (p0) REVERT: D 318 MET cc_start: 0.8250 (mpp) cc_final: 0.7669 (mpp) REVERT: D 570 CYS cc_start: 0.8635 (m) cc_final: 0.8190 (m) REVERT: D 601 MET cc_start: 0.8113 (tmm) cc_final: 0.7718 (tmm) REVERT: D 605 LEU cc_start: 0.9417 (tp) cc_final: 0.9117 (tp) REVERT: D 677 TYR cc_start: 0.9125 (m-80) cc_final: 0.8785 (m-80) outliers start: 0 outliers final: 0 residues processed: 227 average time/residue: 0.1317 time to fit residues: 49.5895 Evaluate side-chains 183 residues out of total 2224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 183 time to evaluate : 0.780 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 38 optimal weight: 2.9990 chunk 244 optimal weight: 20.0000 chunk 106 optimal weight: 3.9990 chunk 93 optimal weight: 0.4980 chunk 225 optimal weight: 0.0020 chunk 179 optimal weight: 9.9990 chunk 182 optimal weight: 7.9990 chunk 162 optimal weight: 4.9990 chunk 201 optimal weight: 9.9990 chunk 66 optimal weight: 20.0000 chunk 95 optimal weight: 0.7980 overall best weight: 1.6592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 170 GLN ** A 316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 375 ASN B 170 GLN ** B 316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 375 ASN C 170 GLN ** C 316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 375 ASN D 170 GLN ** D 316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 375 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.085957 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.061808 restraints weight = 76900.130| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.063695 restraints weight = 48282.164| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.064926 restraints weight = 36318.050| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.065776 restraints weight = 30279.104| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.066384 restraints weight = 26822.052| |-----------------------------------------------------------------------------| r_work (final): 0.3234 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8245 moved from start: 0.3811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 21048 Z= 0.119 Angle : 0.603 9.148 28484 Z= 0.298 Chirality : 0.042 0.154 3360 Planarity : 0.004 0.039 3696 Dihedral : 4.577 23.942 2912 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 9.65 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.83 % Favored : 94.02 % Rotamer: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.32 (0.17), residues: 2708 helix: 0.72 (0.15), residues: 1300 sheet: -2.90 (0.22), residues: 464 loop : -1.96 (0.21), residues: 944 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 96 TYR 0.010 0.001 TYR A 157 PHE 0.008 0.001 PHE B 696 TRP 0.011 0.001 TRP C 304 HIS 0.003 0.001 HIS B 517 Details of bonding type rmsd covalent geometry : bond 0.00259 (21048) covalent geometry : angle 0.60276 (28484) hydrogen bonds : bond 0.03363 ( 952) hydrogen bonds : angle 4.07020 ( 2712) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5416 Ramachandran restraints generated. 2708 Oldfield, 0 Emsley, 2708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5416 Ramachandran restraints generated. 2708 Oldfield, 0 Emsley, 2708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 2224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 250 time to evaluate : 0.834 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 90 GLU cc_start: 0.8149 (mm-30) cc_final: 0.7811 (mm-30) REVERT: A 118 LEU cc_start: 0.9066 (mm) cc_final: 0.8815 (tp) REVERT: A 119 MET cc_start: 0.8269 (tmm) cc_final: 0.7991 (tmm) REVERT: A 123 MET cc_start: 0.8224 (ttm) cc_final: 0.8001 (ttm) REVERT: A 207 ASP cc_start: 0.8696 (p0) cc_final: 0.8492 (p0) REVERT: A 318 MET cc_start: 0.8277 (mpp) cc_final: 0.7795 (mpp) REVERT: A 570 CYS cc_start: 0.8584 (m) cc_final: 0.8081 (m) REVERT: A 601 MET cc_start: 0.8075 (tmm) cc_final: 0.7726 (tmm) REVERT: A 677 TYR cc_start: 0.9125 (m-80) cc_final: 0.8790 (m-80) REVERT: B 90 GLU cc_start: 0.8131 (mm-30) cc_final: 0.7799 (mm-30) REVERT: B 118 LEU cc_start: 0.9062 (mm) cc_final: 0.8812 (tp) REVERT: B 119 MET cc_start: 0.8272 (tmm) cc_final: 0.8000 (tmm) REVERT: B 123 MET cc_start: 0.8228 (ttm) cc_final: 0.8007 (ttm) REVERT: B 207 ASP cc_start: 0.8697 (p0) cc_final: 0.8488 (p0) REVERT: B 318 MET cc_start: 0.8256 (mpp) cc_final: 0.7776 (mpp) REVERT: B 570 CYS cc_start: 0.8557 (m) cc_final: 0.8049 (m) REVERT: B 601 MET cc_start: 0.8115 (tmm) cc_final: 0.7766 (tmm) REVERT: B 677 TYR cc_start: 0.9130 (m-80) cc_final: 0.8788 (m-80) REVERT: C 90 GLU cc_start: 0.8150 (mm-30) cc_final: 0.7812 (mm-30) REVERT: C 118 LEU cc_start: 0.9063 (mm) cc_final: 0.8812 (tp) REVERT: C 119 MET cc_start: 0.8273 (tmm) cc_final: 0.7996 (tmm) REVERT: C 123 MET cc_start: 0.8227 (ttm) cc_final: 0.8006 (ttm) REVERT: C 207 ASP cc_start: 0.8704 (p0) cc_final: 0.8499 (p0) REVERT: C 318 MET cc_start: 0.8268 (mpp) cc_final: 0.7787 (mpp) REVERT: C 570 CYS cc_start: 0.8579 (m) cc_final: 0.8077 (m) REVERT: C 601 MET cc_start: 0.8071 (tmm) cc_final: 0.7723 (tmm) REVERT: C 677 TYR cc_start: 0.9118 (m-80) cc_final: 0.8787 (m-80) REVERT: D 90 GLU cc_start: 0.8129 (mm-30) cc_final: 0.7797 (mm-30) REVERT: D 118 LEU cc_start: 0.9063 (mm) cc_final: 0.8812 (tp) REVERT: D 119 MET cc_start: 0.8271 (tmm) cc_final: 0.7997 (tmm) REVERT: D 123 MET cc_start: 0.8228 (ttm) cc_final: 0.8007 (ttm) REVERT: D 207 ASP cc_start: 0.8698 (p0) cc_final: 0.8489 (p0) REVERT: D 318 MET cc_start: 0.8242 (mpp) cc_final: 0.7763 (mpp) REVERT: D 570 CYS cc_start: 0.8586 (m) cc_final: 0.8095 (m) REVERT: D 601 MET cc_start: 0.8083 (tmm) cc_final: 0.7735 (tmm) REVERT: D 677 TYR cc_start: 0.9122 (m-80) cc_final: 0.8781 (m-80) outliers start: 0 outliers final: 0 residues processed: 250 average time/residue: 0.1414 time to fit residues: 56.9055 Evaluate side-chains 207 residues out of total 2224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 207 time to evaluate : 0.806 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 247 optimal weight: 0.9980 chunk 23 optimal weight: 1.9990 chunk 68 optimal weight: 10.0000 chunk 189 optimal weight: 10.0000 chunk 227 optimal weight: 6.9990 chunk 98 optimal weight: 20.0000 chunk 7 optimal weight: 6.9990 chunk 121 optimal weight: 7.9990 chunk 9 optimal weight: 0.9990 chunk 35 optimal weight: 6.9990 chunk 208 optimal weight: 0.9980 overall best weight: 2.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.085111 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.060959 restraints weight = 76894.760| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.062832 restraints weight = 48716.471| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.064027 restraints weight = 36737.124| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.064875 restraints weight = 30741.496| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.065424 restraints weight = 27346.622| |-----------------------------------------------------------------------------| r_work (final): 0.3212 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8266 moved from start: 0.3905 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 21048 Z= 0.148 Angle : 0.629 8.278 28484 Z= 0.314 Chirality : 0.042 0.138 3360 Planarity : 0.004 0.039 3696 Dihedral : 4.646 23.906 2912 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 10.25 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.87 % Favored : 92.98 % Rotamer: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.22 (0.17), residues: 2708 helix: 0.72 (0.15), residues: 1304 sheet: -2.81 (0.22), residues: 468 loop : -1.79 (0.21), residues: 936 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 96 TYR 0.007 0.001 TYR B 157 PHE 0.007 0.001 PHE D 696 TRP 0.009 0.001 TRP B 304 HIS 0.002 0.001 HIS B 517 Details of bonding type rmsd covalent geometry : bond 0.00321 (21048) covalent geometry : angle 0.62889 (28484) hydrogen bonds : bond 0.03544 ( 952) hydrogen bonds : angle 4.26246 ( 2712) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5416 Ramachandran restraints generated. 2708 Oldfield, 0 Emsley, 2708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5416 Ramachandran restraints generated. 2708 Oldfield, 0 Emsley, 2708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 2224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 236 time to evaluate : 0.860 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 90 GLU cc_start: 0.8125 (mm-30) cc_final: 0.7853 (mm-30) REVERT: A 118 LEU cc_start: 0.9083 (mm) cc_final: 0.8799 (tp) REVERT: A 119 MET cc_start: 0.8352 (tmm) cc_final: 0.8139 (tmm) REVERT: A 318 MET cc_start: 0.8271 (mpp) cc_final: 0.7773 (mpp) REVERT: A 493 LYS cc_start: 0.7669 (pptt) cc_final: 0.7434 (mmmm) REVERT: A 570 CYS cc_start: 0.8627 (m) cc_final: 0.8118 (m) REVERT: A 601 MET cc_start: 0.8080 (tmm) cc_final: 0.7692 (tmm) REVERT: A 677 TYR cc_start: 0.9158 (m-80) cc_final: 0.8799 (m-80) REVERT: B 71 GLU cc_start: 0.8602 (pm20) cc_final: 0.8386 (pm20) REVERT: B 90 GLU cc_start: 0.8085 (mm-30) cc_final: 0.7745 (mm-30) REVERT: B 118 LEU cc_start: 0.9087 (mm) cc_final: 0.8797 (tp) REVERT: B 119 MET cc_start: 0.8363 (tmm) cc_final: 0.8140 (tmm) REVERT: B 318 MET cc_start: 0.8263 (mpp) cc_final: 0.7759 (mpp) REVERT: B 493 LYS cc_start: 0.7698 (pptt) cc_final: 0.7460 (mmmm) REVERT: B 570 CYS cc_start: 0.8593 (m) cc_final: 0.8074 (m) REVERT: B 601 MET cc_start: 0.8105 (tmm) cc_final: 0.7760 (tmm) REVERT: B 677 TYR cc_start: 0.9156 (m-80) cc_final: 0.8806 (m-80) REVERT: C 71 GLU cc_start: 0.8601 (pm20) cc_final: 0.8384 (pm20) REVERT: C 90 GLU cc_start: 0.8102 (mm-30) cc_final: 0.7756 (mm-30) REVERT: C 118 LEU cc_start: 0.9085 (mm) cc_final: 0.8796 (tp) REVERT: C 119 MET cc_start: 0.8366 (tmm) cc_final: 0.8143 (tmm) REVERT: C 318 MET cc_start: 0.8285 (mpp) cc_final: 0.7774 (mpp) REVERT: C 493 LYS cc_start: 0.7672 (pptt) cc_final: 0.7437 (mmmm) REVERT: C 570 CYS cc_start: 0.8628 (m) cc_final: 0.8119 (m) REVERT: C 601 MET cc_start: 0.8082 (tmm) cc_final: 0.7691 (tmm) REVERT: C 677 TYR cc_start: 0.9152 (m-80) cc_final: 0.8794 (m-80) REVERT: D 90 GLU cc_start: 0.8106 (mm-30) cc_final: 0.7841 (mm-30) REVERT: D 118 LEU cc_start: 0.9086 (mm) cc_final: 0.8800 (tp) REVERT: D 119 MET cc_start: 0.8352 (tmm) cc_final: 0.8139 (tmm) REVERT: D 318 MET cc_start: 0.8251 (mpp) cc_final: 0.7753 (mpp) REVERT: D 493 LYS cc_start: 0.7693 (pptt) cc_final: 0.7455 (mmmm) REVERT: D 570 CYS cc_start: 0.8629 (m) cc_final: 0.8112 (m) REVERT: D 601 MET cc_start: 0.8085 (tmm) cc_final: 0.7699 (tmm) REVERT: D 677 TYR cc_start: 0.9159 (m-80) cc_final: 0.8800 (m-80) outliers start: 0 outliers final: 0 residues processed: 236 average time/residue: 0.1401 time to fit residues: 53.0790 Evaluate side-chains 211 residues out of total 2224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 211 time to evaluate : 0.796 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 216 optimal weight: 2.9990 chunk 184 optimal weight: 4.9990 chunk 159 optimal weight: 0.8980 chunk 175 optimal weight: 6.9990 chunk 102 optimal weight: 8.9990 chunk 69 optimal weight: 4.9990 chunk 92 optimal weight: 10.0000 chunk 81 optimal weight: 0.9990 chunk 201 optimal weight: 7.9990 chunk 121 optimal weight: 5.9990 chunk 22 optimal weight: 6.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.084479 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.060398 restraints weight = 77266.834| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.062269 restraints weight = 48809.730| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.063460 restraints weight = 36623.053| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.064307 restraints weight = 30621.914| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.064559 restraints weight = 27207.787| |-----------------------------------------------------------------------------| r_work (final): 0.3187 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8284 moved from start: 0.3912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 21048 Z= 0.171 Angle : 0.644 7.878 28484 Z= 0.323 Chirality : 0.043 0.144 3360 Planarity : 0.004 0.038 3696 Dihedral : 4.719 24.422 2912 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 10.58 Ramachandran Plot: Outliers : 0.15 % Allowed : 7.46 % Favored : 92.39 % Rotamer: Outliers : 0.00 % Allowed : 0.72 % Favored : 99.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.13 (0.17), residues: 2708 helix: 0.80 (0.15), residues: 1280 sheet: -2.76 (0.22), residues: 468 loop : -1.70 (0.21), residues: 960 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 96 TYR 0.008 0.001 TYR D 55 PHE 0.009 0.001 PHE A 178 TRP 0.006 0.001 TRP D 304 HIS 0.002 0.001 HIS D 755 Details of bonding type rmsd covalent geometry : bond 0.00371 (21048) covalent geometry : angle 0.64411 (28484) hydrogen bonds : bond 0.03713 ( 952) hydrogen bonds : angle 4.33443 ( 2712) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5416 Ramachandran restraints generated. 2708 Oldfield, 0 Emsley, 2708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5416 Ramachandran restraints generated. 2708 Oldfield, 0 Emsley, 2708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 2224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 240 time to evaluate : 0.766 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 90 GLU cc_start: 0.8099 (mm-30) cc_final: 0.7821 (mm-30) REVERT: A 118 LEU cc_start: 0.9103 (mm) cc_final: 0.8800 (tp) REVERT: A 119 MET cc_start: 0.8395 (tmm) cc_final: 0.8091 (tmm) REVERT: A 125 GLU cc_start: 0.9155 (tt0) cc_final: 0.8917 (tm-30) REVERT: A 318 MET cc_start: 0.8275 (mpp) cc_final: 0.7761 (mpp) REVERT: A 353 GLU cc_start: 0.8759 (mp0) cc_final: 0.8492 (mp0) REVERT: A 570 CYS cc_start: 0.8605 (m) cc_final: 0.8113 (m) REVERT: A 601 MET cc_start: 0.8068 (tmm) cc_final: 0.7662 (tmm) REVERT: A 677 TYR cc_start: 0.9155 (m-80) cc_final: 0.8806 (m-80) REVERT: B 90 GLU cc_start: 0.8128 (mm-30) cc_final: 0.7863 (mm-30) REVERT: B 118 LEU cc_start: 0.9104 (mm) cc_final: 0.8799 (tp) REVERT: B 119 MET cc_start: 0.8408 (tmm) cc_final: 0.8096 (tmm) REVERT: B 125 GLU cc_start: 0.9155 (tt0) cc_final: 0.8916 (tm-30) REVERT: B 318 MET cc_start: 0.8268 (mpp) cc_final: 0.7744 (mpp) REVERT: B 353 GLU cc_start: 0.8767 (mp0) cc_final: 0.8499 (mp0) REVERT: B 570 CYS cc_start: 0.8594 (m) cc_final: 0.8086 (m) REVERT: B 601 MET cc_start: 0.8062 (tmm) cc_final: 0.7661 (tmm) REVERT: B 677 TYR cc_start: 0.9153 (m-80) cc_final: 0.8809 (m-80) REVERT: C 90 GLU cc_start: 0.8126 (mm-30) cc_final: 0.7866 (mm-30) REVERT: C 118 LEU cc_start: 0.9107 (mm) cc_final: 0.8804 (tp) REVERT: C 119 MET cc_start: 0.8404 (tmm) cc_final: 0.8094 (tmm) REVERT: C 125 GLU cc_start: 0.9158 (tt0) cc_final: 0.8915 (tm-30) REVERT: C 318 MET cc_start: 0.8280 (mpp) cc_final: 0.7755 (mpp) REVERT: C 353 GLU cc_start: 0.8764 (mp0) cc_final: 0.8498 (mp0) REVERT: C 570 CYS cc_start: 0.8600 (m) cc_final: 0.8102 (m) REVERT: C 601 MET cc_start: 0.8067 (tmm) cc_final: 0.7659 (tmm) REVERT: C 677 TYR cc_start: 0.9160 (m-80) cc_final: 0.8810 (m-80) REVERT: D 90 GLU cc_start: 0.8091 (mm-30) cc_final: 0.7815 (mm-30) REVERT: D 118 LEU cc_start: 0.9108 (mm) cc_final: 0.8804 (tp) REVERT: D 119 MET cc_start: 0.8394 (tmm) cc_final: 0.8090 (tmm) REVERT: D 125 GLU cc_start: 0.9147 (tt0) cc_final: 0.8914 (tm-30) REVERT: D 318 MET cc_start: 0.8260 (mpp) cc_final: 0.7744 (mpp) REVERT: D 353 GLU cc_start: 0.8764 (mp0) cc_final: 0.8500 (mp0) REVERT: D 570 CYS cc_start: 0.8627 (m) cc_final: 0.8174 (m) REVERT: D 601 MET cc_start: 0.8078 (tmm) cc_final: 0.7678 (tmm) REVERT: D 677 TYR cc_start: 0.9161 (m-80) cc_final: 0.8813 (m-80) outliers start: 0 outliers final: 0 residues processed: 240 average time/residue: 0.1364 time to fit residues: 52.7887 Evaluate side-chains 203 residues out of total 2224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 203 time to evaluate : 0.829 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 140 optimal weight: 0.9980 chunk 17 optimal weight: 4.9990 chunk 239 optimal weight: 10.0000 chunk 141 optimal weight: 2.9990 chunk 228 optimal weight: 7.9990 chunk 43 optimal weight: 8.9990 chunk 4 optimal weight: 3.9990 chunk 26 optimal weight: 4.9990 chunk 219 optimal weight: 5.9990 chunk 34 optimal weight: 0.1980 chunk 52 optimal weight: 0.6980 overall best weight: 1.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.085930 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.061499 restraints weight = 77915.381| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.063378 restraints weight = 48759.572| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.064622 restraints weight = 36844.407| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.065478 restraints weight = 30877.912| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.066026 restraints weight = 27501.723| |-----------------------------------------------------------------------------| r_work (final): 0.3222 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8256 moved from start: 0.4171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 21048 Z= 0.127 Angle : 0.618 7.769 28484 Z= 0.306 Chirality : 0.043 0.147 3360 Planarity : 0.004 0.035 3696 Dihedral : 4.543 23.938 2912 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 10.15 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.76 % Favored : 93.09 % Rotamer: Outliers : 0.00 % Allowed : 0.22 % Favored : 99.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.96 (0.17), residues: 2708 helix: 0.90 (0.15), residues: 1284 sheet: -2.62 (0.22), residues: 464 loop : -1.61 (0.21), residues: 960 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 96 TYR 0.009 0.001 TYR D 654 PHE 0.006 0.001 PHE A 696 TRP 0.010 0.001 TRP B 304 HIS 0.003 0.001 HIS D 571 Details of bonding type rmsd covalent geometry : bond 0.00277 (21048) covalent geometry : angle 0.61814 (28484) hydrogen bonds : bond 0.03426 ( 952) hydrogen bonds : angle 4.25584 ( 2712) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5416 Ramachandran restraints generated. 2708 Oldfield, 0 Emsley, 2708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5416 Ramachandran restraints generated. 2708 Oldfield, 0 Emsley, 2708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 2224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 251 time to evaluate : 0.718 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: A 90 GLU cc_start: 0.8130 (mm-30) cc_final: 0.7864 (mm-30) REVERT: A 118 LEU cc_start: 0.9053 (mm) cc_final: 0.8771 (tp) REVERT: A 123 MET cc_start: 0.8124 (ttm) cc_final: 0.7859 (tpp) REVERT: A 125 GLU cc_start: 0.9182 (tt0) cc_final: 0.8949 (tm-30) REVERT: A 179 TYR cc_start: 0.8571 (m-80) cc_final: 0.8110 (m-80) REVERT: A 318 MET cc_start: 0.8257 (mpp) cc_final: 0.7773 (mpp) REVERT: A 385 GLU cc_start: 0.8779 (pm20) cc_final: 0.8575 (pm20) REVERT: A 570 CYS cc_start: 0.8597 (m) cc_final: 0.8138 (m) REVERT: A 601 MET cc_start: 0.8105 (tmm) cc_final: 0.7777 (tmm) REVERT: A 677 TYR cc_start: 0.9107 (m-80) cc_final: 0.8798 (m-80) REVERT: B 90 GLU cc_start: 0.8114 (mm-30) cc_final: 0.7852 (mm-30) REVERT: B 118 LEU cc_start: 0.9052 (mm) cc_final: 0.8768 (tp) REVERT: B 123 MET cc_start: 0.8133 (ttm) cc_final: 0.7861 (tpp) REVERT: B 125 GLU cc_start: 0.9185 (tt0) cc_final: 0.8947 (tm-30) REVERT: B 179 TYR cc_start: 0.8567 (m-80) cc_final: 0.8110 (m-80) REVERT: B 318 MET cc_start: 0.8242 (mpp) cc_final: 0.7761 (mpp) REVERT: B 385 GLU cc_start: 0.8785 (pm20) cc_final: 0.8581 (pm20) REVERT: B 570 CYS cc_start: 0.8589 (m) cc_final: 0.8109 (m) REVERT: B 601 MET cc_start: 0.8143 (tmm) cc_final: 0.7838 (tmm) REVERT: B 677 TYR cc_start: 0.9090 (m-80) cc_final: 0.8785 (m-80) REVERT: C 90 GLU cc_start: 0.8119 (mm-30) cc_final: 0.7855 (mm-30) REVERT: C 118 LEU cc_start: 0.9052 (mm) cc_final: 0.8770 (tp) REVERT: C 123 MET cc_start: 0.8123 (ttm) cc_final: 0.7859 (tpp) REVERT: C 125 GLU cc_start: 0.9181 (tt0) cc_final: 0.8943 (tm-30) REVERT: C 179 TYR cc_start: 0.8564 (m-80) cc_final: 0.8109 (m-80) REVERT: C 318 MET cc_start: 0.8262 (mpp) cc_final: 0.7773 (mpp) REVERT: C 570 CYS cc_start: 0.8599 (m) cc_final: 0.8135 (m) REVERT: C 601 MET cc_start: 0.8099 (tmm) cc_final: 0.7771 (tmm) REVERT: C 677 TYR cc_start: 0.9109 (m-80) cc_final: 0.8798 (m-80) REVERT: D 90 GLU cc_start: 0.8115 (mm-30) cc_final: 0.7855 (mm-30) REVERT: D 118 LEU cc_start: 0.9053 (mm) cc_final: 0.8768 (tp) REVERT: D 123 MET cc_start: 0.8136 (ttm) cc_final: 0.7858 (tpp) REVERT: D 125 GLU cc_start: 0.9190 (tt0) cc_final: 0.8948 (tm-30) REVERT: D 179 TYR cc_start: 0.8567 (m-80) cc_final: 0.8108 (m-80) REVERT: D 318 MET cc_start: 0.8250 (mpp) cc_final: 0.7766 (mpp) REVERT: D 385 GLU cc_start: 0.8777 (pm20) cc_final: 0.8576 (pm20) REVERT: D 570 CYS cc_start: 0.8445 (m) cc_final: 0.8095 (m) REVERT: D 601 MET cc_start: 0.7994 (tmm) cc_final: 0.7598 (tmm) REVERT: D 677 TYR cc_start: 0.9090 (m-80) cc_final: 0.8764 (m-80) outliers start: 0 outliers final: 0 residues processed: 251 average time/residue: 0.1297 time to fit residues: 52.9002 Evaluate side-chains 218 residues out of total 2224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 218 time to evaluate : 0.732 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 167 optimal weight: 4.9990 chunk 180 optimal weight: 5.9990 chunk 39 optimal weight: 5.9990 chunk 166 optimal weight: 9.9990 chunk 27 optimal weight: 5.9990 chunk 182 optimal weight: 0.9980 chunk 29 optimal weight: 0.2980 chunk 148 optimal weight: 8.9990 chunk 126 optimal weight: 5.9990 chunk 48 optimal weight: 7.9990 chunk 252 optimal weight: 8.9990 overall best weight: 3.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 344 ASN ** B 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 344 ASN B 454 GLN ** C 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 344 ASN ** D 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 344 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.084183 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.064291 restraints weight = 78160.320| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.065560 restraints weight = 65840.859| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.066745 restraints weight = 47929.158| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.067644 restraints weight = 35252.552| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.067973 restraints weight = 32567.865| |-----------------------------------------------------------------------------| r_work (final): 0.3258 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8213 moved from start: 0.4082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 21048 Z= 0.198 Angle : 0.656 7.339 28484 Z= 0.331 Chirality : 0.043 0.144 3360 Planarity : 0.004 0.035 3696 Dihedral : 4.834 24.448 2912 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 10.99 Ramachandran Plot: Outliers : 0.15 % Allowed : 8.79 % Favored : 91.06 % Rotamer: Outliers : 0.00 % Allowed : 0.13 % Favored : 99.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.03 (0.17), residues: 2708 helix: 0.80 (0.15), residues: 1280 sheet: -2.64 (0.22), residues: 460 loop : -1.60 (0.22), residues: 968 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 96 TYR 0.010 0.001 TYR B 55 PHE 0.008 0.001 PHE B 642 TRP 0.006 0.001 TRP B 304 HIS 0.003 0.001 HIS B 571 Details of bonding type rmsd covalent geometry : bond 0.00424 (21048) covalent geometry : angle 0.65560 (28484) hydrogen bonds : bond 0.03914 ( 952) hydrogen bonds : angle 4.41353 ( 2712) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3192.11 seconds wall clock time: 56 minutes 28.20 seconds (3388.20 seconds total)