Starting phenix.real_space_refine on Sun Sep 29 00:44:38 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f5u_31467/09_2024/7f5u_31467.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f5u_31467/09_2024/7f5u_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f5u_31467/09_2024/7f5u_31467.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f5u_31467/09_2024/7f5u_31467.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f5u_31467/09_2024/7f5u_31467.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f5u_31467/09_2024/7f5u_31467.cif" } resolution = 4.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 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): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/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: C, B, D Time building chain proxies: 11.88, per 1000 atoms: 0.57 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: 4.80 Conformation dependent library (CDL) restraints added in 2.4 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: 2.50 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: 6.73 Time building geometry restraints manager: 5.62 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: 0.00 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: 2.230 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.810 Check model and map are aligned: 0.160 Set scattering table: 0.200 Process input model: 43.990 Find NCS groups from input model: 0.600 Set up NCS constraints: 0.050 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:2.560 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.620 ------------------------------------------------------------------------------- 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= 0.445 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.009 0.002 TRP A 768 HIS 0.008 0.001 HIS D 517 PHE 0.012 0.002 PHE B 760 TYR 0.013 0.002 TYR D 55 ARG 0.004 0.001 ARG A 308 *********************** 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 fitting. rotamer outliers: 0 poor density : 260 time to evaluate : 2.320 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: 0.6644 (mmt) REVERT: A 318 MET cc_start: 0.7948 (mpp) cc_final: 0.7612 (mpp) REVERT: A 605 LEU cc_start: 0.9445 (tp) cc_final: 0.9074 (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: 0.8583 (tm-30) REVERT: B 271 MET cc_start: 0.7789 (tpp) cc_final: 0.6655 (mmt) REVERT: B 318 MET cc_start: 0.7948 (mpp) cc_final: 0.7606 (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: 0.8596 (tm-30) REVERT: C 271 MET cc_start: 0.7778 (tpp) cc_final: 0.6651 (mmt) REVERT: C 318 MET cc_start: 0.7944 (mpp) cc_final: 0.7615 (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: 0.6650 (mmt) REVERT: D 318 MET cc_start: 0.7944 (mpp) cc_final: 0.7612 (mpp) REVERT: D 605 LEU cc_start: 0.9439 (tp) cc_final: 0.9063 (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: 0.4068 time to fit residues: 153.3812 Evaluate side-chains 196 residues out of total 2224 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 196 time to evaluate : 2.597 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 229 optimal weight: 8.9990 chunk 206 optimal weight: 6.9990 chunk 114 optimal weight: 0.4980 chunk 70 optimal weight: 0.7980 chunk 139 optimal weight: 1.9990 chunk 110 optimal weight: 0.7980 chunk 213 optimal weight: 0.9980 chunk 82 optimal weight: 1.9990 chunk 129 optimal weight: 4.9990 chunk 158 optimal weight: 10.0000 chunk 247 optimal weight: 0.6980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 92 HIS A 599 ASN A 675 HIS B 92 HIS B 354 ASN B 599 ASN B 675 HIS C 92 HIS C 599 ASN C 675 HIS D 92 HIS D 599 ASN D 675 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8246 moved from start: 0.2420 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= 0.170 Angle : 0.629 8.222 28484 Z= 0.318 Chirality : 0.043 0.145 3360 Planarity : 0.004 0.038 3696 Dihedral : 4.809 24.489 2912 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 9.55 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.94 % Favored : 92.91 % Rotamer: Outliers : 0.00 % Allowed : 6.16 % Favored : 93.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.89 (0.16), residues: 2708 helix: -0.52 (0.14), residues: 1272 sheet: -3.84 (0.18), residues: 464 loop : -2.64 (0.20), residues: 972 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 748 HIS 0.003 0.001 HIS B 272 PHE 0.015 0.001 PHE B 760 TYR 0.010 0.001 TYR A 157 ARG 0.005 0.001 ARG C 50 *********************** 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 312 residues out of total 2224 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 312 time to evaluate : 2.317 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 90 GLU cc_start: 0.7974 (mm-30) cc_final: 0.7718 (mm-30) REVERT: A 207 ASP cc_start: 0.8817 (p0) cc_final: 0.8552 (p0) REVERT: A 271 MET cc_start: 0.6891 (tpp) cc_final: 0.6345 (tpp) REVERT: A 570 CYS cc_start: 0.8813 (m) cc_final: 0.8273 (m) REVERT: A 601 MET cc_start: 0.8135 (tmm) cc_final: 0.7665 (tmm) REVERT: A 605 LEU cc_start: 0.9421 (tp) cc_final: 0.9095 (mp) REVERT: B 90 GLU cc_start: 0.7985 (mm-30) cc_final: 0.7729 (mm-30) REVERT: B 207 ASP cc_start: 0.8809 (p0) cc_final: 0.8546 (p0) REVERT: B 271 MET cc_start: 0.6904 (tpp) cc_final: 0.6346 (tpp) REVERT: B 570 CYS cc_start: 0.8819 (m) cc_final: 0.8280 (m) REVERT: B 601 MET cc_start: 0.8133 (tmm) cc_final: 0.7665 (tmm) REVERT: B 605 LEU cc_start: 0.9428 (tp) cc_final: 0.9107 (mp) REVERT: C 90 GLU cc_start: 0.7975 (mm-30) cc_final: 0.7717 (mm-30) REVERT: C 207 ASP cc_start: 0.8827 (p0) cc_final: 0.8560 (p0) REVERT: C 271 MET cc_start: 0.6891 (tpp) cc_final: 0.6335 (tpp) REVERT: C 570 CYS cc_start: 0.8797 (m) cc_final: 0.8263 (m) REVERT: C 601 MET cc_start: 0.8126 (tmm) cc_final: 0.7658 (tmm) REVERT: C 605 LEU cc_start: 0.9412 (tp) cc_final: 0.9079 (mp) REVERT: D 90 GLU cc_start: 0.7982 (mm-30) cc_final: 0.7719 (mm-30) REVERT: D 207 ASP cc_start: 0.8807 (p0) cc_final: 0.8543 (p0) REVERT: D 271 MET cc_start: 0.6899 (tpp) cc_final: 0.6339 (tpp) REVERT: D 570 CYS cc_start: 0.8801 (m) cc_final: 0.8270 (m) REVERT: D 601 MET cc_start: 0.8149 (tmm) cc_final: 0.7681 (tmm) REVERT: D 605 LEU cc_start: 0.9413 (tp) cc_final: 0.9085 (mp) outliers start: 0 outliers final: 0 residues processed: 312 average time/residue: 0.3445 time to fit residues: 161.5618 Evaluate side-chains 224 residues out of total 2224 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 224 time to evaluate : 2.456 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 137 optimal weight: 4.9990 chunk 76 optimal weight: 10.0000 chunk 205 optimal weight: 4.9990 chunk 168 optimal weight: 5.9990 chunk 68 optimal weight: 10.0000 chunk 247 optimal weight: 10.0000 chunk 267 optimal weight: 7.9990 chunk 220 optimal weight: 2.9990 chunk 245 optimal weight: 7.9990 chunk 84 optimal weight: 2.9990 chunk 198 optimal weight: 10.0000 overall best weight: 4.3990 ------------------------------------------------------------------------------- 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 354 ASN A 369 GLN A 375 ASN A 565 HIS ** A 770 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 369 GLN B 375 ASN B 392 ASN ** B 517 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 565 HIS ** B 770 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 354 ASN C 369 GLN C 375 ASN C 565 HIS ** C 770 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 354 ASN D 369 GLN D 375 ASN D 392 ASN D 565 HIS ** D 770 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8334 moved from start: 0.2663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 21048 Z= 0.331 Angle : 0.675 7.904 28484 Z= 0.344 Chirality : 0.043 0.141 3360 Planarity : 0.004 0.041 3696 Dihedral : 5.064 26.071 2912 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 11.56 Ramachandran Plot: Outliers : 0.15 % Allowed : 9.27 % Favored : 90.58 % Rotamer: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.41 (0.16), residues: 2708 helix: -0.16 (0.14), residues: 1284 sheet: -3.57 (0.20), residues: 456 loop : -2.42 (0.20), residues: 968 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP D 304 HIS 0.005 0.001 HIS B 517 PHE 0.007 0.001 PHE D 760 TYR 0.010 0.001 TYR D 164 ARG 0.008 0.000 ARG D 588 *********************** 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 244 residues out of total 2224 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 244 time to evaluate : 1.951 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 90 GLU cc_start: 0.8086 (mm-30) cc_final: 0.7690 (mm-30) REVERT: A 118 LEU cc_start: 0.9120 (mm) cc_final: 0.8750 (tp) REVERT: A 193 GLU cc_start: 0.8641 (tm-30) cc_final: 0.8296 (tm-30) REVERT: A 207 ASP cc_start: 0.8787 (p0) cc_final: 0.8557 (p0) REVERT: A 318 MET cc_start: 0.8303 (mpp) cc_final: 0.7938 (mpp) REVERT: A 570 CYS cc_start: 0.8840 (m) cc_final: 0.8332 (m) REVERT: A 601 MET cc_start: 0.8252 (tmm) cc_final: 0.7852 (tmm) REVERT: A 605 LEU cc_start: 0.9441 (tp) cc_final: 0.9158 (tp) REVERT: A 653 GLU cc_start: 0.8950 (pm20) cc_final: 0.8733 (mp0) REVERT: B 90 GLU cc_start: 0.8100 (mm-30) cc_final: 0.7707 (mm-30) REVERT: B 118 LEU cc_start: 0.9119 (mm) cc_final: 0.8748 (tp) REVERT: B 193 GLU cc_start: 0.8636 (tm-30) cc_final: 0.8289 (tm-30) REVERT: B 207 ASP cc_start: 0.8781 (p0) cc_final: 0.8549 (p0) REVERT: B 318 MET cc_start: 0.8302 (mpp) cc_final: 0.7934 (mpp) REVERT: B 570 CYS cc_start: 0.8842 (m) cc_final: 0.8335 (m) REVERT: B 601 MET cc_start: 0.8248 (tmm) cc_final: 0.7849 (tmm) REVERT: B 605 LEU cc_start: 0.9452 (tp) cc_final: 0.9171 (tp) REVERT: B 653 GLU cc_start: 0.8954 (pm20) cc_final: 0.8732 (mp0) REVERT: C 90 GLU cc_start: 0.8086 (mm-30) cc_final: 0.7694 (mm-30) REVERT: C 118 LEU cc_start: 0.9125 (mm) cc_final: 0.8756 (tp) REVERT: C 193 GLU cc_start: 0.8661 (tm-30) cc_final: 0.8313 (tm-30) REVERT: C 207 ASP cc_start: 0.8797 (p0) cc_final: 0.8562 (p0) REVERT: C 318 MET cc_start: 0.8305 (mpp) cc_final: 0.7941 (mpp) REVERT: C 570 CYS cc_start: 0.8831 (m) cc_final: 0.8329 (m) REVERT: C 601 MET cc_start: 0.8243 (tmm) cc_final: 0.7845 (tmm) REVERT: C 605 LEU cc_start: 0.9433 (tp) cc_final: 0.9152 (tp) REVERT: C 653 GLU cc_start: 0.8950 (pm20) cc_final: 0.8737 (mp0) REVERT: D 90 GLU cc_start: 0.8099 (mm-30) cc_final: 0.7701 (mm-30) REVERT: D 118 LEU cc_start: 0.9121 (mm) cc_final: 0.8751 (tp) REVERT: D 193 GLU cc_start: 0.8636 (tm-30) cc_final: 0.8294 (tm-30) REVERT: D 207 ASP cc_start: 0.8776 (p0) cc_final: 0.8547 (p0) REVERT: D 318 MET cc_start: 0.8300 (mpp) cc_final: 0.7936 (mpp) REVERT: D 570 CYS cc_start: 0.8831 (m) cc_final: 0.8332 (m) REVERT: D 601 MET cc_start: 0.8267 (tmm) cc_final: 0.7869 (tmm) REVERT: D 605 LEU cc_start: 0.9436 (tp) cc_final: 0.9152 (tp) REVERT: D 653 GLU cc_start: 0.8935 (pm20) cc_final: 0.8724 (mp0) outliers start: 0 outliers final: 0 residues processed: 244 average time/residue: 0.2899 time to fit residues: 109.9505 Evaluate side-chains 212 residues out of total 2224 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 212 time to evaluate : 1.724 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 244 optimal weight: 5.9990 chunk 186 optimal weight: 5.9990 chunk 128 optimal weight: 2.9990 chunk 27 optimal weight: 6.9990 chunk 118 optimal weight: 8.9990 chunk 166 optimal weight: 20.0000 chunk 248 optimal weight: 9.9990 chunk 262 optimal weight: 9.9990 chunk 129 optimal weight: 2.9990 chunk 235 optimal weight: 10.0000 chunk 70 optimal weight: 3.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 517 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 708 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 770 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 517 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 708 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 770 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 436 ASN ** C 517 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 708 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 770 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 517 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8335 moved from start: 0.2940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 21048 Z= 0.327 Angle : 0.669 8.087 28484 Z= 0.342 Chirality : 0.043 0.136 3360 Planarity : 0.005 0.042 3696 Dihedral : 5.137 25.531 2912 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 12.50 Ramachandran Plot: Outliers : 0.15 % Allowed : 8.42 % Favored : 91.43 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.20 (0.16), residues: 2708 helix: -0.00 (0.15), residues: 1292 sheet: -3.44 (0.20), residues: 456 loop : -2.33 (0.20), residues: 960 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP B 304 HIS 0.006 0.001 HIS B 517 PHE 0.018 0.001 PHE A 696 TYR 0.008 0.001 TYR C 677 ARG 0.008 0.001 ARG A 625 *********************** 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 228 residues out of total 2224 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 228 time to evaluate : 2.394 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 118 LEU cc_start: 0.9083 (mm) cc_final: 0.8734 (tp) REVERT: A 119 MET cc_start: 0.8239 (tmm) cc_final: 0.7976 (tmm) REVERT: A 193 GLU cc_start: 0.8606 (tm-30) cc_final: 0.8387 (tm-30) REVERT: A 207 ASP cc_start: 0.8786 (p0) cc_final: 0.8564 (p0) REVERT: A 271 MET cc_start: 0.7481 (tpp) cc_final: 0.7170 (tpp) REVERT: A 318 MET cc_start: 0.8324 (mpp) cc_final: 0.7932 (mpp) REVERT: A 570 CYS cc_start: 0.8837 (m) cc_final: 0.8337 (m) REVERT: A 601 MET cc_start: 0.8112 (tmm) cc_final: 0.7700 (tmm) REVERT: A 605 LEU cc_start: 0.9451 (tp) cc_final: 0.9101 (mp) REVERT: A 653 GLU cc_start: 0.8938 (pm20) cc_final: 0.8733 (mp0) REVERT: B 118 LEU cc_start: 0.9083 (mm) cc_final: 0.8731 (tp) REVERT: B 119 MET cc_start: 0.8243 (tmm) cc_final: 0.7979 (tmm) REVERT: B 193 GLU cc_start: 0.8593 (tm-30) cc_final: 0.8381 (tm-30) REVERT: B 207 ASP cc_start: 0.8781 (p0) cc_final: 0.8559 (p0) REVERT: B 271 MET cc_start: 0.7487 (tpp) cc_final: 0.7177 (tpp) REVERT: B 318 MET cc_start: 0.8289 (mpp) cc_final: 0.7886 (mpp) REVERT: B 570 CYS cc_start: 0.8840 (m) cc_final: 0.8340 (m) REVERT: B 601 MET cc_start: 0.8108 (tmm) cc_final: 0.7700 (tmm) REVERT: B 605 LEU cc_start: 0.9455 (tp) cc_final: 0.9111 (mp) REVERT: B 653 GLU cc_start: 0.8945 (pm20) cc_final: 0.8686 (mp0) REVERT: C 118 LEU cc_start: 0.9087 (mm) cc_final: 0.8738 (tp) REVERT: C 119 MET cc_start: 0.8237 (tmm) cc_final: 0.7971 (tmm) REVERT: C 193 GLU cc_start: 0.8627 (tm-30) cc_final: 0.8405 (tm-30) REVERT: C 207 ASP cc_start: 0.8794 (p0) cc_final: 0.8569 (p0) REVERT: C 271 MET cc_start: 0.7475 (tpp) cc_final: 0.7174 (tpp) REVERT: C 318 MET cc_start: 0.8322 (mpp) cc_final: 0.7935 (mpp) REVERT: C 570 CYS cc_start: 0.8832 (m) cc_final: 0.8339 (m) REVERT: C 601 MET cc_start: 0.8101 (tmm) cc_final: 0.7694 (tmm) REVERT: C 605 LEU cc_start: 0.9444 (tp) cc_final: 0.9085 (mp) REVERT: C 653 GLU cc_start: 0.8939 (pm20) cc_final: 0.8735 (mp0) REVERT: D 118 LEU cc_start: 0.9082 (mm) cc_final: 0.8733 (tp) REVERT: D 119 MET cc_start: 0.8231 (tmm) cc_final: 0.7967 (tmm) REVERT: D 193 GLU cc_start: 0.8602 (tm-30) cc_final: 0.8388 (tm-30) REVERT: D 207 ASP cc_start: 0.8776 (p0) cc_final: 0.8555 (p0) REVERT: D 271 MET cc_start: 0.7482 (tpp) cc_final: 0.7173 (tpp) REVERT: D 318 MET cc_start: 0.8323 (mpp) cc_final: 0.7935 (mpp) REVERT: D 570 CYS cc_start: 0.8830 (m) cc_final: 0.8337 (m) REVERT: D 601 MET cc_start: 0.8121 (tmm) cc_final: 0.7713 (tmm) REVERT: D 605 LEU cc_start: 0.9440 (tp) cc_final: 0.9087 (mp) REVERT: D 653 GLU cc_start: 0.8921 (pm20) cc_final: 0.8674 (mp0) outliers start: 0 outliers final: 0 residues processed: 228 average time/residue: 0.2983 time to fit residues: 110.0022 Evaluate side-chains 185 residues out of total 2224 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 185 time to evaluate : 2.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 218 optimal weight: 0.5980 chunk 149 optimal weight: 3.9990 chunk 3 optimal weight: 0.8980 chunk 195 optimal weight: 10.0000 chunk 108 optimal weight: 0.0570 chunk 224 optimal weight: 7.9990 chunk 181 optimal weight: 8.9990 chunk 0 optimal weight: 10.0000 chunk 134 optimal weight: 8.9990 chunk 235 optimal weight: 4.9990 chunk 66 optimal weight: 6.9990 overall best weight: 2.1102 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 517 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 708 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 436 ASN ** B 517 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 708 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 517 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 708 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 436 ASN ** D 517 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 708 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8287 moved from start: 0.3365 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= 0.202 Angle : 0.622 6.773 28484 Z= 0.314 Chirality : 0.043 0.190 3360 Planarity : 0.004 0.039 3696 Dihedral : 4.787 25.176 2912 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 10.49 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.98 % Favored : 92.87 % Rotamer: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.80 (0.17), residues: 2708 helix: 0.28 (0.15), residues: 1292 sheet: -3.16 (0.21), residues: 468 loop : -2.07 (0.21), residues: 948 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 304 HIS 0.003 0.001 HIS D 673 PHE 0.028 0.001 PHE A 696 TYR 0.011 0.001 TYR A 164 ARG 0.004 0.000 ARG A 625 *********************** 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 248 residues out of total 2224 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 248 time to evaluate : 2.361 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: 0.8082 (mm-30) cc_final: 0.7771 (mm-30) REVERT: A 118 LEU cc_start: 0.8939 (mm) cc_final: 0.8724 (tp) REVERT: A 207 ASP cc_start: 0.8770 (p0) cc_final: 0.8526 (p0) REVERT: A 234 ASP cc_start: 0.9045 (m-30) cc_final: 0.8746 (m-30) REVERT: A 318 MET cc_start: 0.8290 (mpp) cc_final: 0.7900 (mpp) REVERT: A 570 CYS cc_start: 0.8805 (m) cc_final: 0.8311 (m) REVERT: A 601 MET cc_start: 0.8134 (tmm) cc_final: 0.7737 (tmm) REVERT: A 605 LEU cc_start: 0.9469 (tp) cc_final: 0.9138 (mp) REVERT: A 653 GLU cc_start: 0.8904 (pm20) cc_final: 0.8668 (mp0) REVERT: A 677 TYR cc_start: 0.9019 (m-80) cc_final: 0.8803 (m-80) REVERT: B 90 GLU cc_start: 0.8099 (mm-30) cc_final: 0.7789 (mm-30) REVERT: B 118 LEU cc_start: 0.8939 (mm) cc_final: 0.8720 (tp) REVERT: B 123 MET cc_start: 0.8290 (ttm) cc_final: 0.8064 (ttm) REVERT: B 207 ASP cc_start: 0.8764 (p0) cc_final: 0.8519 (p0) REVERT: B 234 ASP cc_start: 0.9053 (m-30) cc_final: 0.8752 (m-30) REVERT: B 318 MET cc_start: 0.8287 (mpp) cc_final: 0.7895 (mpp) REVERT: B 570 CYS cc_start: 0.8814 (m) cc_final: 0.8320 (m) REVERT: B 601 MET cc_start: 0.8131 (tmm) cc_final: 0.7736 (tmm) REVERT: B 605 LEU cc_start: 0.9472 (tp) cc_final: 0.9143 (mp) REVERT: B 653 GLU cc_start: 0.8911 (pm20) cc_final: 0.8669 (mp0) REVERT: B 677 TYR cc_start: 0.9035 (m-80) cc_final: 0.8811 (m-80) REVERT: C 90 GLU cc_start: 0.8084 (mm-30) cc_final: 0.7778 (mm-30) REVERT: C 118 LEU cc_start: 0.8944 (mm) cc_final: 0.8730 (tp) REVERT: C 207 ASP cc_start: 0.8780 (p0) cc_final: 0.8531 (p0) REVERT: C 234 ASP cc_start: 0.9071 (m-30) cc_final: 0.8768 (m-30) REVERT: C 318 MET cc_start: 0.8290 (mpp) cc_final: 0.7904 (mpp) REVERT: C 570 CYS cc_start: 0.8798 (m) cc_final: 0.8309 (m) REVERT: C 601 MET cc_start: 0.8122 (tmm) cc_final: 0.7728 (tmm) REVERT: C 605 LEU cc_start: 0.9459 (tp) cc_final: 0.9117 (mp) REVERT: C 653 GLU cc_start: 0.8906 (pm20) cc_final: 0.8671 (mp0) REVERT: C 677 TYR cc_start: 0.9007 (m-80) cc_final: 0.8798 (m-80) REVERT: D 90 GLU cc_start: 0.8091 (mm-30) cc_final: 0.7781 (mm-30) REVERT: D 118 LEU cc_start: 0.8938 (mm) cc_final: 0.8723 (tp) REVERT: D 207 ASP cc_start: 0.8758 (p0) cc_final: 0.8514 (p0) REVERT: D 234 ASP cc_start: 0.9062 (m-30) cc_final: 0.8757 (m-30) REVERT: D 318 MET cc_start: 0.8286 (mpp) cc_final: 0.7895 (mpp) REVERT: D 570 CYS cc_start: 0.8798 (m) cc_final: 0.8307 (m) REVERT: D 601 MET cc_start: 0.8143 (tmm) cc_final: 0.7746 (tmm) REVERT: D 605 LEU cc_start: 0.9460 (tp) cc_final: 0.9119 (mp) REVERT: D 653 GLU cc_start: 0.8884 (pm20) cc_final: 0.8659 (mp0) REVERT: D 677 TYR cc_start: 0.8995 (m-80) cc_final: 0.8793 (m-80) outliers start: 0 outliers final: 0 residues processed: 248 average time/residue: 0.2841 time to fit residues: 113.6833 Evaluate side-chains 200 residues out of total 2224 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 200 time to evaluate : 2.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 88 optimal weight: 9.9990 chunk 236 optimal weight: 4.9990 chunk 51 optimal weight: 9.9990 chunk 154 optimal weight: 9.9990 chunk 64 optimal weight: 9.9990 chunk 263 optimal weight: 20.0000 chunk 218 optimal weight: 0.5980 chunk 121 optimal weight: 2.9990 chunk 21 optimal weight: 8.9990 chunk 87 optimal weight: 0.8980 chunk 138 optimal weight: 0.6980 overall best weight: 2.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 369 GLN A 436 ASN ** A 517 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 708 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 369 GLN ** B 517 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 708 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 369 GLN ** C 517 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 708 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 369 GLN ** D 517 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 708 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8269 moved from start: 0.3599 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= 0.195 Angle : 0.594 5.910 28484 Z= 0.300 Chirality : 0.042 0.154 3360 Planarity : 0.004 0.039 3696 Dihedral : 4.638 24.149 2912 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 10.25 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.43 % Favored : 93.43 % Rotamer: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.49 (0.17), residues: 2708 helix: 0.48 (0.15), residues: 1304 sheet: -2.87 (0.22), residues: 464 loop : -1.97 (0.21), residues: 940 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 304 HIS 0.003 0.001 HIS B 517 PHE 0.008 0.001 PHE D 696 TYR 0.010 0.001 TYR D 164 ARG 0.004 0.000 ARG B 308 *********************** 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 254 residues out of total 2224 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 254 time to evaluate : 2.469 Fit side-chains REVERT: A 90 GLU cc_start: 0.8038 (mm-30) cc_final: 0.7746 (mm-30) REVERT: A 118 LEU cc_start: 0.9039 (mm) cc_final: 0.8774 (tp) REVERT: A 207 ASP cc_start: 0.8815 (p0) cc_final: 0.8537 (p0) REVERT: A 318 MET cc_start: 0.8359 (mpp) cc_final: 0.7951 (mpp) REVERT: A 570 CYS cc_start: 0.8816 (m) cc_final: 0.8356 (m) REVERT: A 601 MET cc_start: 0.8154 (tmm) cc_final: 0.7820 (tmm) REVERT: A 653 GLU cc_start: 0.8916 (pm20) cc_final: 0.8715 (mp0) REVERT: A 677 TYR cc_start: 0.9059 (m-80) cc_final: 0.8722 (m-80) REVERT: B 90 GLU cc_start: 0.8057 (mm-30) cc_final: 0.7764 (mm-30) REVERT: B 118 LEU cc_start: 0.9040 (mm) cc_final: 0.8776 (tp) REVERT: B 207 ASP cc_start: 0.8811 (p0) cc_final: 0.8532 (p0) REVERT: B 318 MET cc_start: 0.8351 (mpp) cc_final: 0.7946 (mpp) REVERT: B 570 CYS cc_start: 0.8815 (m) cc_final: 0.8357 (m) REVERT: B 601 MET cc_start: 0.8152 (tmm) cc_final: 0.7819 (tmm) REVERT: B 653 GLU cc_start: 0.8921 (pm20) cc_final: 0.8714 (mp0) REVERT: B 677 TYR cc_start: 0.9077 (m-80) cc_final: 0.8729 (m-80) REVERT: C 90 GLU cc_start: 0.8042 (mm-30) cc_final: 0.7752 (mm-30) REVERT: C 118 LEU cc_start: 0.9041 (mm) cc_final: 0.8776 (tp) REVERT: C 207 ASP cc_start: 0.8825 (p0) cc_final: 0.8543 (p0) REVERT: C 318 MET cc_start: 0.8360 (mpp) cc_final: 0.7955 (mpp) REVERT: C 570 CYS cc_start: 0.8804 (m) cc_final: 0.8350 (m) REVERT: C 601 MET cc_start: 0.8142 (tmm) cc_final: 0.7814 (tmm) REVERT: C 653 GLU cc_start: 0.8916 (pm20) cc_final: 0.8716 (mp0) REVERT: C 677 TYR cc_start: 0.9048 (m-80) cc_final: 0.8717 (m-80) REVERT: D 90 GLU cc_start: 0.8049 (mm-30) cc_final: 0.7755 (mm-30) REVERT: D 118 LEU cc_start: 0.9035 (mm) cc_final: 0.8770 (tp) REVERT: D 207 ASP cc_start: 0.8805 (p0) cc_final: 0.8527 (p0) REVERT: D 318 MET cc_start: 0.8352 (mpp) cc_final: 0.7945 (mpp) REVERT: D 570 CYS cc_start: 0.8810 (m) cc_final: 0.8359 (m) REVERT: D 601 MET cc_start: 0.8165 (tmm) cc_final: 0.7832 (tmm) REVERT: D 677 TYR cc_start: 0.9038 (m-80) cc_final: 0.8709 (m-80) outliers start: 0 outliers final: 0 residues processed: 254 average time/residue: 0.2805 time to fit residues: 114.5378 Evaluate side-chains 201 residues out of total 2224 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 201 time to evaluate : 2.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 253 optimal weight: 0.9980 chunk 29 optimal weight: 6.9990 chunk 149 optimal weight: 4.9990 chunk 192 optimal weight: 20.0000 chunk 148 optimal weight: 4.9990 chunk 221 optimal weight: 4.9990 chunk 146 optimal weight: 0.4980 chunk 262 optimal weight: 9.9990 chunk 164 optimal weight: 1.9990 chunk 159 optimal weight: 1.9990 chunk 121 optimal weight: 2.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 375 ASN A 517 HIS ** A 708 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 375 ASN B 517 HIS B 708 ASN C 375 ASN C 517 HIS ** C 708 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 375 ASN D 517 HIS D 708 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8254 moved from start: 0.3909 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= 0.181 Angle : 0.614 9.159 28484 Z= 0.306 Chirality : 0.042 0.155 3360 Planarity : 0.004 0.040 3696 Dihedral : 4.529 24.847 2912 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.09 % Favored : 93.76 % Rotamer: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.28 (0.17), residues: 2708 helix: 0.66 (0.15), residues: 1304 sheet: -2.80 (0.21), residues: 468 loop : -1.84 (0.21), residues: 936 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 304 HIS 0.002 0.001 HIS D 272 PHE 0.007 0.001 PHE B 696 TYR 0.009 0.001 TYR D 164 ARG 0.002 0.000 ARG B 80 *********************** 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 fitting. rotamer outliers: 0 poor density : 250 time to evaluate : 2.394 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: 0.7847 (mm-30) REVERT: A 118 LEU cc_start: 0.8999 (mm) cc_final: 0.8710 (tp) REVERT: A 207 ASP cc_start: 0.8765 (p0) cc_final: 0.8539 (p0) REVERT: A 318 MET cc_start: 0.8358 (mpp) cc_final: 0.7972 (mpp) REVERT: A 493 LYS cc_start: 0.7738 (pptt) cc_final: 0.7483 (mmmm) REVERT: A 570 CYS cc_start: 0.8766 (m) cc_final: 0.8317 (m) REVERT: A 601 MET cc_start: 0.8146 (tmm) cc_final: 0.7798 (tmm) REVERT: A 677 TYR cc_start: 0.9054 (m-80) cc_final: 0.8709 (m-80) REVERT: B 90 GLU cc_start: 0.8129 (mm-30) cc_final: 0.7867 (mm-30) REVERT: B 118 LEU cc_start: 0.9000 (mm) cc_final: 0.8703 (tp) REVERT: B 125 GLU cc_start: 0.8982 (mt-10) cc_final: 0.8771 (tp30) REVERT: B 207 ASP cc_start: 0.8758 (p0) cc_final: 0.8532 (p0) REVERT: B 318 MET cc_start: 0.8351 (mpp) cc_final: 0.7966 (mpp) REVERT: B 493 LYS cc_start: 0.7724 (pptt) cc_final: 0.7473 (mmmm) REVERT: B 570 CYS cc_start: 0.8772 (m) cc_final: 0.8323 (m) REVERT: B 601 MET cc_start: 0.8141 (tmm) cc_final: 0.7792 (tmm) REVERT: B 677 TYR cc_start: 0.9071 (m-80) cc_final: 0.8717 (m-80) REVERT: C 90 GLU cc_start: 0.8116 (mm-30) cc_final: 0.7851 (mm-30) REVERT: C 118 LEU cc_start: 0.9001 (mm) cc_final: 0.8717 (tp) REVERT: C 207 ASP cc_start: 0.8775 (p0) cc_final: 0.8542 (p0) REVERT: C 318 MET cc_start: 0.8358 (mpp) cc_final: 0.7977 (mpp) REVERT: C 493 LYS cc_start: 0.7723 (pptt) cc_final: 0.7473 (mmmm) REVERT: C 570 CYS cc_start: 0.8752 (m) cc_final: 0.8305 (m) REVERT: C 601 MET cc_start: 0.8130 (tmm) cc_final: 0.7789 (tmm) REVERT: C 677 TYR cc_start: 0.9042 (m-80) cc_final: 0.8704 (m-80) REVERT: D 90 GLU cc_start: 0.8124 (mm-30) cc_final: 0.7858 (mm-30) REVERT: D 118 LEU cc_start: 0.8996 (mm) cc_final: 0.8712 (tp) REVERT: D 207 ASP cc_start: 0.8757 (p0) cc_final: 0.8530 (p0) REVERT: D 318 MET cc_start: 0.8352 (mpp) cc_final: 0.7970 (mpp) REVERT: D 493 LYS cc_start: 0.7735 (pptt) cc_final: 0.7476 (mmmm) REVERT: D 570 CYS cc_start: 0.8760 (m) cc_final: 0.8315 (m) REVERT: D 601 MET cc_start: 0.8150 (tmm) cc_final: 0.7805 (tmm) REVERT: D 677 TYR cc_start: 0.9031 (m-80) cc_final: 0.8694 (m-80) outliers start: 0 outliers final: 0 residues processed: 250 average time/residue: 0.2865 time to fit residues: 116.2298 Evaluate side-chains 215 residues out of total 2224 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 215 time to evaluate : 2.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 162 optimal weight: 6.9990 chunk 104 optimal weight: 3.9990 chunk 156 optimal weight: 7.9990 chunk 78 optimal weight: 0.5980 chunk 51 optimal weight: 20.0000 chunk 50 optimal weight: 4.9990 chunk 166 optimal weight: 20.0000 chunk 178 optimal weight: 8.9990 chunk 129 optimal weight: 8.9990 chunk 24 optimal weight: 10.0000 chunk 206 optimal weight: 1.9990 overall best weight: 3.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 571 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 454 GLN ** B 571 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 571 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 454 GLN ** D 571 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8314 moved from start: 0.3789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 21048 Z= 0.285 Angle : 0.652 9.693 28484 Z= 0.327 Chirality : 0.043 0.139 3360 Planarity : 0.004 0.036 3696 Dihedral : 4.863 25.921 2912 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 10.46 Ramachandran Plot: Outliers : 0.15 % Allowed : 9.05 % Favored : 90.81 % Rotamer: Outliers : 0.00 % Allowed : 0.58 % Favored : 99.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.36 (0.17), residues: 2708 helix: 0.57 (0.15), residues: 1304 sheet: -2.86 (0.21), residues: 468 loop : -1.82 (0.22), residues: 936 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP D 304 HIS 0.003 0.001 HIS A 517 PHE 0.006 0.001 PHE D 642 TYR 0.008 0.001 TYR D 55 ARG 0.003 0.000 ARG A 96 *********************** 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 226 residues out of total 2224 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 226 time to evaluate : 2.121 Fit side-chains REVERT: A 90 GLU cc_start: 0.8058 (mm-30) cc_final: 0.7731 (mm-30) REVERT: A 118 LEU cc_start: 0.9040 (mm) cc_final: 0.8764 (tp) REVERT: A 125 GLU cc_start: 0.9182 (tt0) cc_final: 0.8941 (tm-30) REVERT: A 207 ASP cc_start: 0.8821 (p0) cc_final: 0.8613 (p0) REVERT: A 318 MET cc_start: 0.8395 (mpp) cc_final: 0.7988 (mpp) REVERT: A 353 GLU cc_start: 0.8758 (mp0) cc_final: 0.8480 (mp0) REVERT: A 570 CYS cc_start: 0.8847 (m) cc_final: 0.8405 (m) REVERT: A 601 MET cc_start: 0.8143 (tmm) cc_final: 0.7742 (tmm) REVERT: A 677 TYR cc_start: 0.9154 (m-80) cc_final: 0.8747 (m-80) REVERT: B 90 GLU cc_start: 0.8079 (mm-30) cc_final: 0.7750 (mm-30) REVERT: B 118 LEU cc_start: 0.9038 (mm) cc_final: 0.8769 (tp) REVERT: B 125 GLU cc_start: 0.9044 (mt-10) cc_final: 0.8840 (tp30) REVERT: B 207 ASP cc_start: 0.8818 (p0) cc_final: 0.8606 (p0) REVERT: B 318 MET cc_start: 0.8389 (mpp) cc_final: 0.7980 (mpp) REVERT: B 570 CYS cc_start: 0.8842 (m) cc_final: 0.8404 (m) REVERT: B 601 MET cc_start: 0.8136 (tmm) cc_final: 0.7738 (tmm) REVERT: B 677 TYR cc_start: 0.9168 (m-80) cc_final: 0.8753 (m-80) REVERT: C 90 GLU cc_start: 0.8061 (mm-30) cc_final: 0.7736 (mm-30) REVERT: C 118 LEU cc_start: 0.9041 (mm) cc_final: 0.8766 (tp) REVERT: C 123 MET cc_start: 0.8344 (ttm) cc_final: 0.8113 (tpp) REVERT: C 125 GLU cc_start: 0.9166 (tt0) cc_final: 0.8941 (tm-30) REVERT: C 207 ASP cc_start: 0.8834 (p0) cc_final: 0.8619 (p0) REVERT: C 318 MET cc_start: 0.8396 (mpp) cc_final: 0.7989 (mpp) REVERT: C 353 GLU cc_start: 0.8772 (mp0) cc_final: 0.8493 (mp0) REVERT: C 570 CYS cc_start: 0.8833 (m) cc_final: 0.8395 (m) REVERT: C 601 MET cc_start: 0.8132 (tmm) cc_final: 0.7734 (tmm) REVERT: C 677 TYR cc_start: 0.9142 (m-80) cc_final: 0.8743 (m-80) REVERT: D 90 GLU cc_start: 0.8073 (mm-30) cc_final: 0.7746 (mm-30) REVERT: D 118 LEU cc_start: 0.9036 (mm) cc_final: 0.8758 (tp) REVERT: D 123 MET cc_start: 0.8355 (ttm) cc_final: 0.8112 (tpp) REVERT: D 125 GLU cc_start: 0.9174 (tt0) cc_final: 0.8936 (tm-30) REVERT: D 207 ASP cc_start: 0.8818 (p0) cc_final: 0.8605 (p0) REVERT: D 318 MET cc_start: 0.8394 (mpp) cc_final: 0.7986 (mpp) REVERT: D 353 GLU cc_start: 0.8761 (mp0) cc_final: 0.8486 (mp0) REVERT: D 570 CYS cc_start: 0.8840 (m) cc_final: 0.8403 (m) REVERT: D 601 MET cc_start: 0.8150 (tmm) cc_final: 0.7752 (tmm) REVERT: D 677 TYR cc_start: 0.9130 (m-80) cc_final: 0.8732 (m-80) outliers start: 0 outliers final: 0 residues processed: 226 average time/residue: 0.2741 time to fit residues: 101.7109 Evaluate side-chains 198 residues out of total 2224 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 198 time to evaluate : 2.517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 238 optimal weight: 6.9990 chunk 251 optimal weight: 0.7980 chunk 229 optimal weight: 8.9990 chunk 244 optimal weight: 1.9990 chunk 147 optimal weight: 0.9990 chunk 106 optimal weight: 5.9990 chunk 191 optimal weight: 8.9990 chunk 74 optimal weight: 0.7980 chunk 220 optimal weight: 2.9990 chunk 231 optimal weight: 0.9990 chunk 243 optimal weight: 10.0000 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 316 ASN B 316 ASN C 316 ASN D 316 ASN D 454 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8245 moved from start: 0.4183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 21048 Z= 0.166 Angle : 0.621 9.523 28484 Z= 0.307 Chirality : 0.043 0.152 3360 Planarity : 0.004 0.036 3696 Dihedral : 4.436 24.349 2912 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 9.05 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.06 % Favored : 93.80 % Rotamer: Outliers : 0.00 % Allowed : 0.40 % Favored : 99.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.04 (0.17), residues: 2708 helix: 0.80 (0.15), residues: 1280 sheet: -2.62 (0.21), residues: 464 loop : -1.60 (0.21), residues: 964 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 304 HIS 0.002 0.001 HIS A 755 PHE 0.006 0.001 PHE A 616 TYR 0.010 0.001 TYR D 157 ARG 0.002 0.000 ARG A 124 *********************** 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 259 residues out of total 2224 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 259 time to evaluate : 2.224 Fit side-chains REVERT: A 90 GLU cc_start: 0.8117 (mm-30) cc_final: 0.7861 (mm-30) REVERT: A 118 LEU cc_start: 0.8987 (mm) cc_final: 0.8724 (tp) REVERT: A 123 MET cc_start: 0.8730 (tpt) cc_final: 0.8305 (tpp) REVERT: A 125 GLU cc_start: 0.9132 (tt0) cc_final: 0.8906 (tm-30) REVERT: A 179 TYR cc_start: 0.8571 (m-80) cc_final: 0.8124 (m-80) REVERT: A 207 ASP cc_start: 0.8762 (p0) cc_final: 0.8546 (p0) REVERT: A 318 MET cc_start: 0.8394 (mpp) cc_final: 0.8011 (mpp) REVERT: A 570 CYS cc_start: 0.8759 (m) cc_final: 0.8313 (m) REVERT: A 601 MET cc_start: 0.8149 (tmm) cc_final: 0.7794 (tmm) REVERT: A 677 TYR cc_start: 0.9085 (m-80) cc_final: 0.8751 (m-80) REVERT: B 90 GLU cc_start: 0.8138 (mm-30) cc_final: 0.7880 (mm-30) REVERT: B 118 LEU cc_start: 0.8983 (mm) cc_final: 0.8732 (tp) REVERT: B 179 TYR cc_start: 0.8585 (m-80) cc_final: 0.8130 (m-80) REVERT: B 207 ASP cc_start: 0.8755 (p0) cc_final: 0.8541 (p0) REVERT: B 318 MET cc_start: 0.8393 (mpp) cc_final: 0.8005 (mpp) REVERT: B 570 CYS cc_start: 0.8762 (m) cc_final: 0.8336 (m) REVERT: B 601 MET cc_start: 0.8188 (tmm) cc_final: 0.7858 (tmm) REVERT: B 677 TYR cc_start: 0.9103 (m-80) cc_final: 0.8758 (m-80) REVERT: C 90 GLU cc_start: 0.8121 (mm-30) cc_final: 0.7867 (mm-30) REVERT: C 118 LEU cc_start: 0.8992 (mm) cc_final: 0.8729 (tp) REVERT: C 125 GLU cc_start: 0.9159 (tt0) cc_final: 0.8909 (tm-30) REVERT: C 179 TYR cc_start: 0.8591 (m-80) cc_final: 0.8129 (m-80) REVERT: C 207 ASP cc_start: 0.8773 (p0) cc_final: 0.8551 (p0) REVERT: C 318 MET cc_start: 0.8395 (mpp) cc_final: 0.8018 (mpp) REVERT: C 570 CYS cc_start: 0.8748 (m) cc_final: 0.8310 (m) REVERT: C 601 MET cc_start: 0.8138 (tmm) cc_final: 0.7791 (tmm) REVERT: C 677 TYR cc_start: 0.9072 (m-80) cc_final: 0.8746 (m-80) REVERT: D 90 GLU cc_start: 0.8130 (mm-30) cc_final: 0.7871 (mm-30) REVERT: D 118 LEU cc_start: 0.8987 (mm) cc_final: 0.8724 (tp) REVERT: D 125 GLU cc_start: 0.9170 (tt0) cc_final: 0.8903 (tm-30) REVERT: D 179 TYR cc_start: 0.8580 (m-80) cc_final: 0.8126 (m-80) REVERT: D 207 ASP cc_start: 0.8755 (p0) cc_final: 0.8539 (p0) REVERT: D 318 MET cc_start: 0.8391 (mpp) cc_final: 0.8006 (mpp) REVERT: D 570 CYS cc_start: 0.8754 (m) cc_final: 0.8329 (m) REVERT: D 601 MET cc_start: 0.8200 (tmm) cc_final: 0.7873 (tmm) REVERT: D 677 TYR cc_start: 0.9062 (m-80) cc_final: 0.8740 (m-80) outliers start: 0 outliers final: 0 residues processed: 259 average time/residue: 0.2882 time to fit residues: 119.8168 Evaluate side-chains 208 residues out of total 2224 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 208 time to evaluate : 2.422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 160 optimal weight: 0.9980 chunk 258 optimal weight: 8.9990 chunk 157 optimal weight: 4.9990 chunk 122 optimal weight: 5.9990 chunk 179 optimal weight: 20.0000 chunk 270 optimal weight: 8.9990 chunk 249 optimal weight: 2.9990 chunk 215 optimal weight: 2.9990 chunk 22 optimal weight: 7.9990 chunk 166 optimal weight: 20.0000 chunk 132 optimal weight: 0.0970 overall best weight: 2.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 571 HIS B 454 GLN B 571 HIS C 571 HIS D 571 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8274 moved from start: 0.4187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 21048 Z= 0.217 Angle : 0.633 8.540 28484 Z= 0.317 Chirality : 0.043 0.148 3360 Planarity : 0.004 0.035 3696 Dihedral : 4.530 24.777 2912 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 10.03 Ramachandran Plot: Outliers : 0.15 % Allowed : 7.05 % Favored : 92.80 % Rotamer: Outliers : 0.00 % Allowed : 0.40 % Favored : 99.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.01 (0.17), residues: 2708 helix: 0.84 (0.15), residues: 1284 sheet: -2.64 (0.21), residues: 468 loop : -1.59 (0.21), residues: 956 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 304 HIS 0.002 0.001 HIS B 517 PHE 0.005 0.001 PHE B 696 TYR 0.011 0.001 TYR A 164 ARG 0.004 0.000 ARG C 124 ********************** 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 fitting. rotamer outliers: 0 poor density : 251 time to evaluate : 2.401 Fit side-chains REVERT: A 90 GLU cc_start: 0.8145 (mm-30) cc_final: 0.7876 (mm-30) REVERT: A 118 LEU cc_start: 0.9004 (mm) cc_final: 0.8719 (tp) REVERT: A 125 GLU cc_start: 0.9111 (tt0) cc_final: 0.8909 (tm-30) REVERT: A 179 TYR cc_start: 0.8507 (m-80) cc_final: 0.8102 (m-80) REVERT: A 207 ASP cc_start: 0.8808 (p0) cc_final: 0.8608 (p0) REVERT: A 318 MET cc_start: 0.8409 (mpp) cc_final: 0.7960 (mpp) REVERT: A 540 LEU cc_start: 0.9275 (tp) cc_final: 0.9053 (tt) REVERT: A 570 CYS cc_start: 0.8725 (m) cc_final: 0.8272 (m) REVERT: A 601 MET cc_start: 0.8189 (tmm) cc_final: 0.7823 (tmm) REVERT: A 677 TYR cc_start: 0.9130 (m-80) cc_final: 0.8745 (m-80) REVERT: B 71 GLU cc_start: 0.8546 (pm20) cc_final: 0.8149 (pm20) REVERT: B 90 GLU cc_start: 0.8160 (mm-30) cc_final: 0.7894 (mm-30) REVERT: B 118 LEU cc_start: 0.9000 (mm) cc_final: 0.8723 (tp) REVERT: B 179 TYR cc_start: 0.8516 (m-80) cc_final: 0.8106 (m-80) REVERT: B 207 ASP cc_start: 0.8800 (p0) cc_final: 0.8600 (p0) REVERT: B 318 MET cc_start: 0.8400 (mpp) cc_final: 0.7952 (mpp) REVERT: B 540 LEU cc_start: 0.9280 (tp) cc_final: 0.9056 (tt) REVERT: B 570 CYS cc_start: 0.8731 (m) cc_final: 0.8285 (m) REVERT: B 601 MET cc_start: 0.8180 (tmm) cc_final: 0.7818 (tmm) REVERT: B 677 TYR cc_start: 0.9145 (m-80) cc_final: 0.8752 (m-80) REVERT: C 90 GLU cc_start: 0.8147 (mm-30) cc_final: 0.7881 (mm-30) REVERT: C 118 LEU cc_start: 0.9006 (mm) cc_final: 0.8720 (tp) REVERT: C 179 TYR cc_start: 0.8523 (m-80) cc_final: 0.8106 (m-80) REVERT: C 207 ASP cc_start: 0.8822 (p0) cc_final: 0.8610 (p0) REVERT: C 318 MET cc_start: 0.8409 (mpp) cc_final: 0.7964 (mpp) REVERT: C 540 LEU cc_start: 0.9279 (tp) cc_final: 0.9055 (tt) REVERT: C 570 CYS cc_start: 0.8711 (m) cc_final: 0.8267 (m) REVERT: C 601 MET cc_start: 0.8177 (tmm) cc_final: 0.7816 (tmm) REVERT: C 677 TYR cc_start: 0.9116 (m-80) cc_final: 0.8739 (m-80) REVERT: D 71 GLU cc_start: 0.8532 (pm20) cc_final: 0.8137 (pm20) REVERT: D 90 GLU cc_start: 0.8155 (mm-30) cc_final: 0.7889 (mm-30) REVERT: D 118 LEU cc_start: 0.9001 (mm) cc_final: 0.8714 (tp) REVERT: D 179 TYR cc_start: 0.8508 (m-80) cc_final: 0.8100 (m-80) REVERT: D 207 ASP cc_start: 0.8799 (p0) cc_final: 0.8594 (p0) REVERT: D 318 MET cc_start: 0.8402 (mpp) cc_final: 0.7956 (mpp) REVERT: D 540 LEU cc_start: 0.9276 (tp) cc_final: 0.9050 (tt) REVERT: D 570 CYS cc_start: 0.8728 (m) cc_final: 0.8286 (m) REVERT: D 601 MET cc_start: 0.8194 (tmm) cc_final: 0.7836 (tmm) REVERT: D 677 TYR cc_start: 0.9105 (m-80) cc_final: 0.8730 (m-80) outliers start: 0 outliers final: 0 residues processed: 251 average time/residue: 0.3051 time to fit residues: 120.9895 Evaluate side-chains 205 residues out of total 2224 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 205 time to evaluate : 2.468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 171 optimal weight: 8.9990 chunk 229 optimal weight: 0.1980 chunk 66 optimal weight: 20.0000 chunk 198 optimal weight: 4.9990 chunk 31 optimal weight: 4.9990 chunk 59 optimal weight: 10.0000 chunk 216 optimal weight: 8.9990 chunk 90 optimal weight: 5.9990 chunk 221 optimal weight: 0.5980 chunk 27 optimal weight: 5.9990 chunk 39 optimal weight: 5.9990 overall best weight: 3.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.084105 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.060199 restraints weight = 76891.331| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.062058 restraints weight = 48591.545| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.063318 restraints weight = 36477.506| |-----------------------------------------------------------------------------| r_work (final): 0.3161 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8301 moved from start: 0.4215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 21048 Z= 0.264 Angle : 0.660 9.901 28484 Z= 0.332 Chirality : 0.043 0.151 3360 Planarity : 0.004 0.040 3696 Dihedral : 4.736 24.393 2912 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 10.56 Ramachandran Plot: Outliers : 0.15 % Allowed : 7.90 % Favored : 91.95 % Rotamer: Outliers : 0.00 % Allowed : 0.54 % Favored : 99.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.05 (0.17), residues: 2708 helix: 0.78 (0.15), residues: 1284 sheet: -2.73 (0.22), residues: 468 loop : -1.53 (0.22), residues: 956 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 304 HIS 0.003 0.001 HIS C 517 PHE 0.007 0.001 PHE B 642 TYR 0.008 0.001 TYR D 55 ARG 0.007 0.001 ARG C 96 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3440.09 seconds wall clock time: 64 minutes 54.64 seconds (3894.64 seconds total)