Starting phenix.real_space_refine on Tue Nov 19 14:04:00 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qdx_18342/11_2024/8qdx_18342.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qdx_18342/11_2024/8qdx_18342.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qdx_18342/11_2024/8qdx_18342.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qdx_18342/11_2024/8qdx_18342.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qdx_18342/11_2024/8qdx_18342.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qdx_18342/11_2024/8qdx_18342.cif" } resolution = 3.0 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= 0.002 sd= 0.992 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: 6 Type Number sf(0) Gaussians P 236 5.49 5 S 84 5.16 5 C 16508 2.51 5 N 4850 2.21 5 O 5729 1.98 5 H 25314 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 1.67s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 52721 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 8294 Number of conformers: 1 Conformer: "" Number of residues, atoms: 523, 8294 Classifications: {'peptide': 523} Link IDs: {'PTRANS': 21, 'TRANS': 501} Chain: "B" Number of atoms: 11902 Number of conformers: 1 Conformer: "" Number of residues, atoms: 753, 11902 Classifications: {'peptide': 753} Link IDs: {'PTRANS': 26, 'TRANS': 726} Chain breaks: 3 Chain: "C" Number of atoms: 13172 Number of conformers: 1 Conformer: "" Number of residues, atoms: 837, 13172 Classifications: {'peptide': 837} Link IDs: {'PTRANS': 28, 'TRANS': 808} Chain: "D" Number of atoms: 11919 Number of conformers: 1 Conformer: "" Number of residues, atoms: 754, 11919 Classifications: {'peptide': 754} Link IDs: {'PTRANS': 26, 'TRANS': 727} Chain breaks: 2 Chain: "E" Number of atoms: 3658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 3658 Classifications: {'DNA': 118} Link IDs: {'rna3p': 117} Chain: "F" Number of atoms: 3776 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 3776 Classifications: {'DNA': 118} Link IDs: {'rna3p': 117} Time building chain proxies: 24.35, per 1000 atoms: 0.46 Number of scatterers: 52721 At special positions: 0 Unit cell: (137.92, 156.884, 215.5, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 84 16.00 P 236 15.00 O 5729 8.00 N 4850 7.00 C 16508 6.00 H 25314 1.00 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: 12.42 Conformation dependent library (CDL) restraints added in 3.5 seconds 5698 Ramachandran restraints generated. 2849 Oldfield, 0 Emsley, 2849 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5326 Finding SS restraints... Secondary structure from input PDB file: 96 helices and 35 sheets defined 44.1% alpha, 14.5% beta 108 base pairs and 200 stacking pairs defined. Time for finding SS restraints: 23.34 Creating SS restraints... Processing helix chain 'A' and resid 13 through 32 Processing helix chain 'A' and resid 42 through 56 Processing helix chain 'A' and resid 66 through 77 Processing helix chain 'A' and resid 81 through 94 removed outlier: 3.757A pdb=" N VAL A 85 " --> pdb=" O GLY A 81 " (cutoff:3.500A) Processing helix chain 'A' and resid 128 through 135 removed outlier: 3.752A pdb=" N HIS A 132 " --> pdb=" O ALA A 128 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N GLU A 133 " --> pdb=" O LYS A 129 " (cutoff:3.500A) Processing helix chain 'A' and resid 164 through 170 Processing helix chain 'A' and resid 186 through 200 Processing helix chain 'A' and resid 204 through 212 removed outlier: 3.523A pdb=" N LEU A 208 " --> pdb=" O SER A 204 " (cutoff:3.500A) Processing helix chain 'A' and resid 226 through 236 Processing helix chain 'A' and resid 269 through 283 Processing helix chain 'A' and resid 313 through 324 Processing helix chain 'A' and resid 346 through 389 Processing helix chain 'A' and resid 389 through 400 Processing helix chain 'A' and resid 402 through 413 Processing helix chain 'A' and resid 418 through 425 Processing helix chain 'A' and resid 451 through 460 Processing helix chain 'A' and resid 462 through 466 Processing helix chain 'A' and resid 467 through 494 removed outlier: 3.752A pdb=" N SER A 494 " --> pdb=" O ARG A 490 " (cutoff:3.500A) Processing helix chain 'A' and resid 494 through 514 removed outlier: 3.620A pdb=" N LEU A 498 " --> pdb=" O SER A 494 " (cutoff:3.500A) Processing helix chain 'B' and resid 10 through 22 removed outlier: 3.835A pdb=" N ARG B 22 " --> pdb=" O ALA B 18 " (cutoff:3.500A) Processing helix chain 'B' and resid 23 through 26 Processing helix chain 'B' and resid 33 through 52 removed outlier: 4.070A pdb=" N HIS B 37 " --> pdb=" O GLY B 33 " (cutoff:3.500A) Processing helix chain 'B' and resid 121 through 126 Processing helix chain 'B' and resid 183 through 196 removed outlier: 3.749A pdb=" N LEU B 187 " --> pdb=" O GLU B 183 " (cutoff:3.500A) Processing helix chain 'B' and resid 221 through 230 Processing helix chain 'B' and resid 279 through 301 Processing helix chain 'B' and resid 301 through 307 Processing helix chain 'B' and resid 343 through 364 removed outlier: 4.412A pdb=" N SER B 347 " --> pdb=" O SER B 343 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ALA B 348 " --> pdb=" O GLU B 344 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N ALA B 358 " --> pdb=" O ASN B 354 " (cutoff:3.500A) Processing helix chain 'B' and resid 364 through 385 removed outlier: 3.795A pdb=" N ALA B 368 " --> pdb=" O ASN B 364 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ALA B 385 " --> pdb=" O ALA B 381 " (cutoff:3.500A) Processing helix chain 'B' and resid 425 through 435 removed outlier: 3.551A pdb=" N GLY B 435 " --> pdb=" O SER B 431 " (cutoff:3.500A) Processing helix chain 'B' and resid 458 through 462 removed outlier: 3.591A pdb=" N LEU B 462 " --> pdb=" O ASP B 459 " (cutoff:3.500A) Processing helix chain 'B' and resid 463 through 474 Processing helix chain 'B' and resid 484 through 488 Processing helix chain 'B' and resid 500 through 517 Processing helix chain 'B' and resid 520 through 524 Processing helix chain 'B' and resid 548 through 561 Processing helix chain 'B' and resid 576 through 598 Processing helix chain 'B' and resid 602 through 612 removed outlier: 3.686A pdb=" N ILE B 610 " --> pdb=" O LEU B 606 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N TYR B 611 " --> pdb=" O LYS B 607 " (cutoff:3.500A) Processing helix chain 'B' and resid 616 through 622 removed outlier: 3.646A pdb=" N LEU B 620 " --> pdb=" O THR B 616 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N SER B 621 " --> pdb=" O GLU B 617 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ASP B 622 " --> pdb=" O ALA B 618 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 616 through 622' Processing helix chain 'B' and resid 623 through 640 Processing helix chain 'B' and resid 678 through 683 removed outlier: 3.661A pdb=" N THR B 683 " --> pdb=" O HIS B 679 " (cutoff:3.500A) Processing helix chain 'B' and resid 686 through 696 removed outlier: 3.749A pdb=" N LYS B 696 " --> pdb=" O THR B 692 " (cutoff:3.500A) Processing helix chain 'B' and resid 718 through 731 Processing helix chain 'B' and resid 746 through 755 removed outlier: 3.899A pdb=" N MET B 755 " --> pdb=" O TRP B 751 " (cutoff:3.500A) Processing helix chain 'B' and resid 769 through 782 Processing helix chain 'B' and resid 785 through 801 Processing helix chain 'C' and resid 13 through 32 Processing helix chain 'C' and resid 42 through 56 Processing helix chain 'C' and resid 66 through 77 Processing helix chain 'C' and resid 84 through 94 Processing helix chain 'C' and resid 128 through 135 removed outlier: 3.794A pdb=" N HIS C 132 " --> pdb=" O ALA C 128 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N GLU C 133 " --> pdb=" O LYS C 129 " (cutoff:3.500A) Processing helix chain 'C' and resid 164 through 170 Processing helix chain 'C' and resid 186 through 200 Processing helix chain 'C' and resid 204 through 212 removed outlier: 3.531A pdb=" N LEU C 208 " --> pdb=" O SER C 204 " (cutoff:3.500A) Processing helix chain 'C' and resid 226 through 236 Processing helix chain 'C' and resid 269 through 283 Processing helix chain 'C' and resid 313 through 324 Processing helix chain 'C' and resid 346 through 389 Processing helix chain 'C' and resid 389 through 400 Processing helix chain 'C' and resid 402 through 413 Processing helix chain 'C' and resid 418 through 427 removed outlier: 3.662A pdb=" N ALA C 427 " --> pdb=" O MET C 423 " (cutoff:3.500A) Processing helix chain 'C' and resid 451 through 460 Processing helix chain 'C' and resid 462 through 466 Processing helix chain 'C' and resid 467 through 494 removed outlier: 3.994A pdb=" N HIS C 471 " --> pdb=" O THR C 467 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N GLU C 472 " --> pdb=" O GLY C 468 " (cutoff:3.500A) Processing helix chain 'C' and resid 494 through 514 removed outlier: 3.880A pdb=" N LEU C 498 " --> pdb=" O SER C 494 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N MET C 499 " --> pdb=" O ALA C 495 " (cutoff:3.500A) Processing helix chain 'C' and resid 529 through 535 removed outlier: 3.618A pdb=" N THR C 535 " --> pdb=" O GLU C 531 " (cutoff:3.500A) Processing helix chain 'C' and resid 554 through 558 removed outlier: 3.774A pdb=" N TYR C 557 " --> pdb=" O LEU C 554 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N GLU C 558 " --> pdb=" O SER C 555 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 554 through 558' Processing helix chain 'C' and resid 662 through 665 removed outlier: 3.860A pdb=" N ARG C 665 " --> pdb=" O GLU C 662 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 662 through 665' Processing helix chain 'C' and resid 708 through 712 removed outlier: 3.539A pdb=" N VAL C 711 " --> pdb=" O GLU C 708 " (cutoff:3.500A) Processing helix chain 'C' and resid 812 through 814 No H-bonds generated for 'chain 'C' and resid 812 through 814' Processing helix chain 'D' and resid 10 through 22 removed outlier: 3.930A pdb=" N ARG D 22 " --> pdb=" O ALA D 18 " (cutoff:3.500A) Processing helix chain 'D' and resid 23 through 26 Processing helix chain 'D' and resid 33 through 52 removed outlier: 4.130A pdb=" N HIS D 37 " --> pdb=" O GLY D 33 " (cutoff:3.500A) Processing helix chain 'D' and resid 121 through 126 Processing helix chain 'D' and resid 183 through 196 removed outlier: 3.798A pdb=" N LEU D 187 " --> pdb=" O GLU D 183 " (cutoff:3.500A) Processing helix chain 'D' and resid 221 through 231 Processing helix chain 'D' and resid 279 through 301 Processing helix chain 'D' and resid 301 through 307 Processing helix chain 'D' and resid 342 through 364 removed outlier: 4.425A pdb=" N LYS D 346 " --> pdb=" O SER D 342 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N SER D 347 " --> pdb=" O SER D 343 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ALA D 348 " --> pdb=" O GLU D 344 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ALA D 358 " --> pdb=" O ASN D 354 " (cutoff:3.500A) Processing helix chain 'D' and resid 364 through 385 removed outlier: 3.757A pdb=" N ALA D 385 " --> pdb=" O ALA D 381 " (cutoff:3.500A) Processing helix chain 'D' and resid 425 through 435 removed outlier: 3.693A pdb=" N GLY D 435 " --> pdb=" O SER D 431 " (cutoff:3.500A) Processing helix chain 'D' and resid 463 through 474 Processing helix chain 'D' and resid 484 through 488 Processing helix chain 'D' and resid 500 through 518 Processing helix chain 'D' and resid 518 through 524 Processing helix chain 'D' and resid 548 through 562 Processing helix chain 'D' and resid 576 through 597 Processing helix chain 'D' and resid 602 through 612 removed outlier: 3.758A pdb=" N ILE D 610 " --> pdb=" O LEU D 606 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N TYR D 611 " --> pdb=" O LYS D 607 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N GLN D 612 " --> pdb=" O GLU D 608 " (cutoff:3.500A) Processing helix chain 'D' and resid 616 through 622 removed outlier: 3.706A pdb=" N SER D 621 " --> pdb=" O GLU D 617 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N ASP D 622 " --> pdb=" O ALA D 618 " (cutoff:3.500A) Processing helix chain 'D' and resid 622 through 640 removed outlier: 3.502A pdb=" N VAL D 626 " --> pdb=" O ASP D 622 " (cutoff:3.500A) Processing helix chain 'D' and resid 678 through 683 removed outlier: 3.519A pdb=" N THR D 683 " --> pdb=" O HIS D 679 " (cutoff:3.500A) Processing helix chain 'D' and resid 685 through 697 Processing helix chain 'D' and resid 718 through 731 Processing helix chain 'D' and resid 746 through 754 Processing helix chain 'D' and resid 769 through 782 Processing helix chain 'D' and resid 785 through 801 Processing sheet with id=AA1, first strand: chain 'A' and resid 8 through 12 removed outlier: 6.610A pdb=" N THR A 9 " --> pdb=" O ARG B 764 " (cutoff:3.500A) removed outlier: 7.414A pdb=" N THR B 766 " --> pdb=" O THR A 9 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N VAL A 11 " --> pdb=" O THR B 766 " (cutoff:3.500A) removed outlier: 5.529A pdb=" N VAL B 527 " --> pdb=" O VAL B 765 " (cutoff:3.500A) removed outlier: 6.202A pdb=" N ILE B 493 " --> pdb=" O TYR B 528 " (cutoff:3.500A) removed outlier: 7.103A pdb=" N ALA B 530 " --> pdb=" O ILE B 493 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N ILE B 495 " --> pdb=" O ALA B 530 " (cutoff:3.500A) removed outlier: 6.215A pdb=" N LEU B 420 " --> pdb=" O ILE B 494 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N VAL B 423 " --> pdb=" O LEU B 444 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 64 through 65 Processing sheet with id=AA3, first strand: chain 'A' and resid 145 through 147 Processing sheet with id=AA4, first strand: chain 'A' and resid 171 through 174 Processing sheet with id=AA5, first strand: chain 'A' and resid 328 through 333 Processing sheet with id=AA6, first strand: chain 'A' and resid 246 through 250 removed outlier: 3.554A pdb=" N ILE A 260 " --> pdb=" O GLU A 247 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 335 through 337 Processing sheet with id=AA8, first strand: chain 'A' and resid 415 through 416 removed outlier: 3.578A pdb=" N GLY A 442 " --> pdb=" O TYR A 449 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 155 through 156 removed outlier: 3.626A pdb=" N ALA B 155 " --> pdb=" O ARG B 142 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N LEU B 132 " --> pdb=" O GLN B 143 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LYS B 129 " --> pdb=" O TRP B 170 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N VAL B 69 " --> pdb=" O PHE B 169 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N SER B 68 " --> pdb=" O HIS B 64 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ILE B 60 " --> pdb=" O GLN B 72 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 241 through 243 removed outlier: 3.530A pdb=" N PHE B 241 " --> pdb=" O LEU B 256 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LYS B 247 " --> pdb=" O ILE B 250 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 241 through 243 removed outlier: 3.530A pdb=" N PHE B 241 " --> pdb=" O LEU B 256 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 542 through 546 Processing sheet with id=AB4, first strand: chain 'B' and resid 565 through 567 removed outlier: 4.128A pdb=" N ARG B 712 " --> pdb=" O ARG B 709 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 647 through 654 removed outlier: 3.551A pdb=" N ASN B 654 " --> pdb=" O LEU B 659 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N VAL B 664 " --> pdb=" O TYR B 675 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 11 through 12 removed outlier: 6.303A pdb=" N VAL C 11 " --> pdb=" O THR D 766 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'C' and resid 64 through 65 Processing sheet with id=AB8, first strand: chain 'C' and resid 145 through 147 Processing sheet with id=AB9, first strand: chain 'C' and resid 171 through 174 Processing sheet with id=AC1, first strand: chain 'C' and resid 327 through 333 Processing sheet with id=AC2, first strand: chain 'C' and resid 246 through 250 removed outlier: 3.574A pdb=" N ILE C 303 " --> pdb=" O VAL C 261 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 335 through 337 Processing sheet with id=AC4, first strand: chain 'C' and resid 415 through 416 Processing sheet with id=AC5, first strand: chain 'C' and resid 540 through 545 Processing sheet with id=AC6, first strand: chain 'C' and resid 560 through 561 removed outlier: 7.180A pdb=" N ARG C 561 " --> pdb=" O SER C 810 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N VAL C 805 " --> pdb=" O ALA C 801 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 637 through 638 removed outlier: 3.949A pdb=" N VAL C 672 " --> pdb=" O TYR C 600 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 683 through 689 removed outlier: 3.861A pdb=" N VAL C 655 " --> pdb=" O ALA C 651 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 703 through 707 removed outlier: 3.829A pdb=" N VAL C 703 " --> pdb=" O ALA C 699 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LYS C 707 " --> pdb=" O MET C 695 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N MET C 695 " --> pdb=" O LYS C 707 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N LEU C 735 " --> pdb=" O SER C 698 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 757 through 758 removed outlier: 4.264A pdb=" N VAL C 787 " --> pdb=" O THR C 748 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'D' and resid 155 through 156 removed outlier: 3.569A pdb=" N ALA D 155 " --> pdb=" O ARG D 142 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N LEU D 132 " --> pdb=" O GLN D 143 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N TYR D 145 " --> pdb=" O LEU D 130 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LYS D 129 " --> pdb=" O TRP D 170 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N VAL D 69 " --> pdb=" O PHE D 169 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N SER D 68 " --> pdb=" O HIS D 64 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ILE D 60 " --> pdb=" O GLN D 72 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'D' and resid 241 through 243 removed outlier: 3.554A pdb=" N PHE D 243 " --> pdb=" O VAL D 254 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N VAL D 254 " --> pdb=" O PHE D 243 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N LYS D 247 " --> pdb=" O ILE D 250 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'D' and resid 241 through 243 removed outlier: 3.554A pdb=" N PHE D 243 " --> pdb=" O VAL D 254 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N VAL D 254 " --> pdb=" O PHE D 243 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N GLY D 251 " --> pdb=" O LYS D 326 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ALA D 255 " --> pdb=" O VAL D 322 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N VAL D 322 " --> pdb=" O ALA D 255 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N ASN D 265 " --> pdb=" O ALA D 321 " (cutoff:3.500A) removed outlier: 8.084A pdb=" N VAL D 323 " --> pdb=" O ASN D 265 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N TYR D 267 " --> pdb=" O VAL D 323 " (cutoff:3.500A) removed outlier: 8.150A pdb=" N VAL D 325 " --> pdb=" O TYR D 267 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N PHE D 269 " --> pdb=" O VAL D 325 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'D' and resid 441 through 445 removed outlier: 3.737A pdb=" N VAL D 423 " --> pdb=" O LEU D 444 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N LEU D 420 " --> pdb=" O ILE D 494 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N ILE D 493 " --> pdb=" O TYR D 528 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'D' and resid 542 through 546 Processing sheet with id=AD7, first strand: chain 'D' and resid 565 through 567 Processing sheet with id=AD8, first strand: chain 'D' and resid 647 through 654 1098 hydrogen bonds defined for protein. 3135 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 216 hydrogen bonds 432 hydrogen bond angles 0 basepair planarities 108 basepair parallelities 200 stacking parallelities Total time for adding SS restraints: 24.37 Time building geometry restraints manager: 15.02 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 8263 1.03 - 1.23: 17104 1.23 - 1.42: 11748 1.42 - 1.62: 16389 1.62 - 1.81: 158 Bond restraints: 53662 Sorted by residual: bond pdb=" N LYS C 707 " pdb=" H LYS C 707 " ideal model delta sigma weight residual 0.860 1.284 -0.424 2.00e-02 2.50e+03 4.50e+02 bond pdb=" NE1 TRP C 59 " pdb=" HE1 TRP C 59 " ideal model delta sigma weight residual 0.860 1.082 -0.222 2.00e-02 2.50e+03 1.23e+02 bond pdb=" NE1 TRP B 647 " pdb=" HE1 TRP B 647 " ideal model delta sigma weight residual 0.860 1.082 -0.222 2.00e-02 2.50e+03 1.23e+02 bond pdb=" NE1 TRP D 751 " pdb=" HE1 TRP D 751 " ideal model delta sigma weight residual 0.860 1.082 -0.222 2.00e-02 2.50e+03 1.23e+02 bond pdb=" NE1 TRP B 629 " pdb=" HE1 TRP B 629 " ideal model delta sigma weight residual 0.860 1.082 -0.222 2.00e-02 2.50e+03 1.23e+02 ... (remaining 53657 not shown) Histogram of bond angle deviations from ideal: 0.00 - 8.22: 97239 8.22 - 16.44: 44 16.44 - 24.65: 3 24.65 - 32.87: 0 32.87 - 41.09: 2 Bond angle restraints: 97288 Sorted by residual: angle pdb=" C PHE C 706 " pdb=" CA PHE C 706 " pdb=" CB PHE C 706 " ideal model delta sigma weight residual 110.62 75.13 35.49 1.51e+00 4.39e-01 5.52e+02 angle pdb=" C PHE C 706 " pdb=" N LYS C 707 " pdb=" H LYS C 707 " ideal model delta sigma weight residual 123.61 82.53 41.09 3.00e+00 1.11e-01 1.88e+02 angle pdb=" N PHE C 706 " pdb=" CA PHE C 706 " pdb=" C PHE C 706 " ideal model delta sigma weight residual 108.02 127.58 -19.56 1.78e+00 3.16e-01 1.21e+02 angle pdb=" N CYS C 592 " pdb=" CA CYS C 592 " pdb=" C CYS C 592 " ideal model delta sigma weight residual 108.41 91.34 17.07 1.63e+00 3.76e-01 1.10e+02 angle pdb=" N LYS C 707 " pdb=" CA LYS C 707 " pdb=" CB LYS C 707 " ideal model delta sigma weight residual 110.65 95.19 15.46 1.58e+00 4.01e-01 9.57e+01 ... (remaining 97283 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.20: 22970 34.20 - 68.39: 1465 68.39 - 102.59: 18 102.59 - 136.78: 0 136.78 - 170.98: 4 Dihedral angle restraints: 24457 sinusoidal: 15170 harmonic: 9287 Sorted by residual: dihedral pdb=" C PHE C 706 " pdb=" N PHE C 706 " pdb=" CA PHE C 706 " pdb=" CB PHE C 706 " ideal model delta harmonic sigma weight residual -122.60 -85.68 -36.92 0 2.50e+00 1.60e-01 2.18e+02 dihedral pdb=" N PHE C 706 " pdb=" C PHE C 706 " pdb=" CA PHE C 706 " pdb=" CB PHE C 706 " ideal model delta harmonic sigma weight residual 122.80 102.96 19.84 0 2.50e+00 1.60e-01 6.30e+01 dihedral pdb=" N LYS C 707 " pdb=" C LYS C 707 " pdb=" CA LYS C 707 " pdb=" CB LYS C 707 " ideal model delta harmonic sigma weight residual 122.80 106.97 15.83 0 2.50e+00 1.60e-01 4.01e+01 ... (remaining 24454 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.107: 4168 0.107 - 0.213: 249 0.213 - 0.320: 7 0.320 - 0.427: 1 0.427 - 0.533: 15 Chirality restraints: 4440 Sorted by residual: chirality pdb=" P DT E 68 " pdb=" OP1 DT E 68 " pdb=" OP2 DT E 68 " pdb=" O5' DT E 68 " both_signs ideal model delta sigma weight residual True 2.35 -2.88 -0.53 2.00e-01 2.50e+01 7.11e+00 chirality pdb=" P DA F 53 " pdb=" OP1 DA F 53 " pdb=" OP2 DA F 53 " pdb=" O5' DA F 53 " both_signs ideal model delta sigma weight residual True 2.35 -2.84 -0.49 2.00e-01 2.50e+01 6.12e+00 chirality pdb=" P DT E 22 " pdb=" OP1 DT E 22 " pdb=" OP2 DT E 22 " pdb=" O5' DT E 22 " both_signs ideal model delta sigma weight residual True 2.35 -2.83 -0.49 2.00e-01 2.50e+01 5.91e+00 ... (remaining 4437 not shown) Planarity restraints: 7173 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE C 706 " 0.193 2.00e-02 2.50e+03 2.62e-01 6.85e+02 pdb=" N LYS C 707 " -0.447 2.00e-02 2.50e+03 pdb=" CA LYS C 707 " 0.176 2.00e-02 2.50e+03 pdb=" H LYS C 707 " 0.078 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE C 772 " -0.089 2.00e-02 2.50e+03 1.52e-01 2.32e+02 pdb=" N SER C 773 " 0.264 2.00e-02 2.50e+03 pdb=" CA SER C 773 " -0.074 2.00e-02 2.50e+03 pdb=" H SER C 773 " -0.101 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG C 705 " -0.054 2.00e-02 2.50e+03 1.16e-01 1.33e+02 pdb=" C ARG C 705 " 0.199 2.00e-02 2.50e+03 pdb=" O ARG C 705 " -0.079 2.00e-02 2.50e+03 pdb=" N PHE C 706 " -0.067 2.00e-02 2.50e+03 ... (remaining 7170 not shown) Histogram of nonbonded interaction distances: 1.07 - 1.77: 106 1.77 - 2.48: 30987 2.48 - 3.19: 158754 3.19 - 3.89: 202295 3.89 - 4.60: 323806 Nonbonded interactions: 715948 Sorted by model distance: nonbonded pdb=" H2' DT E 48 " pdb=" H71 DT E 49 " model vdw 1.067 2.440 nonbonded pdb=" H72 DT E 75 " pdb=" H61 DA F 43 " model vdw 1.081 2.270 nonbonded pdb=" H2' DT E 10 " pdb=" H73 DT E 11 " model vdw 1.128 2.440 nonbonded pdb=" H2' DT E 39 " pdb=" H73 DT E 40 " model vdw 1.177 2.440 nonbonded pdb="H2'' DT E 46 " pdb=" H71 DT E 47 " model vdw 1.234 2.440 ... (remaining 715943 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 'B' selection = (chain 'D' and (resid 9 through 517 or resid 519 through 804)) } 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 individual isotropic 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: 7.830 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: 0.850 Extract box with map and model: 2.140 Check model and map are aligned: 0.310 Set scattering table: 0.480 Process input model: 122.790 Find NCS groups from input model: 1.060 Set up NCS constraints: 0.160 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:14.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 149.630 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6870 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 : 0.006 0.126 28348 Z= 0.365 Angle : 0.884 35.490 39325 Z= 0.533 Chirality : 0.057 0.533 4440 Planarity : 0.005 0.116 4297 Dihedral : 17.770 170.979 11569 Min Nonbonded Distance : 1.888 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.93 % Favored : 95.96 % Rotamer: Outliers : 0.17 % Allowed : 2.99 % Favored : 96.85 % Cbeta Deviations : 0.11 % 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: -0.13 (0.15), residues: 2849 helix: 1.97 (0.14), residues: 1143 sheet: -1.46 (0.23), residues: 469 loop : -1.53 (0.16), residues: 1237 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 436 HIS 0.005 0.001 HIS C 545 PHE 0.044 0.002 PHE C 706 TYR 0.019 0.001 TYR C 600 ARG 0.005 0.000 ARG C 561 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5698 Ramachandran restraints generated. 2849 Oldfield, 0 Emsley, 2849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5698 Ramachandran restraints generated. 2849 Oldfield, 0 Emsley, 2849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 507 residues out of total 2409 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 503 time to evaluate : 3.572 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 302 ARG cc_start: 0.8443 (ttt90) cc_final: 0.8226 (ttt-90) REVERT: A 424 LEU cc_start: 0.6991 (tp) cc_final: 0.6123 (tp) REVERT: A 503 ARG cc_start: 0.8087 (ttp-110) cc_final: 0.7775 (ttm-80) REVERT: B 20 ARG cc_start: 0.8163 (ttm170) cc_final: 0.7949 (ttm170) REVERT: B 232 ASN cc_start: 0.7551 (p0) cc_final: 0.7130 (m110) REVERT: B 439 LYS cc_start: 0.8279 (mtpp) cc_final: 0.8073 (mmtt) REVERT: B 450 ILE cc_start: 0.8856 (pt) cc_final: 0.8472 (tt) REVERT: B 487 LYS cc_start: 0.8784 (mttt) cc_final: 0.8577 (mmpt) REVERT: B 754 THR cc_start: 0.8261 (p) cc_final: 0.7708 (t) REVERT: C 356 ARG cc_start: 0.7980 (mmt180) cc_final: 0.7751 (ttp-110) REVERT: D 139 LYS cc_start: 0.7415 (mttp) cc_final: 0.7208 (mttt) REVERT: D 387 ARG cc_start: 0.7614 (ttm-80) cc_final: 0.7055 (ptm160) REVERT: D 406 LYS cc_start: 0.8205 (mttt) cc_final: 0.7968 (mmtt) REVERT: D 439 LYS cc_start: 0.8600 (mmmm) cc_final: 0.8319 (tmtt) outliers start: 4 outliers final: 3 residues processed: 506 average time/residue: 3.4174 time to fit residues: 1973.2579 Evaluate side-chains 260 residues out of total 2409 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 257 time to evaluate : 3.816 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 ASP Chi-restraints excluded: chain C residue 650 THR Chi-restraints excluded: chain C residue 707 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 307 random chunks: chunk 259 optimal weight: 0.7980 chunk 232 optimal weight: 3.9990 chunk 129 optimal weight: 0.9980 chunk 79 optimal weight: 0.9990 chunk 156 optimal weight: 0.9980 chunk 124 optimal weight: 0.9990 chunk 240 optimal weight: 0.9990 chunk 93 optimal weight: 0.9980 chunk 146 optimal weight: 0.8980 chunk 179 optimal weight: 8.9990 chunk 278 optimal weight: 0.9990 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 319 ASN A 413 ASN B 440 ASN B 465 GLN B 591 GLN B 642 GLN B 737 GLN C 453 GLN D 239 ASN D 275 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6933 moved from start: 0.2412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 28348 Z= 0.205 Angle : 0.583 9.182 39325 Z= 0.336 Chirality : 0.041 0.172 4440 Planarity : 0.004 0.054 4297 Dihedral : 21.313 166.082 5987 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 3.12 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.79 % Favored : 96.17 % Rotamer: Outliers : 1.54 % Allowed : 12.29 % Favored : 86.18 % 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: 0.41 (0.16), residues: 2849 helix: 2.64 (0.15), residues: 1173 sheet: -1.48 (0.23), residues: 485 loop : -1.45 (0.17), residues: 1191 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 415 HIS 0.004 0.001 HIS B 679 PHE 0.023 0.001 PHE D 169 TYR 0.009 0.001 TYR A 266 ARG 0.007 0.000 ARG C 444 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5698 Ramachandran restraints generated. 2849 Oldfield, 0 Emsley, 2849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5698 Ramachandran restraints generated. 2849 Oldfield, 0 Emsley, 2849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 2409 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 263 time to evaluate : 3.919 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 503 ARG cc_start: 0.8105 (ttp-110) cc_final: 0.7747 (ttt-90) REVERT: B 20 ARG cc_start: 0.8209 (ttm170) cc_final: 0.7947 (ttm170) REVERT: B 128 GLN cc_start: 0.7849 (pt0) cc_final: 0.7523 (pp30) REVERT: B 232 ASN cc_start: 0.7469 (p0) cc_final: 0.7160 (m110) REVERT: B 450 ILE cc_start: 0.8866 (pt) cc_final: 0.8495 (tt) REVERT: B 538 LYS cc_start: 0.8654 (tttt) cc_final: 0.8416 (tttp) REVERT: B 596 ARG cc_start: 0.7875 (OUTLIER) cc_final: 0.7586 (mtp180) REVERT: B 599 ARG cc_start: 0.7539 (mmp-170) cc_final: 0.7050 (ttm-80) REVERT: B 754 THR cc_start: 0.8388 (p) cc_final: 0.7831 (t) REVERT: C 72 ASP cc_start: 0.8108 (OUTLIER) cc_final: 0.7845 (t0) REVERT: C 413 ASN cc_start: 0.7366 (m-40) cc_final: 0.6649 (t0) REVERT: D 13 LEU cc_start: 0.8739 (mt) cc_final: 0.8168 (pp) REVERT: D 21 LYS cc_start: 0.7797 (mttt) cc_final: 0.6914 (mttt) REVERT: D 72 GLN cc_start: 0.7338 (mt0) cc_final: 0.7111 (tp40) REVERT: D 139 LYS cc_start: 0.7391 (mttp) cc_final: 0.7189 (mttt) REVERT: D 203 ILE cc_start: 0.8481 (OUTLIER) cc_final: 0.8167 (mp) REVERT: D 387 ARG cc_start: 0.7548 (ttm-80) cc_final: 0.6992 (ptm160) REVERT: D 406 LYS cc_start: 0.8287 (mttt) cc_final: 0.7951 (mmtt) REVERT: D 411 GLN cc_start: 0.8584 (OUTLIER) cc_final: 0.7140 (mt0) REVERT: D 439 LYS cc_start: 0.8658 (mmmm) cc_final: 0.8421 (tmtt) REVERT: D 474 LEU cc_start: 0.8249 (OUTLIER) cc_final: 0.7951 (tp) REVERT: D 562 ASP cc_start: 0.7476 (t0) cc_final: 0.6771 (m-30) outliers start: 37 outliers final: 12 residues processed: 293 average time/residue: 3.1411 time to fit residues: 1074.2276 Evaluate side-chains 236 residues out of total 2409 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 219 time to evaluate : 3.680 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 147 ASP Chi-restraints excluded: chain A residue 150 ASP Chi-restraints excluded: chain A residue 171 SER Chi-restraints excluded: chain A residue 394 ILE Chi-restraints excluded: chain B residue 134 ILE Chi-restraints excluded: chain B residue 426 ASP Chi-restraints excluded: chain B residue 596 ARG Chi-restraints excluded: chain C residue 72 ASP Chi-restraints excluded: chain C residue 452 GLU Chi-restraints excluded: chain C residue 543 LEU Chi-restraints excluded: chain C residue 707 LYS Chi-restraints excluded: chain D residue 203 ILE Chi-restraints excluded: chain D residue 290 THR Chi-restraints excluded: chain D residue 411 GLN Chi-restraints excluded: chain D residue 426 ASP Chi-restraints excluded: chain D residue 474 LEU Chi-restraints excluded: chain D residue 548 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 307 random chunks: chunk 154 optimal weight: 1.9990 chunk 86 optimal weight: 1.9990 chunk 232 optimal weight: 10.0000 chunk 189 optimal weight: 7.9990 chunk 76 optimal weight: 4.9990 chunk 279 optimal weight: 2.9990 chunk 301 optimal weight: 10.0000 chunk 248 optimal weight: 1.9990 chunk 276 optimal weight: 1.9990 chunk 95 optimal weight: 2.9990 chunk 224 optimal weight: 3.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 106 GLN A 319 ASN B 239 ASN B 556 GLN B 795 ASN C 94 GLN C 453 GLN ** C 587 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 749 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7003 moved from start: 0.2984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 28348 Z= 0.296 Angle : 0.581 8.208 39325 Z= 0.336 Chirality : 0.043 0.171 4440 Planarity : 0.004 0.064 4297 Dihedral : 21.209 165.960 5984 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 3.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 1.99 % Allowed : 13.49 % Favored : 84.52 % 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: 0.35 (0.16), residues: 2849 helix: 2.59 (0.15), residues: 1172 sheet: -1.40 (0.22), residues: 483 loop : -1.52 (0.17), residues: 1194 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 415 HIS 0.006 0.001 HIS B 237 PHE 0.022 0.002 PHE C 706 TYR 0.012 0.001 TYR C 63 ARG 0.006 0.001 ARG C 285 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5698 Ramachandran restraints generated. 2849 Oldfield, 0 Emsley, 2849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5698 Ramachandran restraints generated. 2849 Oldfield, 0 Emsley, 2849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 2409 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 229 time to evaluate : 3.680 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: A 285 ARG cc_start: 0.7843 (mpt-90) cc_final: 0.7635 (mpp80) REVERT: A 395 GLU cc_start: 0.7791 (OUTLIER) cc_final: 0.7526 (tp30) REVERT: B 20 ARG cc_start: 0.8223 (ttm170) cc_final: 0.7928 (ttm170) REVERT: B 128 GLN cc_start: 0.7952 (pt0) cc_final: 0.7587 (pp30) REVERT: B 276 ARG cc_start: 0.8452 (OUTLIER) cc_final: 0.8049 (ttm110) REVERT: B 450 ILE cc_start: 0.8894 (pt) cc_final: 0.8564 (tt) REVERT: B 538 LYS cc_start: 0.8730 (tttt) cc_final: 0.8416 (tttp) REVERT: B 599 ARG cc_start: 0.7638 (mmp-170) cc_final: 0.7091 (ttm-80) REVERT: B 754 THR cc_start: 0.8599 (p) cc_final: 0.8076 (t) REVERT: B 769 ASP cc_start: 0.7583 (t0) cc_final: 0.7335 (t0) REVERT: C 413 ASN cc_start: 0.7294 (m-40) cc_final: 0.6594 (t0) REVERT: C 423 MET cc_start: 0.7299 (pp-130) cc_final: 0.7052 (ppp) REVERT: D 78 ILE cc_start: 0.7943 (mt) cc_final: 0.7690 (pt) REVERT: D 134 ILE cc_start: 0.7160 (tt) cc_final: 0.6937 (mt) REVERT: D 203 ILE cc_start: 0.8434 (OUTLIER) cc_final: 0.8153 (mp) REVERT: D 387 ARG cc_start: 0.7585 (ttm-80) cc_final: 0.7018 (ptm160) REVERT: D 406 LYS cc_start: 0.8355 (mttt) cc_final: 0.8000 (mmtp) REVERT: D 411 GLN cc_start: 0.8663 (OUTLIER) cc_final: 0.7286 (mt0) REVERT: D 439 LYS cc_start: 0.8710 (mmmm) cc_final: 0.8506 (tmtt) REVERT: D 474 LEU cc_start: 0.8298 (OUTLIER) cc_final: 0.7986 (tp) outliers start: 48 outliers final: 18 residues processed: 261 average time/residue: 2.8372 time to fit residues: 873.8756 Evaluate side-chains 237 residues out of total 2409 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 214 time to evaluate : 3.753 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 ILE Chi-restraints excluded: chain A residue 150 ASP Chi-restraints excluded: chain A residue 171 SER Chi-restraints excluded: chain A residue 202 ASP Chi-restraints excluded: chain A residue 395 GLU Chi-restraints excluded: chain B residue 14 LYS Chi-restraints excluded: chain B residue 134 ILE Chi-restraints excluded: chain B residue 191 LEU Chi-restraints excluded: chain B residue 276 ARG Chi-restraints excluded: chain B residue 351 GLN Chi-restraints excluded: chain B residue 426 ASP Chi-restraints excluded: chain C residue 72 ASP Chi-restraints excluded: chain C residue 543 LEU Chi-restraints excluded: chain C residue 650 THR Chi-restraints excluded: chain C residue 749 GLN Chi-restraints excluded: chain D residue 203 ILE Chi-restraints excluded: chain D residue 290 THR Chi-restraints excluded: chain D residue 313 ASP Chi-restraints excluded: chain D residue 411 GLN Chi-restraints excluded: chain D residue 426 ASP Chi-restraints excluded: chain D residue 474 LEU Chi-restraints excluded: chain D residue 754 THR Chi-restraints excluded: chain D residue 778 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 307 random chunks: chunk 275 optimal weight: 3.9990 chunk 209 optimal weight: 5.9990 chunk 144 optimal weight: 1.9990 chunk 30 optimal weight: 3.9990 chunk 133 optimal weight: 1.9990 chunk 187 optimal weight: 20.0000 chunk 280 optimal weight: 1.9990 chunk 296 optimal weight: 4.9990 chunk 146 optimal weight: 2.9990 chunk 265 optimal weight: 0.9980 chunk 79 optimal weight: 2.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 319 ASN C 453 GLN ** C 587 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 351 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7006 moved from start: 0.3211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 28348 Z= 0.270 Angle : 0.563 7.580 39325 Z= 0.325 Chirality : 0.042 0.156 4440 Planarity : 0.004 0.066 4297 Dihedral : 21.196 165.338 5980 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 3.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 1.87 % Allowed : 14.32 % Favored : 83.81 % 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: 0.31 (0.16), residues: 2849 helix: 2.53 (0.15), residues: 1180 sheet: -1.41 (0.22), residues: 493 loop : -1.55 (0.17), residues: 1176 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 415 HIS 0.005 0.001 HIS A 378 PHE 0.019 0.001 PHE C 706 TYR 0.011 0.001 TYR C 63 ARG 0.007 0.000 ARG C 426 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5698 Ramachandran restraints generated. 2849 Oldfield, 0 Emsley, 2849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5698 Ramachandran restraints generated. 2849 Oldfield, 0 Emsley, 2849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 2409 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 222 time to evaluate : 3.690 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: A 150 ASP cc_start: 0.8634 (OUTLIER) cc_final: 0.8302 (t0) REVERT: B 20 ARG cc_start: 0.8259 (ttm170) cc_final: 0.7970 (ttm170) REVERT: B 206 ARG cc_start: 0.6860 (mtt180) cc_final: 0.6468 (mtt-85) REVERT: B 276 ARG cc_start: 0.8442 (OUTLIER) cc_final: 0.8033 (ttm110) REVERT: B 450 ILE cc_start: 0.8932 (pt) cc_final: 0.8594 (tt) REVERT: B 599 ARG cc_start: 0.7665 (mmp-170) cc_final: 0.7076 (ttm-80) REVERT: B 754 THR cc_start: 0.8625 (p) cc_final: 0.8058 (t) REVERT: C 413 ASN cc_start: 0.7350 (m-40) cc_final: 0.6673 (t0) REVERT: C 423 MET cc_start: 0.7386 (pp-130) cc_final: 0.7102 (ppp) REVERT: C 424 LEU cc_start: 0.7194 (tt) cc_final: 0.6878 (tt) REVERT: D 203 ILE cc_start: 0.8441 (OUTLIER) cc_final: 0.8150 (mp) REVERT: D 313 ASP cc_start: 0.7253 (OUTLIER) cc_final: 0.7016 (m-30) REVERT: D 387 ARG cc_start: 0.7596 (ttm-80) cc_final: 0.7017 (ptm160) REVERT: D 406 LYS cc_start: 0.8332 (mttt) cc_final: 0.7956 (mmtt) REVERT: D 411 GLN cc_start: 0.8657 (OUTLIER) cc_final: 0.7290 (mt0) REVERT: D 439 LYS cc_start: 0.8703 (mmmm) cc_final: 0.8501 (tmtt) REVERT: D 474 LEU cc_start: 0.8302 (OUTLIER) cc_final: 0.7979 (tp) outliers start: 45 outliers final: 20 residues processed: 251 average time/residue: 2.9318 time to fit residues: 884.7275 Evaluate side-chains 231 residues out of total 2409 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 205 time to evaluate : 3.799 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 ILE Chi-restraints excluded: chain A residue 150 ASP Chi-restraints excluded: chain A residue 171 SER Chi-restraints excluded: chain A residue 423 MET Chi-restraints excluded: chain B residue 14 LYS Chi-restraints excluded: chain B residue 74 ASP Chi-restraints excluded: chain B residue 134 ILE Chi-restraints excluded: chain B residue 140 ILE Chi-restraints excluded: chain B residue 191 LEU Chi-restraints excluded: chain B residue 276 ARG Chi-restraints excluded: chain B residue 351 GLN Chi-restraints excluded: chain B residue 426 ASP Chi-restraints excluded: chain C residue 72 ASP Chi-restraints excluded: chain C residue 399 HIS Chi-restraints excluded: chain C residue 452 GLU Chi-restraints excluded: chain C residue 650 THR Chi-restraints excluded: chain D residue 45 ASP Chi-restraints excluded: chain D residue 203 ILE Chi-restraints excluded: chain D residue 290 THR Chi-restraints excluded: chain D residue 297 MET Chi-restraints excluded: chain D residue 313 ASP Chi-restraints excluded: chain D residue 411 GLN Chi-restraints excluded: chain D residue 426 ASP Chi-restraints excluded: chain D residue 474 LEU Chi-restraints excluded: chain D residue 778 THR Chi-restraints excluded: chain D residue 779 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 307 random chunks: chunk 247 optimal weight: 2.9990 chunk 168 optimal weight: 5.9990 chunk 4 optimal weight: 1.9990 chunk 220 optimal weight: 10.0000 chunk 122 optimal weight: 1.9990 chunk 253 optimal weight: 0.9980 chunk 205 optimal weight: 8.9990 chunk 0 optimal weight: 1.9990 chunk 151 optimal weight: 4.9990 chunk 266 optimal weight: 4.9990 chunk 74 optimal weight: 3.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 319 ASN C 453 GLN ** C 587 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7019 moved from start: 0.3428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 28348 Z= 0.276 Angle : 0.566 7.251 39325 Z= 0.326 Chirality : 0.042 0.158 4440 Planarity : 0.004 0.082 4297 Dihedral : 21.212 164.641 5980 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 3.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 1.99 % Allowed : 14.94 % Favored : 83.06 % 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: 0.28 (0.16), residues: 2849 helix: 2.47 (0.15), residues: 1182 sheet: -1.38 (0.22), residues: 493 loop : -1.56 (0.17), residues: 1174 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 415 HIS 0.005 0.001 HIS B 237 PHE 0.016 0.001 PHE B 262 TYR 0.011 0.001 TYR C 63 ARG 0.011 0.000 ARG C 426 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5698 Ramachandran restraints generated. 2849 Oldfield, 0 Emsley, 2849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5698 Ramachandran restraints generated. 2849 Oldfield, 0 Emsley, 2849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 2409 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 211 time to evaluate : 3.717 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: A 150 ASP cc_start: 0.8653 (OUTLIER) cc_final: 0.8324 (t0) REVERT: B 20 ARG cc_start: 0.8260 (ttm170) cc_final: 0.8008 (ttm170) REVERT: B 25 MET cc_start: 0.8140 (OUTLIER) cc_final: 0.7583 (mtm) REVERT: B 206 ARG cc_start: 0.6845 (mtt180) cc_final: 0.6393 (mtt-85) REVERT: B 276 ARG cc_start: 0.8450 (OUTLIER) cc_final: 0.8037 (ttm110) REVERT: B 450 ILE cc_start: 0.8902 (pt) cc_final: 0.8597 (tt) REVERT: B 538 LYS cc_start: 0.8751 (tttt) cc_final: 0.8421 (tttp) REVERT: B 588 ASN cc_start: 0.8317 (m-40) cc_final: 0.8071 (m-40) REVERT: B 599 ARG cc_start: 0.7664 (mmp-170) cc_final: 0.7066 (ttm-80) REVERT: B 754 THR cc_start: 0.8689 (p) cc_final: 0.8129 (t) REVERT: B 761 ARG cc_start: 0.8648 (mmt90) cc_final: 0.8445 (mmm-85) REVERT: C 413 ASN cc_start: 0.7324 (m-40) cc_final: 0.6612 (t0) REVERT: C 423 MET cc_start: 0.7358 (pp-130) cc_final: 0.7096 (ppp) REVERT: C 424 LEU cc_start: 0.7226 (tt) cc_final: 0.6907 (tt) REVERT: D 166 MET cc_start: 0.6878 (tmm) cc_final: 0.6537 (tmm) REVERT: D 253 GLU cc_start: 0.7930 (mt-10) cc_final: 0.7688 (mt-10) REVERT: D 313 ASP cc_start: 0.7298 (OUTLIER) cc_final: 0.7065 (m-30) REVERT: D 387 ARG cc_start: 0.7602 (ttm-80) cc_final: 0.7006 (ptm160) REVERT: D 406 LYS cc_start: 0.8363 (mttt) cc_final: 0.8001 (mmtp) REVERT: D 411 GLN cc_start: 0.8661 (OUTLIER) cc_final: 0.7319 (mt0) REVERT: D 439 LYS cc_start: 0.8719 (mmmm) cc_final: 0.8513 (tmtt) REVERT: D 474 LEU cc_start: 0.8305 (OUTLIER) cc_final: 0.7967 (tp) outliers start: 48 outliers final: 21 residues processed: 243 average time/residue: 2.9449 time to fit residues: 839.6962 Evaluate side-chains 229 residues out of total 2409 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 202 time to evaluate : 3.670 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 ILE Chi-restraints excluded: chain A residue 150 ASP Chi-restraints excluded: chain A residue 171 SER Chi-restraints excluded: chain A residue 394 ILE Chi-restraints excluded: chain A residue 423 MET Chi-restraints excluded: chain B residue 14 LYS Chi-restraints excluded: chain B residue 25 MET Chi-restraints excluded: chain B residue 29 ASP Chi-restraints excluded: chain B residue 74 ASP Chi-restraints excluded: chain B residue 134 ILE Chi-restraints excluded: chain B residue 140 ILE Chi-restraints excluded: chain B residue 276 ARG Chi-restraints excluded: chain B residue 351 GLN Chi-restraints excluded: chain B residue 426 ASP Chi-restraints excluded: chain C residue 72 ASP Chi-restraints excluded: chain C residue 399 HIS Chi-restraints excluded: chain C residue 452 GLU Chi-restraints excluded: chain C residue 511 GLU Chi-restraints excluded: chain C residue 650 THR Chi-restraints excluded: chain D residue 290 THR Chi-restraints excluded: chain D residue 297 MET Chi-restraints excluded: chain D residue 313 ASP Chi-restraints excluded: chain D residue 411 GLN Chi-restraints excluded: chain D residue 426 ASP Chi-restraints excluded: chain D residue 474 LEU Chi-restraints excluded: chain D residue 778 THR Chi-restraints excluded: chain D residue 779 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 307 random chunks: chunk 99 optimal weight: 0.8980 chunk 267 optimal weight: 3.9990 chunk 58 optimal weight: 9.9990 chunk 174 optimal weight: 3.9990 chunk 73 optimal weight: 4.9990 chunk 297 optimal weight: 2.9990 chunk 246 optimal weight: 0.9990 chunk 137 optimal weight: 2.9990 chunk 24 optimal weight: 5.9990 chunk 98 optimal weight: 0.5980 chunk 155 optimal weight: 3.9990 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 319 ASN C 453 GLN ** C 587 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 351 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7015 moved from start: 0.3546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 28348 Z= 0.243 Angle : 0.549 7.165 39325 Z= 0.318 Chirality : 0.041 0.152 4440 Planarity : 0.004 0.085 4297 Dihedral : 21.221 164.144 5980 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 1.83 % Allowed : 15.53 % Favored : 82.65 % 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: 0.32 (0.16), residues: 2849 helix: 2.50 (0.15), residues: 1183 sheet: -1.37 (0.22), residues: 495 loop : -1.52 (0.17), residues: 1171 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 415 HIS 0.004 0.001 HIS A 378 PHE 0.015 0.001 PHE B 262 TYR 0.019 0.001 TYR D 242 ARG 0.010 0.000 ARG C 426 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5698 Ramachandran restraints generated. 2849 Oldfield, 0 Emsley, 2849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5698 Ramachandran restraints generated. 2849 Oldfield, 0 Emsley, 2849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 2409 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 206 time to evaluate : 3.645 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: A 150 ASP cc_start: 0.8619 (OUTLIER) cc_final: 0.8304 (t0) REVERT: B 20 ARG cc_start: 0.8258 (ttm170) cc_final: 0.7995 (ttm170) REVERT: B 25 MET cc_start: 0.8150 (OUTLIER) cc_final: 0.7639 (mtm) REVERT: B 206 ARG cc_start: 0.6871 (mtt180) cc_final: 0.6426 (mtt-85) REVERT: B 276 ARG cc_start: 0.8434 (OUTLIER) cc_final: 0.8020 (ttm110) REVERT: B 356 LEU cc_start: 0.8348 (mm) cc_final: 0.8091 (mp) REVERT: B 450 ILE cc_start: 0.8905 (pt) cc_final: 0.8615 (tt) REVERT: B 538 LYS cc_start: 0.8738 (tttt) cc_final: 0.8419 (tttp) REVERT: B 599 ARG cc_start: 0.7613 (mmp-170) cc_final: 0.7044 (ttm-80) REVERT: B 754 THR cc_start: 0.8712 (p) cc_final: 0.8130 (t) REVERT: B 761 ARG cc_start: 0.8614 (mmt90) cc_final: 0.8374 (mmt-90) REVERT: C 413 ASN cc_start: 0.7297 (m-40) cc_final: 0.6608 (t0) REVERT: C 423 MET cc_start: 0.7378 (pp-130) cc_final: 0.7139 (ppp) REVERT: C 424 LEU cc_start: 0.7148 (tt) cc_final: 0.6786 (tt) REVERT: C 426 ARG cc_start: 0.7596 (tpt90) cc_final: 0.7146 (tpt170) REVERT: D 253 GLU cc_start: 0.7926 (mt-10) cc_final: 0.7682 (mt-10) REVERT: D 313 ASP cc_start: 0.7295 (OUTLIER) cc_final: 0.7072 (m-30) REVERT: D 387 ARG cc_start: 0.7598 (ttm-80) cc_final: 0.6996 (ptm160) REVERT: D 406 LYS cc_start: 0.8364 (mttt) cc_final: 0.7991 (mmtp) REVERT: D 411 GLN cc_start: 0.8660 (OUTLIER) cc_final: 0.7307 (mt0) REVERT: D 439 LYS cc_start: 0.8738 (mmmm) cc_final: 0.8536 (tmtt) REVERT: D 474 LEU cc_start: 0.8355 (OUTLIER) cc_final: 0.8022 (tp) outliers start: 44 outliers final: 25 residues processed: 237 average time/residue: 2.9067 time to fit residues: 809.2391 Evaluate side-chains 232 residues out of total 2409 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 201 time to evaluate : 3.618 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 ILE Chi-restraints excluded: chain A residue 147 ASP Chi-restraints excluded: chain A residue 150 ASP Chi-restraints excluded: chain A residue 171 SER Chi-restraints excluded: chain A residue 394 ILE Chi-restraints excluded: chain B residue 14 LYS Chi-restraints excluded: chain B residue 25 MET Chi-restraints excluded: chain B residue 29 ASP Chi-restraints excluded: chain B residue 74 ASP Chi-restraints excluded: chain B residue 134 ILE Chi-restraints excluded: chain B residue 140 ILE Chi-restraints excluded: chain B residue 191 LEU Chi-restraints excluded: chain B residue 276 ARG Chi-restraints excluded: chain B residue 351 GLN Chi-restraints excluded: chain B residue 426 ASP Chi-restraints excluded: chain B residue 439 LYS Chi-restraints excluded: chain B residue 639 ASP Chi-restraints excluded: chain C residue 72 ASP Chi-restraints excluded: chain C residue 399 HIS Chi-restraints excluded: chain C residue 452 GLU Chi-restraints excluded: chain C residue 511 GLU Chi-restraints excluded: chain C residue 650 THR Chi-restraints excluded: chain D residue 290 THR Chi-restraints excluded: chain D residue 297 MET Chi-restraints excluded: chain D residue 298 ASP Chi-restraints excluded: chain D residue 313 ASP Chi-restraints excluded: chain D residue 411 GLN Chi-restraints excluded: chain D residue 426 ASP Chi-restraints excluded: chain D residue 474 LEU Chi-restraints excluded: chain D residue 754 THR Chi-restraints excluded: chain D residue 778 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 307 random chunks: chunk 286 optimal weight: 10.0000 chunk 33 optimal weight: 0.7980 chunk 169 optimal weight: 0.0570 chunk 216 optimal weight: 9.9990 chunk 168 optimal weight: 5.9990 chunk 250 optimal weight: 3.9990 chunk 165 optimal weight: 0.8980 chunk 295 optimal weight: 2.9990 chunk 185 optimal weight: 20.0000 chunk 180 optimal weight: 4.9990 chunk 136 optimal weight: 0.2980 overall best weight: 1.0100 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 319 ASN C 453 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6996 moved from start: 0.3595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 28348 Z= 0.179 Angle : 0.532 6.896 39325 Z= 0.308 Chirality : 0.041 0.152 4440 Planarity : 0.003 0.070 4297 Dihedral : 21.197 163.350 5980 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 3.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 1.78 % Allowed : 15.65 % Favored : 82.57 % 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: 0.46 (0.16), residues: 2849 helix: 2.61 (0.15), residues: 1186 sheet: -1.33 (0.22), residues: 495 loop : -1.44 (0.17), residues: 1168 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 415 HIS 0.003 0.001 HIS C 378 PHE 0.016 0.001 PHE B 262 TYR 0.009 0.001 TYR C 63 ARG 0.006 0.000 ARG C 426 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5698 Ramachandran restraints generated. 2849 Oldfield, 0 Emsley, 2849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5698 Ramachandran restraints generated. 2849 Oldfield, 0 Emsley, 2849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 2409 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 207 time to evaluate : 3.657 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 150 ASP cc_start: 0.8557 (OUTLIER) cc_final: 0.8283 (t0) REVERT: B 20 ARG cc_start: 0.8254 (ttm170) cc_final: 0.8002 (ttm170) REVERT: B 25 MET cc_start: 0.8159 (OUTLIER) cc_final: 0.7811 (mtp) REVERT: B 276 ARG cc_start: 0.8423 (OUTLIER) cc_final: 0.7989 (ttm110) REVERT: B 356 LEU cc_start: 0.8219 (mm) cc_final: 0.7931 (mp) REVERT: B 450 ILE cc_start: 0.8904 (pt) cc_final: 0.8635 (tt) REVERT: B 538 LYS cc_start: 0.8721 (tttt) cc_final: 0.8420 (tttp) REVERT: B 599 ARG cc_start: 0.7584 (mmp-170) cc_final: 0.7029 (ttm-80) REVERT: B 754 THR cc_start: 0.8697 (p) cc_final: 0.8114 (t) REVERT: B 761 ARG cc_start: 0.8571 (mmt90) cc_final: 0.8351 (mmt-90) REVERT: C 413 ASN cc_start: 0.7293 (m-40) cc_final: 0.6540 (t0) REVERT: C 423 MET cc_start: 0.7342 (pp-130) cc_final: 0.7120 (ppp) REVERT: C 424 LEU cc_start: 0.7114 (tt) cc_final: 0.6749 (tt) REVERT: C 426 ARG cc_start: 0.7586 (tpt90) cc_final: 0.7271 (tpt170) REVERT: D 41 PHE cc_start: 0.7558 (m-10) cc_final: 0.7315 (m-10) REVERT: D 253 GLU cc_start: 0.7893 (mt-10) cc_final: 0.7648 (mt-10) REVERT: D 313 ASP cc_start: 0.7287 (OUTLIER) cc_final: 0.7086 (m-30) REVERT: D 387 ARG cc_start: 0.7578 (ttm-80) cc_final: 0.6972 (ptm160) REVERT: D 406 LYS cc_start: 0.8358 (mttt) cc_final: 0.7984 (mmtp) REVERT: D 411 GLN cc_start: 0.8664 (OUTLIER) cc_final: 0.7303 (mt0) REVERT: D 474 LEU cc_start: 0.8304 (OUTLIER) cc_final: 0.7968 (tp) REVERT: D 698 ARG cc_start: 0.7602 (OUTLIER) cc_final: 0.7236 (mmt90) outliers start: 43 outliers final: 19 residues processed: 234 average time/residue: 3.0265 time to fit residues: 839.5308 Evaluate side-chains 225 residues out of total 2409 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 199 time to evaluate : 3.657 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 ILE Chi-restraints excluded: chain A residue 147 ASP Chi-restraints excluded: chain A residue 150 ASP Chi-restraints excluded: chain A residue 171 SER Chi-restraints excluded: chain B residue 14 LYS Chi-restraints excluded: chain B residue 25 MET Chi-restraints excluded: chain B residue 134 ILE Chi-restraints excluded: chain B residue 191 LEU Chi-restraints excluded: chain B residue 276 ARG Chi-restraints excluded: chain B residue 351 GLN Chi-restraints excluded: chain B residue 426 ASP Chi-restraints excluded: chain B residue 439 LYS Chi-restraints excluded: chain C residue 72 ASP Chi-restraints excluded: chain C residue 399 HIS Chi-restraints excluded: chain C residue 452 GLU Chi-restraints excluded: chain C residue 511 GLU Chi-restraints excluded: chain C residue 650 THR Chi-restraints excluded: chain D residue 290 THR Chi-restraints excluded: chain D residue 298 ASP Chi-restraints excluded: chain D residue 313 ASP Chi-restraints excluded: chain D residue 411 GLN Chi-restraints excluded: chain D residue 426 ASP Chi-restraints excluded: chain D residue 474 LEU Chi-restraints excluded: chain D residue 698 ARG Chi-restraints excluded: chain D residue 778 THR Chi-restraints excluded: chain D residue 779 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 307 random chunks: chunk 183 optimal weight: 20.0000 chunk 118 optimal weight: 0.9990 chunk 176 optimal weight: 0.8980 chunk 89 optimal weight: 2.9990 chunk 58 optimal weight: 4.9990 chunk 57 optimal weight: 0.8980 chunk 188 optimal weight: 8.9990 chunk 201 optimal weight: 30.0000 chunk 146 optimal weight: 1.9990 chunk 27 optimal weight: 2.9990 chunk 232 optimal weight: 2.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 319 ASN C 453 GLN ** C 587 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 351 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7014 moved from start: 0.3710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 28348 Z= 0.229 Angle : 0.542 8.575 39325 Z= 0.313 Chirality : 0.041 0.161 4440 Planarity : 0.003 0.061 4297 Dihedral : 21.220 164.115 5980 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 1.49 % Allowed : 15.98 % Favored : 82.52 % 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: 0.44 (0.16), residues: 2849 helix: 2.59 (0.15), residues: 1186 sheet: -1.38 (0.22), residues: 502 loop : -1.43 (0.17), residues: 1161 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 415 HIS 0.004 0.001 HIS B 237 PHE 0.020 0.001 PHE B 262 TYR 0.018 0.001 TYR D 242 ARG 0.004 0.000 ARG C 426 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5698 Ramachandran restraints generated. 2849 Oldfield, 0 Emsley, 2849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5698 Ramachandran restraints generated. 2849 Oldfield, 0 Emsley, 2849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 2409 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 208 time to evaluate : 3.818 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 150 ASP cc_start: 0.8576 (OUTLIER) cc_final: 0.8279 (t0) REVERT: B 20 ARG cc_start: 0.8256 (ttm170) cc_final: 0.8004 (ttm170) REVERT: B 25 MET cc_start: 0.8170 (OUTLIER) cc_final: 0.7791 (mtp) REVERT: B 276 ARG cc_start: 0.8414 (OUTLIER) cc_final: 0.7977 (ttm110) REVERT: B 356 LEU cc_start: 0.8136 (mm) cc_final: 0.7836 (mp) REVERT: B 450 ILE cc_start: 0.8901 (pt) cc_final: 0.8623 (tt) REVERT: B 538 LYS cc_start: 0.8733 (tttt) cc_final: 0.8413 (tttp) REVERT: B 599 ARG cc_start: 0.7614 (mmp-170) cc_final: 0.7046 (ttm-80) REVERT: B 754 THR cc_start: 0.8721 (p) cc_final: 0.8161 (t) REVERT: B 761 ARG cc_start: 0.8606 (mmt90) cc_final: 0.8368 (mmt-90) REVERT: C 413 ASN cc_start: 0.7294 (m-40) cc_final: 0.6626 (t0) REVERT: C 423 MET cc_start: 0.7367 (pp-130) cc_final: 0.7151 (ppp) REVERT: C 424 LEU cc_start: 0.7147 (tt) cc_final: 0.6844 (tt) REVERT: D 36 LEU cc_start: 0.8598 (mp) cc_final: 0.8119 (mt) REVERT: D 253 GLU cc_start: 0.7933 (mt-10) cc_final: 0.7664 (mt-10) REVERT: D 313 ASP cc_start: 0.7318 (OUTLIER) cc_final: 0.7104 (m-30) REVERT: D 387 ARG cc_start: 0.7584 (ttm-80) cc_final: 0.6976 (ptm160) REVERT: D 406 LYS cc_start: 0.8369 (mttt) cc_final: 0.7997 (mmtp) REVERT: D 411 GLN cc_start: 0.8690 (OUTLIER) cc_final: 0.7318 (mt0) REVERT: D 474 LEU cc_start: 0.8304 (OUTLIER) cc_final: 0.7963 (tp) outliers start: 36 outliers final: 18 residues processed: 233 average time/residue: 2.9495 time to fit residues: 806.0402 Evaluate side-chains 224 residues out of total 2409 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 200 time to evaluate : 3.728 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 ILE Chi-restraints excluded: chain A residue 147 ASP Chi-restraints excluded: chain A residue 150 ASP Chi-restraints excluded: chain A residue 171 SER Chi-restraints excluded: chain B residue 14 LYS Chi-restraints excluded: chain B residue 25 MET Chi-restraints excluded: chain B residue 134 ILE Chi-restraints excluded: chain B residue 140 ILE Chi-restraints excluded: chain B residue 276 ARG Chi-restraints excluded: chain B residue 351 GLN Chi-restraints excluded: chain B residue 426 ASP Chi-restraints excluded: chain B residue 439 LYS Chi-restraints excluded: chain C residue 72 ASP Chi-restraints excluded: chain C residue 399 HIS Chi-restraints excluded: chain C residue 452 GLU Chi-restraints excluded: chain C residue 650 THR Chi-restraints excluded: chain D residue 290 THR Chi-restraints excluded: chain D residue 313 ASP Chi-restraints excluded: chain D residue 411 GLN Chi-restraints excluded: chain D residue 426 ASP Chi-restraints excluded: chain D residue 439 LYS Chi-restraints excluded: chain D residue 474 LEU Chi-restraints excluded: chain D residue 778 THR Chi-restraints excluded: chain D residue 779 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 307 random chunks: chunk 269 optimal weight: 0.0870 chunk 283 optimal weight: 0.5980 chunk 258 optimal weight: 0.6980 chunk 275 optimal weight: 2.9990 chunk 165 optimal weight: 2.9990 chunk 120 optimal weight: 2.9990 chunk 216 optimal weight: 9.9990 chunk 84 optimal weight: 4.9990 chunk 249 optimal weight: 1.9990 chunk 260 optimal weight: 0.5980 chunk 274 optimal weight: 0.5980 overall best weight: 0.5158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 319 ASN C 453 GLN ** C 587 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 351 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6976 moved from start: 0.3750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 28348 Z= 0.150 Angle : 0.520 7.719 39325 Z= 0.301 Chirality : 0.040 0.150 4440 Planarity : 0.003 0.075 4297 Dihedral : 21.164 164.143 5980 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 3.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 1.29 % Allowed : 16.31 % Favored : 82.40 % 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: 0.61 (0.16), residues: 2849 helix: 2.75 (0.15), residues: 1185 sheet: -1.27 (0.22), residues: 497 loop : -1.36 (0.17), residues: 1167 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 415 HIS 0.003 0.001 HIS C 378 PHE 0.020 0.001 PHE B 262 TYR 0.011 0.001 TYR C 149 ARG 0.008 0.000 ARG C 426 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5698 Ramachandran restraints generated. 2849 Oldfield, 0 Emsley, 2849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5698 Ramachandran restraints generated. 2849 Oldfield, 0 Emsley, 2849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 2409 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 208 time to evaluate : 3.740 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 150 ASP cc_start: 0.8512 (OUTLIER) cc_final: 0.8284 (t0) REVERT: B 20 ARG cc_start: 0.8253 (ttm170) cc_final: 0.7998 (ttm170) REVERT: B 25 MET cc_start: 0.8159 (OUTLIER) cc_final: 0.7780 (mtp) REVERT: B 276 ARG cc_start: 0.8394 (OUTLIER) cc_final: 0.7981 (ttm110) REVERT: B 356 LEU cc_start: 0.8032 (mm) cc_final: 0.7709 (mp) REVERT: B 450 ILE cc_start: 0.8897 (pt) cc_final: 0.8649 (tt) REVERT: B 538 LYS cc_start: 0.8702 (tttt) cc_final: 0.8401 (tttp) REVERT: B 599 ARG cc_start: 0.7610 (mmp-170) cc_final: 0.7026 (ttm-80) REVERT: B 754 THR cc_start: 0.8703 (p) cc_final: 0.8091 (t) REVERT: B 761 ARG cc_start: 0.8528 (mmt90) cc_final: 0.8316 (mmt-90) REVERT: C 275 GLU cc_start: 0.7504 (OUTLIER) cc_final: 0.6920 (mp0) REVERT: C 413 ASN cc_start: 0.7331 (m-40) cc_final: 0.6595 (t0) REVERT: C 423 MET cc_start: 0.7429 (pp-130) cc_final: 0.7185 (ppp) REVERT: C 424 LEU cc_start: 0.7075 (tt) cc_final: 0.6771 (tt) REVERT: C 452 GLU cc_start: 0.8353 (OUTLIER) cc_final: 0.8104 (mt-10) REVERT: D 36 LEU cc_start: 0.8576 (mp) cc_final: 0.8066 (mt) REVERT: D 131 GLU cc_start: 0.6971 (tt0) cc_final: 0.6517 (tm-30) REVERT: D 253 GLU cc_start: 0.7848 (mt-10) cc_final: 0.7609 (mt-10) REVERT: D 387 ARG cc_start: 0.7556 (ttm-80) cc_final: 0.6952 (ptm160) REVERT: D 406 LYS cc_start: 0.8351 (mttt) cc_final: 0.7947 (mmtt) REVERT: D 474 LEU cc_start: 0.8256 (OUTLIER) cc_final: 0.7884 (tp) REVERT: D 698 ARG cc_start: 0.7569 (OUTLIER) cc_final: 0.7283 (mmt90) outliers start: 31 outliers final: 14 residues processed: 230 average time/residue: 2.9875 time to fit residues: 805.2397 Evaluate side-chains 220 residues out of total 2409 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 199 time to evaluate : 3.726 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 147 ASP Chi-restraints excluded: chain A residue 150 ASP Chi-restraints excluded: chain B residue 14 LYS Chi-restraints excluded: chain B residue 25 MET Chi-restraints excluded: chain B residue 134 ILE Chi-restraints excluded: chain B residue 191 LEU Chi-restraints excluded: chain B residue 276 ARG Chi-restraints excluded: chain B residue 351 GLN Chi-restraints excluded: chain B residue 439 LYS Chi-restraints excluded: chain C residue 72 ASP Chi-restraints excluded: chain C residue 275 GLU Chi-restraints excluded: chain C residue 399 HIS Chi-restraints excluded: chain C residue 452 GLU Chi-restraints excluded: chain C residue 511 GLU Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 650 THR Chi-restraints excluded: chain C residue 787 VAL Chi-restraints excluded: chain D residue 290 THR Chi-restraints excluded: chain D residue 426 ASP Chi-restraints excluded: chain D residue 474 LEU Chi-restraints excluded: chain D residue 698 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 307 random chunks: chunk 181 optimal weight: 9.9990 chunk 291 optimal weight: 10.0000 chunk 177 optimal weight: 2.9990 chunk 138 optimal weight: 2.9990 chunk 202 optimal weight: 8.9990 chunk 305 optimal weight: 10.0000 chunk 281 optimal weight: 0.7980 chunk 243 optimal weight: 5.9990 chunk 25 optimal weight: 4.9990 chunk 188 optimal weight: 0.3980 chunk 149 optimal weight: 1.9990 overall best weight: 1.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 319 ASN C 453 GLN ** C 587 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 721 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7025 moved from start: 0.3856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 28348 Z= 0.256 Angle : 0.548 6.762 39325 Z= 0.316 Chirality : 0.042 0.161 4440 Planarity : 0.004 0.090 4297 Dihedral : 21.230 165.065 5980 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 0.91 % Allowed : 16.98 % Favored : 82.11 % 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: 0.49 (0.16), residues: 2849 helix: 2.64 (0.15), residues: 1186 sheet: -1.28 (0.22), residues: 497 loop : -1.45 (0.17), residues: 1166 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 415 HIS 0.005 0.001 HIS B 237 PHE 0.023 0.001 PHE B 262 TYR 0.011 0.001 TYR C 149 ARG 0.010 0.000 ARG A 444 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5698 Ramachandran restraints generated. 2849 Oldfield, 0 Emsley, 2849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5698 Ramachandran restraints generated. 2849 Oldfield, 0 Emsley, 2849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 2409 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 199 time to evaluate : 3.850 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 150 ASP cc_start: 0.8621 (OUTLIER) cc_final: 0.8311 (t0) REVERT: B 20 ARG cc_start: 0.8257 (ttm170) cc_final: 0.7997 (ttm170) REVERT: B 25 MET cc_start: 0.8179 (OUTLIER) cc_final: 0.7800 (mtp) REVERT: B 276 ARG cc_start: 0.8417 (OUTLIER) cc_final: 0.7979 (ttm110) REVERT: B 356 LEU cc_start: 0.7991 (mm) cc_final: 0.7685 (mp) REVERT: B 450 ILE cc_start: 0.8880 (pt) cc_final: 0.8630 (tt) REVERT: B 538 LYS cc_start: 0.8743 (tttt) cc_final: 0.8430 (tttp) REVERT: B 599 ARG cc_start: 0.7616 (mmp-170) cc_final: 0.7047 (ttm-80) REVERT: B 754 THR cc_start: 0.8786 (p) cc_final: 0.8276 (t) REVERT: B 761 ARG cc_start: 0.8608 (mmt90) cc_final: 0.8366 (mmt-90) REVERT: C 413 ASN cc_start: 0.7338 (m-40) cc_final: 0.6694 (t0) REVERT: C 423 MET cc_start: 0.7412 (pp-130) cc_final: 0.7187 (ppp) REVERT: C 424 LEU cc_start: 0.7144 (tt) cc_final: 0.6839 (tt) REVERT: D 36 LEU cc_start: 0.8587 (mp) cc_final: 0.8083 (mt) REVERT: D 131 GLU cc_start: 0.7103 (tt0) cc_final: 0.6594 (tm-30) REVERT: D 253 GLU cc_start: 0.7914 (mt-10) cc_final: 0.7654 (mt-10) REVERT: D 387 ARG cc_start: 0.7599 (ttm-80) cc_final: 0.6842 (ptm160) REVERT: D 406 LYS cc_start: 0.8363 (mttt) cc_final: 0.7957 (mmtt) REVERT: D 474 LEU cc_start: 0.8265 (OUTLIER) cc_final: 0.7915 (tp) outliers start: 22 outliers final: 14 residues processed: 216 average time/residue: 3.0161 time to fit residues: 770.6656 Evaluate side-chains 215 residues out of total 2409 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 197 time to evaluate : 3.985 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 150 ASP Chi-restraints excluded: chain A residue 171 SER Chi-restraints excluded: chain B residue 14 LYS Chi-restraints excluded: chain B residue 25 MET Chi-restraints excluded: chain B residue 134 ILE Chi-restraints excluded: chain B residue 276 ARG Chi-restraints excluded: chain B residue 351 GLN Chi-restraints excluded: chain B residue 426 ASP Chi-restraints excluded: chain B residue 439 LYS Chi-restraints excluded: chain C residue 72 ASP Chi-restraints excluded: chain C residue 452 GLU Chi-restraints excluded: chain C residue 511 GLU Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 650 THR Chi-restraints excluded: chain C residue 787 VAL Chi-restraints excluded: chain D residue 290 THR Chi-restraints excluded: chain D residue 426 ASP Chi-restraints excluded: chain D residue 474 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 307 random chunks: chunk 193 optimal weight: 3.9990 chunk 259 optimal weight: 0.9990 chunk 74 optimal weight: 3.9990 chunk 224 optimal weight: 3.9990 chunk 35 optimal weight: 0.4980 chunk 67 optimal weight: 4.9990 chunk 243 optimal weight: 5.9990 chunk 102 optimal weight: 2.9990 chunk 250 optimal weight: 0.0570 chunk 30 optimal weight: 2.9990 chunk 44 optimal weight: 0.6980 overall best weight: 1.0502 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 319 ASN C 453 GLN ** C 587 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4125 r_free = 0.4125 target = 0.162069 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.104709 restraints weight = 103832.327| |-----------------------------------------------------------------------------| r_work (start): 0.3349 rms_B_bonded: 1.94 r_work: 0.3071 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.2947 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.2947 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8535 moved from start: 0.3882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 28348 Z= 0.181 Angle : 0.527 6.454 39325 Z= 0.304 Chirality : 0.040 0.151 4440 Planarity : 0.003 0.067 4297 Dihedral : 21.199 164.990 5980 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 4.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 0.83 % Allowed : 17.02 % Favored : 82.15 % 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: 0.59 (0.16), residues: 2849 helix: 2.73 (0.15), residues: 1186 sheet: -1.23 (0.23), residues: 497 loop : -1.40 (0.17), residues: 1166 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 415 HIS 0.004 0.001 HIS C 378 PHE 0.022 0.001 PHE B 262 TYR 0.018 0.001 TYR D 242 ARG 0.013 0.000 ARG A 444 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 17826.41 seconds wall clock time: 413 minutes 12.56 seconds (24792.56 seconds total)