Starting phenix.real_space_refine on Sun Sep 13 08:27:34 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6yrg_10889/09_2026/6yrg_10889_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/6yrg_10889/09_2026/6yrg_10889.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6yrg_10889/09_2026/6yrg_10889.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6yrg_10889/09_2026/6yrg_10889.map" model { file = "/net/cci-nas-00/data/ceres_data/6yrg_10889/09_2026/6yrg_10889_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6yrg_10889/09_2026/6yrg_10889_neut.cif" } resolution = 4.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.005 sd= 0.100 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 60 5.16 5 C 14024 2.51 5 N 3572 2.21 5 O 4336 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 124 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 21992 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 5498 Number of conformers: 1 Conformer: "" Number of residues, atoms: 684, 5498 Classifications: {'peptide': 684} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 21, 'TRANS': 662} Chain breaks: 1 Chain: "B" Number of atoms: 5498 Number of conformers: 1 Conformer: "" Number of residues, atoms: 684, 5498 Classifications: {'peptide': 684} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 21, 'TRANS': 662} Chain breaks: 1 Chain: "C" Number of atoms: 5498 Number of conformers: 1 Conformer: "" Number of residues, atoms: 684, 5498 Classifications: {'peptide': 684} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 21, 'TRANS': 662} Chain breaks: 1 Chain: "D" Number of atoms: 5498 Number of conformers: 1 Conformer: "" Number of residues, atoms: 684, 5498 Classifications: {'peptide': 684} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 21, 'TRANS': 662} Chain breaks: 1 Time building chain proxies: 5.79, per 1000 atoms: 0.26 Number of scatterers: 21992 At special positions: 0 Unit cell: (145.905, 152.295, 155.49, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 60 16.00 O 4336 8.00 N 3572 7.00 C 14024 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.84 Conformation dependent library (CDL) restraints added in 1.0 seconds 5440 Ramachandran restraints generated. 2720 Oldfield, 0 Emsley, 2720 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5184 Finding SS restraints... Secondary structure from input PDB file: 44 helices and 48 sheets defined 31.7% alpha, 28.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.80 Creating SS restraints... Processing helix chain 'A' and resid 105 through 193 Proline residue: A 129 - end of helix Proline residue: A 181 - end of helix Processing helix chain 'A' and resid 193 through 198 Processing helix chain 'A' and resid 215 through 231 Processing helix chain 'A' and resid 236 through 250 Processing helix chain 'A' and resid 257 through 270 Processing helix chain 'A' and resid 276 through 307 Processing helix chain 'A' and resid 313 through 332 Processing helix chain 'A' and resid 389 through 393 removed outlier: 3.836A pdb=" N TYR A 392 " --> pdb=" O LYS A 389 " (cutoff:3.500A) Processing helix chain 'A' and resid 406 through 412 Processing helix chain 'A' and resid 531 through 538 removed outlier: 3.611A pdb=" N GLU A 538 " --> pdb=" O GLU A 534 " (cutoff:3.500A) Processing helix chain 'A' and resid 607 through 610 Processing helix chain 'B' and resid 106 through 193 Proline residue: B 129 - end of helix Proline residue: B 181 - end of helix Processing helix chain 'B' and resid 193 through 198 Processing helix chain 'B' and resid 215 through 231 Processing helix chain 'B' and resid 236 through 250 Processing helix chain 'B' and resid 257 through 270 Processing helix chain 'B' and resid 276 through 307 Processing helix chain 'B' and resid 313 through 332 Processing helix chain 'B' and resid 407 through 412 Processing helix chain 'B' and resid 456 through 459 removed outlier: 4.121A pdb=" N GLY B 459 " --> pdb=" O PRO B 456 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 456 through 459' Processing helix chain 'B' and resid 518 through 522 Processing helix chain 'B' and resid 531 through 540 removed outlier: 4.871A pdb=" N GLU B 538 " --> pdb=" O GLU B 534 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N THR B 539 " --> pdb=" O SER B 535 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ASP B 540 " --> pdb=" O LEU B 536 " (cutoff:3.500A) Processing helix chain 'C' and resid 106 through 193 Proline residue: C 129 - end of helix Proline residue: C 181 - end of helix Processing helix chain 'C' and resid 193 through 198 Processing helix chain 'C' and resid 215 through 231 Processing helix chain 'C' and resid 236 through 250 Processing helix chain 'C' and resid 257 through 270 Processing helix chain 'C' and resid 276 through 307 Processing helix chain 'C' and resid 313 through 332 Processing helix chain 'C' and resid 389 through 393 removed outlier: 3.837A pdb=" N TYR C 392 " --> pdb=" O LYS C 389 " (cutoff:3.500A) Processing helix chain 'C' and resid 406 through 412 Processing helix chain 'C' and resid 531 through 538 removed outlier: 3.611A pdb=" N GLU C 538 " --> pdb=" O GLU C 534 " (cutoff:3.500A) Processing helix chain 'C' and resid 607 through 610 Processing helix chain 'D' and resid 106 through 193 Proline residue: D 129 - end of helix Proline residue: D 181 - end of helix Processing helix chain 'D' and resid 193 through 198 Processing helix chain 'D' and resid 215 through 231 Processing helix chain 'D' and resid 236 through 250 Processing helix chain 'D' and resid 257 through 270 Processing helix chain 'D' and resid 276 through 307 Processing helix chain 'D' and resid 313 through 332 Processing helix chain 'D' and resid 407 through 412 Processing helix chain 'D' and resid 456 through 459 removed outlier: 4.121A pdb=" N GLY D 459 " --> pdb=" O PRO D 456 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 456 through 459' Processing helix chain 'D' and resid 518 through 522 Processing helix chain 'D' and resid 531 through 540 removed outlier: 4.870A pdb=" N GLU D 538 " --> pdb=" O GLU D 534 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N THR D 539 " --> pdb=" O SER D 535 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ASP D 540 " --> pdb=" O LEU D 536 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 339 through 341 removed outlier: 3.830A pdb=" N PHE A 340 " --> pdb=" O GLY A 528 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N GLY A 528 " --> pdb=" O PHE A 340 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 344 through 348 removed outlier: 4.166A pdb=" N ASN A 348 " --> pdb=" O ILE A 495 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N ILE A 495 " --> pdb=" O ASN A 348 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 357 through 361 removed outlier: 6.755A pdb=" N THR A 450 " --> pdb=" O THR A 434 " (cutoff:3.500A) removed outlier: 6.034A pdb=" N LYS A 465 " --> pdb=" O PHE A 453 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 357 through 361 removed outlier: 6.894A pdb=" N LYS A 419 " --> pdb=" O LEU A 445 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 366 through 374 removed outlier: 5.920A pdb=" N LEU A 368 " --> pdb=" O ALA A 386 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N ALA A 386 " --> pdb=" O LEU A 368 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N GLY A 370 " --> pdb=" O TYR A 384 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N TYR A 384 " --> pdb=" O GLY A 370 " (cutoff:3.500A) removed outlier: 7.350A pdb=" N ILE A 403 " --> pdb=" O LYS A 687 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 366 through 374 removed outlier: 5.920A pdb=" N LEU A 368 " --> pdb=" O ALA A 386 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N ALA A 386 " --> pdb=" O LEU A 368 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N GLY A 370 " --> pdb=" O TYR A 384 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N TYR A 384 " --> pdb=" O GLY A 370 " (cutoff:3.500A) removed outlier: 7.350A pdb=" N ILE A 403 " --> pdb=" O LYS A 687 " (cutoff:3.500A) removed outlier: 4.727A pdb=" N GLY A 678 " --> pdb=" O LYS A 623 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N LYS A 623 " --> pdb=" O GLY A 678 " (cutoff:3.500A) removed outlier: 4.707A pdb=" N ASN A 680 " --> pdb=" O VAL A 621 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N VAL A 621 " --> pdb=" O ASN A 680 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N ASN A 615 " --> pdb=" O ILE A 686 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N THR A 614 " --> pdb=" O SER A 657 " (cutoff:3.500A) removed outlier: 7.530A pdb=" N GLY A 624 " --> pdb=" O ASP A 647 " (cutoff:3.500A) removed outlier: 8.019A pdb=" N ASP A 647 " --> pdb=" O GLY A 624 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 603 through 605 removed outlier: 6.339A pdb=" N ILE A 628 " --> pdb=" O GLU A 639 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N GLU A 639 " --> pdb=" O ILE A 628 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N LEU A 630 " --> pdb=" O LEU A 637 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 603 through 605 Processing sheet with id=AA9, first strand: chain 'A' and resid 702 through 704 removed outlier: 3.681A pdb=" N GLN A 725 " --> pdb=" O ILE A 781 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ILE A 781 " --> pdb=" O GLN A 725 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N ALA A 782 " --> pdb=" O SER A 748 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N SER A 748 " --> pdb=" O ALA A 782 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N VAL A 747 " --> pdb=" O VAL A 759 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N VAL A 759 " --> pdb=" O VAL A 747 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N ILE A 749 " --> pdb=" O LEU A 757 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 707 through 708 removed outlier: 4.116A pdb=" N GLN A 708 " --> pdb=" O GLU A 716 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N GLU A 716 " --> pdb=" O GLN A 708 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 736 through 738 removed outlier: 3.760A pdb=" N LEU A 737 " --> pdb=" O ARG A 768 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ARG A 768 " --> pdb=" O LEU A 737 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'B' and resid 344 through 348 removed outlier: 3.816A pdb=" N ASN B 348 " --> pdb=" O ILE B 495 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N ILE B 495 " --> pdb=" O ASN B 348 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 357 through 361 removed outlier: 5.071A pdb=" N TYR B 431 " --> pdb=" O TYR B 454 " (cutoff:3.500A) removed outlier: 5.989A pdb=" N TYR B 454 " --> pdb=" O TYR B 431 " (cutoff:3.500A) removed outlier: 4.729A pdb=" N ILE B 433 " --> pdb=" O ASN B 452 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N ASN B 452 " --> pdb=" O ILE B 433 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N LYS B 435 " --> pdb=" O THR B 450 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N THR B 450 " --> pdb=" O LYS B 435 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ARG B 441 " --> pdb=" O GLN B 444 " (cutoff:3.500A) removed outlier: 12.476A pdb=" N TYR B 447 " --> pdb=" O VAL B 468 " (cutoff:3.500A) removed outlier: 11.073A pdb=" N VAL B 468 " --> pdb=" O TYR B 447 " (cutoff:3.500A) removed outlier: 11.703A pdb=" N VAL B 449 " --> pdb=" O VAL B 466 " (cutoff:3.500A) removed outlier: 10.438A pdb=" N VAL B 466 " --> pdb=" O VAL B 449 " (cutoff:3.500A) removed outlier: 9.552A pdb=" N ALA B 451 " --> pdb=" O ASN B 464 " (cutoff:3.500A) removed outlier: 8.310A pdb=" N ASN B 464 " --> pdb=" O ALA B 451 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N PHE B 453 " --> pdb=" O ASP B 462 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 357 through 361 removed outlier: 5.071A pdb=" N TYR B 431 " --> pdb=" O TYR B 454 " (cutoff:3.500A) removed outlier: 5.989A pdb=" N TYR B 454 " --> pdb=" O TYR B 431 " (cutoff:3.500A) removed outlier: 4.729A pdb=" N ILE B 433 " --> pdb=" O ASN B 452 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N ASN B 452 " --> pdb=" O ILE B 433 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N LYS B 435 " --> pdb=" O THR B 450 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N THR B 450 " --> pdb=" O LYS B 435 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ARG B 441 " --> pdb=" O GLN B 444 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N TYR B 421 " --> pdb=" O LEU B 445 " (cutoff:3.500A) removed outlier: 7.508A pdb=" N TYR B 447 " --> pdb=" O TYR B 421 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 366 through 370 removed outlier: 6.162A pdb=" N TYR B 384 " --> pdb=" O ILE B 369 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 373 through 374 removed outlier: 4.654A pdb=" N LEU B 381 " --> pdb=" O TYR B 404 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 424 through 426 Processing sheet with id=AB9, first strand: chain 'B' and resid 574 through 575 removed outlier: 3.749A pdb=" N TYR B 629 " --> pdb=" O LEU B 667 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 596 through 597 Processing sheet with id=AC2, first strand: chain 'B' and resid 645 through 649 removed outlier: 5.468A pdb=" N ASP B 647 " --> pdb=" O ILE B 622 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N ILE B 622 " --> pdb=" O ASP B 647 " (cutoff:3.500A) removed outlier: 5.996A pdb=" N GLN B 649 " --> pdb=" O TYR B 620 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N TYR B 620 " --> pdb=" O GLN B 649 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N THR B 614 " --> pdb=" O SER B 657 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N PHE B 655 " --> pdb=" O TYR B 616 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ILE B 618 " --> pdb=" O LYS B 653 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 645 through 649 removed outlier: 5.468A pdb=" N ASP B 647 " --> pdb=" O ILE B 622 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N ILE B 622 " --> pdb=" O ASP B 647 " (cutoff:3.500A) removed outlier: 5.996A pdb=" N GLN B 649 " --> pdb=" O TYR B 620 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N TYR B 620 " --> pdb=" O GLN B 649 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ASN B 615 " --> pdb=" O ILE B 686 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N VAL B 621 " --> pdb=" O ASN B 680 " (cutoff:3.500A) removed outlier: 4.902A pdb=" N ASN B 680 " --> pdb=" O VAL B 621 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 701 through 703 removed outlier: 3.910A pdb=" N GLN B 725 " --> pdb=" O ILE B 781 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ILE B 781 " --> pdb=" O GLN B 725 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N LEU B 757 " --> pdb=" O ILE B 749 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 716 through 717 Processing sheet with id=AC6, first strand: chain 'B' and resid 769 through 770 removed outlier: 3.770A pdb=" N THR B 734 " --> pdb=" O GLU B 803 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 339 through 341 removed outlier: 3.831A pdb=" N PHE C 340 " --> pdb=" O GLY C 528 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N GLY C 528 " --> pdb=" O PHE C 340 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 344 through 348 removed outlier: 4.167A pdb=" N ASN C 348 " --> pdb=" O ILE C 495 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N ILE C 495 " --> pdb=" O ASN C 348 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 357 through 361 removed outlier: 6.755A pdb=" N THR C 450 " --> pdb=" O THR C 434 " (cutoff:3.500A) removed outlier: 6.033A pdb=" N LYS C 465 " --> pdb=" O PHE C 453 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 357 through 361 removed outlier: 6.894A pdb=" N LYS C 419 " --> pdb=" O LEU C 445 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 366 through 374 removed outlier: 5.921A pdb=" N LEU C 368 " --> pdb=" O ALA C 386 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N ALA C 386 " --> pdb=" O LEU C 368 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N GLY C 370 " --> pdb=" O TYR C 384 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N TYR C 384 " --> pdb=" O GLY C 370 " (cutoff:3.500A) removed outlier: 7.350A pdb=" N ILE C 403 " --> pdb=" O LYS C 687 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 366 through 374 removed outlier: 5.921A pdb=" N LEU C 368 " --> pdb=" O ALA C 386 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N ALA C 386 " --> pdb=" O LEU C 368 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N GLY C 370 " --> pdb=" O TYR C 384 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N TYR C 384 " --> pdb=" O GLY C 370 " (cutoff:3.500A) removed outlier: 7.350A pdb=" N ILE C 403 " --> pdb=" O LYS C 687 " (cutoff:3.500A) removed outlier: 4.727A pdb=" N GLY C 678 " --> pdb=" O LYS C 623 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N LYS C 623 " --> pdb=" O GLY C 678 " (cutoff:3.500A) removed outlier: 4.707A pdb=" N ASN C 680 " --> pdb=" O VAL C 621 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N VAL C 621 " --> pdb=" O ASN C 680 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N ASN C 615 " --> pdb=" O ILE C 686 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N THR C 614 " --> pdb=" O SER C 657 " (cutoff:3.500A) removed outlier: 7.530A pdb=" N GLY C 624 " --> pdb=" O ASP C 647 " (cutoff:3.500A) removed outlier: 8.019A pdb=" N ASP C 647 " --> pdb=" O GLY C 624 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 603 through 605 removed outlier: 6.339A pdb=" N ILE C 628 " --> pdb=" O GLU C 639 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N GLU C 639 " --> pdb=" O ILE C 628 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N LEU C 630 " --> pdb=" O LEU C 637 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 603 through 605 Processing sheet with id=AD6, first strand: chain 'C' and resid 702 through 704 removed outlier: 3.681A pdb=" N GLN C 725 " --> pdb=" O ILE C 781 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ILE C 781 " --> pdb=" O GLN C 725 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N ALA C 782 " --> pdb=" O SER C 748 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N SER C 748 " --> pdb=" O ALA C 782 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N VAL C 747 " --> pdb=" O VAL C 759 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N VAL C 759 " --> pdb=" O VAL C 747 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N ILE C 749 " --> pdb=" O LEU C 757 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 707 through 708 removed outlier: 4.117A pdb=" N GLN C 708 " --> pdb=" O GLU C 716 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N GLU C 716 " --> pdb=" O GLN C 708 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 736 through 738 removed outlier: 3.760A pdb=" N LEU C 737 " --> pdb=" O ARG C 768 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ARG C 768 " --> pdb=" O LEU C 737 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD8 Processing sheet with id=AD9, first strand: chain 'D' and resid 344 through 348 removed outlier: 3.815A pdb=" N ASN D 348 " --> pdb=" O ILE D 495 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N ILE D 495 " --> pdb=" O ASN D 348 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'D' and resid 357 through 361 removed outlier: 5.072A pdb=" N TYR D 431 " --> pdb=" O TYR D 454 " (cutoff:3.500A) removed outlier: 5.988A pdb=" N TYR D 454 " --> pdb=" O TYR D 431 " (cutoff:3.500A) removed outlier: 4.729A pdb=" N ILE D 433 " --> pdb=" O ASN D 452 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N ASN D 452 " --> pdb=" O ILE D 433 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N LYS D 435 " --> pdb=" O THR D 450 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N THR D 450 " --> pdb=" O LYS D 435 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ARG D 441 " --> pdb=" O GLN D 444 " (cutoff:3.500A) removed outlier: 12.476A pdb=" N TYR D 447 " --> pdb=" O VAL D 468 " (cutoff:3.500A) removed outlier: 11.073A pdb=" N VAL D 468 " --> pdb=" O TYR D 447 " (cutoff:3.500A) removed outlier: 11.704A pdb=" N VAL D 449 " --> pdb=" O VAL D 466 " (cutoff:3.500A) removed outlier: 10.438A pdb=" N VAL D 466 " --> pdb=" O VAL D 449 " (cutoff:3.500A) removed outlier: 9.552A pdb=" N ALA D 451 " --> pdb=" O ASN D 464 " (cutoff:3.500A) removed outlier: 8.310A pdb=" N ASN D 464 " --> pdb=" O ALA D 451 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N PHE D 453 " --> pdb=" O ASP D 462 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'D' and resid 357 through 361 removed outlier: 5.072A pdb=" N TYR D 431 " --> pdb=" O TYR D 454 " (cutoff:3.500A) removed outlier: 5.988A pdb=" N TYR D 454 " --> pdb=" O TYR D 431 " (cutoff:3.500A) removed outlier: 4.729A pdb=" N ILE D 433 " --> pdb=" O ASN D 452 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N ASN D 452 " --> pdb=" O ILE D 433 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N LYS D 435 " --> pdb=" O THR D 450 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N THR D 450 " --> pdb=" O LYS D 435 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ARG D 441 " --> pdb=" O GLN D 444 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N TYR D 421 " --> pdb=" O LEU D 445 " (cutoff:3.500A) removed outlier: 7.507A pdb=" N TYR D 447 " --> pdb=" O TYR D 421 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'D' and resid 366 through 370 removed outlier: 6.161A pdb=" N TYR D 384 " --> pdb=" O ILE D 369 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'D' and resid 373 through 374 removed outlier: 4.653A pdb=" N LEU D 381 " --> pdb=" O TYR D 404 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'D' and resid 424 through 426 Processing sheet with id=AE6, first strand: chain 'D' and resid 574 through 575 removed outlier: 3.748A pdb=" N TYR D 629 " --> pdb=" O LEU D 667 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'D' and resid 596 through 597 Processing sheet with id=AE8, first strand: chain 'D' and resid 645 through 649 removed outlier: 5.468A pdb=" N ASP D 647 " --> pdb=" O ILE D 622 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N ILE D 622 " --> pdb=" O ASP D 647 " (cutoff:3.500A) removed outlier: 5.996A pdb=" N GLN D 649 " --> pdb=" O TYR D 620 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N TYR D 620 " --> pdb=" O GLN D 649 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N THR D 614 " --> pdb=" O SER D 657 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N PHE D 655 " --> pdb=" O TYR D 616 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ILE D 618 " --> pdb=" O LYS D 653 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'D' and resid 645 through 649 removed outlier: 5.468A pdb=" N ASP D 647 " --> pdb=" O ILE D 622 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N ILE D 622 " --> pdb=" O ASP D 647 " (cutoff:3.500A) removed outlier: 5.996A pdb=" N GLN D 649 " --> pdb=" O TYR D 620 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N TYR D 620 " --> pdb=" O GLN D 649 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ASN D 615 " --> pdb=" O ILE D 686 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N VAL D 621 " --> pdb=" O ASN D 680 " (cutoff:3.500A) removed outlier: 4.902A pdb=" N ASN D 680 " --> pdb=" O VAL D 621 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'D' and resid 701 through 703 removed outlier: 3.910A pdb=" N GLN D 725 " --> pdb=" O ILE D 781 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ILE D 781 " --> pdb=" O GLN D 725 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N LEU D 757 " --> pdb=" O ILE D 749 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'D' and resid 716 through 717 Processing sheet with id=AF3, first strand: chain 'D' and resid 769 through 770 removed outlier: 3.771A pdb=" N THR D 734 " --> pdb=" O GLU D 803 " (cutoff:3.500A) 1033 hydrogen bonds defined for protein. 2871 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.10 Time building geometry restraints manager: 2.51 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 6129 1.34 - 1.46: 5891 1.46 - 1.58: 10276 1.58 - 1.71: 4 1.71 - 1.83: 100 Bond restraints: 22400 Sorted by residual: bond pdb=" N LEU A 336 " pdb=" CA LEU A 336 " ideal model delta sigma weight residual 1.457 1.570 -0.112 1.29e-02 6.01e+03 7.57e+01 bond pdb=" N LEU C 336 " pdb=" CA LEU C 336 " ideal model delta sigma weight residual 1.457 1.568 -0.111 1.29e-02 6.01e+03 7.42e+01 bond pdb=" C LEU B 336 " pdb=" N SER B 337 " ideal model delta sigma weight residual 1.331 1.425 -0.095 1.23e-02 6.61e+03 5.92e+01 bond pdb=" C LEU D 336 " pdb=" N SER D 337 " ideal model delta sigma weight residual 1.331 1.424 -0.093 1.23e-02 6.61e+03 5.75e+01 bond pdb=" N THR C 335 " pdb=" CA THR C 335 " ideal model delta sigma weight residual 1.454 1.543 -0.089 1.23e-02 6.61e+03 5.28e+01 ... (remaining 22395 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.88: 30058 4.88 - 9.77: 220 9.77 - 14.65: 20 14.65 - 19.53: 8 19.53 - 24.42: 2 Bond angle restraints: 30308 Sorted by residual: angle pdb=" O PRO A 334 " pdb=" C PRO A 334 " pdb=" N THR A 335 " ideal model delta sigma weight residual 122.64 105.61 17.03 1.35e+00 5.49e-01 1.59e+02 angle pdb=" O PRO C 334 " pdb=" C PRO C 334 " pdb=" N THR C 335 " ideal model delta sigma weight residual 122.64 105.75 16.89 1.35e+00 5.49e-01 1.57e+02 angle pdb=" C THR B 335 " pdb=" CA THR B 335 " pdb=" CB THR B 335 " ideal model delta sigma weight residual 110.42 134.84 -24.42 1.99e+00 2.53e-01 1.51e+02 angle pdb=" C THR D 335 " pdb=" CA THR D 335 " pdb=" CB THR D 335 " ideal model delta sigma weight residual 110.42 133.61 -23.19 1.99e+00 2.53e-01 1.36e+02 angle pdb=" CA THR A 335 " pdb=" C THR A 335 " pdb=" O THR A 335 " ideal model delta sigma weight residual 121.11 109.36 11.75 1.13e+00 7.83e-01 1.08e+02 ... (remaining 30303 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.66: 12299 17.66 - 35.33: 1035 35.33 - 52.99: 182 52.99 - 70.66: 36 70.66 - 88.32: 12 Dihedral angle restraints: 13564 sinusoidal: 5524 harmonic: 8040 Sorted by residual: dihedral pdb=" CA THR B 335 " pdb=" C THR B 335 " pdb=" N LEU B 336 " pdb=" CA LEU B 336 " ideal model delta harmonic sigma weight residual 180.00 -114.21 -65.79 0 5.00e+00 4.00e-02 1.73e+02 dihedral pdb=" CA THR D 335 " pdb=" C THR D 335 " pdb=" N LEU D 336 " pdb=" CA LEU D 336 " ideal model delta harmonic sigma weight residual -180.00 -114.78 -65.22 0 5.00e+00 4.00e-02 1.70e+02 dihedral pdb=" C THR B 335 " pdb=" N THR B 335 " pdb=" CA THR B 335 " pdb=" CB THR B 335 " ideal model delta harmonic sigma weight residual -122.00 -146.73 24.73 0 2.50e+00 1.60e-01 9.78e+01 ... (remaining 13561 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.150: 3251 0.150 - 0.300: 161 0.300 - 0.450: 21 0.450 - 0.600: 5 0.600 - 0.751: 2 Chirality restraints: 3440 Sorted by residual: chirality pdb=" CA THR B 335 " pdb=" N THR B 335 " pdb=" C THR B 335 " pdb=" CB THR B 335 " both_signs ideal model delta sigma weight residual False 2.53 1.78 0.75 2.00e-01 2.50e+01 1.41e+01 chirality pdb=" CA THR D 335 " pdb=" N THR D 335 " pdb=" C THR D 335 " pdb=" CB THR D 335 " both_signs ideal model delta sigma weight residual False 2.53 1.88 0.65 2.00e-01 2.50e+01 1.04e+01 chirality pdb=" CA THR B 180 " pdb=" N THR B 180 " pdb=" C THR B 180 " pdb=" CB THR B 180 " both_signs ideal model delta sigma weight residual False 2.53 2.06 0.47 2.00e-01 2.50e+01 5.42e+00 ... (remaining 3437 not shown) Planarity restraints: 3892 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PRO D 334 " 0.086 2.00e-02 2.50e+03 1.77e-01 3.14e+02 pdb=" C PRO D 334 " -0.306 2.00e-02 2.50e+03 pdb=" O PRO D 334 " 0.125 2.00e-02 2.50e+03 pdb=" N THR D 335 " 0.096 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PRO B 334 " -0.085 2.00e-02 2.50e+03 1.75e-01 3.08e+02 pdb=" C PRO B 334 " 0.303 2.00e-02 2.50e+03 pdb=" O PRO B 334 " -0.123 2.00e-02 2.50e+03 pdb=" N THR B 335 " -0.095 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PRO A 334 " 0.086 2.00e-02 2.50e+03 1.55e-01 2.41e+02 pdb=" C PRO A 334 " -0.268 2.00e-02 2.50e+03 pdb=" O PRO A 334 " 0.099 2.00e-02 2.50e+03 pdb=" N THR A 335 " 0.084 2.00e-02 2.50e+03 ... (remaining 3889 not shown) Histogram of nonbonded interaction distances: 1.27 - 2.00: 12 2.00 - 2.72: 1394 2.72 - 3.45: 35339 3.45 - 4.17: 59931 4.17 - 4.90: 101166 Nonbonded interactions: 197842 Sorted by model distance: nonbonded pdb=" O ILE B 332 " pdb=" CG2 THR B 335 " model vdw 1.270 3.460 nonbonded pdb=" O ILE D 332 " pdb=" CG2 THR D 335 " model vdw 1.324 3.460 nonbonded pdb=" O LEU D 333 " pdb=" OG1 THR D 335 " model vdw 1.500 3.040 nonbonded pdb=" O LEU B 333 " pdb=" OG1 THR B 335 " model vdw 1.657 3.040 nonbonded pdb=" NZ LYS B 325 " pdb=" ND2 ASN B 543 " model vdw 1.777 3.200 ... (remaining 197837 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints Number of NCS constrained groups: 1 pdb_interpretation.ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } Set refine NCS operators NCS operators will be refined. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.860 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.410 Check model and map are aligned: 0.080 Set scattering table: 0.070 Process input model: 22.830 Find NCS groups from input model: 0.390 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.010 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.070 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3162 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 : 0.009 0.112 22400 Z= 0.552 Angle : 1.413 24.415 30308 Z= 0.952 Chirality : 0.081 0.751 3440 Planarity : 0.010 0.177 3892 Dihedral : 13.689 88.322 8380 Min Nonbonded Distance : 1.270 Molprobity Statistics. All-atom Clashscore : 31.64 Ramachandran Plot: Outliers : 0.29 % Allowed : 9.38 % Favored : 90.33 % Rotamer: Outliers : 0.48 % Allowed : 4.99 % Favored : 94.53 % Cbeta Deviations : 0.69 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.26 (0.16), residues: 2720 helix: 2.81 (0.17), residues: 780 sheet: -3.12 (0.20), residues: 538 loop : -3.58 (0.13), residues: 1402 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.035 0.003 ARG D 185 TYR 0.063 0.006 TYR A 127 PHE 0.035 0.004 PHE C 239 TRP 0.012 0.002 TRP C 563 HIS 0.005 0.001 HIS C 597 Details of bonding type rmsd/Z covalent geometry : bond 0.00917 / 0.55 (22400) covalent geometry : angle 1.41302 / 0.95 (30308) hydrogen bonds : bond 0.24264 / 15.94 ( 975) hydrogen bonds : angle 9.05349 / 6.45 ( 2871) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5440 Ramachandran restraints generated. 2720 Oldfield, 0 Emsley, 2720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5440 Ramachandran restraints generated. 2720 Oldfield, 0 Emsley, 2720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 93 time to evaluate : 0.221 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 168 LEU cc_start: 0.7801 (tp) cc_final: 0.7528 (tp) REVERT: A 245 HIS cc_start: 0.4639 (t-90) cc_final: 0.4366 (t-90) REVERT: A 497 MET cc_start: 0.7234 (ptm) cc_final: 0.6770 (ttp) REVERT: A 645 PHE cc_start: 0.6276 (m-80) cc_final: 0.5914 (m-80) REVERT: A 730 GLU cc_start: 0.8371 (mm-30) cc_final: 0.8162 (tp30) outliers start: 4 outliers final: 1 residues processed: 96 average time/residue: 0.1016 time to fit residues: 11.9619 Evaluate side-chains 46 residues out of total 626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 45 time to evaluate : 0.234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 197 optimal weight: 0.0040 chunk 215 optimal weight: 0.8980 chunk 20 optimal weight: 0.5980 chunk 132 optimal weight: 0.0170 chunk 261 optimal weight: 0.4980 chunk 248 optimal weight: 0.0070 chunk 207 optimal weight: 10.0000 chunk 155 optimal weight: 0.0870 chunk 244 optimal weight: 0.0270 chunk 183 optimal weight: 0.8980 chunk 111 optimal weight: 9.9990 overall best weight: 0.0284 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 141 GLN A 242 GLN A 319 HIS ** A 348 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 569 ASN A 577 ASN A 604 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4657 r_free = 0.4657 target = 0.107581 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.4198 r_free = 0.4198 target = 0.074177 restraints weight = 44317.851| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 66)----------------| | r_work = 0.4214 r_free = 0.4214 target = 0.074949 restraints weight = 38022.410| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4233 r_free = 0.4233 target = 0.075839 restraints weight = 33408.986| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.4247 r_free = 0.4247 target = 0.076585 restraints weight = 30405.912| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.4258 r_free = 0.4258 target = 0.077109 restraints weight = 28149.678| |-----------------------------------------------------------------------------| r_work (final): 0.4143 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4974 moved from start: 1.4388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.013 0.361 22400 Z= 0.805 Angle : 1.280 26.858 30308 Z= 0.772 Chirality : 0.071 0.818 3440 Planarity : 0.007 0.056 3892 Dihedral : 7.240 50.531 2928 Min Nonbonded Distance : 1.077 Molprobity Statistics. All-atom Clashscore : 32.87 Ramachandran Plot: Outliers : 2.21 % Allowed : 9.56 % Favored : 88.24 % Rotamer: Outliers : 0.48 % Allowed : 5.59 % Favored : 93.93 % Cbeta Deviations : 0.31 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.30 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.89 (0.16), residues: 2720 helix: 2.23 (0.18), residues: 744 sheet: -1.93 (0.21), residues: 636 loop : -3.10 (0.14), residues: 1340 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 185 TYR 0.046 0.003 TYR B 127 PHE 0.020 0.002 PHE D 666 TRP 0.009 0.002 TRP C 471 HIS 0.021 0.003 HIS D 112 Details of bonding type rmsd/Z covalent geometry : bond 0.01299 / 0.80 (22400) covalent geometry : angle 1.27972 / 0.77 (30308) hydrogen bonds : bond 0.19347 / 12.14 ( 975) hydrogen bonds : angle 7.89016 / 5.62 ( 2871) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5440 Ramachandran restraints generated. 2720 Oldfield, 0 Emsley, 2720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5440 Ramachandran restraints generated. 2720 Oldfield, 0 Emsley, 2720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 75 time to evaluate : 0.214 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 319 HIS cc_start: 0.8709 (m-70) cc_final: 0.8155 (m90) REVERT: C 387 ARG cc_start: 0.5447 (mmt90) cc_final: 0.5243 (mmm160) REVERT: C 467 LYS cc_start: 0.9237 (ttpt) cc_final: 0.8973 (tttm) REVERT: C 497 MET cc_start: 0.6848 (ptm) cc_final: 0.6585 (ptm) REVERT: C 685 GLU cc_start: 0.8164 (tt0) cc_final: 0.7804 (tm-30) REVERT: C 695 MET cc_start: 0.7830 (ptp) cc_final: 0.7479 (ppp) REVERT: C 730 GLU cc_start: 0.8314 (mm-30) cc_final: 0.8074 (tp30) outliers start: 3 outliers final: 1 residues processed: 77 average time/residue: 0.0892 time to fit residues: 8.7498 Evaluate side-chains 43 residues out of total 626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 42 time to evaluate : 0.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 64 optimal weight: 0.0670 chunk 25 optimal weight: 0.7980 chunk 149 optimal weight: 2.9990 chunk 100 optimal weight: 3.9990 chunk 185 optimal weight: 0.0050 chunk 124 optimal weight: 7.9990 chunk 42 optimal weight: 0.0570 chunk 114 optimal weight: 9.9990 chunk 221 optimal weight: 0.0670 chunk 162 optimal weight: 0.0970 chunk 146 optimal weight: 6.9990 overall best weight: 0.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 141 GLN C 292 GLN ** C 320 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 324 GLN C 348 ASN C 569 ASN C 577 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4677 r_free = 0.4677 target = 0.108429 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4206 r_free = 0.4206 target = 0.074310 restraints weight = 44591.714| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4232 r_free = 0.4232 target = 0.075440 restraints weight = 37946.868| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 66)----------------| | r_work = 0.4246 r_free = 0.4246 target = 0.076398 restraints weight = 32937.206| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 19)----------------| | r_work = 0.4261 r_free = 0.4261 target = 0.077087 restraints weight = 29608.535| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.4268 r_free = 0.4268 target = 0.077418 restraints weight = 27279.202| |-----------------------------------------------------------------------------| r_work (final): 0.4212 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4972 moved from start: 1.5289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.356 22400 Z= 0.762 Angle : 1.188 29.759 30308 Z= 0.705 Chirality : 0.065 0.649 3440 Planarity : 0.005 0.048 3892 Dihedral : 6.513 29.370 2928 Min Nonbonded Distance : 1.113 Molprobity Statistics. All-atom Clashscore : 26.73 Ramachandran Plot: Outliers : 0.15 % Allowed : 10.00 % Favored : 89.85 % Rotamer: Outliers : 0.32 % Allowed : 4.31 % Favored : 95.37 % Cbeta Deviations : 0.31 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.87 (0.16), residues: 2720 helix: 1.71 (0.18), residues: 736 sheet: -1.61 (0.20), residues: 628 loop : -2.88 (0.15), residues: 1356 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 185 TYR 0.028 0.002 TYR C 127 PHE 0.024 0.002 PHE B 780 TRP 0.011 0.001 TRP C 573 HIS 0.016 0.003 HIS C 112 Details of bonding type rmsd/Z covalent geometry : bond 0.01130 / 0.76 (22400) covalent geometry : angle 1.18843 / 0.71 (30308) hydrogen bonds : bond 0.17703 / 10.97 ( 975) hydrogen bonds : angle 7.46017 / 5.28 ( 2871) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5440 Ramachandran restraints generated. 2720 Oldfield, 0 Emsley, 2720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5440 Ramachandran restraints generated. 2720 Oldfield, 0 Emsley, 2720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 62 time to evaluate : 0.211 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 134 MET cc_start: -0.3942 (mtt) cc_final: -0.4160 (mtp) REVERT: C 241 LEU cc_start: 0.7904 (mm) cc_final: 0.7539 (pp) REVERT: C 319 HIS cc_start: 0.8656 (m-70) cc_final: 0.8021 (m90) REVERT: C 467 LYS cc_start: 0.9198 (ttpt) cc_final: 0.8915 (tttm) REVERT: C 685 GLU cc_start: 0.8069 (tt0) cc_final: 0.7754 (tm-30) REVERT: C 695 MET cc_start: 0.7218 (ptp) cc_final: 0.6559 (ppp) REVERT: C 709 MET cc_start: 0.5108 (mpp) cc_final: 0.4611 (mmm) outliers start: 2 outliers final: 0 residues processed: 64 average time/residue: 0.0819 time to fit residues: 6.8415 Evaluate side-chains 42 residues out of total 626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 42 time to evaluate : 0.216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 257 optimal weight: 0.0270 chunk 151 optimal weight: 1.9990 chunk 137 optimal weight: 50.0000 chunk 53 optimal weight: 0.4980 chunk 199 optimal weight: 0.3980 chunk 267 optimal weight: 6.9990 chunk 176 optimal weight: 9.9990 chunk 41 optimal weight: 2.9990 chunk 135 optimal weight: 0.0040 chunk 191 optimal weight: 30.0000 chunk 106 optimal weight: 0.8980 overall best weight: 0.3650 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 141 GLN ** C 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 604 GLN C 670 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4757 r_free = 0.4757 target = 0.128086 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.4530 r_free = 0.4530 target = 0.096689 restraints weight = 50031.235| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 66)----------------| | r_work = 0.4564 r_free = 0.4564 target = 0.099186 restraints weight = 33305.054| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4582 r_free = 0.4582 target = 0.100658 restraints weight = 24793.351| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.4600 r_free = 0.4600 target = 0.101752 restraints weight = 20687.949| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.4603 r_free = 0.4603 target = 0.101979 restraints weight = 18176.167| |-----------------------------------------------------------------------------| r_work (final): 0.4333 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5165 moved from start: 1.5886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.338 22400 Z= 0.708 Angle : 1.149 25.490 30308 Z= 0.689 Chirality : 0.073 1.200 3440 Planarity : 0.005 0.051 3892 Dihedral : 6.060 40.488 2928 Min Nonbonded Distance : 1.358 Molprobity Statistics. All-atom Clashscore : 24.18 Ramachandran Plot: Outliers : 0.29 % Allowed : 9.71 % Favored : 90.00 % Rotamer: Outliers : 0.32 % Allowed : 4.15 % Favored : 95.53 % Cbeta Deviations : 0.46 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.30 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.68 (0.16), residues: 2720 helix: 1.47 (0.18), residues: 740 sheet: -1.41 (0.22), residues: 628 loop : -2.56 (0.15), residues: 1352 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 185 TYR 0.023 0.002 TYR C 240 PHE 0.034 0.002 PHE A 237 TRP 0.011 0.001 TRP C 563 HIS 0.010 0.002 HIS A 320 Details of bonding type rmsd/Z covalent geometry : bond 0.01090 / 0.71 (22400) covalent geometry : angle 1.14893 / 0.69 (30308) hydrogen bonds : bond 0.18542 / 11.59 ( 975) hydrogen bonds : angle 7.33934 / 5.19 ( 2871) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5440 Ramachandran restraints generated. 2720 Oldfield, 0 Emsley, 2720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5440 Ramachandran restraints generated. 2720 Oldfield, 0 Emsley, 2720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 58 time to evaluate : 0.240 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: C 319 HIS cc_start: 0.8940 (m-70) cc_final: 0.8588 (m90) REVERT: C 497 MET cc_start: 0.7659 (ptm) cc_final: 0.7004 (ttp) REVERT: C 532 LEU cc_start: 0.6644 (tp) cc_final: 0.6444 (tp) REVERT: C 685 GLU cc_start: 0.8365 (tt0) cc_final: 0.8086 (tm-30) REVERT: C 695 MET cc_start: 0.8863 (ptp) cc_final: 0.8300 (ppp) REVERT: C 709 MET cc_start: 0.5282 (mpp) cc_final: 0.4995 (mmm) outliers start: 2 outliers final: 0 residues processed: 60 average time/residue: 0.0742 time to fit residues: 5.8644 Evaluate side-chains 43 residues out of total 626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 43 time to evaluate : 0.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 97 optimal weight: 8.9990 chunk 145 optimal weight: 7.9990 chunk 25 optimal weight: 0.8980 chunk 198 optimal weight: 0.0270 chunk 269 optimal weight: 0.2980 chunk 233 optimal weight: 20.0000 chunk 210 optimal weight: 2.9990 chunk 120 optimal weight: 6.9990 chunk 44 optimal weight: 0.2980 chunk 177 optimal weight: 0.0570 chunk 163 optimal weight: 1.9990 overall best weight: 0.3156 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 114 ASN C 118 ASN C 270 ASN C 604 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4755 r_free = 0.4755 target = 0.128398 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4542 r_free = 0.4542 target = 0.096165 restraints weight = 50990.027| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.4577 r_free = 0.4577 target = 0.098927 restraints weight = 32401.070| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.4600 r_free = 0.4600 target = 0.100554 restraints weight = 24402.627| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4604 r_free = 0.4604 target = 0.101284 restraints weight = 20056.213| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.4604 r_free = 0.4604 target = 0.101284 restraints weight = 17941.702| |-----------------------------------------------------------------------------| r_work (final): 0.4319 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5213 moved from start: 1.6452 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.242 22400 Z= 0.497 Angle : 1.296 59.165 30308 Z= 0.721 Chirality : 0.116 2.900 3440 Planarity : 0.006 0.094 3892 Dihedral : 6.136 63.198 2928 Min Nonbonded Distance : 1.525 Molprobity Statistics. All-atom Clashscore : 21.35 Ramachandran Plot: Outliers : 0.29 % Allowed : 8.97 % Favored : 90.74 % Rotamer: Outliers : 0.32 % Allowed : 2.88 % Favored : 96.81 % Cbeta Deviations : 0.46 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.30 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.59 (0.16), residues: 2720 helix: 1.28 (0.19), residues: 756 sheet: -1.34 (0.22), residues: 644 loop : -2.38 (0.15), residues: 1320 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 185 TYR 0.023 0.002 TYR B 127 PHE 0.024 0.002 PHE B 581 TRP 0.016 0.002 TRP C 573 HIS 0.041 0.005 HIS D 112 Details of bonding type rmsd/Z covalent geometry : bond 0.00780 / 0.50 (22400) covalent geometry : angle 1.29611 / 0.72 (30308) hydrogen bonds : bond 0.17476 / 11.21 ( 975) hydrogen bonds : angle 7.33281 / 5.14 ( 2871) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5440 Ramachandran restraints generated. 2720 Oldfield, 0 Emsley, 2720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5440 Ramachandran restraints generated. 2720 Oldfield, 0 Emsley, 2720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 62 time to evaluate : 0.222 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 317 MET cc_start: 0.0594 (tmm) cc_final: -0.0176 (tmm) REVERT: C 319 HIS cc_start: 0.8926 (m-70) cc_final: 0.8471 (m90) REVERT: C 497 MET cc_start: 0.8053 (ptm) cc_final: 0.7614 (ttp) REVERT: C 511 TYR cc_start: 0.7683 (p90) cc_final: 0.7433 (p90) REVERT: C 532 LEU cc_start: 0.6978 (tp) cc_final: 0.6609 (tp) REVERT: C 685 GLU cc_start: 0.8500 (tt0) cc_final: 0.8222 (tm-30) REVERT: C 695 MET cc_start: 0.8605 (ptp) cc_final: 0.7728 (ppp) REVERT: C 768 ARG cc_start: 0.5687 (mmt-90) cc_final: 0.5411 (ptt-90) outliers start: 2 outliers final: 1 residues processed: 64 average time/residue: 0.0888 time to fit residues: 7.3238 Evaluate side-chains 45 residues out of total 626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 44 time to evaluate : 0.198 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 207 optimal weight: 9.9990 chunk 248 optimal weight: 0.0870 chunk 246 optimal weight: 7.9990 chunk 114 optimal weight: 3.9990 chunk 53 optimal weight: 0.9980 chunk 4 optimal weight: 8.9990 chunk 166 optimal weight: 0.0030 chunk 227 optimal weight: 0.9990 chunk 83 optimal weight: 9.9990 chunk 202 optimal weight: 0.0170 chunk 197 optimal weight: 9.9990 overall best weight: 0.4208 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 604 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4748 r_free = 0.4748 target = 0.128036 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.4525 r_free = 0.4525 target = 0.095961 restraints weight = 50372.257| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 64)----------------| | r_work = 0.4562 r_free = 0.4562 target = 0.098411 restraints weight = 32213.448| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 61)----------------| | r_work = 0.4561 r_free = 0.4561 target = 0.099720 restraints weight = 24267.160| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 21)----------------| | r_work = 0.4566 r_free = 0.4566 target = 0.100126 restraints weight = 20039.262| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.4585 r_free = 0.4585 target = 0.101362 restraints weight = 17920.686| |-----------------------------------------------------------------------------| r_work (final): 0.4315 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5189 moved from start: 1.6568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.258 22400 Z= 0.507 Angle : 1.351 63.699 30308 Z= 0.738 Chirality : 0.097 2.199 3440 Planarity : 0.008 0.140 3892 Dihedral : 6.269 62.881 2928 Min Nonbonded Distance : 1.465 Molprobity Statistics. All-atom Clashscore : 25.48 Ramachandran Plot: Outliers : 0.15 % Allowed : 8.68 % Favored : 91.18 % Rotamer: Outliers : 0.00 % Allowed : 0.96 % Favored : 99.04 % Cbeta Deviations : 0.62 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.30 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.63 (0.16), residues: 2720 helix: 1.07 (0.19), residues: 764 sheet: -1.26 (0.22), residues: 644 loop : -2.36 (0.15), residues: 1312 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.059 0.002 ARG B 533 TYR 0.015 0.002 TYR D 240 PHE 0.015 0.001 PHE C 780 TRP 0.011 0.002 TRP C 573 HIS 0.026 0.004 HIS A 112 Details of bonding type rmsd/Z covalent geometry : bond 0.00815 / 0.51 (22400) covalent geometry : angle 1.35087 / 0.74 (30308) hydrogen bonds : bond 0.16358 / 10.32 ( 975) hydrogen bonds : angle 7.21560 / 5.05 ( 2871) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5440 Ramachandran restraints generated. 2720 Oldfield, 0 Emsley, 2720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5440 Ramachandran restraints generated. 2720 Oldfield, 0 Emsley, 2720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 56 time to evaluate : 0.258 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 319 HIS cc_start: 0.8947 (m-70) cc_final: 0.8541 (m90) REVERT: C 497 MET cc_start: 0.8055 (ptm) cc_final: 0.7652 (ttp) REVERT: C 532 LEU cc_start: 0.6928 (tp) cc_final: 0.6712 (tp) REVERT: C 685 GLU cc_start: 0.8552 (tt0) cc_final: 0.8263 (tm-30) REVERT: C 695 MET cc_start: 0.8187 (ptp) cc_final: 0.7288 (ppp) REVERT: C 768 ARG cc_start: 0.5534 (mmt-90) cc_final: 0.5269 (ptt-90) outliers start: 0 outliers final: 0 residues processed: 56 average time/residue: 0.0899 time to fit residues: 6.6247 Evaluate side-chains 43 residues out of total 626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 43 time to evaluate : 0.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 188 optimal weight: 0.7980 chunk 105 optimal weight: 0.6980 chunk 87 optimal weight: 2.9990 chunk 173 optimal weight: 0.0370 chunk 15 optimal weight: 5.9990 chunk 8 optimal weight: 0.7980 chunk 248 optimal weight: 0.6980 chunk 50 optimal weight: 0.6980 chunk 253 optimal weight: 6.9990 chunk 121 optimal weight: 3.9990 chunk 203 optimal weight: 0.0050 overall best weight: 0.4272 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 604 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4746 r_free = 0.4746 target = 0.128021 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4529 r_free = 0.4529 target = 0.095398 restraints weight = 51110.704| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 59)----------------| | r_work = 0.4553 r_free = 0.4553 target = 0.098115 restraints weight = 32646.774| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.4575 r_free = 0.4575 target = 0.099723 restraints weight = 24431.654| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 62)----------------| | r_work = 0.4575 r_free = 0.4575 target = 0.100590 restraints weight = 20244.851| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.4583 r_free = 0.4583 target = 0.101202 restraints weight = 17983.258| |-----------------------------------------------------------------------------| r_work (final): 0.4315 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5190 moved from start: 1.6574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.258 22400 Z= 0.507 Angle : 1.351 63.699 30308 Z= 0.738 Chirality : 0.097 2.199 3440 Planarity : 0.008 0.140 3892 Dihedral : 6.269 62.881 2928 Min Nonbonded Distance : 1.465 Molprobity Statistics. All-atom Clashscore : 28.21 Ramachandran Plot: Outliers : 0.15 % Allowed : 8.68 % Favored : 91.18 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.62 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.30 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.63 (0.16), residues: 2720 helix: 1.07 (0.19), residues: 764 sheet: -1.26 (0.22), residues: 644 loop : -2.36 (0.15), residues: 1312 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.059 0.002 ARG C 533 TYR 0.015 0.002 TYR C 240 PHE 0.015 0.001 PHE A 780 TRP 0.011 0.002 TRP C 573 HIS 0.026 0.004 HIS C 112 Details of bonding type rmsd/Z covalent geometry : bond 0.00815 / 0.51 (22400) covalent geometry : angle 1.35087 / 0.74 (30308) hydrogen bonds : bond 0.16358 / 10.32 ( 975) hydrogen bonds : angle 7.21560 / 5.05 ( 2871) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5440 Ramachandran restraints generated. 2720 Oldfield, 0 Emsley, 2720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5440 Ramachandran restraints generated. 2720 Oldfield, 0 Emsley, 2720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 55 time to evaluate : 0.202 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 319 HIS cc_start: 0.8954 (m-70) cc_final: 0.8577 (m90) REVERT: C 497 MET cc_start: 0.8037 (ptm) cc_final: 0.7639 (ttp) REVERT: C 532 LEU cc_start: 0.6836 (tp) cc_final: 0.6629 (tp) REVERT: C 685 GLU cc_start: 0.8557 (tt0) cc_final: 0.8267 (tm-30) REVERT: C 695 MET cc_start: 0.8262 (ptp) cc_final: 0.7391 (ppp) REVERT: C 768 ARG cc_start: 0.5553 (mmt-90) cc_final: 0.5290 (ptt-90) outliers start: 0 outliers final: 0 residues processed: 55 average time/residue: 0.0865 time to fit residues: 6.2269 Evaluate side-chains 43 residues out of total 626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 43 time to evaluate : 0.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 204 optimal weight: 50.0000 chunk 179 optimal weight: 9.9990 chunk 253 optimal weight: 0.6980 chunk 242 optimal weight: 6.9990 chunk 191 optimal weight: 0.3980 chunk 5 optimal weight: 4.9990 chunk 22 optimal weight: 0.9990 chunk 239 optimal weight: 0.0470 chunk 7 optimal weight: 0.8980 chunk 249 optimal weight: 0.3980 chunk 222 optimal weight: 8.9990 overall best weight: 0.4878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 604 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4746 r_free = 0.4746 target = 0.128021 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4524 r_free = 0.4524 target = 0.095519 restraints weight = 50397.102| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 57)----------------| | r_work = 0.4550 r_free = 0.4550 target = 0.097996 restraints weight = 33110.545| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4573 r_free = 0.4573 target = 0.099633 restraints weight = 24614.542| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.4577 r_free = 0.4577 target = 0.100389 restraints weight = 20257.921| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.4577 r_free = 0.4577 target = 0.100389 restraints weight = 18178.687| |-----------------------------------------------------------------------------| r_work (final): 0.4314 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5236 moved from start: 1.6574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.258 22400 Z= 0.507 Angle : 1.351 63.699 30308 Z= 0.738 Chirality : 0.097 2.199 3440 Planarity : 0.008 0.140 3892 Dihedral : 6.269 62.881 2928 Min Nonbonded Distance : 1.465 Molprobity Statistics. All-atom Clashscore : 28.21 Ramachandran Plot: Outliers : 0.15 % Allowed : 8.68 % Favored : 91.18 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.62 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.30 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.63 (0.16), residues: 2720 helix: 1.07 (0.19), residues: 764 sheet: -1.26 (0.22), residues: 644 loop : -2.36 (0.15), residues: 1312 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.059 0.002 ARG D 533 TYR 0.015 0.002 TYR D 240 PHE 0.015 0.001 PHE C 780 TRP 0.011 0.002 TRP C 573 HIS 0.026 0.004 HIS A 112 Details of bonding type rmsd/Z covalent geometry : bond 0.00815 / 0.51 (22400) covalent geometry : angle 1.35087 / 0.74 (30308) hydrogen bonds : bond 0.16358 / 10.32 ( 975) hydrogen bonds : angle 7.21560 / 5.05 ( 2871) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5440 Ramachandran restraints generated. 2720 Oldfield, 0 Emsley, 2720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5440 Ramachandran restraints generated. 2720 Oldfield, 0 Emsley, 2720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 55 time to evaluate : 0.219 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 319 HIS cc_start: 0.8959 (m-70) cc_final: 0.8579 (m90) REVERT: C 497 MET cc_start: 0.8027 (ptm) cc_final: 0.7620 (ttp) REVERT: C 532 LEU cc_start: 0.6844 (tp) cc_final: 0.6637 (tp) REVERT: C 685 GLU cc_start: 0.8556 (tt0) cc_final: 0.8263 (tm-30) REVERT: C 695 MET cc_start: 0.8697 (ptp) cc_final: 0.7970 (ppp) REVERT: C 768 ARG cc_start: 0.5786 (mmt-90) cc_final: 0.5518 (ptt-90) outliers start: 0 outliers final: 0 residues processed: 55 average time/residue: 0.0897 time to fit residues: 6.4304 Evaluate side-chains 43 residues out of total 626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 43 time to evaluate : 0.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 121 optimal weight: 3.9990 chunk 202 optimal weight: 2.9990 chunk 139 optimal weight: 1.9990 chunk 165 optimal weight: 0.0970 chunk 156 optimal weight: 0.0980 chunk 161 optimal weight: 0.7980 chunk 120 optimal weight: 1.9990 chunk 73 optimal weight: 2.9990 chunk 229 optimal weight: 0.0000 chunk 41 optimal weight: 3.9990 chunk 187 optimal weight: 0.9980 overall best weight: 0.3982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 604 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4746 r_free = 0.4746 target = 0.128021 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.4525 r_free = 0.4525 target = 0.095559 restraints weight = 50394.358| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 73)----------------| | r_work = 0.4554 r_free = 0.4554 target = 0.098189 restraints weight = 32558.141| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4560 r_free = 0.4560 target = 0.099089 restraints weight = 24249.874| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.4584 r_free = 0.4584 target = 0.100483 restraints weight = 20852.912| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.4589 r_free = 0.4589 target = 0.101001 restraints weight = 18416.619| |-----------------------------------------------------------------------------| r_work (final): 0.4332 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5213 moved from start: 1.6574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.258 22400 Z= 0.507 Angle : 1.351 63.699 30308 Z= 0.738 Chirality : 0.097 2.199 3440 Planarity : 0.008 0.140 3892 Dihedral : 6.269 62.881 2928 Min Nonbonded Distance : 1.465 Molprobity Statistics. All-atom Clashscore : 28.21 Ramachandran Plot: Outliers : 0.15 % Allowed : 8.68 % Favored : 91.18 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.62 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.30 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.63 (0.16), residues: 2720 helix: 1.07 (0.19), residues: 764 sheet: -1.26 (0.22), residues: 644 loop : -2.36 (0.15), residues: 1312 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.059 0.002 ARG A 533 TYR 0.015 0.002 TYR B 240 PHE 0.015 0.001 PHE C 780 TRP 0.011 0.002 TRP C 573 HIS 0.026 0.004 HIS A 112 Details of bonding type rmsd/Z covalent geometry : bond 0.00815 / 0.51 (22400) covalent geometry : angle 1.35087 / 0.74 (30308) hydrogen bonds : bond 0.16358 / 10.32 ( 975) hydrogen bonds : angle 7.21560 / 5.05 ( 2871) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5440 Ramachandran restraints generated. 2720 Oldfield, 0 Emsley, 2720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5440 Ramachandran restraints generated. 2720 Oldfield, 0 Emsley, 2720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 55 time to evaluate : 0.215 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 319 HIS cc_start: 0.8939 (m-70) cc_final: 0.8470 (m90) REVERT: C 497 MET cc_start: 0.8043 (ptm) cc_final: 0.7608 (ttp) REVERT: C 685 GLU cc_start: 0.8550 (tt0) cc_final: 0.8230 (tm-30) REVERT: C 695 MET cc_start: 0.8509 (ptp) cc_final: 0.7703 (ppp) REVERT: C 768 ARG cc_start: 0.5716 (mmt-90) cc_final: 0.5443 (ptt-90) outliers start: 0 outliers final: 0 residues processed: 55 average time/residue: 0.0830 time to fit residues: 5.9804 Evaluate side-chains 42 residues out of total 626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 42 time to evaluate : 0.203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 252 optimal weight: 1.9990 chunk 183 optimal weight: 0.0010 chunk 102 optimal weight: 0.9990 chunk 69 optimal weight: 6.9990 chunk 83 optimal weight: 7.9990 chunk 162 optimal weight: 0.0060 chunk 239 optimal weight: 0.0000 chunk 11 optimal weight: 0.0060 chunk 123 optimal weight: 0.0370 chunk 270 optimal weight: 0.0030 chunk 248 optimal weight: 0.9980 overall best weight: 0.0032 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 604 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4746 r_free = 0.4746 target = 0.128022 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4530 r_free = 0.4530 target = 0.095481 restraints weight = 50685.644| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.4553 r_free = 0.4553 target = 0.098133 restraints weight = 32457.357| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.4575 r_free = 0.4575 target = 0.099775 restraints weight = 24278.001| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4576 r_free = 0.4576 target = 0.100399 restraints weight = 20150.238| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 19)----------------| | r_work = 0.4584 r_free = 0.4584 target = 0.101022 restraints weight = 18367.059| |-----------------------------------------------------------------------------| r_work (final): 0.4329 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5223 moved from start: 1.6574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.258 22400 Z= 0.507 Angle : 1.351 63.700 30308 Z= 0.738 Chirality : 0.097 2.199 3440 Planarity : 0.008 0.140 3892 Dihedral : 6.269 62.880 2928 Min Nonbonded Distance : 1.465 Molprobity Statistics. All-atom Clashscore : 28.12 Ramachandran Plot: Outliers : 0.15 % Allowed : 8.68 % Favored : 91.18 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.62 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.30 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.63 (0.16), residues: 2720 helix: 1.07 (0.19), residues: 764 sheet: -1.26 (0.22), residues: 644 loop : -2.36 (0.15), residues: 1312 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.059 0.002 ARG D 533 TYR 0.015 0.002 TYR C 240 PHE 0.015 0.001 PHE A 780 TRP 0.011 0.002 TRP C 573 HIS 0.026 0.004 HIS A 112 Details of bonding type rmsd/Z covalent geometry : bond 0.00814 / 0.51 (22400) covalent geometry : angle 1.35085 / 0.74 (30308) hydrogen bonds : bond 0.16358 / 10.32 ( 975) hydrogen bonds : angle 7.21561 / 5.05 ( 2871) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5440 Ramachandran restraints generated. 2720 Oldfield, 0 Emsley, 2720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5440 Ramachandran restraints generated. 2720 Oldfield, 0 Emsley, 2720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 55 time to evaluate : 0.207 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 319 HIS cc_start: 0.8955 (m-70) cc_final: 0.8572 (m90) REVERT: C 497 MET cc_start: 0.8020 (ptm) cc_final: 0.7614 (ttp) REVERT: C 532 LEU cc_start: 0.6540 (tp) cc_final: 0.6283 (tp) REVERT: C 685 GLU cc_start: 0.8558 (tt0) cc_final: 0.8264 (tm-30) REVERT: C 695 MET cc_start: 0.8670 (ptp) cc_final: 0.7943 (ppp) REVERT: C 768 ARG cc_start: 0.5769 (mmt-90) cc_final: 0.5499 (ptt-90) outliers start: 0 outliers final: 0 residues processed: 55 average time/residue: 0.0880 time to fit residues: 6.3572 Evaluate side-chains 43 residues out of total 626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 43 time to evaluate : 0.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 264 optimal weight: 0.9990 chunk 191 optimal weight: 3.9990 chunk 43 optimal weight: 5.9990 chunk 125 optimal weight: 0.8980 chunk 174 optimal weight: 0.9980 chunk 45 optimal weight: 1.9990 chunk 213 optimal weight: 6.9990 chunk 36 optimal weight: 0.9990 chunk 258 optimal weight: 5.9990 chunk 52 optimal weight: 0.4980 chunk 212 optimal weight: 0.7980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 604 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4746 r_free = 0.4746 target = 0.128022 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.4527 r_free = 0.4527 target = 0.095678 restraints weight = 50354.208| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 60)----------------| | r_work = 0.4558 r_free = 0.4558 target = 0.098315 restraints weight = 32534.757| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 76)----------------| | r_work = 0.4565 r_free = 0.4565 target = 0.099811 restraints weight = 24244.634| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 19)----------------| | r_work = 0.4567 r_free = 0.4567 target = 0.100470 restraints weight = 19896.648| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.4584 r_free = 0.4584 target = 0.101287 restraints weight = 17937.162| |-----------------------------------------------------------------------------| r_work (final): 0.4323 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5023 moved from start: 1.6574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.258 22400 Z= 0.507 Angle : 1.351 63.700 30308 Z= 0.738 Chirality : 0.097 2.199 3440 Planarity : 0.008 0.140 3892 Dihedral : 6.269 62.880 2928 Min Nonbonded Distance : 1.465 Molprobity Statistics. All-atom Clashscore : 28.12 Ramachandran Plot: Outliers : 0.15 % Allowed : 8.68 % Favored : 91.18 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.62 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.30 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.63 (0.16), residues: 2720 helix: 1.07 (0.19), residues: 764 sheet: -1.26 (0.22), residues: 644 loop : -2.36 (0.15), residues: 1312 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.059 0.002 ARG D 533 TYR 0.015 0.002 TYR D 240 PHE 0.015 0.001 PHE C 780 TRP 0.011 0.002 TRP C 573 HIS 0.026 0.004 HIS A 112 Details of bonding type rmsd/Z covalent geometry : bond 0.00814 / 0.51 (22400) covalent geometry : angle 1.35085 / 0.74 (30308) hydrogen bonds : bond 0.16358 / 10.32 ( 975) hydrogen bonds : angle 7.21561 / 5.05 ( 2871) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2532.75 seconds wall clock time: 45 minutes 30.68 seconds (2730.68 seconds total)