Starting phenix.real_space_refine on Thu Mar 5 11:47:21 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6yrg_10889/03_2026/6yrg_10889_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/6yrg_10889/03_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 { model { file = "/net/cci-nas-00/data/ceres_data/6yrg_10889/03_2026/6yrg_10889_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6yrg_10889/03_2026/6yrg_10889_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6yrg_10889/03_2026/6yrg_10889.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6yrg_10889/03_2026/6yrg_10889.map" } 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 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: 5.36, per 1000 atoms: 0.24 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: 1.70 Conformation dependent library (CDL) restraints added in 955.5 milliseconds 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: 1.00 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: 5.25 Time building geometry restraints manager: 2.41 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: 2.550 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: 0.280 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 22.910 Find NCS groups from input model: 0.390 Set up NCS constraints: 0.030 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:1.430 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.720 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3241 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 covalent geometry : bond 0.00917 (22400) covalent geometry : angle 1.41302 (30308) hydrogen bonds : bond 0.24264 ( 975) hydrogen bonds : angle 9.05349 ( 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 : 0.206 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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: 0.1068 time to fit residues: 12.5593 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 : 0.201 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: C 141 GLN C 242 GLN C 319 HIS ** C 348 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 569 ASN C 577 ASN C 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 = 0.4658 r_free = 0.4658 target = 0.107621 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.4200 r_free = 0.4200 target = 0.074129 restraints weight = 44487.265| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.4220 r_free = 0.4220 target = 0.075066 restraints weight = 38128.081| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 20)----------------| | r_work = 0.4235 r_free = 0.4235 target = 0.075800 restraints weight = 33447.320| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.4248 r_free = 0.4248 target = 0.076447 restraints weight = 30498.387| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4254 r_free = 0.4254 target = 0.076766 restraints weight = 28275.169| |-----------------------------------------------------------------------------| r_work (final): 0.4206 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4889 moved from start: 1.4403 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 : 32.78 Ramachandran Plot: Outliers : 2.21 % Allowed : 9.56 % Favored : 88.24 % Rotamer: Outliers : 0.48 % Allowed : 5.75 % Favored : 93.77 % 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 covalent geometry : bond 0.01299 (22400) covalent geometry : angle 1.27972 (30308) hydrogen bonds : bond 0.19347 ( 975) hydrogen bonds : angle 7.89016 ( 2871) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 76 time to evaluate : 0.211 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 319 HIS cc_start: 0.8500 (m90) cc_final: 0.7967 (m90) REVERT: C 467 LYS cc_start: 0.9212 (ttpt) cc_final: 0.8941 (tttm) REVERT: C 497 MET cc_start: 0.6738 (ptm) cc_final: 0.6497 (ptm) REVERT: C 685 GLU cc_start: 0.8143 (tt0) cc_final: 0.7782 (tm-30) REVERT: C 695 MET cc_start: 0.7680 (ptp) cc_final: 0.7359 (ppp) REVERT: C 730 GLU cc_start: 0.8329 (mm-30) cc_final: 0.8089 (tp30) outliers start: 3 outliers final: 1 residues processed: 78 average time/residue: 0.0965 time to fit residues: 9.5090 Evaluate side-chains 42 residues out of total 626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 41 time to evaluate : 0.159 ------------------------------------------------------------------------------- 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: 0.3980 chunk 100 optimal weight: 3.9990 chunk 185 optimal weight: 3.9990 chunk 124 optimal weight: 7.9990 chunk 42 optimal weight: 0.0050 chunk 114 optimal weight: 9.9990 chunk 221 optimal weight: 0.0670 chunk 162 optimal weight: 0.0670 chunk 146 optimal weight: 0.6980 overall best weight: 0.1208 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 141 GLN C 292 GLN ** C 320 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 324 GLN C 348 ASN C 604 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4763 r_free = 0.4763 target = 0.128820 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4559 r_free = 0.4559 target = 0.097969 restraints weight = 49335.679| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.4573 r_free = 0.4573 target = 0.100112 restraints weight = 32490.377| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4596 r_free = 0.4596 target = 0.101658 restraints weight = 24492.412| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 74)----------------| | r_work = 0.4599 r_free = 0.4599 target = 0.102874 restraints weight = 20276.015| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4601 r_free = 0.4601 target = 0.103318 restraints weight = 18126.501| |-----------------------------------------------------------------------------| r_work (final): 0.4364 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4810 moved from start: 1.5347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.363 22400 Z= 0.765 Angle : 1.172 29.050 30308 Z= 0.699 Chirality : 0.064 0.657 3440 Planarity : 0.005 0.049 3892 Dihedral : 6.384 29.178 2928 Min Nonbonded Distance : 1.135 Molprobity Statistics. All-atom Clashscore : 25.98 Ramachandran Plot: Outliers : 0.15 % Allowed : 10.44 % Favored : 89.41 % 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: -2.08 (0.15), residues: 2720 helix: 1.40 (0.18), residues: 736 sheet: -1.68 (0.20), residues: 624 loop : -2.96 (0.14), residues: 1360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 533 TYR 0.027 0.002 TYR C 240 PHE 0.023 0.002 PHE B 780 TRP 0.018 0.002 TRP C 573 HIS 0.014 0.003 HIS A 112 Details of bonding type rmsd covalent geometry : bond 0.01144 (22400) covalent geometry : angle 1.17161 (30308) hydrogen bonds : bond 0.17772 ( 975) hydrogen bonds : angle 7.43145 ( 2871) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 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 : 0.157 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: -0.3885 (mtt) cc_final: -0.4091 (mtp) REVERT: C 173 ASN cc_start: 0.9046 (m110) cc_final: 0.8830 (m110) REVERT: C 241 LEU cc_start: 0.8042 (mm) cc_final: 0.7651 (pp) REVERT: C 319 HIS cc_start: 0.8415 (m90) cc_final: 0.7699 (m90) REVERT: C 467 LYS cc_start: 0.9202 (ttpt) cc_final: 0.8930 (tttm) REVERT: C 685 GLU cc_start: 0.7938 (tt0) cc_final: 0.7677 (tm-30) REVERT: C 695 MET cc_start: 0.7512 (ptp) cc_final: 0.6776 (ppp) REVERT: C 709 MET cc_start: 0.5086 (mpp) cc_final: 0.4662 (mmm) REVERT: C 730 GLU cc_start: 0.8023 (mm-30) cc_final: 0.7817 (tp30) outliers start: 2 outliers final: 0 residues processed: 64 average time/residue: 0.0763 time to fit residues: 6.5098 Evaluate side-chains 41 residues out of total 626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 41 time to evaluate : 0.220 ------------------------------------------------------------------------------- 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: 0.3980 chunk 151 optimal weight: 3.9990 chunk 137 optimal weight: 30.0000 chunk 53 optimal weight: 0.0010 chunk 199 optimal weight: 5.9990 chunk 267 optimal weight: 2.9990 chunk 176 optimal weight: 8.9990 chunk 41 optimal weight: 3.9990 chunk 135 optimal weight: 1.9990 chunk 191 optimal weight: 0.3980 chunk 106 optimal weight: 0.5980 overall best weight: 0.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 141 GLN C 252 ASN C 604 GLN C 670 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4754 r_free = 0.4754 target = 0.127754 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.4541 r_free = 0.4541 target = 0.096084 restraints weight = 50036.054| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.4567 r_free = 0.4567 target = 0.098586 restraints weight = 32442.330| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4583 r_free = 0.4583 target = 0.100009 restraints weight = 24157.662| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.4601 r_free = 0.4601 target = 0.101180 restraints weight = 19872.078| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4603 r_free = 0.4603 target = 0.101609 restraints weight = 17683.426| |-----------------------------------------------------------------------------| r_work (final): 0.4348 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5157 moved from start: 1.5878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.352 22400 Z= 0.730 Angle : 1.145 26.137 30308 Z= 0.690 Chirality : 0.068 0.806 3440 Planarity : 0.005 0.051 3892 Dihedral : 5.849 39.895 2928 Min Nonbonded Distance : 1.430 Molprobity Statistics. All-atom Clashscore : 24.57 Ramachandran Plot: Outliers : 0.29 % Allowed : 10.44 % Favored : 89.26 % Rotamer: Outliers : 0.32 % Allowed : 4.63 % Favored : 95.05 % 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: -1.95 (0.15), residues: 2720 helix: 1.09 (0.18), residues: 744 sheet: -1.48 (0.22), residues: 628 loop : -2.69 (0.14), residues: 1348 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 185 TYR 0.022 0.002 TYR C 240 PHE 0.019 0.002 PHE B 239 TRP 0.015 0.001 TRP D 573 HIS 0.010 0.002 HIS C 320 Details of bonding type rmsd covalent geometry : bond 0.01127 (22400) covalent geometry : angle 1.14513 (30308) hydrogen bonds : bond 0.18062 ( 975) hydrogen bonds : angle 7.31275 ( 2871) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 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 : 0.204 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: 0.8812 (m90) cc_final: 0.8375 (m-70) REVERT: C 467 LYS cc_start: 0.9309 (ttpt) cc_final: 0.9095 (tttm) REVERT: C 685 GLU cc_start: 0.8385 (tt0) cc_final: 0.8113 (tm-30) REVERT: C 695 MET cc_start: 0.8752 (ptp) cc_final: 0.8024 (ppp) REVERT: C 709 MET cc_start: 0.5442 (mpp) cc_final: 0.5138 (mmm) outliers start: 2 outliers final: 0 residues processed: 64 average time/residue: 0.0849 time to fit residues: 7.1030 Evaluate side-chains 47 residues out of total 626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 47 time to evaluate : 0.217 ------------------------------------------------------------------------------- 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: 4.9990 chunk 145 optimal weight: 8.9990 chunk 25 optimal weight: 0.4980 chunk 198 optimal weight: 0.0670 chunk 269 optimal weight: 0.0770 chunk 233 optimal weight: 0.2980 chunk 210 optimal weight: 3.9990 chunk 120 optimal weight: 0.0670 chunk 44 optimal weight: 0.0270 chunk 177 optimal weight: 0.9980 chunk 163 optimal weight: 0.0040 overall best weight: 0.0484 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 106 GLN C 114 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 = 0.4756 r_free = 0.4756 target = 0.128311 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4779 r_free = 0.4779 target = 0.108440 restraints weight = 51526.089| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.4573 r_free = 0.4573 target = 0.108944 restraints weight = 31116.716| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4610 r_free = 0.4610 target = 0.109288 restraints weight = 25796.331| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.4614 r_free = 0.4614 target = 0.109340 restraints weight = 24045.354| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4614 r_free = 0.4614 target = 0.109373 restraints weight = 21816.023| |-----------------------------------------------------------------------------| r_work (final): 0.4334 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4881 moved from start: 1.6216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.222 22400 Z= 0.293 Angle : 1.248 63.402 30308 Z= 0.638 Chirality : 0.077 1.652 3440 Planarity : 0.005 0.080 3892 Dihedral : 5.938 50.184 2928 Min Nonbonded Distance : 1.780 Molprobity Statistics. All-atom Clashscore : 20.98 Ramachandran Plot: Outliers : 0.15 % Allowed : 9.71 % Favored : 90.15 % Rotamer: Outliers : 0.16 % Allowed : 2.40 % Favored : 97.44 % 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: -1.82 (0.16), residues: 2720 helix: 1.08 (0.18), residues: 760 sheet: -1.43 (0.22), residues: 644 loop : -2.55 (0.15), residues: 1316 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 329 TYR 0.013 0.001 TYR D 240 PHE 0.022 0.001 PHE C 581 TRP 0.010 0.001 TRP D 573 HIS 0.011 0.002 HIS A 320 Details of bonding type rmsd covalent geometry : bond 0.00581 (22400) covalent geometry : angle 1.24764 (30308) hydrogen bonds : bond 0.14560 ( 975) hydrogen bonds : angle 7.07973 ( 2871) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 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: 1 poor density : 63 time to evaluate : 0.210 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: 0.8798 (m90) cc_final: 0.8297 (m90) REVERT: C 467 LYS cc_start: 0.9311 (ttpt) cc_final: 0.9063 (tttt) REVERT: C 497 MET cc_start: 0.7873 (ptm) cc_final: 0.7322 (ttp) REVERT: C 532 LEU cc_start: 0.6850 (tp) cc_final: 0.6436 (tp) REVERT: C 685 GLU cc_start: 0.8480 (tt0) cc_final: 0.8196 (tm-30) REVERT: C 695 MET cc_start: 0.7501 (ptp) cc_final: 0.6887 (ppp) REVERT: C 709 MET cc_start: 0.5452 (mpp) cc_final: 0.5068 (mmm) outliers start: 1 outliers final: 0 residues processed: 64 average time/residue: 0.0908 time to fit residues: 7.4711 Evaluate side-chains 45 residues out of total 626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 45 time to evaluate : 0.208 ------------------------------------------------------------------------------- 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: 3.9990 chunk 248 optimal weight: 0.0010 chunk 246 optimal weight: 0.0980 chunk 114 optimal weight: 0.0870 chunk 53 optimal weight: 2.9990 chunk 4 optimal weight: 4.9990 chunk 166 optimal weight: 0.0570 chunk 227 optimal weight: 0.9990 chunk 83 optimal weight: 0.0370 chunk 202 optimal weight: 0.9980 chunk 197 optimal weight: 0.0010 overall best weight: 0.0366 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 292 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 562 ASN C 604 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4748 r_free = 0.4748 target = 0.127783 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4774 r_free = 0.4774 target = 0.107978 restraints weight = 50691.039| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.4558 r_free = 0.4558 target = 0.108241 restraints weight = 30760.270| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4600 r_free = 0.4600 target = 0.108655 restraints weight = 26009.677| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.4602 r_free = 0.4602 target = 0.108733 restraints weight = 23918.663| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4604 r_free = 0.4604 target = 0.108800 restraints weight = 21395.026| |-----------------------------------------------------------------------------| r_work (final): 0.4331 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4919 moved from start: 1.6247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.274 22400 Z= 0.319 Angle : 1.247 63.699 30308 Z= 0.638 Chirality : 0.072 1.524 3440 Planarity : 0.006 0.083 3892 Dihedral : 5.726 39.294 2928 Min Nonbonded Distance : 1.794 Molprobity Statistics. All-atom Clashscore : 23.08 Ramachandran Plot: Outliers : 0.15 % Allowed : 9.41 % Favored : 90.44 % Rotamer: Outliers : 0.00 % Allowed : 1.28 % Favored : 98.72 % Cbeta Deviations : 0.62 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.45 % 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: -1.86 (0.16), residues: 2720 helix: 0.88 (0.18), residues: 768 sheet: -1.38 (0.22), residues: 644 loop : -2.53 (0.15), residues: 1308 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 303 TYR 0.025 0.002 TYR B 188 PHE 0.016 0.001 PHE A 581 TRP 0.009 0.001 TRP B 573 HIS 0.026 0.004 HIS A 245 Details of bonding type rmsd covalent geometry : bond 0.00686 (22400) covalent geometry : angle 1.24664 (30308) hydrogen bonds : bond 0.12591 ( 975) hydrogen bonds : angle 6.85669 ( 2871) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 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 : 0.206 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 319 HIS cc_start: 0.8839 (m90) cc_final: 0.8305 (m90) REVERT: C 467 LYS cc_start: 0.9333 (ttpt) cc_final: 0.9096 (tttt) REVERT: C 497 MET cc_start: 0.7887 (ptm) cc_final: 0.7339 (ttp) REVERT: C 532 LEU cc_start: 0.7071 (tp) cc_final: 0.6602 (tp) REVERT: C 685 GLU cc_start: 0.8533 (tt0) cc_final: 0.8211 (tm-30) REVERT: C 695 MET cc_start: 0.7610 (ptp) cc_final: 0.6674 (ppp) REVERT: C 709 MET cc_start: 0.5437 (mpp) cc_final: 0.5063 (mmm) outliers start: 0 outliers final: 0 residues processed: 56 average time/residue: 0.0965 time to fit residues: 6.9136 Evaluate side-chains 44 residues out of total 626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 44 time to evaluate : 0.232 ------------------------------------------------------------------------------- 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: 1.9990 chunk 105 optimal weight: 3.9990 chunk 87 optimal weight: 0.8980 chunk 173 optimal weight: 10.0000 chunk 15 optimal weight: 5.9990 chunk 8 optimal weight: 0.1980 chunk 248 optimal weight: 0.0980 chunk 50 optimal weight: 0.0980 chunk 253 optimal weight: 0.0470 chunk 121 optimal weight: 0.7980 chunk 203 optimal weight: 20.0000 overall best weight: 0.2478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 292 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 604 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4746 r_free = 0.4746 target = 0.127804 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4787 r_free = 0.4787 target = 0.107333 restraints weight = 51418.866| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4537 r_free = 0.4537 target = 0.107372 restraints weight = 31636.557| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4589 r_free = 0.4589 target = 0.107802 restraints weight = 26315.895| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.4591 r_free = 0.4591 target = 0.107868 restraints weight = 24312.871| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4593 r_free = 0.4593 target = 0.107981 restraints weight = 21696.068| |-----------------------------------------------------------------------------| r_work (final): 0.4313 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4935 moved from start: 1.6285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.195 22400 Z= 0.290 Angle : 1.225 63.669 30308 Z= 0.628 Chirality : 0.060 0.963 3440 Planarity : 0.006 0.074 3892 Dihedral : 5.808 41.830 2928 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 24.02 Ramachandran Plot: Outliers : 0.15 % Allowed : 9.41 % Favored : 90.44 % Rotamer: Outliers : 0.00 % Allowed : 0.80 % Favored : 99.20 % Cbeta Deviations : 0.46 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.45 % 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: -1.91 (0.16), residues: 2720 helix: 0.76 (0.18), residues: 768 sheet: -1.37 (0.22), residues: 644 loop : -2.53 (0.15), residues: 1308 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.051 0.002 ARG C 185 TYR 0.041 0.002 TYR D 240 PHE 0.015 0.001 PHE B 581 TRP 0.008 0.001 TRP D 573 HIS 0.015 0.004 HIS D 112 Details of bonding type rmsd covalent geometry : bond 0.00635 (22400) covalent geometry : angle 1.22541 (30308) hydrogen bonds : bond 0.12043 ( 975) hydrogen bonds : angle 6.80038 ( 2871) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 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 : 0.274 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: 0.8786 (m90) cc_final: 0.8193 (m90) REVERT: C 467 LYS cc_start: 0.9329 (ttpt) cc_final: 0.9085 (tttm) REVERT: C 497 MET cc_start: 0.7870 (ptm) cc_final: 0.7311 (ttp) REVERT: C 532 LEU cc_start: 0.7142 (tp) cc_final: 0.6716 (tp) REVERT: C 685 GLU cc_start: 0.8507 (tt0) cc_final: 0.8170 (tm-30) REVERT: C 695 MET cc_start: 0.7537 (ptp) cc_final: 0.6600 (ppp) REVERT: C 709 MET cc_start: 0.5418 (mpp) cc_final: 0.5039 (mmm) outliers start: 0 outliers final: 0 residues processed: 55 average time/residue: 0.0884 time to fit residues: 6.3869 Evaluate side-chains 45 residues out of total 626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 45 time to evaluate : 0.148 ------------------------------------------------------------------------------- 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: 0.0980 chunk 253 optimal weight: 0.9980 chunk 242 optimal weight: 0.0270 chunk 191 optimal weight: 8.9990 chunk 5 optimal weight: 0.0470 chunk 22 optimal weight: 0.0000 chunk 239 optimal weight: 0.0060 chunk 7 optimal weight: 0.0870 chunk 249 optimal weight: 1.9990 chunk 222 optimal weight: 1.9990 overall best weight: 0.0334 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 292 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 443 ASN C 604 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4750 r_free = 0.4750 target = 0.127816 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4718 r_free = 0.4718 target = 0.106443 restraints weight = 50450.513| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4542 r_free = 0.4542 target = 0.105577 restraints weight = 40015.405| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4570 r_free = 0.4570 target = 0.106867 restraints weight = 30123.706| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.4572 r_free = 0.4572 target = 0.106901 restraints weight = 26544.209| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 20)----------------| | r_work = 0.4577 r_free = 0.4577 target = 0.107012 restraints weight = 23683.130| |-----------------------------------------------------------------------------| r_work (final): 0.4313 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4781 moved from start: 1.6303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.207 22400 Z= 0.292 Angle : 1.222 63.700 30308 Z= 0.619 Chirality : 0.067 1.353 3440 Planarity : 0.005 0.062 3892 Dihedral : 5.686 38.442 2928 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 23.04 Ramachandran Plot: Outliers : 0.15 % Allowed : 9.41 % Favored : 90.44 % Rotamer: Outliers : 0.16 % Allowed : 0.48 % Favored : 99.36 % Cbeta Deviations : 0.31 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.45 % 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: -1.92 (0.16), residues: 2720 helix: 0.73 (0.18), residues: 768 sheet: -1.36 (0.22), residues: 644 loop : -2.52 (0.15), residues: 1308 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 185 TYR 0.037 0.002 TYR D 240 PHE 0.012 0.001 PHE C 581 TRP 0.008 0.001 TRP D 573 HIS 0.025 0.005 HIS C 112 Details of bonding type rmsd covalent geometry : bond 0.00594 (22400) covalent geometry : angle 1.22187 (30308) hydrogen bonds : bond 0.11780 ( 975) hydrogen bonds : angle 6.76338 ( 2871) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 53 time to evaluate : 0.148 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 173 ASN cc_start: 0.9026 (m110) cc_final: 0.8810 (m110) REVERT: C 319 HIS cc_start: 0.8462 (m90) cc_final: 0.7857 (m90) REVERT: C 467 LYS cc_start: 0.9252 (ttpt) cc_final: 0.8921 (tttm) REVERT: C 497 MET cc_start: 0.7504 (ptm) cc_final: 0.6870 (ttp) REVERT: C 532 LEU cc_start: 0.7237 (tp) cc_final: 0.7002 (tp) REVERT: C 685 GLU cc_start: 0.8322 (tt0) cc_final: 0.8050 (tm-30) REVERT: C 695 MET cc_start: 0.6848 (ptp) cc_final: 0.6283 (ppp) REVERT: C 709 MET cc_start: 0.5265 (mpp) cc_final: 0.4859 (mmm) outliers start: 1 outliers final: 0 residues processed: 54 average time/residue: 0.0919 time to fit residues: 6.4808 Evaluate side-chains 44 residues out of total 626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 44 time to evaluate : 0.232 ------------------------------------------------------------------------------- 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: 0.8980 chunk 202 optimal weight: 0.7980 chunk 139 optimal weight: 10.0000 chunk 165 optimal weight: 0.0870 chunk 156 optimal weight: 0.8980 chunk 161 optimal weight: 0.3980 chunk 120 optimal weight: 9.9990 chunk 73 optimal weight: 0.0170 chunk 229 optimal weight: 0.0970 chunk 41 optimal weight: 0.0010 chunk 187 optimal weight: 0.3980 overall best weight: 0.1200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 292 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 604 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4749 r_free = 0.4749 target = 0.127914 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.4535 r_free = 0.4535 target = 0.096032 restraints weight = 50548.902| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.4561 r_free = 0.4561 target = 0.098466 restraints weight = 32016.817| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 68)----------------| | r_work = 0.4570 r_free = 0.4570 target = 0.099931 restraints weight = 24108.097| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.4584 r_free = 0.4584 target = 0.100991 restraints weight = 19851.475| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.4588 r_free = 0.4588 target = 0.101201 restraints weight = 17509.490| |-----------------------------------------------------------------------------| r_work (final): 0.4295 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5169 moved from start: 1.6311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.207 22400 Z= 0.292 Angle : 1.222 63.700 30308 Z= 0.619 Chirality : 0.067 1.353 3440 Planarity : 0.005 0.062 3892 Dihedral : 5.686 38.442 2928 Min Nonbonded Distance : 1.811 Molprobity Statistics. All-atom Clashscore : 26.25 Ramachandran Plot: Outliers : 0.15 % Allowed : 9.41 % Favored : 90.44 % Rotamer: Outliers : 0.00 % Allowed : 0.16 % Favored : 99.84 % Cbeta Deviations : 0.31 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.45 % 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: -1.92 (0.16), residues: 2720 helix: 0.73 (0.18), residues: 768 sheet: -1.36 (0.22), residues: 644 loop : -2.52 (0.15), residues: 1308 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG D 185 TYR 0.037 0.002 TYR D 240 PHE 0.012 0.001 PHE D 581 TRP 0.008 0.001 TRP B 573 HIS 0.025 0.005 HIS A 112 Details of bonding type rmsd covalent geometry : bond 0.00594 (22400) covalent geometry : angle 1.22187 (30308) hydrogen bonds : bond 0.11780 ( 975) hydrogen bonds : angle 6.76338 ( 2871) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 52 time to evaluate : 0.214 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 319 HIS cc_start: 0.8866 (m90) cc_final: 0.8369 (m90) REVERT: C 497 MET cc_start: 0.7955 (ptm) cc_final: 0.7414 (ttp) REVERT: C 532 LEU cc_start: 0.7030 (tp) cc_final: 0.6545 (tp) REVERT: C 685 GLU cc_start: 0.8554 (tt0) cc_final: 0.8235 (tm-30) REVERT: C 695 MET cc_start: 0.8349 (ptp) cc_final: 0.7786 (ppp) REVERT: C 709 MET cc_start: 0.5561 (mpp) cc_final: 0.5241 (mmm) outliers start: 0 outliers final: 0 residues processed: 52 average time/residue: 0.0898 time to fit residues: 6.1392 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 : 0.218 ------------------------------------------------------------------------------- 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: 0.0870 chunk 183 optimal weight: 0.0170 chunk 102 optimal weight: 0.0670 chunk 69 optimal weight: 40.0000 chunk 83 optimal weight: 0.0370 chunk 162 optimal weight: 1.9990 chunk 239 optimal weight: 0.9990 chunk 11 optimal weight: 2.9990 chunk 123 optimal weight: 0.1980 chunk 270 optimal weight: 0.0870 chunk 248 optimal weight: 2.9990 overall best weight: 0.0590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 292 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 604 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4674 r_free = 0.4674 target = 0.118103 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.4198 r_free = 0.4198 target = 0.086300 restraints weight = 33827.956| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4232 r_free = 0.4232 target = 0.088007 restraints weight = 26007.597| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4254 r_free = 0.4254 target = 0.089112 restraints weight = 21297.707| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.4274 r_free = 0.4274 target = 0.090143 restraints weight = 18527.097| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4291 r_free = 0.4291 target = 0.090986 restraints weight = 16472.410| |-----------------------------------------------------------------------------| r_work (final): 0.4241 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4837 moved from start: 1.6319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.206 22400 Z= 0.291 Angle : 1.222 63.685 30308 Z= 0.619 Chirality : 0.067 1.353 3440 Planarity : 0.005 0.062 3892 Dihedral : 5.686 38.438 2928 Min Nonbonded Distance : 1.812 Molprobity Statistics. All-atom Clashscore : 27.16 Ramachandran Plot: Outliers : 0.15 % Allowed : 9.41 % Favored : 90.44 % Rotamer: Outliers : 0.00 % Allowed : 0.32 % Favored : 99.68 % Cbeta Deviations : 0.31 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.45 % 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: -1.92 (0.16), residues: 2720 helix: 0.73 (0.18), residues: 768 sheet: -1.36 (0.22), residues: 644 loop : -2.52 (0.15), residues: 1308 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 185 TYR 0.037 0.002 TYR D 240 PHE 0.012 0.001 PHE C 581 TRP 0.008 0.001 TRP D 573 HIS 0.025 0.005 HIS C 112 Details of bonding type rmsd covalent geometry : bond 0.00594 (22400) covalent geometry : angle 1.22166 (30308) hydrogen bonds : bond 0.11781 ( 975) hydrogen bonds : angle 6.76320 ( 2871) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 53 time to evaluate : 0.214 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: 0.8669 (m90) cc_final: 0.8049 (m90) REVERT: C 497 MET cc_start: 0.8038 (ptm) cc_final: 0.7490 (ttp) REVERT: C 532 LEU cc_start: 0.7281 (tp) cc_final: 0.6947 (tp) REVERT: C 685 GLU cc_start: 0.8433 (tt0) cc_final: 0.8113 (tm-30) REVERT: C 695 MET cc_start: 0.6982 (ptp) cc_final: 0.6352 (ppp) REVERT: C 709 MET cc_start: 0.5421 (mpp) cc_final: 0.5033 (mmm) outliers start: 0 outliers final: 0 residues processed: 53 average time/residue: 0.0853 time to fit residues: 5.9034 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 : 0.218 ------------------------------------------------------------------------------- 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: 0.4980 chunk 191 optimal weight: 0.9990 chunk 43 optimal weight: 20.0000 chunk 125 optimal weight: 0.3980 chunk 174 optimal weight: 0.4980 chunk 45 optimal weight: 1.9990 chunk 213 optimal weight: 5.9990 chunk 36 optimal weight: 20.0000 chunk 258 optimal weight: 0.7980 chunk 52 optimal weight: 0.7980 chunk 212 optimal weight: 0.8980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 292 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 604 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4674 r_free = 0.4674 target = 0.118094 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.4199 r_free = 0.4199 target = 0.086338 restraints weight = 33628.123| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4234 r_free = 0.4234 target = 0.088046 restraints weight = 25895.893| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4260 r_free = 0.4260 target = 0.089361 restraints weight = 21156.352| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.4279 r_free = 0.4279 target = 0.090373 restraints weight = 18110.623| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.4293 r_free = 0.4293 target = 0.091116 restraints weight = 16062.771| |-----------------------------------------------------------------------------| r_work (final): 0.4244 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4824 moved from start: 1.6319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.206 22400 Z= 0.291 Angle : 1.222 63.684 30308 Z= 0.619 Chirality : 0.067 1.353 3440 Planarity : 0.005 0.062 3892 Dihedral : 5.686 38.438 2928 Min Nonbonded Distance : 1.812 Molprobity Statistics. All-atom Clashscore : 26.94 Ramachandran Plot: Outliers : 0.15 % Allowed : 9.41 % Favored : 90.44 % Rotamer: Outliers : 0.00 % Allowed : 0.16 % Favored : 99.84 % Cbeta Deviations : 0.31 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.45 % 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: -1.92 (0.16), residues: 2720 helix: 0.73 (0.18), residues: 768 sheet: -1.36 (0.22), residues: 644 loop : -2.52 (0.15), residues: 1308 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG B 185 TYR 0.037 0.002 TYR D 240 PHE 0.012 0.001 PHE B 581 TRP 0.008 0.001 TRP D 573 HIS 0.025 0.005 HIS A 112 Details of bonding type rmsd covalent geometry : bond 0.00593 (22400) covalent geometry : angle 1.22165 (30308) hydrogen bonds : bond 0.11781 ( 975) hydrogen bonds : angle 6.76319 ( 2871) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2277.23 seconds wall clock time: 41 minutes 2.41 seconds (2462.41 seconds total)