Starting phenix.real_space_refine on Sun Sep 29 09:55:12 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6yrg_10889/09_2024/6yrg_10889_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6yrg_10889/09_2024/6yrg_10889.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6yrg_10889/09_2024/6yrg_10889.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6yrg_10889/09_2024/6yrg_10889.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6yrg_10889/09_2024/6yrg_10889_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6yrg_10889/09_2024/6yrg_10889_neut.cif" } resolution = 4.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.005 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): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/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: 13.31, per 1000 atoms: 0.61 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: 5.43 Conformation dependent library (CDL) restraints added in 2.8 seconds 5440 Ramachandran restraints generated. 2720 Oldfield, 0 Emsley, 2720 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5184 Finding SS restraints... Secondary structure from input PDB file: 44 helices and 48 sheets defined 31.7% alpha, 28.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.25 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: 8.70 Time building geometry restraints manager: 6.28 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: 0.00 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: 1.380 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: 0.030 Extract box with map and model: 0.930 Check model and map are aligned: 0.190 Set scattering table: 0.240 Process input model: 50.790 Find NCS groups from input model: 0.760 Set up NCS constraints: 0.070 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:2.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 57.170 ------------------------------------------------------------------------------- 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= 0.596 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 : 31.61 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.26 (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 TRP 0.012 0.002 TRP C 563 HIS 0.005 0.001 HIS C 597 PHE 0.035 0.004 PHE C 239 TYR 0.063 0.006 TYR A 127 ARG 0.035 0.003 ARG D 185 *********************** 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 fitting. rotamer outliers: 4 poor density : 93 time to evaluate : 0.619 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 511 TYR cc_start: 0.8403 (p90) cc_final: 0.8201 (p90) 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: 0.2595 time to fit residues: 30.5189 Evaluate side-chains 46 residues out of total 626 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 45 time to evaluate : 0.593 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 229 optimal weight: 0.0050 chunk 206 optimal weight: 30.0000 chunk 114 optimal weight: 9.9990 chunk 70 optimal weight: 20.0000 chunk 139 optimal weight: 8.9990 chunk 110 optimal weight: 0.0000 chunk 213 optimal weight: 5.9990 chunk 82 optimal weight: 0.9990 chunk 129 optimal weight: 5.9990 chunk 158 optimal weight: 3.9990 chunk 247 optimal weight: 7.9990 overall best weight: 2.2004 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** C 604 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3184 moved from start: 1.4417 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.013 0.317 22400 Z= 0.865 Angle : 1.281 27.451 30308 Z= 0.770 Chirality : 0.071 0.786 3440 Planarity : 0.007 0.057 3892 Dihedral : 7.274 51.555 2928 Min Nonbonded Distance : 1.073 Molprobity Statistics. All-atom Clashscore : 37.16 Ramachandran Plot: Outliers : 2.21 % Allowed : 9.71 % Favored : 88.09 % Rotamer: Outliers : 0.64 % Allowed : 5.91 % Favored : 93.45 % Cbeta Deviations : 0.31 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.30 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.00 (0.16), residues: 2720 helix: 2.10 (0.18), residues: 744 sheet: -2.02 (0.20), residues: 648 loop : -3.13 (0.14), residues: 1328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP C 471 HIS 0.019 0.003 HIS D 112 PHE 0.020 0.002 PHE D 666 TYR 0.040 0.003 TYR B 127 ARG 0.006 0.001 ARG D 574 *********************** 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 80 residues out of total 626 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 76 time to evaluate : 0.655 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 316 ILE cc_start: 0.5791 (mt) cc_final: 0.4665 (tt) REVERT: C 317 MET cc_start: 0.2801 (tmm) cc_final: 0.2399 (tmm) REVERT: C 336 LEU cc_start: 0.1741 (OUTLIER) cc_final: 0.1507 (mt) REVERT: C 387 ARG cc_start: 0.5656 (mmt90) cc_final: 0.5307 (mmm160) REVERT: C 685 GLU cc_start: 0.8553 (tt0) cc_final: 0.8274 (tm-30) REVERT: C 695 MET cc_start: 0.8232 (ptp) cc_final: 0.7833 (ppp) REVERT: C 709 MET cc_start: 0.4779 (mpp) cc_final: 0.4263 (mmm) REVERT: C 730 GLU cc_start: 0.8314 (mm-30) cc_final: 0.8009 (tp30) outliers start: 4 outliers final: 2 residues processed: 79 average time/residue: 0.2213 time to fit residues: 22.2114 Evaluate side-chains 46 residues out of total 626 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 43 time to evaluate : 0.664 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 137 optimal weight: 8.9990 chunk 76 optimal weight: 2.9990 chunk 205 optimal weight: 8.9990 chunk 168 optimal weight: 7.9990 chunk 68 optimal weight: 50.0000 chunk 247 optimal weight: 8.9990 chunk 267 optimal weight: 8.9990 chunk 220 optimal weight: 2.9990 chunk 245 optimal weight: 3.9990 chunk 84 optimal weight: 0.2980 chunk 198 optimal weight: 0.0970 overall best weight: 2.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 141 GLN C 270 ASN ** C 320 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 324 GLN C 348 ASN ** C 577 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 604 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3425 moved from start: 1.5525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.412 22400 Z= 0.730 Angle : 1.299 40.541 30308 Z= 0.741 Chirality : 0.073 1.161 3440 Planarity : 0.006 0.080 3892 Dihedral : 6.738 40.638 2928 Min Nonbonded Distance : 0.979 Molprobity Statistics. All-atom Clashscore : 30.13 Ramachandran Plot: Outliers : 0.44 % Allowed : 9.56 % Favored : 90.00 % Rotamer: Outliers : 0.64 % Allowed : 4.63 % Favored : 94.73 % Cbeta Deviations : 0.62 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.45 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.45 (0.15), residues: 2720 helix: 1.10 (0.18), residues: 736 sheet: -2.17 (0.19), residues: 640 loop : -3.03 (0.14), residues: 1344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP C 573 HIS 0.019 0.004 HIS D 112 PHE 0.028 0.002 PHE D 254 TYR 0.026 0.002 TYR C 240 ARG 0.005 0.001 ARG A 303 *********************** 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 69 residues out of total 626 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 65 time to evaluate : 0.645 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 234 MET cc_start: -0.0231 (mmp) cc_final: -0.1061 (mmt) REVERT: C 312 ASP cc_start: 0.3865 (t0) cc_final: 0.3343 (t0) REVERT: C 387 ARG cc_start: 0.5416 (mmt90) cc_final: 0.5141 (mmm160) REVERT: C 497 MET cc_start: 0.8088 (ptm) cc_final: 0.7576 (ttp) REVERT: C 685 GLU cc_start: 0.8718 (tt0) cc_final: 0.8512 (tm-30) REVERT: C 695 MET cc_start: 0.8244 (ptp) cc_final: 0.7713 (ppp) REVERT: C 709 MET cc_start: 0.4891 (mpp) cc_final: 0.4520 (mmm) REVERT: C 730 GLU cc_start: 0.7987 (mm-30) cc_final: 0.7628 (tp30) outliers start: 4 outliers final: 2 residues processed: 69 average time/residue: 0.1847 time to fit residues: 16.8535 Evaluate side-chains 47 residues out of total 626 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 45 time to evaluate : 0.687 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 244 optimal weight: 0.9990 chunk 186 optimal weight: 0.0370 chunk 128 optimal weight: 0.8980 chunk 27 optimal weight: 5.9990 chunk 118 optimal weight: 0.9990 chunk 166 optimal weight: 0.6980 chunk 248 optimal weight: 0.6980 chunk 262 optimal weight: 0.0040 chunk 129 optimal weight: 0.0870 chunk 235 optimal weight: 0.0010 chunk 70 optimal weight: 6.9990 overall best weight: 0.1654 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 141 GLN ** C 597 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 604 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3354 moved from start: 1.5971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.444 22400 Z= 0.556 Angle : 1.048 26.650 30308 Z= 0.615 Chirality : 0.068 1.196 3440 Planarity : 0.005 0.080 3892 Dihedral : 6.186 38.509 2928 Min Nonbonded Distance : 1.087 Molprobity Statistics. All-atom Clashscore : 22.45 Ramachandran Plot: Outliers : 0.15 % Allowed : 11.03 % Favored : 88.82 % Rotamer: Outliers : 0.48 % Allowed : 3.83 % Favored : 95.69 % Cbeta Deviations : 0.46 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.45 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.22 (0.15), residues: 2720 helix: 0.84 (0.18), residues: 768 sheet: -1.66 (0.21), residues: 620 loop : -2.88 (0.14), residues: 1332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 573 HIS 0.018 0.004 HIS D 112 PHE 0.025 0.002 PHE B 780 TYR 0.034 0.002 TYR D 240 ARG 0.002 0.000 ARG C 185 *********************** 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 63 residues out of total 626 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 60 time to evaluate : 0.682 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 316 ILE cc_start: 0.5695 (tt) cc_final: 0.5224 (tp) REVERT: C 387 ARG cc_start: 0.5505 (mmt90) cc_final: 0.5257 (mmm160) REVERT: C 497 MET cc_start: 0.8136 (ptm) cc_final: 0.7753 (ptm) REVERT: C 685 GLU cc_start: 0.8669 (tt0) cc_final: 0.8436 (tm-30) REVERT: C 695 MET cc_start: 0.8002 (ptp) cc_final: 0.7663 (ppp) REVERT: C 709 MET cc_start: 0.5103 (mpp) cc_final: 0.4749 (mmm) REVERT: C 730 GLU cc_start: 0.7773 (mm-30) cc_final: 0.7473 (tp30) outliers start: 3 outliers final: 2 residues processed: 63 average time/residue: 0.2115 time to fit residues: 17.1517 Evaluate side-chains 45 residues out of total 626 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 43 time to evaluate : 0.657 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 218 optimal weight: 1.9990 chunk 149 optimal weight: 0.6980 chunk 3 optimal weight: 6.9990 chunk 195 optimal weight: 0.3980 chunk 108 optimal weight: 4.9990 chunk 224 optimal weight: 3.9990 chunk 181 optimal weight: 0.9980 chunk 0 optimal weight: 50.0000 chunk 134 optimal weight: 0.0370 chunk 235 optimal weight: 0.8980 chunk 66 optimal weight: 0.2980 overall best weight: 0.4658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 597 HIS C 604 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3377 moved from start: 1.6367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.435 22400 Z= 0.507 Angle : 0.988 26.381 30308 Z= 0.584 Chirality : 0.069 1.327 3440 Planarity : 0.005 0.079 3892 Dihedral : 6.157 40.784 2928 Min Nonbonded Distance : 1.068 Molprobity Statistics. All-atom Clashscore : 20.46 Ramachandran Plot: Outliers : 0.15 % Allowed : 10.29 % Favored : 89.56 % Rotamer: Outliers : 0.32 % Allowed : 3.67 % Favored : 96.01 % Cbeta Deviations : 0.15 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.45 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.13 (0.16), residues: 2720 helix: 0.74 (0.18), residues: 768 sheet: -1.47 (0.22), residues: 636 loop : -2.79 (0.15), residues: 1316 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 573 HIS 0.011 0.002 HIS C 320 PHE 0.016 0.002 PHE C 780 TYR 0.026 0.002 TYR C 188 ARG 0.004 0.000 ARG B 303 *********************** 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 62 residues out of total 626 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 60 time to evaluate : 0.618 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: C 316 ILE cc_start: 0.5800 (tt) cc_final: 0.5124 (tp) REVERT: C 387 ARG cc_start: 0.5461 (mmt90) cc_final: 0.5208 (mmm160) REVERT: C 497 MET cc_start: 0.8309 (ptm) cc_final: 0.7915 (ttp) REVERT: C 685 GLU cc_start: 0.8720 (tt0) cc_final: 0.8517 (tm-30) REVERT: C 695 MET cc_start: 0.7895 (ptp) cc_final: 0.7140 (ppp) REVERT: C 709 MET cc_start: 0.5294 (mpp) cc_final: 0.4916 (mmm) REVERT: C 730 GLU cc_start: 0.7708 (mm-30) cc_final: 0.7423 (tp30) outliers start: 2 outliers final: 1 residues processed: 62 average time/residue: 0.2003 time to fit residues: 16.1233 Evaluate side-chains 47 residues out of total 626 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 46 time to evaluate : 0.675 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 88 optimal weight: 2.9990 chunk 236 optimal weight: 0.6980 chunk 51 optimal weight: 0.0030 chunk 154 optimal weight: 0.0670 chunk 64 optimal weight: 0.0000 chunk 263 optimal weight: 0.0470 chunk 218 optimal weight: 0.7980 chunk 121 optimal weight: 0.0010 chunk 21 optimal weight: 0.6980 chunk 87 optimal weight: 5.9990 chunk 138 optimal weight: 20.0000 overall best weight: 0.0236 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 562 ASN ** C 597 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 604 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3306 moved from start: 1.6686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.440 22400 Z= 0.506 Angle : 0.972 25.590 30308 Z= 0.575 Chirality : 0.064 1.090 3440 Planarity : 0.005 0.086 3892 Dihedral : 5.994 42.421 2928 Min Nonbonded Distance : 1.070 Molprobity Statistics. All-atom Clashscore : 17.93 Ramachandran Plot: Outliers : 0.15 % Allowed : 10.29 % Favored : 89.56 % Rotamer: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Cbeta Deviations : 0.46 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.45 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.98 (0.16), residues: 2720 helix: 0.74 (0.18), residues: 752 sheet: -1.30 (0.22), residues: 644 loop : -2.63 (0.15), residues: 1324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 573 HIS 0.012 0.002 HIS C 320 PHE 0.015 0.001 PHE C 254 TYR 0.013 0.001 TYR B 188 ARG 0.014 0.001 ARG A 185 *********************** 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 60 residues out of total 626 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 60 time to evaluate : 0.609 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 316 ILE cc_start: 0.5442 (tt) cc_final: 0.4868 (tp) REVERT: C 387 ARG cc_start: 0.5497 (mmt90) cc_final: 0.5217 (mmm160) REVERT: C 497 MET cc_start: 0.8366 (ptm) cc_final: 0.8011 (ttp) REVERT: C 685 GLU cc_start: 0.8755 (tt0) cc_final: 0.8526 (tm-30) REVERT: C 695 MET cc_start: 0.7775 (ptp) cc_final: 0.6951 (ppp) REVERT: C 709 MET cc_start: 0.5422 (mpp) cc_final: 0.5093 (mmm) REVERT: C 730 GLU cc_start: 0.7726 (mm-30) cc_final: 0.7437 (tp30) outliers start: 0 outliers final: 0 residues processed: 60 average time/residue: 0.1955 time to fit residues: 15.3221 Evaluate side-chains 44 residues out of total 626 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 44 time to evaluate : 0.602 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 253 optimal weight: 0.0030 chunk 29 optimal weight: 1.9990 chunk 149 optimal weight: 0.0970 chunk 192 optimal weight: 0.0050 chunk 148 optimal weight: 0.6980 chunk 221 optimal weight: 0.9980 chunk 146 optimal weight: 0.9990 chunk 262 optimal weight: 0.0980 chunk 164 optimal weight: 10.0000 chunk 159 optimal weight: 0.1980 chunk 121 optimal weight: 0.0000 overall best weight: 0.0406 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 292 GLN ** C 597 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 604 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3275 moved from start: 1.7076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.439 22400 Z= 0.501 Angle : 0.947 25.780 30308 Z= 0.566 Chirality : 0.063 1.088 3440 Planarity : 0.005 0.082 3892 Dihedral : 5.716 41.597 2928 Min Nonbonded Distance : 1.068 Molprobity Statistics. All-atom Clashscore : 16.95 Ramachandran Plot: Outliers : 0.15 % Allowed : 9.85 % Favored : 90.00 % Rotamer: Outliers : 0.16 % Allowed : 1.60 % Favored : 98.24 % Cbeta Deviations : 0.46 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.45 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.85 (0.16), residues: 2720 helix: 0.92 (0.18), residues: 752 sheet: -1.15 (0.22), residues: 652 loop : -2.65 (0.15), residues: 1316 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 573 HIS 0.013 0.002 HIS C 320 PHE 0.014 0.001 PHE C 780 TYR 0.015 0.001 TYR A 282 ARG 0.006 0.001 ARG D 185 *********************** 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 61 residues out of total 626 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 60 time to evaluate : 0.691 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 292 GLN cc_start: 0.2972 (OUTLIER) cc_final: 0.2550 (pp30) REVERT: C 316 ILE cc_start: 0.5410 (tt) cc_final: 0.4943 (tp) REVERT: C 387 ARG cc_start: 0.5639 (mmt90) cc_final: 0.5329 (mmm160) REVERT: C 497 MET cc_start: 0.8424 (ptm) cc_final: 0.8072 (ttp) REVERT: C 695 MET cc_start: 0.7739 (ptp) cc_final: 0.6851 (ppp) REVERT: C 709 MET cc_start: 0.5480 (mpp) cc_final: 0.5157 (mmm) REVERT: C 730 GLU cc_start: 0.7673 (mm-30) cc_final: 0.7414 (tp30) outliers start: 1 outliers final: 0 residues processed: 61 average time/residue: 0.2097 time to fit residues: 16.6771 Evaluate side-chains 46 residues out of total 626 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 45 time to evaluate : 0.646 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 162 optimal weight: 4.9990 chunk 104 optimal weight: 0.0870 chunk 156 optimal weight: 1.9990 chunk 78 optimal weight: 0.9980 chunk 51 optimal weight: 20.0000 chunk 50 optimal weight: 0.9990 chunk 166 optimal weight: 0.5980 chunk 178 optimal weight: 0.6980 chunk 129 optimal weight: 0.4980 chunk 24 optimal weight: 0.8980 chunk 206 optimal weight: 0.0010 overall best weight: 0.3764 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** C 331 ASN C 443 ASN ** C 597 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 604 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3331 moved from start: 1.7300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.440 22400 Z= 0.499 Angle : 0.947 25.544 30308 Z= 0.562 Chirality : 0.061 1.009 3440 Planarity : 0.005 0.081 3892 Dihedral : 5.643 42.272 2928 Min Nonbonded Distance : 1.060 Molprobity Statistics. All-atom Clashscore : 17.70 Ramachandran Plot: Outliers : 0.15 % Allowed : 10.29 % Favored : 89.56 % Rotamer: Outliers : 0.00 % Allowed : 1.12 % Favored : 98.88 % Cbeta Deviations : 0.46 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.45 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.76 (0.16), residues: 2720 helix: 0.98 (0.18), residues: 752 sheet: -1.13 (0.22), residues: 660 loop : -2.57 (0.15), residues: 1308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 573 HIS 0.015 0.002 HIS A 320 PHE 0.013 0.001 PHE C 780 TYR 0.012 0.001 TYR D 183 ARG 0.003 0.000 ARG D 329 *********************** 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 58 residues out of total 626 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 58 time to evaluate : 0.598 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 168 LEU cc_start: 0.8224 (tp) cc_final: 0.7889 (tp) REVERT: C 316 ILE cc_start: 0.5391 (tt) cc_final: 0.4838 (tp) REVERT: C 387 ARG cc_start: 0.5594 (mmt90) cc_final: 0.5307 (mmm160) REVERT: C 497 MET cc_start: 0.8401 (ptm) cc_final: 0.8072 (ttp) REVERT: C 695 MET cc_start: 0.7774 (ptp) cc_final: 0.7252 (ppp) REVERT: C 709 MET cc_start: 0.5551 (mpp) cc_final: 0.5209 (mmm) REVERT: C 730 GLU cc_start: 0.7664 (mm-30) cc_final: 0.7417 (tp30) outliers start: 0 outliers final: 0 residues processed: 58 average time/residue: 0.2097 time to fit residues: 15.7559 Evaluate side-chains 43 residues out of total 626 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 43 time to evaluate : 0.655 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 238 optimal weight: 0.8980 chunk 251 optimal weight: 0.1980 chunk 229 optimal weight: 0.5980 chunk 244 optimal weight: 0.0980 chunk 147 optimal weight: 0.2980 chunk 106 optimal weight: 0.0870 chunk 191 optimal weight: 8.9990 chunk 74 optimal weight: 1.9990 chunk 220 optimal weight: 0.9990 chunk 231 optimal weight: 1.9990 chunk 243 optimal weight: 0.0570 overall best weight: 0.1476 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 597 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 604 GLN C 619 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3301 moved from start: 1.7454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.440 22400 Z= 0.498 Angle : 0.944 25.409 30308 Z= 0.561 Chirality : 0.061 0.987 3440 Planarity : 0.005 0.082 3892 Dihedral : 5.655 46.888 2928 Min Nonbonded Distance : 1.055 Molprobity Statistics. All-atom Clashscore : 16.56 Ramachandran Plot: Outliers : 0.15 % Allowed : 10.15 % Favored : 89.71 % Rotamer: Outliers : 0.00 % Allowed : 0.64 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.64 (0.16), residues: 2720 helix: 1.04 (0.18), residues: 756 sheet: -1.05 (0.22), residues: 660 loop : -2.47 (0.15), residues: 1304 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 573 HIS 0.015 0.002 HIS C 320 PHE 0.015 0.001 PHE B 254 TYR 0.009 0.001 TYR A 282 ARG 0.006 0.001 ARG B 185 *********************** 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 61 residues out of total 626 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 61 time to evaluate : 0.650 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 316 ILE cc_start: 0.5557 (tt) cc_final: 0.4957 (tp) REVERT: C 387 ARG cc_start: 0.5743 (mmt90) cc_final: 0.5474 (mmm160) REVERT: C 497 MET cc_start: 0.8404 (ptm) cc_final: 0.8090 (ttp) REVERT: C 695 MET cc_start: 0.7618 (ptp) cc_final: 0.6697 (ppp) REVERT: C 709 MET cc_start: 0.5596 (mpp) cc_final: 0.5265 (mmm) REVERT: C 730 GLU cc_start: 0.7698 (mm-30) cc_final: 0.7463 (tp30) outliers start: 0 outliers final: 0 residues processed: 61 average time/residue: 0.2158 time to fit residues: 16.9942 Evaluate side-chains 45 residues out of total 626 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 45 time to evaluate : 0.645 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 160 optimal weight: 3.9990 chunk 258 optimal weight: 3.9990 chunk 157 optimal weight: 4.9990 chunk 122 optimal weight: 0.3980 chunk 179 optimal weight: 0.0970 chunk 270 optimal weight: 0.0270 chunk 249 optimal weight: 1.9990 chunk 215 optimal weight: 0.0570 chunk 22 optimal weight: 8.9990 chunk 166 optimal weight: 4.9990 chunk 132 optimal weight: 0.7980 overall best weight: 0.2754 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 292 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 543 ASN ** C 597 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 604 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3324 moved from start: 1.7658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.434 22400 Z= 0.496 Angle : 0.907 25.109 30308 Z= 0.545 Chirality : 0.055 0.765 3440 Planarity : 0.005 0.074 3892 Dihedral : 5.648 57.038 2928 Min Nonbonded Distance : 1.041 Molprobity Statistics. All-atom Clashscore : 16.20 Ramachandran Plot: Outliers : 0.29 % Allowed : 10.15 % Favored : 89.56 % Rotamer: Outliers : 0.00 % Allowed : 0.48 % Favored : 99.52 % Cbeta Deviations : 0.15 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.45 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.55 (0.16), residues: 2720 helix: 0.99 (0.18), residues: 760 sheet: -1.00 (0.22), residues: 660 loop : -2.36 (0.16), residues: 1300 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 563 HIS 0.014 0.002 HIS C 320 PHE 0.013 0.001 PHE A 780 TYR 0.014 0.001 TYR B 282 ARG 0.006 0.001 ARG A 185 ********************** 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 59 residues out of total 626 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 59 time to evaluate : 0.625 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 316 ILE cc_start: 0.5460 (tt) cc_final: 0.4908 (tp) REVERT: C 387 ARG cc_start: 0.5704 (mmt90) cc_final: 0.5431 (mmm160) REVERT: C 497 MET cc_start: 0.8498 (ptm) cc_final: 0.8271 (ttp) REVERT: C 532 LEU cc_start: 0.4607 (tp) cc_final: 0.3809 (tp) REVERT: C 695 MET cc_start: 0.7487 (ptp) cc_final: 0.6557 (ppp) REVERT: C 709 MET cc_start: 0.5702 (mpp) cc_final: 0.5412 (mmm) outliers start: 0 outliers final: 0 residues processed: 59 average time/residue: 0.2217 time to fit residues: 16.5643 Evaluate side-chains 40 residues out of total 626 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 40 time to evaluate : 0.590 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 171 optimal weight: 0.0020 chunk 229 optimal weight: 4.9990 chunk 66 optimal weight: 5.9990 chunk 198 optimal weight: 10.0000 chunk 31 optimal weight: 0.0070 chunk 59 optimal weight: 0.0050 chunk 216 optimal weight: 0.9980 chunk 90 optimal weight: 9.9990 chunk 221 optimal weight: 0.7980 chunk 27 optimal weight: 0.7980 chunk 39 optimal weight: 7.9990 overall best weight: 0.3220 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 292 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 543 ASN ** C 597 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4779 r_free = 0.4779 target = 0.127692 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.4519 r_free = 0.4519 target = 0.093634 restraints weight = 49356.420| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.4548 r_free = 0.4548 target = 0.096283 restraints weight = 32091.650| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.4561 r_free = 0.4561 target = 0.097894 restraints weight = 23946.478| |-----------------------------------------------------------------------------| r_work (final): 0.4282 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5535 moved from start: 1.7808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.436 22400 Z= 0.494 Angle : 0.914 25.399 30308 Z= 0.548 Chirality : 0.057 0.838 3440 Planarity : 0.005 0.076 3892 Dihedral : 5.610 54.305 2928 Min Nonbonded Distance : 1.048 Molprobity Statistics. All-atom Clashscore : 16.33 Ramachandran Plot: Outliers : 0.29 % Allowed : 9.71 % Favored : 90.00 % Rotamer: Outliers : 0.00 % Allowed : 0.64 % Favored : 99.36 % Cbeta Deviations : 0.15 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.45 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.40 (0.16), residues: 2720 helix: 1.10 (0.18), residues: 756 sheet: -0.79 (0.22), residues: 644 loop : -2.29 (0.16), residues: 1320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 573 HIS 0.012 0.002 HIS A 320 PHE 0.015 0.001 PHE D 254 TYR 0.010 0.001 TYR B 282 ARG 0.012 0.001 ARG A 329 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3008.30 seconds wall clock time: 55 minutes 46.79 seconds (3346.79 seconds total)