Starting phenix.real_space_refine on Thu Jun 19 04:14:25 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6yrg_10889/06_2025/6yrg_10889_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/6yrg_10889/06_2025/6yrg_10889.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6yrg_10889/06_2025/6yrg_10889.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6yrg_10889/06_2025/6yrg_10889.map" model { file = "/net/cci-nas-00/data/ceres_data/6yrg_10889/06_2025/6yrg_10889_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6yrg_10889/06_2025/6yrg_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): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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: 12.61, per 1000 atoms: 0.57 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: 4.89 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: 2.97 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: 9.05 Time building geometry restraints manager: 5.92 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: 0.10 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: 2.360 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.800 Check model and map are aligned: 0.150 Set scattering table: 0.200 Process input model: 50.200 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:2.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 57.440 ------------------------------------------------------------------------------- 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 : 31.61 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 Details of bonding type rmsd hydrogen bonds : bond 0.24264 ( 975) hydrogen bonds : angle 9.05349 ( 2871) covalent geometry : bond 0.00917 (22400) covalent geometry : angle 1.41302 (30308) *********************** 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 : 0.599 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: 0.2566 time to fit residues: 30.2842 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 : 0.637 ------------------------------------------------------------------------------- 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 ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4627 r_free = 0.4627 target = 0.104707 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4155 r_free = 0.4155 target = 0.071444 restraints weight = 45039.614| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 66)----------------| | r_work = 0.4171 r_free = 0.4171 target = 0.072223 restraints weight = 38895.531| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4187 r_free = 0.4187 target = 0.072991 restraints weight = 34776.201| |-----------------------------------------------------------------------------| r_work (final): 0.4124 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5112 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= 0.792 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 A 127 ARG 0.006 0.001 ARG B 574 Details of bonding type rmsd hydrogen bonds : bond 0.19025 ( 975) hydrogen bonds : angle 7.97995 ( 2871) covalent geometry : bond 0.01278 (22400) covalent geometry : angle 1.28082 (30308) *********************** 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 to be fit. rotamer outliers: 4 poor density : 76 time to evaluate : 0.721 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 316 ILE cc_start: 0.8191 (mt) cc_final: 0.7547 (tt) REVERT: C 319 HIS cc_start: 0.8510 (m90) cc_final: 0.7981 (m90) REVERT: C 387 ARG cc_start: 0.5427 (mmt90) cc_final: 0.5213 (mmm160) REVERT: C 467 LYS cc_start: 0.9255 (ttpt) cc_final: 0.8827 (tttm) REVERT: C 685 GLU cc_start: 0.8241 (tt0) cc_final: 0.7844 (tm-30) REVERT: C 695 MET cc_start: 0.7663 (ptp) cc_final: 0.7230 (ppp) REVERT: C 709 MET cc_start: 0.4966 (mpp) cc_final: 0.4221 (mmm) REVERT: C 730 GLU cc_start: 0.8383 (mm-30) cc_final: 0.8135 (tp30) outliers start: 4 outliers final: 2 residues processed: 79 average time/residue: 0.2522 time to fit residues: 25.3925 Evaluate side-chains 45 residues out of total 626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 43 time to evaluate : 0.683 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 80 optimal weight: 0.9980 chunk 93 optimal weight: 0.9990 chunk 36 optimal weight: 8.9990 chunk 130 optimal weight: 0.0470 chunk 241 optimal weight: 4.9990 chunk 139 optimal weight: 4.9990 chunk 207 optimal weight: 5.9990 chunk 105 optimal weight: 0.9990 chunk 269 optimal weight: 5.9990 chunk 94 optimal weight: 0.0980 chunk 83 optimal weight: 6.9990 overall best weight: 0.6282 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4743 r_free = 0.4743 target = 0.126591 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.4526 r_free = 0.4526 target = 0.095702 restraints weight = 49665.212| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.4543 r_free = 0.4543 target = 0.097972 restraints weight = 32027.251| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.4564 r_free = 0.4564 target = 0.099565 restraints weight = 24161.079| |-----------------------------------------------------------------------------| r_work (final): 0.4306 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5215 moved from start: 1.5286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.411 22400 Z= 0.751 Angle : 1.270 39.679 30308 Z= 0.728 Chirality : 0.069 1.023 3440 Planarity : 0.006 0.071 3892 Dihedral : 6.562 34.380 2928 Min Nonbonded Distance : 0.989 Molprobity Statistics. All-atom Clashscore : 27.69 Ramachandran Plot: Outliers : 0.29 % Allowed : 10.29 % Favored : 89.41 % Rotamer: Outliers : 0.32 % Allowed : 4.31 % Favored : 95.37 % Cbeta Deviations : 0.46 % 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: -2.30 (0.15), residues: 2720 helix: 1.30 (0.18), residues: 736 sheet: -2.06 (0.20), residues: 640 loop : -2.99 (0.14), residues: 1344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP C 573 HIS 0.017 0.003 HIS D 112 PHE 0.026 0.002 PHE B 254 TYR 0.032 0.002 TYR C 240 ARG 0.006 0.001 ARG B 185 Details of bonding type rmsd hydrogen bonds : bond 0.16834 ( 975) hydrogen bonds : angle 7.41760 ( 2871) covalent geometry : bond 0.01108 (22400) covalent geometry : angle 1.26997 (30308) *********************** 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 66 residues out of total 626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 64 time to evaluate : 0.684 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 134 MET cc_start: -0.3973 (mtt) cc_final: -0.4179 (mtp) REVERT: C 241 LEU cc_start: 0.8606 (mm) cc_final: 0.8206 (pp) REVERT: C 316 ILE cc_start: 0.8274 (mt) cc_final: 0.7906 (tt) REVERT: C 319 HIS cc_start: 0.8858 (m90) cc_final: 0.8423 (m-70) REVERT: C 497 MET cc_start: 0.7646 (ptm) cc_final: 0.6882 (ttp) REVERT: C 532 LEU cc_start: 0.6878 (tp) cc_final: 0.6254 (tp) REVERT: C 685 GLU cc_start: 0.8334 (tt0) cc_final: 0.8084 (tm-30) REVERT: C 695 MET cc_start: 0.8895 (ptp) cc_final: 0.8343 (ppp) REVERT: C 730 GLU cc_start: 0.8190 (mm-30) cc_final: 0.7980 (tp30) outliers start: 2 outliers final: 1 residues processed: 66 average time/residue: 0.1954 time to fit residues: 16.9621 Evaluate side-chains 45 residues out of total 626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 44 time to evaluate : 0.610 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 216 optimal weight: 2.9990 chunk 198 optimal weight: 8.9990 chunk 166 optimal weight: 0.2980 chunk 67 optimal weight: 0.0060 chunk 52 optimal weight: 0.0970 chunk 226 optimal weight: 0.9990 chunk 22 optimal weight: 0.0470 chunk 28 optimal weight: 0.1980 chunk 45 optimal weight: 0.0070 chunk 149 optimal weight: 6.9990 chunk 142 optimal weight: 0.9990 overall best weight: 0.0710 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 577 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 597 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.4733 r_free = 0.4733 target = 0.126145 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.4512 r_free = 0.4512 target = 0.094611 restraints weight = 51123.964| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.4537 r_free = 0.4537 target = 0.097143 restraints weight = 32576.218| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 55)----------------| | r_work = 0.4537 r_free = 0.4537 target = 0.098515 restraints weight = 24474.802| |-----------------------------------------------------------------------------| r_work (final): 0.4272 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5070 moved from start: 1.5496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.421 22400 Z= 0.687 Angle : 1.455 63.700 30308 Z= 0.784 Chirality : 0.109 2.694 3440 Planarity : 0.006 0.075 3892 Dihedral : 6.480 30.372 2928 Min Nonbonded Distance : 1.009 Molprobity Statistics. All-atom Clashscore : 30.70 Ramachandran Plot: Outliers : 0.29 % Allowed : 10.74 % Favored : 88.97 % Rotamer: Outliers : 0.32 % Allowed : 2.88 % Favored : 96.81 % Cbeta Deviations : 0.46 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % 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: -2.37 (0.15), residues: 2720 helix: 1.01 (0.19), residues: 752 sheet: -1.98 (0.20), residues: 640 loop : -3.00 (0.14), residues: 1328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 573 HIS 0.021 0.005 HIS D 112 PHE 0.020 0.002 PHE D 237 TYR 0.024 0.002 TYR C 240 ARG 0.014 0.001 ARG A 533 Details of bonding type rmsd hydrogen bonds : bond 0.14590 ( 975) hydrogen bonds : angle 7.29334 ( 2871) covalent geometry : bond 0.01042 (22400) covalent geometry : angle 1.45516 (30308) *********************** 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 61 residues out of total 626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 59 time to evaluate : 0.602 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 173 ASN cc_start: 0.8970 (m110) cc_final: 0.8733 (m110) REVERT: C 316 ILE cc_start: 0.8088 (mt) cc_final: 0.7456 (tt) REVERT: C 319 HIS cc_start: 0.8510 (m90) cc_final: 0.7902 (m-70) REVERT: C 497 MET cc_start: 0.7295 (ptm) cc_final: 0.6664 (ttp) REVERT: C 532 LEU cc_start: 0.6837 (tp) cc_final: 0.6398 (tp) REVERT: C 685 GLU cc_start: 0.8190 (tt0) cc_final: 0.7900 (tm-30) REVERT: C 695 MET cc_start: 0.7975 (ptp) cc_final: 0.7308 (ppp) REVERT: C 709 MET cc_start: 0.4760 (mpp) cc_final: 0.4267 (mmm) REVERT: C 730 GLU cc_start: 0.8006 (mm-30) cc_final: 0.7734 (tp30) outliers start: 2 outliers final: 1 residues processed: 60 average time/residue: 0.1694 time to fit residues: 13.8259 Evaluate side-chains 48 residues out of total 626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 47 time to evaluate : 0.632 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 68 optimal weight: 9.9990 chunk 254 optimal weight: 3.9990 chunk 147 optimal weight: 8.9990 chunk 209 optimal weight: 3.9990 chunk 97 optimal weight: 8.9990 chunk 249 optimal weight: 0.1980 chunk 104 optimal weight: 1.9990 chunk 219 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 chunk 253 optimal weight: 2.9990 chunk 224 optimal weight: 0.9980 overall best weight: 1.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 577 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 597 HIS ** 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 = 0.4645 r_free = 0.4645 target = 0.115369 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.4176 r_free = 0.4176 target = 0.084279 restraints weight = 33455.377| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4209 r_free = 0.4209 target = 0.085880 restraints weight = 26558.840| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4231 r_free = 0.4231 target = 0.087045 restraints weight = 22244.231| |-----------------------------------------------------------------------------| r_work (final): 0.4177 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4937 moved from start: 1.5554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.018 0.589 22400 Z= 0.827 Angle : 1.602 63.700 30308 Z= 0.816 Chirality : 0.091 1.913 3440 Planarity : 0.006 0.090 3892 Dihedral : 6.494 39.479 2928 Min Nonbonded Distance : 0.989 Molprobity Statistics. All-atom Clashscore : 33.51 Ramachandran Plot: Outliers : 0.15 % Allowed : 11.18 % Favored : 88.68 % Rotamer: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Cbeta Deviations : 0.62 % 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: -2.36 (0.15), residues: 2720 helix: 1.01 (0.19), residues: 752 sheet: -1.96 (0.20), residues: 640 loop : -2.99 (0.14), residues: 1328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.003 TRP D 677 HIS 0.012 0.003 HIS D 597 PHE 0.021 0.002 PHE B 237 TYR 0.036 0.003 TYR D 127 ARG 0.016 0.001 ARG D 533 Details of bonding type rmsd hydrogen bonds : bond 0.15657 ( 975) hydrogen bonds : angle 7.38749 ( 2871) covalent geometry : bond 0.01755 (22400) covalent geometry : angle 1.60232 (30308) *********************** 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 56 residues out of total 626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 56 time to evaluate : 0.629 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 238 GLU cc_start: 0.8434 (tm-30) cc_final: 0.8221 (pp20) REVERT: C 241 LEU cc_start: 0.8462 (mm) cc_final: 0.7974 (pp) REVERT: C 316 ILE cc_start: 0.8212 (mt) cc_final: 0.7687 (tt) REVERT: C 319 HIS cc_start: 0.8757 (m90) cc_final: 0.8173 (m-70) REVERT: C 497 MET cc_start: 0.7730 (ptm) cc_final: 0.7050 (ttp) REVERT: C 685 GLU cc_start: 0.8229 (tt0) cc_final: 0.7859 (tm-30) REVERT: C 695 MET cc_start: 0.7447 (ptp) cc_final: 0.7111 (ppp) REVERT: C 709 MET cc_start: 0.4687 (mpp) cc_final: 0.4150 (mmm) REVERT: C 730 GLU cc_start: 0.7920 (mm-30) cc_final: 0.7673 (tp30) outliers start: 0 outliers final: 0 residues processed: 56 average time/residue: 0.1448 time to fit residues: 11.6309 Evaluate side-chains 46 residues out of total 626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 46 time to evaluate : 0.638 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 236 optimal weight: 0.9990 chunk 35 optimal weight: 0.2980 chunk 85 optimal weight: 0.0980 chunk 3 optimal weight: 7.9990 chunk 251 optimal weight: 0.0570 chunk 31 optimal weight: 0.0060 chunk 202 optimal weight: 0.4980 chunk 63 optimal weight: 0.3980 chunk 214 optimal weight: 0.9980 chunk 30 optimal weight: 0.0030 chunk 240 optimal weight: 0.2980 overall best weight: 0.0924 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 577 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 597 HIS ** 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 = 0.4727 r_free = 0.4727 target = 0.125615 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.4514 r_free = 0.4514 target = 0.094422 restraints weight = 50775.375| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.4534 r_free = 0.4534 target = 0.096896 restraints weight = 32800.761| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.4555 r_free = 0.4555 target = 0.098505 restraints weight = 24719.870| |-----------------------------------------------------------------------------| r_work (final): 0.4278 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5110 moved from start: 1.5575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.014 0.458 22400 Z= 0.754 Angle : 1.564 63.622 30308 Z= 0.805 Chirality : 0.085 1.547 3440 Planarity : 0.008 0.121 3892 Dihedral : 6.457 39.728 2928 Min Nonbonded Distance : 1.012 Molprobity Statistics. All-atom Clashscore : 34.49 Ramachandran Plot: Outliers : 0.15 % Allowed : 10.74 % Favored : 89.12 % Rotamer: Outliers : 0.00 % Allowed : 1.12 % Favored : 98.88 % Cbeta Deviations : 0.62 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % 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: -2.37 (0.15), residues: 2720 helix: 0.95 (0.19), residues: 752 sheet: -1.94 (0.21), residues: 640 loop : -2.99 (0.14), residues: 1328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP C 573 HIS 0.017 0.003 HIS B 112 PHE 0.057 0.003 PHE B 239 TYR 0.019 0.002 TYR D 282 ARG 0.016 0.001 ARG D 533 Details of bonding type rmsd hydrogen bonds : bond 0.14743 ( 975) hydrogen bonds : angle 7.48298 ( 2871) covalent geometry : bond 0.01426 (22400) covalent geometry : angle 1.56388 (30308) *********************** 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 55 residues out of total 626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 55 time to evaluate : 0.592 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 173 ASN cc_start: 0.8914 (m110) cc_final: 0.8655 (m110) REVERT: C 241 LEU cc_start: 0.8355 (mm) cc_final: 0.7867 (pp) REVERT: C 316 ILE cc_start: 0.8143 (mt) cc_final: 0.7516 (tt) REVERT: C 319 HIS cc_start: 0.8501 (m90) cc_final: 0.7893 (m-70) REVERT: C 497 MET cc_start: 0.7324 (ptm) cc_final: 0.6656 (ttp) REVERT: C 511 TYR cc_start: 0.7833 (p90) cc_final: 0.7633 (p90) REVERT: C 685 GLU cc_start: 0.8192 (tt0) cc_final: 0.7798 (tm-30) REVERT: C 695 MET cc_start: 0.8502 (ptp) cc_final: 0.8094 (ppp) REVERT: C 709 MET cc_start: 0.4827 (mpp) cc_final: 0.4417 (mmm) REVERT: C 730 GLU cc_start: 0.8066 (mm-30) cc_final: 0.7809 (tp30) outliers start: 0 outliers final: 0 residues processed: 55 average time/residue: 0.1745 time to fit residues: 13.3021 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 : 0.585 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 34 optimal weight: 0.0040 chunk 238 optimal weight: 3.9990 chunk 72 optimal weight: 8.9990 chunk 188 optimal weight: 0.1980 chunk 115 optimal weight: 9.9990 chunk 107 optimal weight: 2.9990 chunk 163 optimal weight: 20.0000 chunk 248 optimal weight: 0.9980 chunk 218 optimal weight: 0.3980 chunk 87 optimal weight: 0.2980 chunk 41 optimal weight: 0.0770 overall best weight: 0.1950 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 577 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 597 HIS ** 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 = 0.4726 r_free = 0.4726 target = 0.125737 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.4501 r_free = 0.4501 target = 0.094757 restraints weight = 50713.579| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 57)----------------| | r_work = 0.4530 r_free = 0.4530 target = 0.097185 restraints weight = 33237.517| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.4551 r_free = 0.4551 target = 0.098770 restraints weight = 25173.621| |-----------------------------------------------------------------------------| r_work (final): 0.4272 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5107 moved from start: 1.5568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.014 0.460 22400 Z= 0.753 Angle : 1.563 63.698 30308 Z= 0.804 Chirality : 0.084 1.544 3440 Planarity : 0.008 0.121 3892 Dihedral : 6.457 39.737 2928 Min Nonbonded Distance : 1.012 Molprobity Statistics. All-atom Clashscore : 36.95 Ramachandran Plot: Outliers : 0.15 % Allowed : 10.74 % Favored : 89.12 % Rotamer: Outliers : 0.00 % Allowed : 0.16 % Favored : 99.84 % Cbeta Deviations : 0.62 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % 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: -2.37 (0.15), residues: 2720 helix: 0.95 (0.19), residues: 752 sheet: -1.94 (0.21), residues: 640 loop : -2.99 (0.14), residues: 1328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP C 573 HIS 0.017 0.003 HIS D 112 PHE 0.058 0.003 PHE A 239 TYR 0.019 0.002 TYR A 282 ARG 0.016 0.001 ARG C 533 Details of bonding type rmsd hydrogen bonds : bond 0.14744 ( 975) hydrogen bonds : angle 7.48249 ( 2871) covalent geometry : bond 0.01425 (22400) covalent geometry : angle 1.56328 (30308) *********************** 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 56 residues out of total 626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 56 time to evaluate : 0.658 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 173 ASN cc_start: 0.8916 (m110) cc_final: 0.8658 (m110) REVERT: C 238 GLU cc_start: 0.8279 (tm-30) cc_final: 0.8048 (pp20) REVERT: C 241 LEU cc_start: 0.8346 (mm) cc_final: 0.7858 (pp) REVERT: C 316 ILE cc_start: 0.8082 (mt) cc_final: 0.7525 (tt) REVERT: C 319 HIS cc_start: 0.8510 (m90) cc_final: 0.7896 (m-70) REVERT: C 497 MET cc_start: 0.7348 (ptm) cc_final: 0.6685 (ttp) REVERT: C 685 GLU cc_start: 0.8191 (tt0) cc_final: 0.7797 (tm-30) REVERT: C 695 MET cc_start: 0.8448 (ptp) cc_final: 0.8049 (ppp) REVERT: C 709 MET cc_start: 0.4793 (mpp) cc_final: 0.4363 (mmm) REVERT: C 730 GLU cc_start: 0.8051 (mm-30) cc_final: 0.7789 (tp30) outliers start: 0 outliers final: 0 residues processed: 56 average time/residue: 0.1629 time to fit residues: 12.8675 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 : 0.685 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 186 optimal weight: 0.0980 chunk 24 optimal weight: 0.0770 chunk 120 optimal weight: 3.9990 chunk 7 optimal weight: 0.8980 chunk 199 optimal weight: 0.1980 chunk 173 optimal weight: 9.9990 chunk 43 optimal weight: 20.0000 chunk 13 optimal weight: 8.9990 chunk 57 optimal weight: 0.3980 chunk 204 optimal weight: 9.9990 chunk 18 optimal weight: 2.9990 overall best weight: 0.3338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 338 ASN ** C 577 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 597 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.4725 r_free = 0.4725 target = 0.125628 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.4499 r_free = 0.4499 target = 0.094613 restraints weight = 50702.439| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.4529 r_free = 0.4529 target = 0.096916 restraints weight = 33412.876| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4538 r_free = 0.4538 target = 0.098308 restraints weight = 25234.330| |-----------------------------------------------------------------------------| r_work (final): 0.4281 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5252 moved from start: 1.5586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.014 0.460 22400 Z= 0.753 Angle : 1.563 63.700 30308 Z= 0.804 Chirality : 0.084 1.544 3440 Planarity : 0.008 0.121 3892 Dihedral : 6.457 39.737 2928 Min Nonbonded Distance : 1.012 Molprobity Statistics. All-atom Clashscore : 37.66 Ramachandran Plot: Outliers : 0.15 % Allowed : 10.74 % Favored : 89.12 % Rotamer: Outliers : 0.16 % Allowed : 0.16 % Favored : 99.68 % Cbeta Deviations : 0.62 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % 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: -2.37 (0.15), residues: 2720 helix: 0.95 (0.19), residues: 752 sheet: -1.94 (0.21), residues: 640 loop : -2.99 (0.14), residues: 1328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP C 573 HIS 0.017 0.003 HIS B 112 PHE 0.058 0.003 PHE A 239 TYR 0.019 0.002 TYR B 282 ARG 0.016 0.001 ARG D 533 Details of bonding type rmsd hydrogen bonds : bond 0.14744 ( 975) hydrogen bonds : angle 7.48248 ( 2871) covalent geometry : bond 0.01425 (22400) covalent geometry : angle 1.56327 (30308) *********************** 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 57 residues out of total 626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 56 time to evaluate : 0.585 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 238 GLU cc_start: 0.8329 (tm-30) cc_final: 0.8028 (pp20) REVERT: C 241 LEU cc_start: 0.8516 (mm) cc_final: 0.8021 (pp) REVERT: C 316 ILE cc_start: 0.8287 (mt) cc_final: 0.7905 (tt) REVERT: C 319 HIS cc_start: 0.8860 (m90) cc_final: 0.8415 (m-70) REVERT: C 497 MET cc_start: 0.7598 (ptm) cc_final: 0.6875 (ttp) REVERT: C 511 TYR cc_start: 0.8204 (p90) cc_final: 0.7822 (p90) REVERT: C 532 LEU cc_start: 0.6955 (tp) cc_final: 0.6680 (tp) REVERT: C 685 GLU cc_start: 0.8385 (tt0) cc_final: 0.7988 (tm-30) REVERT: C 695 MET cc_start: 0.8898 (ptp) cc_final: 0.8537 (ppp) REVERT: C 709 MET cc_start: 0.4972 (mpp) cc_final: 0.4625 (mmm) REVERT: C 730 GLU cc_start: 0.8136 (mm-30) cc_final: 0.7917 (tp30) outliers start: 1 outliers final: 0 residues processed: 57 average time/residue: 0.1537 time to fit residues: 12.3583 Evaluate side-chains 48 residues out of total 626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 48 time to evaluate : 0.607 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 177 optimal weight: 0.0060 chunk 22 optimal weight: 0.1980 chunk 106 optimal weight: 8.9990 chunk 230 optimal weight: 6.9990 chunk 163 optimal weight: 0.1980 chunk 57 optimal weight: 0.0050 chunk 7 optimal weight: 0.7980 chunk 53 optimal weight: 3.9990 chunk 75 optimal weight: 0.6980 chunk 95 optimal weight: 30.0000 chunk 131 optimal weight: 0.0060 overall best weight: 0.0826 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 338 ASN ** C 577 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 597 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.4725 r_free = 0.4725 target = 0.125626 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.4503 r_free = 0.4503 target = 0.094736 restraints weight = 50650.313| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.4529 r_free = 0.4529 target = 0.097124 restraints weight = 33302.757| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4550 r_free = 0.4550 target = 0.098769 restraints weight = 24989.864| |-----------------------------------------------------------------------------| r_work (final): 0.4272 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5102 moved from start: 1.5586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.014 0.460 22400 Z= 0.753 Angle : 1.563 63.700 30308 Z= 0.804 Chirality : 0.084 1.544 3440 Planarity : 0.008 0.121 3892 Dihedral : 6.457 39.737 2928 Min Nonbonded Distance : 1.012 Molprobity Statistics. All-atom Clashscore : 37.55 Ramachandran Plot: Outliers : 0.15 % Allowed : 10.74 % Favored : 89.12 % Rotamer: Outliers : 0.16 % Allowed : 0.16 % Favored : 99.68 % Cbeta Deviations : 0.62 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % 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: -2.37 (0.15), residues: 2720 helix: 0.95 (0.19), residues: 752 sheet: -1.94 (0.21), residues: 640 loop : -2.99 (0.14), residues: 1328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP C 573 HIS 0.017 0.003 HIS D 112 PHE 0.058 0.003 PHE C 239 TYR 0.019 0.002 TYR A 282 ARG 0.016 0.001 ARG D 533 Details of bonding type rmsd hydrogen bonds : bond 0.14744 ( 975) hydrogen bonds : angle 7.48248 ( 2871) covalent geometry : bond 0.01425 (22400) covalent geometry : angle 1.56327 (30308) *********************** 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 57 residues out of total 626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 56 time to evaluate : 0.610 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 173 ASN cc_start: 0.8885 (m110) cc_final: 0.8630 (m110) REVERT: C 238 GLU cc_start: 0.8288 (tm-30) cc_final: 0.8057 (pp20) REVERT: C 241 LEU cc_start: 0.8361 (mm) cc_final: 0.7867 (pp) REVERT: C 316 ILE cc_start: 0.8089 (mt) cc_final: 0.7539 (tt) REVERT: C 319 HIS cc_start: 0.8520 (m90) cc_final: 0.7906 (m-70) REVERT: C 497 MET cc_start: 0.7358 (ptm) cc_final: 0.6690 (ttp) REVERT: C 511 TYR cc_start: 0.7629 (p90) cc_final: 0.7206 (p90) REVERT: C 685 GLU cc_start: 0.8192 (tt0) cc_final: 0.7797 (tm-30) REVERT: C 695 MET cc_start: 0.8471 (ptp) cc_final: 0.8065 (ppp) REVERT: C 709 MET cc_start: 0.4801 (mpp) cc_final: 0.4379 (mmm) REVERT: C 730 GLU cc_start: 0.8055 (mm-30) cc_final: 0.7792 (tp30) outliers start: 1 outliers final: 0 residues processed: 57 average time/residue: 0.1568 time to fit residues: 12.5580 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 : 0.640 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 222 optimal weight: 0.8980 chunk 109 optimal weight: 0.0070 chunk 153 optimal weight: 1.9990 chunk 189 optimal weight: 0.7980 chunk 139 optimal weight: 8.9990 chunk 113 optimal weight: 10.0000 chunk 8 optimal weight: 3.9990 chunk 260 optimal weight: 0.8980 chunk 119 optimal weight: 0.6980 chunk 68 optimal weight: 40.0000 chunk 4 optimal weight: 9.9990 overall best weight: 0.6598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 338 ASN ** C 577 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 597 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.4725 r_free = 0.4725 target = 0.125626 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.4517 r_free = 0.4517 target = 0.094686 restraints weight = 51242.985| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.4530 r_free = 0.4530 target = 0.097048 restraints weight = 33224.865| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.4545 r_free = 0.4545 target = 0.098556 restraints weight = 25191.605| |-----------------------------------------------------------------------------| r_work (final): 0.4269 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5103 moved from start: 1.5586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.014 0.460 22400 Z= 0.753 Angle : 1.563 63.700 30308 Z= 0.804 Chirality : 0.084 1.544 3440 Planarity : 0.008 0.121 3892 Dihedral : 6.457 39.737 2928 Min Nonbonded Distance : 1.012 Molprobity Statistics. All-atom Clashscore : 37.55 Ramachandran Plot: Outliers : 0.15 % Allowed : 10.74 % Favored : 89.12 % Rotamer: Outliers : 0.16 % Allowed : 0.16 % Favored : 99.68 % Cbeta Deviations : 0.62 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % 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: -2.37 (0.15), residues: 2720 helix: 0.95 (0.19), residues: 752 sheet: -1.94 (0.21), residues: 640 loop : -2.99 (0.14), residues: 1328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP C 573 HIS 0.017 0.003 HIS D 112 PHE 0.058 0.003 PHE D 239 TYR 0.019 0.002 TYR A 282 ARG 0.016 0.001 ARG A 533 Details of bonding type rmsd hydrogen bonds : bond 0.14744 ( 975) hydrogen bonds : angle 7.48248 ( 2871) covalent geometry : bond 0.01425 (22400) covalent geometry : angle 1.56327 (30308) ********************** 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 57 residues out of total 626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 56 time to evaluate : 0.622 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 173 ASN cc_start: 0.8898 (m110) cc_final: 0.8644 (m110) REVERT: C 238 GLU cc_start: 0.8277 (tm-30) cc_final: 0.8044 (pp20) REVERT: C 241 LEU cc_start: 0.8351 (mm) cc_final: 0.7858 (pp) REVERT: C 316 ILE cc_start: 0.8088 (mt) cc_final: 0.7534 (tt) REVERT: C 319 HIS cc_start: 0.8509 (m90) cc_final: 0.7896 (m-70) REVERT: C 497 MET cc_start: 0.7339 (ptm) cc_final: 0.6675 (ttp) REVERT: C 511 TYR cc_start: 0.7616 (p90) cc_final: 0.7194 (p90) REVERT: C 685 GLU cc_start: 0.8190 (tt0) cc_final: 0.7796 (tm-30) REVERT: C 695 MET cc_start: 0.8401 (ptp) cc_final: 0.8004 (ppp) REVERT: C 709 MET cc_start: 0.4781 (mpp) cc_final: 0.4346 (mmm) REVERT: C 730 GLU cc_start: 0.8035 (mm-30) cc_final: 0.7770 (tp30) outliers start: 1 outliers final: 0 residues processed: 57 average time/residue: 0.1566 time to fit residues: 12.6807 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 : 0.686 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 41 optimal weight: 0.0770 chunk 242 optimal weight: 0.0670 chunk 33 optimal weight: 20.0000 chunk 56 optimal weight: 0.0570 chunk 27 optimal weight: 0.0010 chunk 206 optimal weight: 0.0000 chunk 77 optimal weight: 10.0000 chunk 167 optimal weight: 0.9990 chunk 221 optimal weight: 0.7980 chunk 228 optimal weight: 7.9990 chunk 52 optimal weight: 2.9990 overall best weight: 0.0404 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 338 ASN ** C 577 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 597 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.4725 r_free = 0.4725 target = 0.125626 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4501 r_free = 0.4501 target = 0.094621 restraints weight = 51314.903| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.4533 r_free = 0.4533 target = 0.097059 restraints weight = 33123.115| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4552 r_free = 0.4552 target = 0.098738 restraints weight = 24687.837| |-----------------------------------------------------------------------------| r_work (final): 0.4274 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5103 moved from start: 1.5586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.014 0.460 22400 Z= 0.753 Angle : 1.563 63.700 30308 Z= 0.804 Chirality : 0.084 1.544 3440 Planarity : 0.008 0.121 3892 Dihedral : 6.457 39.737 2928 Min Nonbonded Distance : 1.012 Molprobity Statistics. All-atom Clashscore : 37.55 Ramachandran Plot: Outliers : 0.15 % Allowed : 10.74 % Favored : 89.12 % Rotamer: Outliers : 0.16 % Allowed : 0.16 % Favored : 99.68 % Cbeta Deviations : 0.62 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % 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: -2.37 (0.15), residues: 2720 helix: 0.95 (0.19), residues: 752 sheet: -1.94 (0.21), residues: 640 loop : -2.99 (0.14), residues: 1328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP C 573 HIS 0.017 0.003 HIS D 112 PHE 0.058 0.003 PHE D 239 TYR 0.019 0.002 TYR D 282 ARG 0.016 0.001 ARG A 533 Details of bonding type rmsd hydrogen bonds : bond 0.14744 ( 975) hydrogen bonds : angle 7.48248 ( 2871) covalent geometry : bond 0.01425 (22400) covalent geometry : angle 1.56327 (30308) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4720.15 seconds wall clock time: 84 minutes 18.47 seconds (5058.47 seconds total)