Starting phenix.real_space_refine on Sun Jun 22 02:41:51 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8juz_36667/06_2025/8juz_36667_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8juz_36667/06_2025/8juz_36667.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.29 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8juz_36667/06_2025/8juz_36667.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8juz_36667/06_2025/8juz_36667.map" model { file = "/net/cci-nas-00/data/ceres_data/8juz_36667/06_2025/8juz_36667_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8juz_36667/06_2025/8juz_36667_neut.cif" } resolution = 4.29 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= 0.000 sd= 0.002 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: 5 Type Number sf(0) Gaussians P 17 5.49 5 S 110 5.16 5 C 16130 2.51 5 N 4361 2.21 5 O 4656 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 48 residue(s): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 25274 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 4149 Number of conformers: 1 Conformer: "" Number of residues, atoms: 522, 4149 Classifications: {'peptide': 522} Link IDs: {'CIS': 3, 'PCIS': 2, 'PTRANS': 30, 'TRANS': 486} Chain breaks: 5 Chain: "B" Number of atoms: 4210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 529, 4210 Classifications: {'peptide': 529} Link IDs: {'CIS': 3, 'PCIS': 2, 'PTRANS': 32, 'TRANS': 491} Chain breaks: 2 Chain: "C" Number of atoms: 4199 Number of conformers: 1 Conformer: "" Number of residues, atoms: 528, 4199 Classifications: {'peptide': 528} Link IDs: {'PCIS': 2, 'PTRANS': 32, 'TRANS': 493} Chain breaks: 2 Chain: "D" Number of atoms: 4213 Number of conformers: 1 Conformer: "" Number of residues, atoms: 530, 4213 Classifications: {'peptide': 530} Link IDs: {'PCIS': 2, 'PTRANS': 32, 'TRANS': 495} Chain breaks: 2 Chain: "E" Number of atoms: 4202 Number of conformers: 1 Conformer: "" Number of residues, atoms: 528, 4202 Classifications: {'peptide': 528} Link IDs: {'CIS': 2, 'PCIS': 2, 'PTRANS': 32, 'TRANS': 491} Chain breaks: 2 Chain: "F" Number of atoms: 4119 Number of conformers: 1 Conformer: "" Number of residues, atoms: 518, 4119 Classifications: {'peptide': 518} Link IDs: {'CIS': 2, 'PCIS': 2, 'PTRANS': 30, 'TRANS': 483} Chain breaks: 4 Chain: "A" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 14.40, per 1000 atoms: 0.57 Number of scatterers: 25274 At special positions: 0 Unit cell: (148.5, 152.9, 146.3, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 110 16.00 P 17 15.00 O 4656 8.00 N 4361 7.00 C 16130 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 5.77 Conformation dependent library (CDL) restraints added in 3.0 seconds 6218 Ramachandran restraints generated. 3109 Oldfield, 0 Emsley, 3109 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6022 Finding SS restraints... Secondary structure from input PDB file: 159 helices and 13 sheets defined 53.5% alpha, 7.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.46 Creating SS restraints... Processing helix chain 'A' and resid 432 through 440 removed outlier: 3.580A pdb=" N GLU A 440 " --> pdb=" O ALA A 436 " (cutoff:3.500A) Processing helix chain 'A' and resid 442 through 448 removed outlier: 3.617A pdb=" N LEU A 446 " --> pdb=" O VAL A 442 " (cutoff:3.500A) Processing helix chain 'A' and resid 472 through 485 removed outlier: 3.504A pdb=" N VAL A 476 " --> pdb=" O GLY A 472 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N ALA A 477 " --> pdb=" O LYS A 473 " (cutoff:3.500A) Processing helix chain 'A' and resid 507 through 524 removed outlier: 4.080A pdb=" N ARG A 511 " --> pdb=" O GLY A 507 " (cutoff:3.500A) Processing helix chain 'A' and resid 533 through 536 Processing helix chain 'A' and resid 548 through 562 Processing helix chain 'A' and resid 576 through 580 removed outlier: 3.844A pdb=" N SER A 579 " --> pdb=" O ARG A 576 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ILE A 580 " --> pdb=" O LEU A 577 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 576 through 580' Processing helix chain 'A' and resid 581 through 585 Processing helix chain 'A' and resid 600 through 612 Processing helix chain 'A' and resid 620 through 631 Processing helix chain 'A' and resid 636 through 655 removed outlier: 3.743A pdb=" N ALA A 647 " --> pdb=" O CYS A 643 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N LEU A 648 " --> pdb=" O ALA A 644 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N TYR A 655 " --> pdb=" O LEU A 651 " (cutoff:3.500A) Processing helix chain 'A' and resid 656 through 659 removed outlier: 3.756A pdb=" N TYR A 659 " --> pdb=" O PRO A 656 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 656 through 659' Processing helix chain 'A' and resid 679 through 685 removed outlier: 3.915A pdb=" N LYS A 685 " --> pdb=" O VAL A 681 " (cutoff:3.500A) Processing helix chain 'A' and resid 705 through 721 removed outlier: 6.048A pdb=" N ASN A 711 " --> pdb=" O PRO A 707 " (cutoff:3.500A) removed outlier: 5.557A pdb=" N THR A 712 " --> pdb=" O LEU A 708 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N LEU A 717 " --> pdb=" O VAL A 713 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N GLU A 718 " --> pdb=" O ASP A 714 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ALA A 719 " --> pdb=" O LYS A 715 " (cutoff:3.500A) Processing helix chain 'A' and resid 724 through 729 Processing helix chain 'A' and resid 808 through 817 Processing helix chain 'A' and resid 826 through 831 Processing helix chain 'A' and resid 838 through 852 removed outlier: 4.031A pdb=" N CYS A 842 " --> pdb=" O PRO A 838 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N ALA A 843 " --> pdb=" O GLU A 839 " (cutoff:3.500A) Processing helix chain 'A' and resid 861 through 866 Processing helix chain 'A' and resid 870 through 881 removed outlier: 3.620A pdb=" N LEU A 881 " --> pdb=" O PHE A 877 " (cutoff:3.500A) Processing helix chain 'A' and resid 904 through 909 Processing helix chain 'A' and resid 910 through 911 No H-bonds generated for 'chain 'A' and resid 910 through 911' Processing helix chain 'A' and resid 912 through 916 Processing helix chain 'A' and resid 926 through 938 removed outlier: 4.519A pdb=" N ASP A 935 " --> pdb=" O LYS A 931 " (cutoff:3.500A) removed outlier: 4.650A pdb=" N LEU A 936 " --> pdb=" O PHE A 932 " (cutoff:3.500A) Processing helix chain 'A' and resid 939 through 943 removed outlier: 3.811A pdb=" N LYS A 943 " --> pdb=" O GLN A 940 " (cutoff:3.500A) Processing helix chain 'A' and resid 1331 through 1344 removed outlier: 3.939A pdb=" N ASN A1335 " --> pdb=" O GLU A1331 " (cutoff:3.500A) Processing helix chain 'A' and resid 1348 through 1366 removed outlier: 3.504A pdb=" N LEU A1355 " --> pdb=" O GLN A1351 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N TYR A1356 " --> pdb=" O LEU A1352 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N GLN A1361 " --> pdb=" O ALA A1357 " (cutoff:3.500A) Processing helix chain 'A' and resid 1375 through 1386 removed outlier: 3.506A pdb=" N GLU A1384 " --> pdb=" O GLU A1380 " (cutoff:3.500A) Processing helix chain 'B' and resid 432 through 443 removed outlier: 3.559A pdb=" N VAL B 442 " --> pdb=" O LEU B 438 " (cutoff:3.500A) Processing helix chain 'B' and resid 444 through 447 Processing helix chain 'B' and resid 450 through 456 removed outlier: 3.636A pdb=" N PHE B 455 " --> pdb=" O VAL B 451 " (cutoff:3.500A) Processing helix chain 'B' and resid 472 through 485 removed outlier: 3.635A pdb=" N VAL B 476 " --> pdb=" O GLY B 472 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N ALA B 477 " --> pdb=" O LYS B 473 " (cutoff:3.500A) Processing helix chain 'B' and resid 508 through 523 removed outlier: 4.041A pdb=" N LEU B 513 " --> pdb=" O SER B 509 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N ARG B 514 " --> pdb=" O GLU B 510 " (cutoff:3.500A) Processing helix chain 'B' and resid 532 through 536 Processing helix chain 'B' and resid 545 through 560 removed outlier: 3.966A pdb=" N SER B 549 " --> pdb=" O ASP B 545 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N ASP B 560 " --> pdb=" O LEU B 556 " (cutoff:3.500A) Processing helix chain 'B' and resid 576 through 580 Processing helix chain 'B' and resid 600 through 612 removed outlier: 3.819A pdb=" N ARG B 604 " --> pdb=" O ASP B 600 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N LYS B 605 " --> pdb=" O LYS B 601 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N GLU B 606 " --> pdb=" O GLU B 602 " (cutoff:3.500A) Processing helix chain 'B' and resid 620 through 629 Processing helix chain 'B' and resid 636 through 655 removed outlier: 3.796A pdb=" N LYS B 640 " --> pdb=" O GLY B 636 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N ALA B 647 " --> pdb=" O CYS B 643 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N LEU B 648 " --> pdb=" O ALA B 644 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N CYS B 649 " --> pdb=" O GLU B 645 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ALA B 650 " --> pdb=" O ALA B 646 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LEU B 651 " --> pdb=" O ALA B 647 " (cutoff:3.500A) Processing helix chain 'B' and resid 675 through 686 removed outlier: 4.152A pdb=" N PHE B 679 " --> pdb=" O SER B 675 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N GLU B 680 " --> pdb=" O ALA B 676 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N VAL B 681 " --> pdb=" O LYS B 677 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ALA B 682 " --> pdb=" O ASP B 678 " (cutoff:3.500A) Processing helix chain 'B' and resid 689 through 693 removed outlier: 3.520A pdb=" N ARG B 692 " --> pdb=" O ALA B 689 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N ALA B 693 " --> pdb=" O SER B 690 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 689 through 693' Processing helix chain 'B' and resid 705 through 724 removed outlier: 7.044A pdb=" N ASN B 711 " --> pdb=" O PRO B 707 " (cutoff:3.500A) removed outlier: 5.851A pdb=" N THR B 712 " --> pdb=" O LEU B 708 " (cutoff:3.500A) Processing helix chain 'B' and resid 725 through 728 Processing helix chain 'B' and resid 804 through 817 removed outlier: 3.550A pdb=" N LEU B 809 " --> pdb=" O GLN B 805 " (cutoff:3.500A) removed outlier: 6.089A pdb=" N ALA B 810 " --> pdb=" O GLY B 806 " (cutoff:3.500A) Proline residue: B 811 - end of helix Processing helix chain 'B' and resid 826 through 831 Processing helix chain 'B' and resid 837 through 852 Processing helix chain 'B' and resid 861 through 866 Processing helix chain 'B' and resid 867 through 869 No H-bonds generated for 'chain 'B' and resid 867 through 869' Processing helix chain 'B' and resid 870 through 883 Processing helix chain 'B' and resid 899 through 903 Processing helix chain 'B' and resid 904 through 909 Processing helix chain 'B' and resid 910 through 911 No H-bonds generated for 'chain 'B' and resid 910 through 911' Processing helix chain 'B' and resid 912 through 916 Processing helix chain 'B' and resid 925 through 935 removed outlier: 4.274A pdb=" N ASP B 935 " --> pdb=" O LYS B 931 " (cutoff:3.500A) Processing helix chain 'B' and resid 935 through 940 removed outlier: 3.531A pdb=" N LYS B 939 " --> pdb=" O ASP B 935 " (cutoff:3.500A) Processing helix chain 'B' and resid 1331 through 1344 removed outlier: 3.864A pdb=" N ASN B1335 " --> pdb=" O GLU B1331 " (cutoff:3.500A) Processing helix chain 'B' and resid 1348 through 1365 removed outlier: 3.600A pdb=" N ILE B1359 " --> pdb=" O LEU B1355 " (cutoff:3.500A) Processing helix chain 'B' and resid 1375 through 1386 removed outlier: 3.563A pdb=" N GLU B1384 " --> pdb=" O GLU B1380 " (cutoff:3.500A) Processing helix chain 'C' and resid 432 through 443 removed outlier: 4.038A pdb=" N GLU C 440 " --> pdb=" O ALA C 436 " (cutoff:3.500A) removed outlier: 4.782A pdb=" N MET C 441 " --> pdb=" O ALA C 437 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N VAL C 442 " --> pdb=" O LEU C 438 " (cutoff:3.500A) Processing helix chain 'C' and resid 443 through 448 Processing helix chain 'C' and resid 451 through 456 removed outlier: 3.712A pdb=" N PHE C 455 " --> pdb=" O VAL C 451 " (cutoff:3.500A) Processing helix chain 'C' and resid 473 through 486 removed outlier: 3.692A pdb=" N ALA C 477 " --> pdb=" O LYS C 473 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N GLN C 486 " --> pdb=" O ASN C 482 " (cutoff:3.500A) Processing helix chain 'C' and resid 510 through 523 removed outlier: 3.587A pdb=" N ARG C 514 " --> pdb=" O GLU C 510 " (cutoff:3.500A) Processing helix chain 'C' and resid 532 through 536 Processing helix chain 'C' and resid 546 through 559 Processing helix chain 'C' and resid 576 through 580 removed outlier: 3.509A pdb=" N SER C 579 " --> pdb=" O ARG C 576 " (cutoff:3.500A) Processing helix chain 'C' and resid 581 through 585 Processing helix chain 'C' and resid 600 through 612 Processing helix chain 'C' and resid 620 through 631 removed outlier: 3.875A pdb=" N GLU C 629 " --> pdb=" O GLU C 625 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N ASN C 630 " --> pdb=" O GLU C 626 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N CYS C 631 " --> pdb=" O LEU C 627 " (cutoff:3.500A) Processing helix chain 'C' and resid 636 through 655 removed outlier: 4.145A pdb=" N ALA C 647 " --> pdb=" O CYS C 643 " (cutoff:3.500A) Processing helix chain 'C' and resid 675 through 686 removed outlier: 3.748A pdb=" N PHE C 679 " --> pdb=" O SER C 675 " (cutoff:3.500A) Processing helix chain 'C' and resid 689 through 693 removed outlier: 3.743A pdb=" N ARG C 692 " --> pdb=" O ALA C 689 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N ALA C 693 " --> pdb=" O SER C 690 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 689 through 693' Processing helix chain 'C' and resid 705 through 708 Processing helix chain 'C' and resid 709 through 724 Processing helix chain 'C' and resid 809 through 817 Processing helix chain 'C' and resid 826 through 831 Processing helix chain 'C' and resid 837 through 852 Processing helix chain 'C' and resid 861 through 866 Processing helix chain 'C' and resid 870 through 881 removed outlier: 3.574A pdb=" N LEU C 881 " --> pdb=" O PHE C 877 " (cutoff:3.500A) Processing helix chain 'C' and resid 912 through 916 Processing helix chain 'C' and resid 925 through 939 removed outlier: 3.518A pdb=" N PHE C 933 " --> pdb=" O ARG C 929 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N ASP C 935 " --> pdb=" O LYS C 931 " (cutoff:3.500A) removed outlier: 4.759A pdb=" N LEU C 936 " --> pdb=" O PHE C 932 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LYS C 939 " --> pdb=" O ASP C 935 " (cutoff:3.500A) Processing helix chain 'C' and resid 1331 through 1344 removed outlier: 3.548A pdb=" N ASN C1335 " --> pdb=" O GLU C1331 " (cutoff:3.500A) Processing helix chain 'C' and resid 1348 through 1366 removed outlier: 4.028A pdb=" N CYS C1362 " --> pdb=" O VAL C1358 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ILE C1363 " --> pdb=" O ILE C1359 " (cutoff:3.500A) Processing helix chain 'C' and resid 1374 through 1386 removed outlier: 4.364A pdb=" N LYS C1378 " --> pdb=" O SER C1374 " (cutoff:3.500A) Processing helix chain 'D' and resid 432 through 448 removed outlier: 3.523A pdb=" N GLU D 440 " --> pdb=" O ALA D 436 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N MET D 441 " --> pdb=" O ALA D 437 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N VAL D 442 " --> pdb=" O LEU D 438 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N PHE D 444 " --> pdb=" O GLU D 440 " (cutoff:3.500A) Proline residue: D 445 - end of helix Processing helix chain 'D' and resid 451 through 456 removed outlier: 4.167A pdb=" N PHE D 455 " --> pdb=" O VAL D 451 " (cutoff:3.500A) Processing helix chain 'D' and resid 472 through 486 removed outlier: 3.718A pdb=" N ALA D 477 " --> pdb=" O LYS D 473 " (cutoff:3.500A) Processing helix chain 'D' and resid 507 through 523 removed outlier: 3.602A pdb=" N LEU D 513 " --> pdb=" O SER D 509 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ARG D 514 " --> pdb=" O GLU D 510 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N MET D 523 " --> pdb=" O GLN D 519 " (cutoff:3.500A) Processing helix chain 'D' and resid 533 through 536 Processing helix chain 'D' and resid 546 through 557 Processing helix chain 'D' and resid 600 through 612 Processing helix chain 'D' and resid 620 through 631 removed outlier: 4.007A pdb=" N ASN D 630 " --> pdb=" O GLU D 626 " (cutoff:3.500A) Processing helix chain 'D' and resid 636 through 655 removed outlier: 3.815A pdb=" N CYS D 643 " --> pdb=" O ILE D 639 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N ALA D 644 " --> pdb=" O LYS D 640 " (cutoff:3.500A) Processing helix chain 'D' and resid 677 through 685 removed outlier: 3.779A pdb=" N VAL D 681 " --> pdb=" O LYS D 677 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N LYS D 685 " --> pdb=" O VAL D 681 " (cutoff:3.500A) Processing helix chain 'D' and resid 689 through 693 removed outlier: 3.707A pdb=" N ARG D 692 " --> pdb=" O ALA D 689 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N ALA D 693 " --> pdb=" O SER D 690 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 689 through 693' Processing helix chain 'D' and resid 705 through 724 removed outlier: 5.677A pdb=" N ASN D 711 " --> pdb=" O PRO D 707 " (cutoff:3.500A) removed outlier: 5.670A pdb=" N THR D 712 " --> pdb=" O LEU D 708 " (cutoff:3.500A) Processing helix chain 'D' and resid 808 through 817 removed outlier: 3.937A pdb=" N ALA D 812 " --> pdb=" O HIS D 808 " (cutoff:3.500A) Processing helix chain 'D' and resid 826 through 831 Processing helix chain 'D' and resid 837 through 852 removed outlier: 3.624A pdb=" N THR D 841 " --> pdb=" O SER D 837 " (cutoff:3.500A) Processing helix chain 'D' and resid 861 through 866 Processing helix chain 'D' and resid 870 through 882 removed outlier: 3.801A pdb=" N GLN D 882 " --> pdb=" O THR D 878 " (cutoff:3.500A) Processing helix chain 'D' and resid 899 through 903 Processing helix chain 'D' and resid 904 through 910 removed outlier: 3.794A pdb=" N LEU D 910 " --> pdb=" O GLU D 906 " (cutoff:3.500A) Processing helix chain 'D' and resid 911 through 916 removed outlier: 6.360A pdb=" N ASP D 914 " --> pdb=" O PHE D 911 " (cutoff:3.500A) Processing helix chain 'D' and resid 925 through 938 removed outlier: 4.312A pdb=" N ASP D 935 " --> pdb=" O LYS D 931 " (cutoff:3.500A) removed outlier: 5.003A pdb=" N LEU D 936 " --> pdb=" O PHE D 932 " (cutoff:3.500A) Processing helix chain 'D' and resid 1331 through 1344 removed outlier: 4.173A pdb=" N ASN D1335 " --> pdb=" O GLU D1331 " (cutoff:3.500A) Processing helix chain 'D' and resid 1348 through 1366 removed outlier: 4.032A pdb=" N HIS D1366 " --> pdb=" O CYS D1362 " (cutoff:3.500A) Processing helix chain 'D' and resid 1375 through 1386 Processing helix chain 'E' and resid 433 through 440 removed outlier: 3.914A pdb=" N ALA E 437 " --> pdb=" O ASN E 433 " (cutoff:3.500A) Processing helix chain 'E' and resid 443 through 448 removed outlier: 3.832A pdb=" N LEU E 447 " --> pdb=" O VAL E 443 " (cutoff:3.500A) Processing helix chain 'E' and resid 450 through 455 removed outlier: 4.506A pdb=" N LYS E 454 " --> pdb=" O GLU E 450 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N PHE E 455 " --> pdb=" O VAL E 451 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 450 through 455' Processing helix chain 'E' and resid 474 through 486 Processing helix chain 'E' and resid 510 through 523 removed outlier: 3.740A pdb=" N ARG E 514 " --> pdb=" O GLU E 510 " (cutoff:3.500A) Processing helix chain 'E' and resid 533 through 536 Processing helix chain 'E' and resid 545 through 561 removed outlier: 4.218A pdb=" N SER E 549 " --> pdb=" O ASP E 545 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N LEU E 558 " --> pdb=" O THR E 554 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N GLY E 561 " --> pdb=" O ALA E 557 " (cutoff:3.500A) Processing helix chain 'E' and resid 600 through 612 Processing helix chain 'E' and resid 620 through 631 removed outlier: 4.256A pdb=" N ASN E 630 " --> pdb=" O GLU E 626 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N CYS E 631 " --> pdb=" O LEU E 627 " (cutoff:3.500A) Processing helix chain 'E' and resid 635 through 655 removed outlier: 3.692A pdb=" N ALA E 644 " --> pdb=" O LYS E 640 " (cutoff:3.500A) Processing helix chain 'E' and resid 675 through 686 removed outlier: 3.605A pdb=" N LYS E 685 " --> pdb=" O VAL E 681 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N MET E 686 " --> pdb=" O ALA E 682 " (cutoff:3.500A) Processing helix chain 'E' and resid 705 through 724 removed outlier: 6.717A pdb=" N ASN E 711 " --> pdb=" O PRO E 707 " (cutoff:3.500A) removed outlier: 5.479A pdb=" N THR E 712 " --> pdb=" O LEU E 708 " (cutoff:3.500A) Processing helix chain 'E' and resid 725 through 728 Processing helix chain 'E' and resid 800 through 804 removed outlier: 4.033A pdb=" N GLY E 804 " --> pdb=" O PRO E 801 " (cutoff:3.500A) Processing helix chain 'E' and resid 808 through 817 Processing helix chain 'E' and resid 826 through 831 Processing helix chain 'E' and resid 837 through 852 removed outlier: 3.523A pdb=" N THR E 852 " --> pdb=" O GLU E 848 " (cutoff:3.500A) Processing helix chain 'E' and resid 861 through 866 Processing helix chain 'E' and resid 870 through 881 removed outlier: 3.836A pdb=" N LEU E 881 " --> pdb=" O PHE E 877 " (cutoff:3.500A) Processing helix chain 'E' and resid 882 through 884 No H-bonds generated for 'chain 'E' and resid 882 through 884' Processing helix chain 'E' and resid 904 through 909 removed outlier: 3.771A pdb=" N GLU E 909 " --> pdb=" O GLU E 905 " (cutoff:3.500A) Processing helix chain 'E' and resid 912 through 916 Processing helix chain 'E' and resid 925 through 935 removed outlier: 3.987A pdb=" N ASP E 935 " --> pdb=" O LYS E 931 " (cutoff:3.500A) Processing helix chain 'E' and resid 1331 through 1344 Processing helix chain 'E' and resid 1348 through 1365 Processing helix chain 'E' and resid 1375 through 1386 Processing helix chain 'F' and resid 431 through 448 removed outlier: 3.642A pdb=" N ALA F 436 " --> pdb=" O SER F 432 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N MET F 441 " --> pdb=" O ALA F 437 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N VAL F 442 " --> pdb=" O LEU F 438 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N PHE F 444 " --> pdb=" O GLU F 440 " (cutoff:3.500A) Proline residue: F 445 - end of helix Processing helix chain 'F' and resid 449 through 452 removed outlier: 3.681A pdb=" N PHE F 452 " --> pdb=" O PRO F 449 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 449 through 452' Processing helix chain 'F' and resid 472 through 486 Processing helix chain 'F' and resid 509 through 520 removed outlier: 4.290A pdb=" N LEU F 513 " --> pdb=" O SER F 509 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N ARG F 514 " --> pdb=" O GLU F 510 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N ASP F 518 " --> pdb=" O ARG F 514 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLN F 519 " --> pdb=" O LEU F 515 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N ALA F 520 " --> pdb=" O LEU F 516 " (cutoff:3.500A) Processing helix chain 'F' and resid 532 through 537 removed outlier: 4.487A pdb=" N LEU F 536 " --> pdb=" O GLN F 532 " (cutoff:3.500A) Processing helix chain 'F' and resid 545 through 562 removed outlier: 3.928A pdb=" N ASP F 560 " --> pdb=" O LEU F 556 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N GLY F 561 " --> pdb=" O ALA F 557 " (cutoff:3.500A) Processing helix chain 'F' and resid 576 through 580 removed outlier: 3.699A pdb=" N ILE F 580 " --> pdb=" O LEU F 577 " (cutoff:3.500A) Processing helix chain 'F' and resid 581 through 585 Processing helix chain 'F' and resid 602 through 612 removed outlier: 4.089A pdb=" N GLU F 606 " --> pdb=" O GLU F 602 " (cutoff:3.500A) Processing helix chain 'F' and resid 620 through 631 removed outlier: 3.616A pdb=" N LEU F 624 " --> pdb=" O LEU F 620 " (cutoff:3.500A) Processing helix chain 'F' and resid 636 through 654 removed outlier: 3.651A pdb=" N CYS F 643 " --> pdb=" O ILE F 639 " (cutoff:3.500A) Processing helix chain 'F' and resid 655 through 659 removed outlier: 3.907A pdb=" N TYR F 659 " --> pdb=" O PRO F 656 " (cutoff:3.500A) Processing helix chain 'F' and resid 675 through 683 removed outlier: 3.809A pdb=" N PHE F 679 " --> pdb=" O SER F 675 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N GLU F 680 " --> pdb=" O ALA F 676 " (cutoff:3.500A) Processing helix chain 'F' and resid 705 through 724 removed outlier: 3.574A pdb=" N LEU F 709 " --> pdb=" O VAL F 705 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N ASN F 711 " --> pdb=" O PRO F 707 " (cutoff:3.500A) removed outlier: 5.348A pdb=" N THR F 712 " --> pdb=" O LEU F 708 " (cutoff:3.500A) Processing helix chain 'F' and resid 808 through 817 Processing helix chain 'F' and resid 826 through 831 Processing helix chain 'F' and resid 837 through 852 removed outlier: 3.776A pdb=" N GLN F 844 " --> pdb=" O GLU F 840 " (cutoff:3.500A) Processing helix chain 'F' and resid 861 through 866 removed outlier: 3.590A pdb=" N TRP F 866 " --> pdb=" O ILE F 862 " (cutoff:3.500A) Processing helix chain 'F' and resid 870 through 883 removed outlier: 3.576A pdb=" N LYS F 874 " --> pdb=" O GLY F 870 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ALA F 875 " --> pdb=" O PRO F 871 " (cutoff:3.500A) Processing helix chain 'F' and resid 899 through 903 Processing helix chain 'F' and resid 904 through 909 Processing helix chain 'F' and resid 925 through 933 removed outlier: 3.740A pdb=" N PHE F 933 " --> pdb=" O ARG F 929 " (cutoff:3.500A) Processing helix chain 'F' and resid 1332 through 1344 Processing helix chain 'F' and resid 1348 through 1366 removed outlier: 3.520A pdb=" N ILE F1363 " --> pdb=" O ILE F1359 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N TYR F1364 " --> pdb=" O SER F1360 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N HIS F1366 " --> pdb=" O CYS F1362 " (cutoff:3.500A) Processing helix chain 'F' and resid 1374 through 1386 removed outlier: 3.633A pdb=" N GLU F1384 " --> pdb=" O GLU F1380 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 492 through 497 removed outlier: 6.110A pdb=" N ALA A 492 " --> pdb=" O ILE A 527 " (cutoff:3.500A) removed outlier: 7.420A pdb=" N PHE A 529 " --> pdb=" O ALA A 492 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N PHE A 494 " --> pdb=" O PHE A 529 " (cutoff:3.500A) removed outlier: 7.177A pdb=" N ASP A 531 " --> pdb=" O PHE A 494 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N ARG A 496 " --> pdb=" O ASP A 531 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N VAL A 569 " --> pdb=" O SER A 526 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N GLY A 572 " --> pdb=" O CYS A 463 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N ARG A 592 " --> pdb=" O GLY A 462 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 821 through 824 removed outlier: 6.687A pdb=" N THR A 821 " --> pdb=" O ILE A 856 " (cutoff:3.500A) removed outlier: 7.810A pdb=" N TYR A 858 " --> pdb=" O THR A 821 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N TYR A 823 " --> pdb=" O TYR A 858 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N SER A 855 " --> pdb=" O LEU A 891 " (cutoff:3.500A) removed outlier: 7.848A pdb=" N LEU A 893 " --> pdb=" O SER A 855 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N VAL A 857 " --> pdb=" O LEU A 893 " (cutoff:3.500A) removed outlier: 8.374A pdb=" N THR A 895 " --> pdb=" O VAL A 857 " (cutoff:3.500A) removed outlier: 7.593A pdb=" N VAL A 859 " --> pdb=" O THR A 895 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ILE A 795 " --> pdb=" O LEU A 892 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N ALA A 894 " --> pdb=" O ILE A 795 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 494 through 496 removed outlier: 3.651A pdb=" N VAL B 569 " --> pdb=" O SER B 526 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ALA B 573 " --> pdb=" O PHE B 530 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N GLY B 572 " --> pdb=" O CYS B 463 " (cutoff:3.500A) removed outlier: 8.195A pdb=" N PHE B 594 " --> pdb=" O GLY B 462 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N LEU B 464 " --> pdb=" O PHE B 594 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 821 through 824 removed outlier: 6.642A pdb=" N THR B 821 " --> pdb=" O ILE B 856 " (cutoff:3.500A) removed outlier: 7.596A pdb=" N TYR B 858 " --> pdb=" O THR B 821 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N TYR B 823 " --> pdb=" O TYR B 858 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N THR B 895 " --> pdb=" O VAL B 859 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ALA B 894 " --> pdb=" O ILE B 795 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 494 through 496 removed outlier: 4.152A pdb=" N VAL C 569 " --> pdb=" O SER C 526 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ALA C 573 " --> pdb=" O PHE C 530 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N GLY C 572 " --> pdb=" O CYS C 463 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N GLY C 462 " --> pdb=" O ARG C 592 " (cutoff:3.500A) removed outlier: 7.808A pdb=" N PHE C 594 " --> pdb=" O GLY C 462 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N LEU C 464 " --> pdb=" O PHE C 594 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 822 through 824 removed outlier: 7.026A pdb=" N TYR C 823 " --> pdb=" O TYR C 858 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N SER C 855 " --> pdb=" O LEU C 891 " (cutoff:3.500A) removed outlier: 7.925A pdb=" N LEU C 893 " --> pdb=" O SER C 855 " (cutoff:3.500A) removed outlier: 6.177A pdb=" N VAL C 857 " --> pdb=" O LEU C 893 " (cutoff:3.500A) removed outlier: 8.266A pdb=" N THR C 895 " --> pdb=" O VAL C 857 " (cutoff:3.500A) removed outlier: 7.535A pdb=" N VAL C 859 " --> pdb=" O THR C 895 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N ILE C 795 " --> pdb=" O ALA C 894 " (cutoff:3.500A) removed outlier: 7.927A pdb=" N SER C 896 " --> pdb=" O ILE C 795 " (cutoff:3.500A) removed outlier: 6.227A pdb=" N ILE C 797 " --> pdb=" O SER C 896 " (cutoff:3.500A) removed outlier: 7.990A pdb=" N PHE C 919 " --> pdb=" O ARG C 794 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N LEU C 796 " --> pdb=" O PHE C 919 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'D' and resid 492 through 496 removed outlier: 3.689A pdb=" N VAL D 569 " --> pdb=" O SER D 526 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N GLY D 572 " --> pdb=" O CYS D 463 " (cutoff:3.500A) removed outlier: 8.161A pdb=" N PHE D 594 " --> pdb=" O GLY D 462 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N LEU D 464 " --> pdb=" O PHE D 594 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 821 through 824 removed outlier: 3.775A pdb=" N THR D 895 " --> pdb=" O VAL D 859 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N ILE D 795 " --> pdb=" O ALA D 894 " (cutoff:3.500A) removed outlier: 7.998A pdb=" N SER D 896 " --> pdb=" O ILE D 795 " (cutoff:3.500A) removed outlier: 5.949A pdb=" N ILE D 797 " --> pdb=" O SER D 896 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N LEU D 796 " --> pdb=" O PHE D 919 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 463 through 466 removed outlier: 6.507A pdb=" N LEU E 464 " --> pdb=" O PHE E 594 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'E' and resid 492 through 495 removed outlier: 3.554A pdb=" N ILE E 527 " --> pdb=" O ALA E 492 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N VAL E 569 " --> pdb=" O SER E 526 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 821 through 824 removed outlier: 3.700A pdb=" N THR E 895 " --> pdb=" O VAL E 859 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ALA E 894 " --> pdb=" O ILE E 795 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 492 through 494 removed outlier: 6.303A pdb=" N ALA F 492 " --> pdb=" O ILE F 527 " (cutoff:3.500A) removed outlier: 8.027A pdb=" N PHE F 529 " --> pdb=" O ALA F 492 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N PHE F 494 " --> pdb=" O PHE F 529 " (cutoff:3.500A) removed outlier: 8.184A pdb=" N ASP F 531 " --> pdb=" O PHE F 494 " (cutoff:3.500A) removed outlier: 7.421A pdb=" N SER F 526 " --> pdb=" O VAL F 569 " (cutoff:3.500A) removed outlier: 8.183A pdb=" N ILE F 571 " --> pdb=" O SER F 526 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N ILE F 528 " --> pdb=" O ILE F 571 " (cutoff:3.500A) removed outlier: 8.189A pdb=" N ALA F 573 " --> pdb=" O ILE F 528 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N PHE F 530 " --> pdb=" O ALA F 573 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N CYS F 463 " --> pdb=" O VAL F 570 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N GLY F 572 " --> pdb=" O CYS F 463 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'F' and resid 821 through 824 removed outlier: 3.698A pdb=" N THR F 895 " --> pdb=" O VAL F 859 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ILE F 795 " --> pdb=" O LEU F 892 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N ALA F 894 " --> pdb=" O ILE F 795 " (cutoff:3.500A) removed outlier: 8.332A pdb=" N PHE F 919 " --> pdb=" O ARG F 794 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N LEU F 796 " --> pdb=" O PHE F 919 " (cutoff:3.500A) 1008 hydrogen bonds defined for protein. 2883 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: 7.21 Time building geometry restraints manager: 6.74 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 7388 1.33 - 1.45: 3717 1.45 - 1.57: 14537 1.57 - 1.69: 28 1.69 - 1.81: 159 Bond restraints: 25829 Sorted by residual: bond pdb=" C4 ATP C1401 " pdb=" C5 ATP C1401 " ideal model delta sigma weight residual 1.388 1.472 -0.084 1.00e-02 1.00e+04 7.01e+01 bond pdb=" C4 ATP B1401 " pdb=" C5 ATP B1401 " ideal model delta sigma weight residual 1.388 1.471 -0.083 1.00e-02 1.00e+04 6.96e+01 bond pdb=" C4 ATP D1401 " pdb=" C5 ATP D1401 " ideal model delta sigma weight residual 1.388 1.470 -0.082 1.00e-02 1.00e+04 6.78e+01 bond pdb=" C5 ATP C1401 " pdb=" C6 ATP C1401 " ideal model delta sigma weight residual 1.409 1.482 -0.073 1.00e-02 1.00e+04 5.39e+01 bond pdb=" C5 ATP D1401 " pdb=" C6 ATP D1401 " ideal model delta sigma weight residual 1.409 1.482 -0.073 1.00e-02 1.00e+04 5.29e+01 ... (remaining 25824 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.90: 34847 3.90 - 7.81: 147 7.81 - 11.71: 14 11.71 - 15.62: 0 15.62 - 19.52: 6 Bond angle restraints: 35014 Sorted by residual: angle pdb=" PB ATP D1401 " pdb=" O3B ATP D1401 " pdb=" PG ATP D1401 " ideal model delta sigma weight residual 139.87 120.35 19.52 1.00e+00 1.00e+00 3.81e+02 angle pdb=" PB ATP C1401 " pdb=" O3B ATP C1401 " pdb=" PG ATP C1401 " ideal model delta sigma weight residual 139.87 120.53 19.34 1.00e+00 1.00e+00 3.74e+02 angle pdb=" PB ATP B1401 " pdb=" O3B ATP B1401 " pdb=" PG ATP B1401 " ideal model delta sigma weight residual 139.87 120.81 19.06 1.00e+00 1.00e+00 3.63e+02 angle pdb=" PA ATP C1401 " pdb=" O3A ATP C1401 " pdb=" PB ATP C1401 " ideal model delta sigma weight residual 136.83 120.42 16.41 1.00e+00 1.00e+00 2.69e+02 angle pdb=" PA ATP B1401 " pdb=" O3A ATP B1401 " pdb=" PB ATP B1401 " ideal model delta sigma weight residual 136.83 120.51 16.32 1.00e+00 1.00e+00 2.66e+02 ... (remaining 35009 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.53: 14599 21.53 - 43.07: 1119 43.07 - 64.60: 116 64.60 - 86.13: 63 86.13 - 107.66: 9 Dihedral angle restraints: 15906 sinusoidal: 6675 harmonic: 9231 Sorted by residual: dihedral pdb=" C5' ADP A1401 " pdb=" O5' ADP A1401 " pdb=" PA ADP A1401 " pdb=" O2A ADP A1401 " ideal model delta sinusoidal sigma weight residual -60.00 47.67 -107.66 1 2.00e+01 2.50e-03 3.13e+01 dihedral pdb=" O1B ADP A1401 " pdb=" O3A ADP A1401 " pdb=" PB ADP A1401 " pdb=" PA ADP A1401 " ideal model delta sinusoidal sigma weight residual -60.00 -149.55 89.55 1 2.00e+01 2.50e-03 2.38e+01 dihedral pdb=" CA PHE B 911 " pdb=" C PHE B 911 " pdb=" N ILE B 912 " pdb=" CA ILE B 912 " ideal model delta harmonic sigma weight residual -180.00 -158.07 -21.93 0 5.00e+00 4.00e-02 1.92e+01 ... (remaining 15903 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 2800 0.041 - 0.081: 862 0.081 - 0.122: 258 0.122 - 0.163: 24 0.163 - 0.204: 4 Chirality restraints: 3948 Sorted by residual: chirality pdb=" CA GLU E1382 " pdb=" N GLU E1382 " pdb=" C GLU E1382 " pdb=" CB GLU E1382 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 1.04e+00 chirality pdb=" CA ASN A 616 " pdb=" N ASN A 616 " pdb=" C ASN A 616 " pdb=" CB ASN A 616 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 9.36e-01 chirality pdb=" CB ILE B 672 " pdb=" CA ILE B 672 " pdb=" CG1 ILE B 672 " pdb=" CG2 ILE B 672 " both_signs ideal model delta sigma weight residual False 2.64 2.84 -0.19 2.00e-01 2.50e+01 9.26e-01 ... (remaining 3945 not shown) Planarity restraints: 4488 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG D 586 " -0.032 5.00e-02 4.00e+02 4.80e-02 3.69e+00 pdb=" N PRO D 587 " 0.083 5.00e-02 4.00e+02 pdb=" CA PRO D 587 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO D 587 " -0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG F 586 " -0.030 5.00e-02 4.00e+02 4.52e-02 3.27e+00 pdb=" N PRO F 587 " 0.078 5.00e-02 4.00e+02 pdb=" CA PRO F 587 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO F 587 " -0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP E 865 " -0.010 2.00e-02 2.50e+03 1.11e-02 3.09e+00 pdb=" CG TRP E 865 " 0.030 2.00e-02 2.50e+03 pdb=" CD1 TRP E 865 " -0.014 2.00e-02 2.50e+03 pdb=" CD2 TRP E 865 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP E 865 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP E 865 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP E 865 " -0.004 2.00e-02 2.50e+03 pdb=" CZ2 TRP E 865 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP E 865 " -0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP E 865 " -0.000 2.00e-02 2.50e+03 ... (remaining 4485 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.68: 458 2.68 - 3.24: 25087 3.24 - 3.79: 37111 3.79 - 4.35: 46992 4.35 - 4.90: 76572 Nonbonded interactions: 186220 Sorted by model distance: nonbonded pdb=" OE1 GLU D 440 " pdb=" OH TYR E 659 " model vdw 2.131 3.040 nonbonded pdb=" O GLN F 657 " pdb=" OG1 THR F 661 " model vdw 2.178 3.040 nonbonded pdb=" O ARG F 576 " pdb=" OG SER F 579 " model vdw 2.220 3.040 nonbonded pdb=" OD2 ASP C 668 " pdb=" OG SER C 670 " model vdw 2.221 3.040 nonbonded pdb=" O LYS C 706 " pdb=" NE2 GLN C 710 " model vdw 2.232 3.120 ... (remaining 186215 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 422 through 598 or resid 601 through 688 or resid 696 thro \ ugh 727 or resid 787 through 943 or resid 1331 through 1388)) selection = (chain 'B' and (resid 422 through 539 or resid 546 through 598 or resid 601 thro \ ugh 659 or resid 666 through 688 or resid 696 through 727 or resid 787 through 9 \ 23 or resid 925 through 943 or resid 1331 through 1388)) selection = (chain 'C' and (resid 422 through 539 or resid 546 through 598 or resid 601 thro \ ugh 659 or resid 666 through 688 or resid 696 through 727 or resid 787 through 9 \ 23 or resid 925 through 943 or resid 1331 through 1388)) selection = (chain 'D' and (resid 422 through 539 or resid 546 through 598 or resid 601 thro \ ugh 659 or resid 666 through 688 or resid 696 through 727 or resid 787 through 9 \ 23 or resid 925 through 943 or resid 1331 through 1388)) selection = (chain 'E' and (resid 422 through 539 or resid 546 through 598 or resid 601 thro \ ugh 659 or resid 666 through 688 or resid 696 through 727 or resid 787 through 9 \ 23 or resid 925 through 943 or resid 1331 through 1388)) selection = (chain 'F' and (resid 422 through 539 or resid 546 through 659 or resid 666 thro \ ugh 727 or resid 787 through 923 or resid 925 through 943 or resid 1331 through \ 1388)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 2.370 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.840 Check model and map are aligned: 0.170 Set scattering table: 0.210 Process input model: 50.840 Find NCS groups from input model: 1.650 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.580 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 58.790 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4999 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.677 25831 Z= 0.554 Angle : 0.723 19.522 35014 Z= 0.456 Chirality : 0.042 0.204 3948 Planarity : 0.004 0.052 4488 Dihedral : 15.177 107.663 9884 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 9.33 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.56 % Favored : 93.34 % Rotamer: Outliers : 0.07 % Allowed : 0.32 % Favored : 99.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.00 % Cis-general : 0.34 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.25 (0.16), residues: 3109 helix: 0.67 (0.15), residues: 1391 sheet: 0.46 (0.28), residues: 377 loop : -1.22 (0.18), residues: 1341 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP E 865 HIS 0.003 0.001 HIS C1366 PHE 0.010 0.001 PHE D 724 TYR 0.017 0.001 TYR C1364 ARG 0.006 0.000 ARG F 576 Details of bonding type rmsd hydrogen bonds : bond 0.20268 ( 1008) hydrogen bonds : angle 6.26622 ( 2883) covalent geometry : bond 0.00327 (25829) covalent geometry : angle 0.72320 (35014) Misc. bond : bond 0.58085 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6218 Ramachandran restraints generated. 3109 Oldfield, 0 Emsley, 3109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6218 Ramachandran restraints generated. 3109 Oldfield, 0 Emsley, 3109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 635 residues out of total 2778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 633 time to evaluate : 2.856 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 639 ILE cc_start: 0.5841 (mm) cc_final: 0.5634 (mm) REVERT: A 686 MET cc_start: 0.0558 (pmm) cc_final: 0.0352 (mtt) REVERT: A 1379 MET cc_start: -0.5244 (mmt) cc_final: -0.5850 (mmp) REVERT: B 686 MET cc_start: 0.3895 (ppp) cc_final: 0.3091 (ppp) REVERT: C 441 MET cc_start: 0.5248 (ttm) cc_final: 0.4280 (ttt) REVERT: C 642 ILE cc_start: 0.8023 (mm) cc_final: 0.7230 (tp) REVERT: C 876 THR cc_start: 0.8155 (m) cc_final: 0.7449 (p) REVERT: C 883 ASN cc_start: 0.7292 (m110) cc_final: 0.6995 (m-40) REVERT: D 789 MET cc_start: 0.6822 (ttp) cc_final: 0.6153 (ppp) REVERT: D 857 VAL cc_start: 0.9198 (t) cc_final: 0.8976 (m) REVERT: E 578 ASP cc_start: 0.1467 (m-30) cc_final: 0.1254 (m-30) REVERT: E 789 MET cc_start: 0.7885 (tpt) cc_final: 0.7620 (tpt) REVERT: E 827 ILE cc_start: 0.7117 (mm) cc_final: 0.6868 (mm) REVERT: F 548 HIS cc_start: 0.7333 (m90) cc_final: 0.6979 (m170) REVERT: F 789 MET cc_start: -0.1316 (ppp) cc_final: -0.1828 (ttt) REVERT: F 1355 LEU cc_start: 0.8742 (tp) cc_final: 0.8542 (tt) outliers start: 2 outliers final: 1 residues processed: 634 average time/residue: 0.4085 time to fit residues: 386.2433 Evaluate side-chains 293 residues out of total 2778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 292 time to evaluate : 2.934 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 263 optimal weight: 0.6980 chunk 236 optimal weight: 0.2980 chunk 131 optimal weight: 10.0000 chunk 80 optimal weight: 1.9990 chunk 159 optimal weight: 4.9990 chunk 126 optimal weight: 0.8980 chunk 244 optimal weight: 0.9990 chunk 94 optimal weight: 3.9990 chunk 148 optimal weight: 4.9990 chunk 182 optimal weight: 2.9990 chunk 283 optimal weight: 0.8980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 546 GLN ** A 861 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 883 ASN A1381 GLN ** B 512 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 548 HIS B 882 GLN ** C 691 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 710 GLN C 808 HIS C 882 GLN C1361 GLN ** D 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 532 GLN D 691 GLN D1361 GLN E 815 HIS E1330 HIS E1351 GLN ** F 544 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 611 HIS ** F 940 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4509 r_free = 0.4509 target = 0.150135 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4155 r_free = 0.4155 target = 0.125575 restraints weight = 131161.152| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.4197 r_free = 0.4197 target = 0.127578 restraints weight = 97861.361| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4193 r_free = 0.4193 target = 0.127648 restraints weight = 73758.515| |-----------------------------------------------------------------------------| r_work (final): 0.4137 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6404 moved from start: 0.2779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 25831 Z= 0.146 Angle : 0.667 10.543 35014 Z= 0.334 Chirality : 0.044 0.192 3948 Planarity : 0.005 0.050 4488 Dihedral : 8.887 104.128 3581 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 9.33 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.72 % Favored : 93.18 % Rotamer: Outliers : 0.14 % Allowed : 4.75 % Favored : 95.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.00 % Cis-general : 0.34 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.16 (0.16), residues: 3109 helix: 0.65 (0.14), residues: 1421 sheet: 0.71 (0.28), residues: 375 loop : -1.17 (0.18), residues: 1313 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 505 HIS 0.015 0.001 HIS A 861 PHE 0.028 0.001 PHE C 517 TYR 0.025 0.002 TYR C 823 ARG 0.007 0.001 ARG B 524 Details of bonding type rmsd hydrogen bonds : bond 0.04743 ( 1008) hydrogen bonds : angle 4.91173 ( 2883) covalent geometry : bond 0.00319 (25829) covalent geometry : angle 0.66720 (35014) Misc. bond : bond 0.00597 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6218 Ramachandran restraints generated. 3109 Oldfield, 0 Emsley, 3109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6218 Ramachandran restraints generated. 3109 Oldfield, 0 Emsley, 3109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 392 residues out of total 2778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 388 time to evaluate : 2.746 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 523 MET cc_start: 0.2309 (mmp) cc_final: 0.2005 (tpt) REVERT: A 825 LEU cc_start: 0.7685 (mt) cc_final: 0.7040 (tp) REVERT: A 858 TYR cc_start: 0.5790 (t80) cc_final: 0.5512 (t80) REVERT: A 861 HIS cc_start: 0.5513 (p-80) cc_final: 0.4885 (p90) REVERT: A 1379 MET cc_start: -0.4726 (mmt) cc_final: -0.5078 (mmp) REVERT: B 495 MET cc_start: 0.7310 (tpt) cc_final: 0.7080 (tmm) REVERT: B 528 ILE cc_start: 0.7148 (mt) cc_final: 0.6938 (mt) REVERT: B 1353 GLU cc_start: 0.6219 (OUTLIER) cc_final: 0.5910 (pt0) REVERT: C 527 ILE cc_start: 0.6820 (mp) cc_final: 0.6580 (mp) REVERT: C 839 GLU cc_start: 0.8040 (mm-30) cc_final: 0.7836 (mm-30) REVERT: C 876 THR cc_start: 0.8204 (m) cc_final: 0.7560 (p) REVERT: C 1379 MET cc_start: 0.7910 (mmt) cc_final: 0.7549 (mmm) REVERT: D 424 ARG cc_start: 0.6133 (mmt180) cc_final: 0.5465 (tpp80) REVERT: D 789 MET cc_start: 0.6957 (ttp) cc_final: 0.6677 (ppp) REVERT: D 821 THR cc_start: 0.7601 (p) cc_final: 0.7244 (t) REVERT: D 857 VAL cc_start: 0.9123 (t) cc_final: 0.8822 (m) REVERT: E 620 LEU cc_start: 0.7423 (pt) cc_final: 0.7163 (mt) REVERT: E 670 SER cc_start: 0.6944 (m) cc_final: 0.6605 (p) REVERT: F 548 HIS cc_start: 0.8411 (m90) cc_final: 0.8162 (m90) REVERT: F 652 ARG cc_start: 0.8886 (tmm160) cc_final: 0.8318 (tpp-160) REVERT: F 789 MET cc_start: -0.3254 (ppp) cc_final: -0.4226 (ttt) outliers start: 4 outliers final: 1 residues processed: 392 average time/residue: 0.3887 time to fit residues: 237.4904 Evaluate side-chains 253 residues out of total 2778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 251 time to evaluate : 2.753 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 126 optimal weight: 1.9990 chunk 74 optimal weight: 10.0000 chunk 210 optimal weight: 7.9990 chunk 8 optimal weight: 10.0000 chunk 278 optimal weight: 0.8980 chunk 91 optimal weight: 6.9990 chunk 84 optimal weight: 10.0000 chunk 199 optimal weight: 0.9980 chunk 48 optimal weight: 0.9990 chunk 137 optimal weight: 5.9990 chunk 117 optimal weight: 0.9980 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 691 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 883 ASN C1361 GLN D 434 HIS ** D 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 691 GLN D1361 GLN E 630 ASN E 726 HIS ** E 815 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 940 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4473 r_free = 0.4473 target = 0.146792 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4115 r_free = 0.4115 target = 0.122879 restraints weight = 129508.689| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4127 r_free = 0.4127 target = 0.123539 restraints weight = 103216.228| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4129 r_free = 0.4129 target = 0.123766 restraints weight = 84910.910| |-----------------------------------------------------------------------------| r_work (final): 0.4082 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6468 moved from start: 0.3664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 25831 Z= 0.146 Angle : 0.652 11.214 35014 Z= 0.324 Chirality : 0.044 0.214 3948 Planarity : 0.005 0.130 4488 Dihedral : 8.577 101.426 3581 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 8.88 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.50 % Favored : 93.41 % Rotamer: Outliers : 0.18 % Allowed : 4.21 % Favored : 95.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.00 % Cis-general : 0.34 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.09 (0.16), residues: 3109 helix: 0.70 (0.14), residues: 1422 sheet: 0.83 (0.28), residues: 379 loop : -1.16 (0.18), residues: 1308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP E 865 HIS 0.010 0.001 HIS A 861 PHE 0.022 0.001 PHE C 517 TYR 0.025 0.001 TYR B 466 ARG 0.021 0.001 ARG E 847 Details of bonding type rmsd hydrogen bonds : bond 0.03960 ( 1008) hydrogen bonds : angle 4.67609 ( 2883) covalent geometry : bond 0.00310 (25829) covalent geometry : angle 0.65225 (35014) Misc. bond : bond 0.01645 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6218 Ramachandran restraints generated. 3109 Oldfield, 0 Emsley, 3109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6218 Ramachandran restraints generated. 3109 Oldfield, 0 Emsley, 3109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 339 residues out of total 2778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 334 time to evaluate : 2.980 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 639 ILE cc_start: 0.6543 (mm) cc_final: 0.6307 (mm) REVERT: A 708 LEU cc_start: 0.3130 (OUTLIER) cc_final: 0.2856 (tp) REVERT: A 789 MET cc_start: 0.1611 (ttt) cc_final: 0.0351 (ttt) REVERT: A 825 LEU cc_start: 0.7457 (mt) cc_final: 0.6792 (tp) REVERT: A 1379 MET cc_start: -0.5237 (mmt) cc_final: -0.5559 (mmp) REVERT: B 495 MET cc_start: 0.7376 (tpt) cc_final: 0.7138 (tmm) REVERT: B 528 ILE cc_start: 0.7379 (mt) cc_final: 0.7167 (mt) REVERT: B 686 MET cc_start: 0.3946 (ppp) cc_final: 0.3288 (ppp) REVERT: B 1353 GLU cc_start: 0.6146 (OUTLIER) cc_final: 0.5222 (pt0) REVERT: B 1380 GLU cc_start: 0.7980 (mt-10) cc_final: 0.7670 (mt-10) REVERT: C 459 PRO cc_start: 0.7865 (Cg_endo) cc_final: 0.7624 (Cg_exo) REVERT: C 839 GLU cc_start: 0.8447 (mm-30) cc_final: 0.8131 (mm-30) REVERT: C 876 THR cc_start: 0.8598 (m) cc_final: 0.7914 (p) REVERT: C 1379 MET cc_start: 0.7938 (mmt) cc_final: 0.7636 (mmp) REVERT: C 1382 GLU cc_start: 0.7527 (tt0) cc_final: 0.7098 (tt0) REVERT: D 424 ARG cc_start: 0.6153 (mmt180) cc_final: 0.5709 (tpp80) REVERT: D 821 THR cc_start: 0.7654 (p) cc_final: 0.7303 (t) REVERT: E 626 GLU cc_start: 0.8844 (mm-30) cc_final: 0.8468 (tt0) REVERT: E 670 SER cc_start: 0.6865 (m) cc_final: 0.6439 (p) REVERT: F 531 ASP cc_start: 0.8387 (t0) cc_final: 0.8034 (p0) REVERT: F 548 HIS cc_start: 0.8322 (m90) cc_final: 0.8025 (m90) REVERT: F 626 GLU cc_start: 0.7787 (tm-30) cc_final: 0.7332 (tm-30) REVERT: F 652 ARG cc_start: 0.8922 (tmm160) cc_final: 0.8201 (ttm-80) REVERT: F 789 MET cc_start: -0.2260 (ppp) cc_final: -0.2915 (ttp) REVERT: F 891 LEU cc_start: 0.8558 (tp) cc_final: 0.8341 (tp) REVERT: F 893 LEU cc_start: 0.5374 (mt) cc_final: 0.4876 (pp) outliers start: 5 outliers final: 2 residues processed: 339 average time/residue: 0.3745 time to fit residues: 199.5528 Evaluate side-chains 230 residues out of total 2778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 226 time to evaluate : 2.748 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 216 optimal weight: 0.7980 chunk 46 optimal weight: 0.0270 chunk 153 optimal weight: 0.9990 chunk 203 optimal weight: 6.9990 chunk 154 optimal weight: 0.6980 chunk 86 optimal weight: 7.9990 chunk 227 optimal weight: 0.8980 chunk 277 optimal weight: 7.9990 chunk 108 optimal weight: 2.9990 chunk 110 optimal weight: 5.9990 chunk 128 optimal weight: 20.0000 overall best weight: 0.6840 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 863 HIS ** A1351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 691 GLN C 883 ASN D 458 GLN D 691 GLN D 726 HIS D1361 GLN E 630 ASN E 815 HIS ** E1351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 940 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4461 r_free = 0.4461 target = 0.146151 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4114 r_free = 0.4114 target = 0.122155 restraints weight = 130441.074| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4115 r_free = 0.4115 target = 0.122573 restraints weight = 100648.733| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4129 r_free = 0.4129 target = 0.123094 restraints weight = 86929.990| |-----------------------------------------------------------------------------| r_work (final): 0.4079 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6533 moved from start: 0.4123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 25831 Z= 0.119 Angle : 0.624 11.172 35014 Z= 0.306 Chirality : 0.043 0.204 3948 Planarity : 0.004 0.067 4488 Dihedral : 8.383 100.040 3581 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.27 % Favored : 93.66 % Rotamer: Outliers : 0.07 % Allowed : 3.17 % Favored : 96.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.00 % Cis-general : 0.34 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.04 (0.16), residues: 3109 helix: 0.84 (0.14), residues: 1410 sheet: 0.90 (0.28), residues: 371 loop : -1.10 (0.18), residues: 1328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 505 HIS 0.006 0.001 HIS A 863 PHE 0.025 0.001 PHE C 517 TYR 0.013 0.001 TYR C 823 ARG 0.007 0.000 ARG D 514 Details of bonding type rmsd hydrogen bonds : bond 0.03454 ( 1008) hydrogen bonds : angle 4.56711 ( 2883) covalent geometry : bond 0.00262 (25829) covalent geometry : angle 0.62421 (35014) Misc. bond : bond 0.00333 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6218 Ramachandran restraints generated. 3109 Oldfield, 0 Emsley, 3109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6218 Ramachandran restraints generated. 3109 Oldfield, 0 Emsley, 3109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 314 residues out of total 2778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 312 time to evaluate : 3.047 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 441 MET cc_start: 0.0586 (tpp) cc_final: 0.0373 (tpp) REVERT: A 523 MET cc_start: 0.2419 (mmp) cc_final: 0.2209 (tpt) REVERT: A 616 ASN cc_start: 0.2997 (p0) cc_final: 0.2066 (m-40) REVERT: A 639 ILE cc_start: 0.6463 (mm) cc_final: 0.6232 (mm) REVERT: A 825 LEU cc_start: 0.7603 (mt) cc_final: 0.6932 (tp) REVERT: A 1379 MET cc_start: -0.4927 (mmt) cc_final: -0.5283 (mmp) REVERT: B 528 ILE cc_start: 0.7394 (mt) cc_final: 0.7162 (mt) REVERT: B 686 MET cc_start: 0.3704 (ppp) cc_final: 0.3117 (ppp) REVERT: B 932 PHE cc_start: 0.7045 (t80) cc_final: 0.6731 (t80) REVERT: B 1380 GLU cc_start: 0.7830 (mt-10) cc_final: 0.7574 (mt-10) REVERT: C 459 PRO cc_start: 0.7775 (Cg_endo) cc_final: 0.7526 (Cg_exo) REVERT: C 876 THR cc_start: 0.8568 (m) cc_final: 0.8166 (p) REVERT: C 1356 TYR cc_start: 0.8254 (t80) cc_final: 0.7954 (t80) REVERT: C 1379 MET cc_start: 0.7673 (mmt) cc_final: 0.7352 (mmp) REVERT: C 1382 GLU cc_start: 0.7304 (tt0) cc_final: 0.7001 (tt0) REVERT: D 496 ARG cc_start: 0.5372 (mtm-85) cc_final: 0.4905 (ttt90) REVERT: D 724 PHE cc_start: 0.8260 (t80) cc_final: 0.8018 (t80) REVERT: D 789 MET cc_start: 0.7653 (ppp) cc_final: 0.7306 (ppp) REVERT: D 821 THR cc_start: 0.7761 (p) cc_final: 0.7217 (t) REVERT: E 670 SER cc_start: 0.6788 (m) cc_final: 0.6441 (p) REVERT: E 1379 MET cc_start: 0.8749 (mpp) cc_final: 0.8252 (mpp) REVERT: F 531 ASP cc_start: 0.8480 (t0) cc_final: 0.7965 (p0) REVERT: F 626 GLU cc_start: 0.7639 (tm-30) cc_final: 0.7389 (tm-30) REVERT: F 652 ARG cc_start: 0.8911 (tmm160) cc_final: 0.8187 (ttm-80) REVERT: F 789 MET cc_start: -0.2379 (ppp) cc_final: -0.2917 (ttp) REVERT: F 863 HIS cc_start: 0.7754 (p90) cc_final: 0.7526 (p-80) REVERT: F 891 LEU cc_start: 0.8650 (tp) cc_final: 0.8434 (tp) REVERT: F 893 LEU cc_start: 0.5610 (mt) cc_final: 0.5149 (pp) REVERT: F 1346 ASN cc_start: 0.6527 (t0) cc_final: 0.6116 (p0) REVERT: F 1379 MET cc_start: 0.8601 (mpp) cc_final: 0.8137 (mmt) outliers start: 2 outliers final: 0 residues processed: 314 average time/residue: 0.3622 time to fit residues: 180.7405 Evaluate side-chains 221 residues out of total 2778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 221 time to evaluate : 2.725 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 76 optimal weight: 0.0870 chunk 114 optimal weight: 5.9990 chunk 50 optimal weight: 0.1980 chunk 198 optimal weight: 6.9990 chunk 183 optimal weight: 0.7980 chunk 238 optimal weight: 0.7980 chunk 188 optimal weight: 1.9990 chunk 44 optimal weight: 0.5980 chunk 155 optimal weight: 7.9990 chunk 137 optimal weight: 4.9990 chunk 291 optimal weight: 0.0470 overall best weight: 0.3456 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1351 GLN A1354 ASN B 611 HIS ** B1366 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 512 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 548 HIS ** C 691 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 883 ASN D 691 GLN ** E 815 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 940 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4463 r_free = 0.4463 target = 0.146125 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4127 r_free = 0.4127 target = 0.122890 restraints weight = 129548.276| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4125 r_free = 0.4125 target = 0.123440 restraints weight = 112403.540| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4129 r_free = 0.4129 target = 0.123562 restraints weight = 92365.291| |-----------------------------------------------------------------------------| r_work (final): 0.4087 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6485 moved from start: 0.4378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 25831 Z= 0.112 Angle : 0.624 10.858 35014 Z= 0.302 Chirality : 0.043 0.211 3948 Planarity : 0.005 0.141 4488 Dihedral : 8.226 98.717 3581 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.24 % Favored : 93.70 % Rotamer: Outliers : 0.04 % Allowed : 2.81 % Favored : 97.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.00 % Cis-general : 0.34 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.09 (0.16), residues: 3109 helix: 0.82 (0.14), residues: 1428 sheet: 0.96 (0.28), residues: 370 loop : -1.04 (0.18), residues: 1311 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 505 HIS 0.011 0.001 HIS B1366 PHE 0.025 0.001 PHE C 517 TYR 0.009 0.001 TYR C 823 ARG 0.019 0.000 ARG D 424 Details of bonding type rmsd hydrogen bonds : bond 0.03252 ( 1008) hydrogen bonds : angle 4.43819 ( 2883) covalent geometry : bond 0.00242 (25829) covalent geometry : angle 0.62449 (35014) Misc. bond : bond 0.00243 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6218 Ramachandran restraints generated. 3109 Oldfield, 0 Emsley, 3109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6218 Ramachandran restraints generated. 3109 Oldfield, 0 Emsley, 3109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 308 residues out of total 2778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 307 time to evaluate : 2.720 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 523 MET cc_start: 0.2784 (mmp) cc_final: 0.1871 (mtp) REVERT: A 616 ASN cc_start: 0.2766 (p0) cc_final: 0.1853 (m-40) REVERT: A 639 ILE cc_start: 0.6552 (mm) cc_final: 0.6302 (mm) REVERT: A 803 PHE cc_start: 0.6618 (m-10) cc_final: 0.6372 (m-10) REVERT: A 825 LEU cc_start: 0.7395 (mt) cc_final: 0.6769 (tp) REVERT: A 1379 MET cc_start: -0.5248 (mmt) cc_final: -0.5749 (mmp) REVERT: B 495 MET cc_start: 0.7520 (tmm) cc_final: 0.7086 (ttm) REVERT: B 528 ILE cc_start: 0.7422 (mt) cc_final: 0.7184 (mt) REVERT: B 686 MET cc_start: 0.3700 (ppp) cc_final: 0.3446 (ppp) REVERT: B 842 CYS cc_start: 0.8842 (t) cc_final: 0.8638 (t) REVERT: B 905 GLU cc_start: 0.8059 (pp20) cc_final: 0.7789 (tt0) REVERT: B 1365 ARG cc_start: 0.5515 (ppt170) cc_final: 0.5092 (tmm-80) REVERT: B 1380 GLU cc_start: 0.8038 (mt-10) cc_final: 0.7742 (mt-10) REVERT: C 459 PRO cc_start: 0.8009 (Cg_endo) cc_final: 0.7691 (Cg_exo) REVERT: C 876 THR cc_start: 0.8475 (m) cc_final: 0.8035 (p) REVERT: C 1379 MET cc_start: 0.7749 (mmt) cc_final: 0.7522 (mmm) REVERT: C 1382 GLU cc_start: 0.7355 (tt0) cc_final: 0.6970 (tt0) REVERT: D 444 PHE cc_start: 0.6211 (m-10) cc_final: 0.5550 (m-10) REVERT: D 495 MET cc_start: 0.7786 (tmm) cc_final: 0.6145 (tmm) REVERT: D 496 ARG cc_start: 0.5677 (mtm-85) cc_final: 0.4898 (ttt90) REVERT: D 724 PHE cc_start: 0.8240 (t80) cc_final: 0.7975 (t80) REVERT: D 789 MET cc_start: 0.7577 (ppp) cc_final: 0.7111 (ppp) REVERT: D 821 THR cc_start: 0.7648 (p) cc_final: 0.7121 (t) REVERT: E 670 SER cc_start: 0.6786 (m) cc_final: 0.6470 (p) REVERT: E 1379 MET cc_start: 0.8643 (mpp) cc_final: 0.8083 (mpp) REVERT: F 531 ASP cc_start: 0.8337 (t0) cc_final: 0.7866 (p0) REVERT: F 626 GLU cc_start: 0.7607 (tm-30) cc_final: 0.7343 (tm-30) REVERT: F 652 ARG cc_start: 0.8885 (tmm160) cc_final: 0.8178 (ttm-80) REVERT: F 789 MET cc_start: -0.2632 (ppp) cc_final: -0.3257 (ttp) REVERT: F 863 HIS cc_start: 0.7530 (p90) cc_final: 0.6425 (t-170) REVERT: F 893 LEU cc_start: 0.5478 (mt) cc_final: 0.5142 (pp) outliers start: 1 outliers final: 0 residues processed: 308 average time/residue: 0.3500 time to fit residues: 171.9939 Evaluate side-chains 219 residues out of total 2778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 219 time to evaluate : 2.674 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 243 optimal weight: 0.8980 chunk 2 optimal weight: 9.9990 chunk 168 optimal weight: 2.9990 chunk 7 optimal weight: 20.0000 chunk 31 optimal weight: 6.9990 chunk 83 optimal weight: 5.9990 chunk 34 optimal weight: 10.0000 chunk 25 optimal weight: 30.0000 chunk 182 optimal weight: 4.9990 chunk 142 optimal weight: 4.9990 chunk 246 optimal weight: 3.9990 overall best weight: 3.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 863 HIS ** B 544 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 548 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 844 GLN B 861 HIS ** C 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 611 HIS ** C 691 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 883 ASN C 922 GLN ** C1366 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 691 GLN D 726 HIS ** E 532 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 575 ASN E 726 HIS E 787 GLN ** E 815 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 900 HIS ** E1351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E1381 GLN ** F 544 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 808 HIS F 815 HIS ** F 940 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4228 r_free = 0.4228 target = 0.129806 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.102488 restraints weight = 118971.400| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.101159 restraints weight = 104171.364| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.101431 restraints weight = 89656.297| |-----------------------------------------------------------------------------| r_work (final): 0.3740 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7135 moved from start: 0.6938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.100 25831 Z= 0.293 Angle : 0.978 11.487 35014 Z= 0.497 Chirality : 0.054 0.277 3948 Planarity : 0.008 0.088 4488 Dihedral : 9.477 100.063 3581 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 16.30 Ramachandran Plot: Outliers : 0.13 % Allowed : 8.11 % Favored : 91.77 % Rotamer: Outliers : 0.11 % Allowed : 4.10 % Favored : 95.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.00 % Cis-general : 0.34 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.02 (0.15), residues: 3109 helix: -0.28 (0.13), residues: 1464 sheet: 0.12 (0.27), residues: 376 loop : -1.29 (0.18), residues: 1269 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.056 0.003 TRP A 615 HIS 0.024 0.003 HIS B1366 PHE 0.059 0.004 PHE E 517 TYR 0.031 0.003 TYR F 823 ARG 0.033 0.001 ARG B1365 Details of bonding type rmsd hydrogen bonds : bond 0.05923 ( 1008) hydrogen bonds : angle 5.46904 ( 2883) covalent geometry : bond 0.00653 (25829) covalent geometry : angle 0.97754 (35014) Misc. bond : bond 0.00210 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6218 Ramachandran restraints generated. 3109 Oldfield, 0 Emsley, 3109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6218 Ramachandran restraints generated. 3109 Oldfield, 0 Emsley, 3109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 2778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 301 time to evaluate : 2.984 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 616 ASN cc_start: 0.2935 (p0) cc_final: 0.1915 (m-40) REVERT: A 825 LEU cc_start: 0.6777 (mt) cc_final: 0.5715 (tt) REVERT: A 1379 MET cc_start: -0.4209 (mmt) cc_final: -0.4428 (mmp) REVERT: B 495 MET cc_start: 0.7517 (tmm) cc_final: 0.7159 (tmm) REVERT: B 528 ILE cc_start: 0.7781 (mt) cc_final: 0.7394 (mt) REVERT: C 448 TYR cc_start: 0.7949 (m-10) cc_final: 0.7639 (m-80) REVERT: C 459 PRO cc_start: 0.8969 (Cg_endo) cc_final: 0.8671 (Cg_exo) REVERT: C 1383 VAL cc_start: 0.8846 (t) cc_final: 0.8368 (p) REVERT: D 523 MET cc_start: 0.6302 (tpt) cc_final: 0.5813 (ptp) REVERT: E 478 ARG cc_start: 0.7421 (mtm180) cc_final: 0.5947 (tpt170) REVERT: E 638 ASP cc_start: 0.8803 (m-30) cc_final: 0.8450 (m-30) REVERT: E 1379 MET cc_start: 0.8605 (mpp) cc_final: 0.7978 (mpp) REVERT: F 531 ASP cc_start: 0.8238 (t0) cc_final: 0.7548 (p0) REVERT: F 620 LEU cc_start: 0.7381 (mp) cc_final: 0.7170 (mt) REVERT: F 652 ARG cc_start: 0.9197 (tmm160) cc_final: 0.8897 (ttp80) REVERT: F 789 MET cc_start: -0.2458 (ppp) cc_final: -0.2837 (ttt) REVERT: F 877 PHE cc_start: 0.6799 (t80) cc_final: 0.6433 (t80) REVERT: F 893 LEU cc_start: 0.6257 (mt) cc_final: 0.5903 (mt) REVERT: F 921 VAL cc_start: 0.4668 (OUTLIER) cc_final: 0.4126 (t) outliers start: 3 outliers final: 0 residues processed: 304 average time/residue: 0.3796 time to fit residues: 182.3967 Evaluate side-chains 197 residues out of total 2778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 196 time to evaluate : 3.015 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 27 optimal weight: 0.9990 chunk 265 optimal weight: 0.9980 chunk 228 optimal weight: 1.9990 chunk 251 optimal weight: 0.8980 chunk 271 optimal weight: 5.9990 chunk 211 optimal weight: 0.6980 chunk 26 optimal weight: 2.9990 chunk 15 optimal weight: 20.0000 chunk 176 optimal weight: 3.9990 chunk 89 optimal weight: 0.9990 chunk 11 optimal weight: 10.0000 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 863 HIS B 611 HIS B1351 GLN B1385 ASN C 575 ASN C 691 GLN C 883 ASN C1361 GLN ** C1366 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 691 GLN D 726 HIS ** E 815 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 863 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 548 HIS ** F 863 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 900 HIS ** F 940 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4273 r_free = 0.4273 target = 0.132372 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.103288 restraints weight = 117183.826| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.104736 restraints weight = 88205.140| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.104468 restraints weight = 66244.993| |-----------------------------------------------------------------------------| r_work (final): 0.3788 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7087 moved from start: 0.7146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 25831 Z= 0.134 Angle : 0.698 11.316 35014 Z= 0.345 Chirality : 0.045 0.335 3948 Planarity : 0.005 0.079 4488 Dihedral : 8.719 100.775 3581 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 10.61 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.24 % Favored : 93.66 % Rotamer: Outliers : 0.11 % Allowed : 1.48 % Favored : 98.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.00 % Cis-general : 0.34 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.44 (0.16), residues: 3109 helix: 0.32 (0.14), residues: 1455 sheet: 0.27 (0.27), residues: 377 loop : -1.11 (0.19), residues: 1277 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 615 HIS 0.004 0.001 HIS C 863 PHE 0.043 0.002 PHE C 517 TYR 0.029 0.002 TYR A 915 ARG 0.008 0.001 ARG D 929 Details of bonding type rmsd hydrogen bonds : bond 0.03985 ( 1008) hydrogen bonds : angle 4.87464 ( 2883) covalent geometry : bond 0.00295 (25829) covalent geometry : angle 0.69820 (35014) Misc. bond : bond 0.00231 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6218 Ramachandran restraints generated. 3109 Oldfield, 0 Emsley, 3109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6218 Ramachandran restraints generated. 3109 Oldfield, 0 Emsley, 3109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 2778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 283 time to evaluate : 2.837 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 616 ASN cc_start: 0.3394 (p0) cc_final: 0.2497 (m-40) REVERT: A 1379 MET cc_start: -0.4149 (mmt) cc_final: -0.4514 (mmp) REVERT: B 495 MET cc_start: 0.7376 (tmm) cc_final: 0.7075 (tmm) REVERT: B 556 LEU cc_start: 0.8108 (mm) cc_final: 0.7611 (mm) REVERT: B 581 ASP cc_start: 0.7452 (t70) cc_final: 0.7138 (t70) REVERT: C 691 GLN cc_start: 0.7549 (OUTLIER) cc_final: 0.7307 (pp30) REVERT: C 876 THR cc_start: 0.8933 (m) cc_final: 0.8502 (p) REVERT: D 496 ARG cc_start: 0.6940 (mtm-85) cc_final: 0.6597 (ttt180) REVERT: D 523 MET cc_start: 0.6010 (tpt) cc_final: 0.5739 (ptp) REVERT: E 638 ASP cc_start: 0.8933 (m-30) cc_final: 0.8517 (m-30) REVERT: F 531 ASP cc_start: 0.8353 (t0) cc_final: 0.7882 (p0) REVERT: F 556 LEU cc_start: 0.8113 (pp) cc_final: 0.7637 (tp) REVERT: F 652 ARG cc_start: 0.9229 (tmm160) cc_final: 0.8934 (ttp80) REVERT: F 789 MET cc_start: -0.2302 (ppp) cc_final: -0.2563 (ttp) REVERT: F 877 PHE cc_start: 0.6896 (t80) cc_final: 0.6568 (t80) REVERT: F 893 LEU cc_start: 0.6583 (mt) cc_final: 0.6353 (mt) outliers start: 3 outliers final: 0 residues processed: 286 average time/residue: 0.3757 time to fit residues: 169.1756 Evaluate side-chains 197 residues out of total 2778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 196 time to evaluate : 2.889 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 161 optimal weight: 1.9990 chunk 100 optimal weight: 0.9990 chunk 147 optimal weight: 6.9990 chunk 289 optimal weight: 0.9990 chunk 126 optimal weight: 10.0000 chunk 174 optimal weight: 1.9990 chunk 163 optimal weight: 5.9990 chunk 73 optimal weight: 9.9990 chunk 223 optimal weight: 7.9990 chunk 68 optimal weight: 2.9990 chunk 81 optimal weight: 0.8980 overall best weight: 1.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 699 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1385 ASN ** C 691 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1366 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 458 GLN D 482 ASN D 691 GLN ** E 815 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 548 HIS ** F 940 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4246 r_free = 0.4246 target = 0.130490 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.101571 restraints weight = 117723.250| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.101783 restraints weight = 98544.611| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.102129 restraints weight = 81343.395| |-----------------------------------------------------------------------------| r_work (final): 0.3765 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7132 moved from start: 0.7599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.081 25831 Z= 0.139 Angle : 0.689 10.180 35014 Z= 0.341 Chirality : 0.044 0.193 3948 Planarity : 0.005 0.072 4488 Dihedral : 8.493 100.181 3581 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 10.55 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.20 % Favored : 92.73 % Rotamer: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.00 % Cis-general : 0.34 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.31 (0.16), residues: 3109 helix: 0.49 (0.14), residues: 1463 sheet: 0.28 (0.27), residues: 376 loop : -1.13 (0.19), residues: 1270 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A 615 HIS 0.004 0.001 HIS C 863 PHE 0.030 0.002 PHE E 494 TYR 0.020 0.002 TYR B1364 ARG 0.012 0.001 ARG C 424 Details of bonding type rmsd hydrogen bonds : bond 0.03759 ( 1008) hydrogen bonds : angle 4.73983 ( 2883) covalent geometry : bond 0.00313 (25829) covalent geometry : angle 0.68856 (35014) Misc. bond : bond 0.00231 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6218 Ramachandran restraints generated. 3109 Oldfield, 0 Emsley, 3109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6218 Ramachandran restraints generated. 3109 Oldfield, 0 Emsley, 3109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 2778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 264 time to evaluate : 3.067 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 616 ASN cc_start: 0.3497 (p0) cc_final: 0.2634 (m-40) REVERT: A 789 MET cc_start: 0.1464 (ttp) cc_final: 0.0010 (mmm) REVERT: A 1379 MET cc_start: -0.4384 (mmt) cc_final: -0.4676 (mmp) REVERT: B 495 MET cc_start: 0.7573 (tmm) cc_final: 0.7268 (tmm) REVERT: B 545 ASP cc_start: 0.8074 (m-30) cc_final: 0.7863 (m-30) REVERT: B 1380 GLU cc_start: 0.7955 (mt-10) cc_final: 0.7746 (mt-10) REVERT: C 518 ASP cc_start: 0.8579 (t0) cc_final: 0.8355 (t0) REVERT: C 631 CYS cc_start: 0.6654 (p) cc_final: 0.6298 (p) REVERT: C 876 THR cc_start: 0.8669 (m) cc_final: 0.8295 (p) REVERT: D 527 ILE cc_start: 0.7646 (mp) cc_final: 0.7424 (mp) REVERT: D 631 CYS cc_start: 0.7277 (p) cc_final: 0.6964 (p) REVERT: E 435 ILE cc_start: 0.8603 (mt) cc_final: 0.8290 (tt) REVERT: E 638 ASP cc_start: 0.9047 (m-30) cc_final: 0.8567 (m-30) REVERT: E 645 GLU cc_start: 0.8286 (tp30) cc_final: 0.8052 (tp30) REVERT: E 683 MET cc_start: 0.8479 (tmm) cc_final: 0.8196 (tmm) REVERT: E 1379 MET cc_start: 0.8404 (mpp) cc_final: 0.8130 (mtm) REVERT: F 531 ASP cc_start: 0.8316 (t0) cc_final: 0.7803 (p0) REVERT: F 556 LEU cc_start: 0.8160 (pp) cc_final: 0.7701 (tp) REVERT: F 789 MET cc_start: -0.2349 (ppp) cc_final: -0.2641 (ttp) REVERT: F 877 PHE cc_start: 0.7118 (t80) cc_final: 0.6764 (t80) REVERT: F 893 LEU cc_start: 0.6552 (mt) cc_final: 0.5938 (mt) REVERT: F 1379 MET cc_start: 0.9177 (mmm) cc_final: 0.8892 (mmt) outliers start: 0 outliers final: 0 residues processed: 264 average time/residue: 0.3449 time to fit residues: 147.9982 Evaluate side-chains 186 residues out of total 2778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 186 time to evaluate : 2.904 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 197 optimal weight: 5.9990 chunk 112 optimal weight: 0.0770 chunk 87 optimal weight: 6.9990 chunk 127 optimal weight: 8.9990 chunk 241 optimal weight: 4.9990 chunk 121 optimal weight: 0.7980 chunk 94 optimal weight: 3.9990 chunk 309 optimal weight: 3.9990 chunk 39 optimal weight: 0.7980 chunk 229 optimal weight: 7.9990 chunk 221 optimal weight: 9.9990 overall best weight: 1.9342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 699 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 691 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 883 ASN C1361 GLN ** C1366 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 546 GLN D 691 GLN E 815 HIS ** E1351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 548 HIS F 630 ASN ** F 940 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4206 r_free = 0.4206 target = 0.127981 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.101504 restraints weight = 115695.793| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.099232 restraints weight = 115067.252| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.099837 restraints weight = 101855.699| |-----------------------------------------------------------------------------| r_work (final): 0.3719 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7150 moved from start: 0.8254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 25831 Z= 0.159 Angle : 0.724 14.441 35014 Z= 0.359 Chirality : 0.046 0.241 3948 Planarity : 0.005 0.074 4488 Dihedral : 8.405 101.618 3581 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 11.74 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.72 % Favored : 93.18 % Rotamer: Outliers : 0.04 % Allowed : 0.68 % Favored : 99.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.00 % Cis-general : 0.34 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.29 (0.16), residues: 3109 helix: 0.51 (0.14), residues: 1452 sheet: 0.31 (0.26), residues: 387 loop : -1.12 (0.19), residues: 1270 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP A 615 HIS 0.016 0.001 HIS A1366 PHE 0.027 0.002 PHE C 517 TYR 0.018 0.002 TYR F 448 ARG 0.011 0.001 ARG E 592 Details of bonding type rmsd hydrogen bonds : bond 0.03982 ( 1008) hydrogen bonds : angle 4.83136 ( 2883) covalent geometry : bond 0.00356 (25829) covalent geometry : angle 0.72401 (35014) Misc. bond : bond 0.00194 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6218 Ramachandran restraints generated. 3109 Oldfield, 0 Emsley, 3109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6218 Ramachandran restraints generated. 3109 Oldfield, 0 Emsley, 3109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 2778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 266 time to evaluate : 3.157 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 616 ASN cc_start: 0.3395 (p0) cc_final: 0.2445 (m-40) REVERT: A 789 MET cc_start: 0.0578 (ttp) cc_final: -0.0938 (mtp) REVERT: A 867 GLU cc_start: 0.8375 (mm-30) cc_final: 0.8151 (pm20) REVERT: A 1379 MET cc_start: -0.4989 (mmt) cc_final: -0.5244 (mmp) REVERT: B 495 MET cc_start: 0.7474 (tmm) cc_final: 0.7157 (tmm) REVERT: B 545 ASP cc_start: 0.8261 (m-30) cc_final: 0.7997 (m-30) REVERT: B 556 LEU cc_start: 0.8171 (mm) cc_final: 0.7639 (mm) REVERT: B 591 ASP cc_start: 0.8452 (p0) cc_final: 0.8164 (p0) REVERT: B 842 CYS cc_start: 0.8986 (t) cc_final: 0.8722 (t) REVERT: C 480 LEU cc_start: 0.9002 (tp) cc_final: 0.8575 (tp) REVERT: C 631 CYS cc_start: 0.6815 (p) cc_final: 0.6486 (p) REVERT: D 527 ILE cc_start: 0.7949 (mp) cc_final: 0.7735 (mp) REVERT: D 631 CYS cc_start: 0.7029 (p) cc_final: 0.6640 (p) REVERT: E 435 ILE cc_start: 0.8862 (mt) cc_final: 0.8480 (tt) REVERT: E 592 ARG cc_start: 0.6455 (mmm160) cc_final: 0.5986 (mmm160) REVERT: E 638 ASP cc_start: 0.9115 (m-30) cc_final: 0.8577 (m-30) REVERT: E 1379 MET cc_start: 0.8343 (mpp) cc_final: 0.7923 (mpp) REVERT: F 531 ASP cc_start: 0.8250 (t0) cc_final: 0.7739 (p0) REVERT: F 556 LEU cc_start: 0.8086 (pp) cc_final: 0.7614 (tp) REVERT: F 825 LEU cc_start: 0.8386 (tp) cc_final: 0.8185 (tp) REVERT: F 877 PHE cc_start: 0.6975 (t80) cc_final: 0.6618 (t80) REVERT: F 893 LEU cc_start: 0.6164 (mt) cc_final: 0.5854 (mt) REVERT: F 1362 CYS cc_start: 0.7734 (m) cc_final: 0.7126 (m) REVERT: F 1379 MET cc_start: 0.9197 (mmm) cc_final: 0.8834 (mmm) outliers start: 1 outliers final: 0 residues processed: 267 average time/residue: 0.3850 time to fit residues: 170.0260 Evaluate side-chains 196 residues out of total 2778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 196 time to evaluate : 3.086 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 26 optimal weight: 6.9990 chunk 258 optimal weight: 0.9980 chunk 86 optimal weight: 6.9990 chunk 68 optimal weight: 0.2980 chunk 24 optimal weight: 0.0070 chunk 133 optimal weight: 0.9980 chunk 227 optimal weight: 4.9990 chunk 58 optimal weight: 0.0000 chunk 32 optimal weight: 9.9990 chunk 229 optimal weight: 2.9990 chunk 308 optimal weight: 4.9990 overall best weight: 0.4602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 863 HIS C 434 HIS C 691 GLN C1361 GLN ** C1366 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 512 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 548 HIS ** F 863 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 940 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4238 r_free = 0.4238 target = 0.129834 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.103669 restraints weight = 125060.740| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.104689 restraints weight = 92445.396| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.104525 restraints weight = 72539.993| |-----------------------------------------------------------------------------| r_work (final): 0.3748 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7168 moved from start: 0.8338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 25831 Z= 0.124 Angle : 0.687 10.165 35014 Z= 0.337 Chirality : 0.045 0.317 3948 Planarity : 0.005 0.074 4488 Dihedral : 8.138 101.039 3581 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 10.16 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.79 % Favored : 93.12 % Rotamer: Outliers : 0.07 % Allowed : 0.25 % Favored : 99.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.00 % Cis-general : 0.34 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.14 (0.16), residues: 3109 helix: 0.64 (0.14), residues: 1446 sheet: 0.47 (0.27), residues: 385 loop : -1.07 (0.19), residues: 1278 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP A 615 HIS 0.007 0.001 HIS A 900 PHE 0.029 0.001 PHE C 517 TYR 0.017 0.001 TYR B 521 ARG 0.019 0.001 ARG A 913 Details of bonding type rmsd hydrogen bonds : bond 0.03448 ( 1008) hydrogen bonds : angle 4.67850 ( 2883) covalent geometry : bond 0.00271 (25829) covalent geometry : angle 0.68695 (35014) Misc. bond : bond 0.00232 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6218 Ramachandran restraints generated. 3109 Oldfield, 0 Emsley, 3109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6218 Ramachandran restraints generated. 3109 Oldfield, 0 Emsley, 3109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 2778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 260 time to evaluate : 2.786 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 639 ILE cc_start: 0.6330 (mm) cc_final: 0.6107 (mm) REVERT: A 683 MET cc_start: -0.3764 (mmt) cc_final: -0.4565 (mtm) REVERT: A 789 MET cc_start: 0.0958 (ttp) cc_final: -0.0529 (mtp) REVERT: A 825 LEU cc_start: 0.6993 (mm) cc_final: 0.6793 (mm) REVERT: A 1379 MET cc_start: -0.4566 (mmt) cc_final: -0.4838 (mmp) REVERT: B 495 MET cc_start: 0.7325 (tmm) cc_final: 0.7085 (tmm) REVERT: B 545 ASP cc_start: 0.8183 (m-30) cc_final: 0.7898 (m-30) REVERT: C 480 LEU cc_start: 0.9016 (tp) cc_final: 0.8492 (tp) REVERT: C 484 CYS cc_start: 0.7683 (m) cc_final: 0.7186 (m) REVERT: C 631 CYS cc_start: 0.6502 (p) cc_final: 0.6150 (p) REVERT: E 435 ILE cc_start: 0.8829 (mt) cc_final: 0.8165 (tt) REVERT: E 592 ARG cc_start: 0.6428 (mmm160) cc_final: 0.5608 (mmm160) REVERT: E 638 ASP cc_start: 0.8985 (m-30) cc_final: 0.8575 (m-30) REVERT: E 1379 MET cc_start: 0.8320 (mpp) cc_final: 0.7943 (mpp) REVERT: F 531 ASP cc_start: 0.8348 (t0) cc_final: 0.7902 (p0) REVERT: F 556 LEU cc_start: 0.8181 (pp) cc_final: 0.7776 (tp) REVERT: F 825 LEU cc_start: 0.8480 (tp) cc_final: 0.8074 (tp) REVERT: F 858 TYR cc_start: 0.5951 (t80) cc_final: 0.5704 (t80) REVERT: F 877 PHE cc_start: 0.6959 (t80) cc_final: 0.6647 (t80) REVERT: F 893 LEU cc_start: 0.6733 (mt) cc_final: 0.6002 (mt) REVERT: F 1379 MET cc_start: 0.9242 (mmm) cc_final: 0.8868 (mmt) outliers start: 2 outliers final: 0 residues processed: 262 average time/residue: 0.3418 time to fit residues: 147.0031 Evaluate side-chains 187 residues out of total 2778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 187 time to evaluate : 2.862 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 52 optimal weight: 10.0000 chunk 303 optimal weight: 0.8980 chunk 297 optimal weight: 1.9990 chunk 183 optimal weight: 0.9990 chunk 105 optimal weight: 1.9990 chunk 185 optimal weight: 5.9990 chunk 227 optimal weight: 4.9990 chunk 146 optimal weight: 7.9990 chunk 98 optimal weight: 1.9990 chunk 143 optimal weight: 1.9990 chunk 68 optimal weight: 3.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 699 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 458 GLN C 691 GLN C1361 GLN ** C1366 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 512 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 691 GLN ** E1351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 548 HIS ** F 940 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4185 r_free = 0.4185 target = 0.126189 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.099341 restraints weight = 118736.372| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.098339 restraints weight = 104521.019| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.098544 restraints weight = 86526.188| |-----------------------------------------------------------------------------| r_work (final): 0.3697 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7228 moved from start: 0.8803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 25831 Z= 0.148 Angle : 0.704 12.471 35014 Z= 0.348 Chirality : 0.045 0.228 3948 Planarity : 0.005 0.069 4488 Dihedral : 8.138 101.655 3581 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 11.66 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.20 % Favored : 92.73 % Rotamer: Outliers : 0.07 % Allowed : 0.50 % Favored : 99.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.00 % Cis-general : 0.34 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.15 (0.16), residues: 3109 helix: 0.64 (0.14), residues: 1452 sheet: 0.39 (0.27), residues: 388 loop : -1.07 (0.19), residues: 1269 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 615 HIS 0.004 0.001 HIS C 863 PHE 0.032 0.002 PHE C 517 TYR 0.018 0.002 TYR B 521 ARG 0.009 0.001 ARG E 592 Details of bonding type rmsd hydrogen bonds : bond 0.03772 ( 1008) hydrogen bonds : angle 4.76317 ( 2883) covalent geometry : bond 0.00335 (25829) covalent geometry : angle 0.70377 (35014) Misc. bond : bond 0.00255 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8033.09 seconds wall clock time: 140 minutes 22.90 seconds (8422.90 seconds total)