Starting phenix.real_space_refine on Mon Aug 25 05:05:56 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8juz_36667/08_2025/8juz_36667_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8juz_36667/08_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_36667/08_2025/8juz_36667.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8juz_36667/08_2025/8juz_36667.map" model { file = "/net/cci-nas-00/data/ceres_data/8juz_36667/08_2025/8juz_36667_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8juz_36667/08_2025/8juz_36667_neut.cif" } resolution = 4.29 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: 5.30, per 1000 atoms: 0.21 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: 1.76 Conformation dependent library (CDL) restraints added in 1.4 seconds Enol-peptide restraints added in 715.3 nanoseconds 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: 0.82 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: 3.92 Time building geometry restraints manager: 2.31 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: 1.620 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.360 Check model and map are aligned: 0.070 Set scattering table: 0.070 Process input model: 19.840 Find NCS groups from input model: 0.770 Set up NCS constraints: 0.050 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:1.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.000 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.006 0.000 ARG F 576 TYR 0.017 0.001 TYR C1364 PHE 0.010 0.001 PHE D 724 TRP 0.030 0.001 TRP E 865 HIS 0.003 0.001 HIS C1366 Details of bonding type rmsd covalent geometry : bond 0.00327 (25829) covalent geometry : angle 0.72320 (35014) hydrogen bonds : bond 0.20268 ( 1008) hydrogen bonds : angle 6.26622 ( 2883) 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 : 0.625 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: 0.1761 time to fit residues: 166.9620 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 : 0.934 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 197 optimal weight: 0.7980 chunk 215 optimal weight: 10.0000 chunk 20 optimal weight: 0.6980 chunk 132 optimal weight: 10.0000 chunk 261 optimal weight: 20.0000 chunk 248 optimal weight: 5.9990 chunk 207 optimal weight: 2.9990 chunk 155 optimal weight: 0.6980 chunk 244 optimal weight: 0.0980 chunk 183 optimal weight: 2.9990 chunk 298 optimal weight: 10.0000 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 482 ASN A 546 GLN ** A 861 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 512 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 548 HIS ** C 691 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 710 GLN C 808 HIS C 882 GLN C1361 GLN D 691 GLN D1361 GLN E 815 HIS E1330 HIS E1351 GLN F 611 HIS ** F 940 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4492 r_free = 0.4492 target = 0.148874 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4131 r_free = 0.4131 target = 0.123994 restraints weight = 131427.950| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4168 r_free = 0.4168 target = 0.125834 restraints weight = 97858.456| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4169 r_free = 0.4169 target = 0.126083 restraints weight = 74129.475| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.4185 r_free = 0.4185 target = 0.126916 restraints weight = 62109.245| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4185 r_free = 0.4185 target = 0.126925 restraints weight = 55657.529| |-----------------------------------------------------------------------------| r_work (final): 0.4133 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6440 moved from start: 0.2988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 25831 Z= 0.152 Angle : 0.681 10.670 35014 Z= 0.340 Chirality : 0.044 0.193 3948 Planarity : 0.005 0.050 4488 Dihedral : 8.910 104.740 3581 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.75 % Favored : 93.15 % Rotamer: Outliers : 0.18 % Allowed : 5.18 % Favored : 94.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.00 % Cis-general : 0.34 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.22 (0.16), residues: 3109 helix: 0.57 (0.14), residues: 1422 sheet: 0.66 (0.28), residues: 376 loop : -1.16 (0.18), residues: 1311 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 524 TYR 0.025 0.002 TYR C 823 PHE 0.031 0.001 PHE C 517 TRP 0.018 0.001 TRP A 505 HIS 0.015 0.001 HIS A 861 Details of bonding type rmsd covalent geometry : bond 0.00323 (25829) covalent geometry : angle 0.68105 (35014) hydrogen bonds : bond 0.04358 ( 1008) hydrogen bonds : angle 4.85797 ( 2883) Misc. bond : bond 0.01121 ( 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 395 residues out of total 2778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 390 time to evaluate : 0.979 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: A 523 MET cc_start: 0.2192 (mmp) cc_final: 0.1923 (tpt) REVERT: A 616 ASN cc_start: 0.3485 (p0) cc_final: 0.2650 (m-40) REVERT: A 825 LEU cc_start: 0.7688 (mt) cc_final: 0.6999 (tp) REVERT: A 858 TYR cc_start: 0.5914 (t80) cc_final: 0.5678 (t80) REVERT: A 861 HIS cc_start: 0.5512 (p-80) cc_final: 0.5110 (p90) REVERT: A 1379 MET cc_start: -0.4671 (mmt) cc_final: -0.5061 (mmp) REVERT: B 528 ILE cc_start: 0.7291 (mt) cc_final: 0.7074 (mt) REVERT: B 905 GLU cc_start: 0.8191 (pp20) cc_final: 0.7990 (tt0) REVERT: B 1353 GLU cc_start: 0.6491 (OUTLIER) cc_final: 0.6273 (pt0) REVERT: C 459 PRO cc_start: 0.7751 (Cg_endo) cc_final: 0.7532 (Cg_exo) REVERT: C 527 ILE cc_start: 0.7047 (mp) cc_final: 0.6816 (mp) REVERT: C 839 GLU cc_start: 0.8372 (mm-30) cc_final: 0.8164 (mm-30) REVERT: C 848 GLU cc_start: 0.8546 (tm-30) cc_final: 0.8346 (tm-30) REVERT: C 876 THR cc_start: 0.8364 (m) cc_final: 0.7739 (p) REVERT: C 1379 MET cc_start: 0.7949 (mmt) cc_final: 0.7632 (mmp) REVERT: C 1384 GLU cc_start: 0.7226 (OUTLIER) cc_final: 0.6988 (mp0) REVERT: D 424 ARG cc_start: 0.6139 (mmt180) cc_final: 0.5541 (tpp80) REVERT: D 495 MET cc_start: 0.8018 (tmm) cc_final: 0.7794 (tmm) REVERT: D 789 MET cc_start: 0.6988 (ttp) cc_final: 0.6663 (ppp) REVERT: D 821 THR cc_start: 0.7659 (p) cc_final: 0.7335 (t) REVERT: D 857 VAL cc_start: 0.9279 (t) cc_final: 0.8952 (m) REVERT: E 620 LEU cc_start: 0.7441 (pt) cc_final: 0.7186 (mt) REVERT: E 670 SER cc_start: 0.6745 (m) cc_final: 0.6389 (p) REVERT: F 548 HIS cc_start: 0.8376 (m90) cc_final: 0.8106 (m90) REVERT: F 620 LEU cc_start: 0.6969 (mp) cc_final: 0.6716 (mt) REVERT: F 652 ARG cc_start: 0.8967 (tmm160) cc_final: 0.8283 (ttm-80) REVERT: F 789 MET cc_start: -0.3188 (ppp) cc_final: -0.4083 (ttt) outliers start: 5 outliers final: 2 residues processed: 395 average time/residue: 0.1561 time to fit residues: 96.5944 Evaluate side-chains 248 residues out of total 2778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 244 time to evaluate : 0.725 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 129 optimal weight: 0.6980 chunk 74 optimal weight: 20.0000 chunk 5 optimal weight: 6.9990 chunk 81 optimal weight: 2.9990 chunk 262 optimal weight: 9.9990 chunk 175 optimal weight: 3.9990 chunk 160 optimal weight: 5.9990 chunk 82 optimal weight: 2.9990 chunk 52 optimal weight: 20.0000 chunk 305 optimal weight: 5.9990 chunk 309 optimal weight: 0.9990 overall best weight: 2.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 611 HIS ** A 861 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1351 GLN C 611 HIS C 691 GLN C 883 ASN C1361 GLN D 434 HIS D 691 GLN E 630 ASN E 726 HIS ** E 815 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 900 HIS F 815 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 = 0.4370 r_free = 0.4370 target = 0.139871 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.114072 restraints weight = 128877.821| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.115432 restraints weight = 91759.094| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.115464 restraints weight = 73475.282| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.115879 restraints weight = 65355.704| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.4004 r_free = 0.4004 target = 0.116132 restraints weight = 59149.555| |-----------------------------------------------------------------------------| r_work (final): 0.3952 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6789 moved from start: 0.4757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.075 25831 Z= 0.208 Angle : 0.772 12.541 35014 Z= 0.389 Chirality : 0.047 0.248 3948 Planarity : 0.006 0.160 4488 Dihedral : 8.821 101.935 3581 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 10.89 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.72 % Favored : 93.21 % Rotamer: Outliers : 0.32 % Allowed : 6.62 % Favored : 93.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.00 % Cis-general : 0.34 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.36 (0.16), residues: 3109 helix: 0.42 (0.14), residues: 1439 sheet: 0.52 (0.27), residues: 393 loop : -1.19 (0.18), residues: 1277 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG E 847 TYR 0.031 0.002 TYR B 466 PHE 0.054 0.002 PHE E 529 TRP 0.027 0.002 TRP A 505 HIS 0.017 0.002 HIS C 863 Details of bonding type rmsd covalent geometry : bond 0.00466 (25829) covalent geometry : angle 0.77204 (35014) hydrogen bonds : bond 0.04765 ( 1008) hydrogen bonds : angle 4.86263 ( 2883) Misc. bond : bond 0.00928 ( 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 338 residues out of total 2778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 329 time to evaluate : 0.990 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 616 ASN cc_start: 0.3069 (p0) cc_final: 0.2291 (m-40) REVERT: A 639 ILE cc_start: 0.6555 (mm) cc_final: 0.6353 (mm) REVERT: A 789 MET cc_start: 0.1843 (ttt) cc_final: 0.0744 (ttt) REVERT: A 825 LEU cc_start: 0.7233 (mt) cc_final: 0.6462 (tp) REVERT: A 861 HIS cc_start: 0.5896 (p-80) cc_final: 0.5680 (p-80) REVERT: A 1379 MET cc_start: -0.4502 (mmt) cc_final: -0.5096 (mmp) REVERT: B 528 ILE cc_start: 0.7486 (mt) cc_final: 0.7279 (mt) REVERT: B 932 PHE cc_start: 0.7019 (t80) cc_final: 0.6808 (t80) REVERT: C 876 THR cc_start: 0.8805 (m) cc_final: 0.8428 (p) REVERT: C 1379 MET cc_start: 0.7709 (mmt) cc_final: 0.7242 (mmp) REVERT: C 1382 GLU cc_start: 0.7542 (tt0) cc_final: 0.7009 (tt0) REVERT: E 626 GLU cc_start: 0.8680 (mm-30) cc_final: 0.8381 (mm-30) REVERT: E 627 LEU cc_start: 0.9099 (mt) cc_final: 0.8899 (mt) REVERT: E 842 CYS cc_start: 0.7051 (t) cc_final: 0.6727 (t) REVERT: E 1379 MET cc_start: 0.8841 (mpp) cc_final: 0.8280 (mpp) REVERT: F 531 ASP cc_start: 0.8463 (t0) cc_final: 0.7984 (p0) REVERT: F 551 ILE cc_start: 0.7765 (tt) cc_final: 0.7540 (tt) REVERT: F 626 GLU cc_start: 0.7803 (tm-30) cc_final: 0.7353 (tm-30) REVERT: F 652 ARG cc_start: 0.9136 (tmm160) cc_final: 0.8902 (ttp80) REVERT: F 863 HIS cc_start: 0.8099 (p90) cc_final: 0.7618 (p90) REVERT: F 1382 GLU cc_start: 0.8710 (tm-30) cc_final: 0.8306 (tp30) outliers start: 9 outliers final: 2 residues processed: 337 average time/residue: 0.1557 time to fit residues: 82.3032 Evaluate side-chains 224 residues out of total 2778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 222 time to evaluate : 0.822 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 135 optimal weight: 0.9980 chunk 59 optimal weight: 9.9990 chunk 221 optimal weight: 2.9990 chunk 293 optimal weight: 9.9990 chunk 96 optimal weight: 5.9990 chunk 311 optimal weight: 0.9980 chunk 68 optimal weight: 2.9990 chunk 232 optimal weight: 0.3980 chunk 50 optimal weight: 9.9990 chunk 49 optimal weight: 0.9990 chunk 40 optimal weight: 5.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 863 HIS B 548 HIS B 575 ASN B 699 GLN C 548 HIS ** C 691 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 883 ASN D 691 GLN D 726 HIS E 575 ASN E 630 ASN ** 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: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4368 r_free = 0.4368 target = 0.139438 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.113979 restraints weight = 126877.233| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.114551 restraints weight = 94042.097| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3982 r_free = 0.3982 target = 0.114822 restraints weight = 82812.094| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.115503 restraints weight = 66160.427| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.115504 restraints weight = 60281.688| |-----------------------------------------------------------------------------| r_work (final): 0.3940 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6810 moved from start: 0.5296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 25831 Z= 0.130 Angle : 0.646 10.913 35014 Z= 0.319 Chirality : 0.044 0.193 3948 Planarity : 0.005 0.059 4488 Dihedral : 8.685 100.956 3581 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 10.10 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.59 % Favored : 93.34 % Rotamer: Outliers : 0.11 % Allowed : 3.38 % Favored : 96.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.00 % Cis-general : 0.34 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.18 (0.16), residues: 3109 helix: 0.62 (0.14), residues: 1438 sheet: 0.50 (0.27), residues: 392 loop : -1.12 (0.19), residues: 1279 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG C 592 TYR 0.015 0.001 TYR C1364 PHE 0.024 0.001 PHE C 517 TRP 0.018 0.001 TRP A 615 HIS 0.008 0.001 HIS A 861 Details of bonding type rmsd covalent geometry : bond 0.00287 (25829) covalent geometry : angle 0.64632 (35014) hydrogen bonds : bond 0.03689 ( 1008) hydrogen bonds : angle 4.66296 ( 2883) Misc. bond : bond 0.00290 ( 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 319 residues out of total 2778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 316 time to evaluate : 0.900 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 441 MET cc_start: 0.0378 (tpp) cc_final: 0.0140 (tpp) REVERT: A 616 ASN cc_start: 0.2899 (p0) cc_final: 0.2026 (m-40) REVERT: A 825 LEU cc_start: 0.7243 (mt) cc_final: 0.6198 (tp) REVERT: A 1379 MET cc_start: -0.4563 (mmt) cc_final: -0.5109 (mmp) REVERT: B 528 ILE cc_start: 0.7610 (mt) cc_final: 0.7369 (mt) REVERT: B 559 MET cc_start: 0.7747 (mtt) cc_final: 0.7459 (mtt) REVERT: B 560 ASP cc_start: 0.7108 (m-30) cc_final: 0.6860 (p0) REVERT: B 686 MET cc_start: 0.3066 (ppp) cc_final: 0.2456 (ppp) REVERT: B 842 CYS cc_start: 0.8917 (t) cc_final: 0.8707 (t) REVERT: B 932 PHE cc_start: 0.7022 (t80) cc_final: 0.6806 (t80) REVERT: B 1380 GLU cc_start: 0.8020 (mt-10) cc_final: 0.7664 (mt-10) REVERT: C 876 THR cc_start: 0.8908 (m) cc_final: 0.8465 (p) REVERT: C 1379 MET cc_start: 0.7827 (mmt) cc_final: 0.7406 (mmp) REVERT: C 1382 GLU cc_start: 0.7623 (tt0) cc_final: 0.7181 (tt0) REVERT: E 1379 MET cc_start: 0.8687 (mpp) cc_final: 0.8169 (mpp) REVERT: F 531 ASP cc_start: 0.8424 (t0) cc_final: 0.8107 (p0) REVERT: F 620 LEU cc_start: 0.7369 (tp) cc_final: 0.7156 (mp) REVERT: F 652 ARG cc_start: 0.9177 (tmm160) cc_final: 0.8944 (ttp80) REVERT: F 1382 GLU cc_start: 0.8754 (tm-30) cc_final: 0.8432 (tp30) outliers start: 3 outliers final: 0 residues processed: 318 average time/residue: 0.1628 time to fit residues: 81.9072 Evaluate side-chains 213 residues out of total 2778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 213 time to evaluate : 0.985 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 37 optimal weight: 0.0370 chunk 132 optimal weight: 3.9990 chunk 196 optimal weight: 0.7980 chunk 277 optimal weight: 2.9990 chunk 83 optimal weight: 0.5980 chunk 157 optimal weight: 4.9990 chunk 147 optimal weight: 5.9990 chunk 208 optimal weight: 3.9990 chunk 103 optimal weight: 5.9990 chunk 41 optimal weight: 3.9990 chunk 13 optimal weight: 5.9990 overall best weight: 1.6862 ------------------------------------------------------------------------------- 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 D 482 ASN D 691 GLN E 630 ASN ** E 815 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E1351 GLN F 548 HIS F 900 HIS ** 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 = 0.4323 r_free = 0.4323 target = 0.136152 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.110127 restraints weight = 125820.931| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.111480 restraints weight = 95979.318| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.111237 restraints weight = 79636.644| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.112139 restraints weight = 67633.303| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.112257 restraints weight = 54323.208| |-----------------------------------------------------------------------------| r_work (final): 0.3886 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6928 moved from start: 0.6064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 25831 Z= 0.152 Angle : 0.678 11.324 35014 Z= 0.336 Chirality : 0.044 0.213 3948 Planarity : 0.005 0.139 4488 Dihedral : 8.574 98.788 3581 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 10.32 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.66 % Favored : 93.28 % Rotamer: Outliers : 0.14 % Allowed : 3.28 % Favored : 96.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.00 % Cis-general : 0.34 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.18 (0.16), residues: 3109 helix: 0.64 (0.14), residues: 1429 sheet: 0.44 (0.27), residues: 389 loop : -1.11 (0.19), residues: 1291 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.023 0.001 ARG B1365 TYR 0.015 0.002 TYR D 655 PHE 0.035 0.002 PHE C 517 TRP 0.018 0.002 TRP A 505 HIS 0.022 0.001 HIS B1366 Details of bonding type rmsd covalent geometry : bond 0.00339 (25829) covalent geometry : angle 0.67797 (35014) hydrogen bonds : bond 0.03724 ( 1008) hydrogen bonds : angle 4.57209 ( 2883) 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 301 residues out of total 2778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 297 time to evaluate : 0.997 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 616 ASN cc_start: 0.3359 (p0) cc_final: 0.2417 (m-40) REVERT: A 789 MET cc_start: 0.0428 (ttt) cc_final: -0.0468 (ttt) REVERT: A 825 LEU cc_start: 0.6852 (mt) cc_final: 0.5791 (tp) REVERT: A 1379 MET cc_start: -0.4336 (mmt) cc_final: -0.4792 (mmp) REVERT: B 686 MET cc_start: 0.2967 (ppp) cc_final: 0.2400 (ppp) REVERT: B 932 PHE cc_start: 0.7422 (t80) cc_final: 0.6474 (t80) REVERT: B 1366 HIS cc_start: 0.1235 (OUTLIER) cc_final: 0.1023 (m-70) REVERT: C 876 THR cc_start: 0.9106 (m) cc_final: 0.8674 (p) REVERT: C 932 PHE cc_start: 0.6074 (t80) cc_final: 0.5818 (t80) REVERT: C 1379 MET cc_start: 0.7740 (mmt) cc_final: 0.7145 (mmp) REVERT: C 1382 GLU cc_start: 0.7805 (tt0) cc_final: 0.7288 (tt0) REVERT: C 1383 VAL cc_start: 0.8606 (t) cc_final: 0.8068 (t) REVERT: E 626 GLU cc_start: 0.8493 (mm-30) cc_final: 0.7993 (mm-30) REVERT: E 842 CYS cc_start: 0.8002 (t) cc_final: 0.7355 (t) REVERT: E 1379 MET cc_start: 0.8661 (mpp) cc_final: 0.8184 (mpp) REVERT: F 531 ASP cc_start: 0.8426 (t0) cc_final: 0.8008 (p0) REVERT: F 556 LEU cc_start: 0.7914 (pp) cc_final: 0.7465 (tp) REVERT: F 620 LEU cc_start: 0.7216 (tp) cc_final: 0.6985 (mt) REVERT: F 652 ARG cc_start: 0.9160 (tmm160) cc_final: 0.8906 (ttp80) REVERT: F 1346 ASN cc_start: 0.7603 (t0) cc_final: 0.7398 (t0) REVERT: F 1382 GLU cc_start: 0.8608 (tm-30) cc_final: 0.8401 (tp30) outliers start: 4 outliers final: 2 residues processed: 301 average time/residue: 0.1496 time to fit residues: 72.4715 Evaluate side-chains 211 residues out of total 2778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 208 time to evaluate : 1.003 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 47 optimal weight: 4.9990 chunk 28 optimal weight: 2.9990 chunk 250 optimal weight: 5.9990 chunk 186 optimal weight: 0.8980 chunk 294 optimal weight: 0.7980 chunk 306 optimal weight: 3.9990 chunk 199 optimal weight: 0.9990 chunk 225 optimal weight: 0.1980 chunk 154 optimal weight: 5.9990 chunk 239 optimal weight: 5.9990 chunk 59 optimal weight: 2.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- 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** B 883 ASN B1351 GLN B1366 HIS C 575 ASN C 691 GLN C 883 ASN C1361 GLN D 691 GLN E 630 ASN ** E 815 HIS ** 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: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4314 r_free = 0.4314 target = 0.135098 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.107564 restraints weight = 120332.782| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.107253 restraints weight = 93614.262| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.107964 restraints weight = 78698.950| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.108327 restraints weight = 61612.947| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.108364 restraints weight = 61974.706| |-----------------------------------------------------------------------------| r_work (final): 0.3873 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6956 moved from start: 0.6476 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= 0.126 Angle : 0.656 11.409 35014 Z= 0.323 Chirality : 0.043 0.210 3948 Planarity : 0.004 0.065 4488 Dihedral : 8.419 100.147 3581 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 9.96 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.56 % Favored : 93.37 % Rotamer: Outliers : 0.07 % Allowed : 2.23 % Favored : 97.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.00 % Cis-general : 0.34 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.12 (0.16), residues: 3109 helix: 0.68 (0.14), residues: 1435 sheet: 0.49 (0.27), residues: 382 loop : -1.08 (0.19), residues: 1292 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 847 TYR 0.016 0.001 TYR C1364 PHE 0.025 0.001 PHE A1386 TRP 0.018 0.001 TRP F 866 HIS 0.006 0.001 HIS A 900 Details of bonding type rmsd covalent geometry : bond 0.00282 (25829) covalent geometry : angle 0.65649 (35014) hydrogen bonds : bond 0.03484 ( 1008) hydrogen bonds : angle 4.61300 ( 2883) Misc. bond : bond 0.00224 ( 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 288 residues out of total 2778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 286 time to evaluate : 1.050 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: A 616 ASN cc_start: 0.3614 (p0) cc_final: 0.2704 (m-40) REVERT: A 789 MET cc_start: 0.0931 (ttt) cc_final: -0.0986 (ttt) REVERT: A 825 LEU cc_start: 0.6702 (mt) cc_final: 0.5660 (tp) REVERT: A 1379 MET cc_start: -0.4322 (mmt) cc_final: -0.4728 (mmp) REVERT: B 686 MET cc_start: 0.3550 (ppp) cc_final: 0.2915 (ppp) REVERT: C 691 GLN cc_start: 0.7422 (OUTLIER) cc_final: 0.7058 (pp30) REVERT: C 876 THR cc_start: 0.9089 (m) cc_final: 0.8670 (p) REVERT: C 932 PHE cc_start: 0.6147 (t80) cc_final: 0.5867 (t80) REVERT: C 1379 MET cc_start: 0.7952 (mmt) cc_final: 0.7536 (mmm) REVERT: C 1382 GLU cc_start: 0.7815 (tt0) cc_final: 0.7568 (tt0) REVERT: E 626 GLU cc_start: 0.8443 (mm-30) cc_final: 0.8099 (mm-30) REVERT: E 638 ASP cc_start: 0.8791 (m-30) cc_final: 0.8362 (m-30) REVERT: E 842 CYS cc_start: 0.8238 (t) cc_final: 0.7779 (t) REVERT: E 1379 MET cc_start: 0.8690 (mpp) cc_final: 0.8042 (mpp) REVERT: F 531 ASP cc_start: 0.8413 (t0) cc_final: 0.7945 (p0) REVERT: F 556 LEU cc_start: 0.7894 (pp) cc_final: 0.7396 (tp) REVERT: F 620 LEU cc_start: 0.7374 (tp) cc_final: 0.7083 (mt) REVERT: F 652 ARG cc_start: 0.9154 (tmm160) cc_final: 0.8903 (ttp80) REVERT: F 825 LEU cc_start: 0.8405 (tp) cc_final: 0.8090 (tp) REVERT: F 866 TRP cc_start: 0.3591 (t-100) cc_final: 0.2574 (t-100) outliers start: 2 outliers final: 1 residues processed: 288 average time/residue: 0.1716 time to fit residues: 78.9326 Evaluate side-chains 202 residues out of total 2778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 200 time to evaluate : 0.673 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 165 optimal weight: 0.9990 chunk 309 optimal weight: 0.8980 chunk 188 optimal weight: 0.9990 chunk 71 optimal weight: 0.5980 chunk 199 optimal weight: 0.8980 chunk 193 optimal weight: 4.9990 chunk 118 optimal weight: 4.9990 chunk 242 optimal weight: 1.9990 chunk 307 optimal weight: 4.9990 chunk 296 optimal weight: 1.9990 chunk 23 optimal weight: 0.5980 overall best weight: 0.7982 ------------------------------------------------------------------------------- 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 575 ASN ** C 691 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1361 GLN D 482 ASN D 691 GLN D1361 GLN E 630 ASN ** E 815 HIS ** 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: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4307 r_free = 0.4307 target = 0.135189 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.107697 restraints weight = 119781.350| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.106966 restraints weight = 108976.988| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.107294 restraints weight = 90203.240| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.107317 restraints weight = 81745.589| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.107471 restraints weight = 72678.273| |-----------------------------------------------------------------------------| r_work (final): 0.3848 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6973 moved from start: 0.6738 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= 0.117 Angle : 0.645 10.385 35014 Z= 0.315 Chirality : 0.043 0.234 3948 Planarity : 0.004 0.070 4488 Dihedral : 8.231 99.493 3581 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 9.39 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.69 % Favored : 93.25 % Rotamer: Outliers : 0.04 % Allowed : 1.73 % Favored : 98.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.00 % Cis-general : 0.34 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.07 (0.16), residues: 3109 helix: 0.73 (0.14), residues: 1449 sheet: 0.59 (0.27), residues: 365 loop : -1.09 (0.19), residues: 1295 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG E 592 TYR 0.018 0.001 TYR E 823 PHE 0.030 0.001 PHE C 517 TRP 0.024 0.001 TRP A 615 HIS 0.004 0.001 HIS A 900 Details of bonding type rmsd covalent geometry : bond 0.00259 (25829) covalent geometry : angle 0.64504 (35014) hydrogen bonds : bond 0.03269 ( 1008) hydrogen bonds : angle 4.45110 ( 2883) Misc. bond : bond 0.00234 ( 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 281 residues out of total 2778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 280 time to evaluate : 1.041 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 825 LEU cc_start: 0.6714 (mt) cc_final: 0.5665 (tp) REVERT: A 1379 MET cc_start: -0.4382 (mmt) cc_final: -0.4763 (mmp) REVERT: B 495 MET cc_start: 0.7112 (tmm) cc_final: 0.6804 (tmm) REVERT: B 581 ASP cc_start: 0.7671 (t70) cc_final: 0.7349 (t70) REVERT: B 686 MET cc_start: 0.3702 (ppp) cc_final: 0.2960 (ppp) REVERT: B 842 CYS cc_start: 0.8895 (t) cc_final: 0.8624 (t) REVERT: B 932 PHE cc_start: 0.7142 (t80) cc_final: 0.6765 (t80) REVERT: C 876 THR cc_start: 0.9105 (m) cc_final: 0.8623 (p) REVERT: C 932 PHE cc_start: 0.6316 (t80) cc_final: 0.6081 (t80) REVERT: C 1379 MET cc_start: 0.8174 (mmt) cc_final: 0.7745 (mmm) REVERT: C 1382 GLU cc_start: 0.7874 (tt0) cc_final: 0.7567 (tt0) REVERT: D 523 MET cc_start: 0.5837 (tpt) cc_final: 0.5531 (ptp) REVERT: E 592 ARG cc_start: 0.6321 (mmm160) cc_final: 0.5879 (mmm160) REVERT: E 626 GLU cc_start: 0.8593 (mm-30) cc_final: 0.8182 (mm-30) REVERT: E 638 ASP cc_start: 0.8992 (m-30) cc_final: 0.8506 (m-30) REVERT: E 842 CYS cc_start: 0.8057 (t) cc_final: 0.7429 (t) REVERT: E 1379 MET cc_start: 0.8698 (mpp) cc_final: 0.8175 (mpp) REVERT: F 531 ASP cc_start: 0.8347 (t0) cc_final: 0.7868 (p0) REVERT: F 556 LEU cc_start: 0.7972 (pp) cc_final: 0.7477 (tp) REVERT: F 652 ARG cc_start: 0.9158 (tmm160) cc_final: 0.8873 (ttp80) REVERT: F 825 LEU cc_start: 0.8341 (tp) cc_final: 0.7892 (tp) REVERT: F 866 TRP cc_start: 0.3422 (t-100) cc_final: 0.2271 (t-100) outliers start: 1 outliers final: 1 residues processed: 281 average time/residue: 0.1663 time to fit residues: 74.7573 Evaluate side-chains 201 residues out of total 2778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 200 time to evaluate : 0.950 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 221 optimal weight: 6.9990 chunk 281 optimal weight: 0.9980 chunk 191 optimal weight: 0.0570 chunk 277 optimal weight: 4.9990 chunk 138 optimal weight: 4.9990 chunk 293 optimal weight: 0.6980 chunk 179 optimal weight: 0.9990 chunk 109 optimal weight: 5.9990 chunk 285 optimal weight: 7.9990 chunk 250 optimal weight: 3.9990 chunk 4 optimal weight: 7.9990 overall best weight: 1.3502 ------------------------------------------------------------------------------- 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** ** C1366 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 691 GLN E 630 ASN E 726 HIS ** E 815 HIS ** 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4280 r_free = 0.4280 target = 0.133316 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.106684 restraints weight = 125990.169| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.107478 restraints weight = 95610.991| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.107614 restraints weight = 81428.815| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.108587 restraints weight = 66356.665| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.108774 restraints weight = 55085.284| |-----------------------------------------------------------------------------| r_work (final): 0.3839 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7023 moved from start: 0.7097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 25831 Z= 0.131 Angle : 0.661 10.318 35014 Z= 0.325 Chirality : 0.044 0.283 3948 Planarity : 0.004 0.071 4488 Dihedral : 8.178 99.934 3581 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 10.08 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.34 % Favored : 93.60 % Rotamer: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.00 % Cis-general : 0.34 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.09 (0.16), residues: 3109 helix: 0.71 (0.14), residues: 1447 sheet: 0.54 (0.27), residues: 366 loop : -1.08 (0.19), residues: 1296 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 592 TYR 0.012 0.001 TYR C 634 PHE 0.037 0.001 PHE C 425 TRP 0.022 0.001 TRP A 615 HIS 0.006 0.001 HIS A1366 Details of bonding type rmsd covalent geometry : bond 0.00295 (25829) covalent geometry : angle 0.66127 (35014) hydrogen bonds : bond 0.03496 ( 1008) hydrogen bonds : angle 4.57697 ( 2883) Misc. bond : bond 0.00216 ( 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 260 residues out of total 2778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 260 time to evaluate : 1.007 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 639 ILE cc_start: 0.6463 (mm) cc_final: 0.6261 (mm) REVERT: A 825 LEU cc_start: 0.6624 (mt) cc_final: 0.5488 (tp) REVERT: A 1379 MET cc_start: -0.4235 (mmt) cc_final: -0.4618 (mmp) REVERT: B 495 MET cc_start: 0.7178 (tmm) cc_final: 0.6916 (tmm) REVERT: B 686 MET cc_start: 0.3490 (ppp) cc_final: 0.2825 (ppp) REVERT: B 932 PHE cc_start: 0.7257 (t80) cc_final: 0.6858 (t80) REVERT: C 876 THR cc_start: 0.9135 (m) cc_final: 0.8719 (p) REVERT: C 1382 GLU cc_start: 0.8015 (tt0) cc_final: 0.7378 (tt0) REVERT: D 580 ILE cc_start: 0.8281 (mm) cc_final: 0.8011 (mm) REVERT: E 592 ARG cc_start: 0.6315 (mmm160) cc_final: 0.5868 (mmm160) REVERT: E 626 GLU cc_start: 0.8664 (mm-30) cc_final: 0.8203 (mm-30) REVERT: E 638 ASP cc_start: 0.9006 (m-30) cc_final: 0.8527 (m-30) REVERT: E 842 CYS cc_start: 0.8338 (t) cc_final: 0.7793 (t) REVERT: F 531 ASP cc_start: 0.8415 (t0) cc_final: 0.7930 (p0) REVERT: F 556 LEU cc_start: 0.8061 (pp) cc_final: 0.7625 (tp) REVERT: F 626 GLU cc_start: 0.7824 (tm-30) cc_final: 0.7335 (tm-30) REVERT: F 652 ARG cc_start: 0.9272 (tmm160) cc_final: 0.8963 (ttp80) REVERT: F 825 LEU cc_start: 0.8296 (tp) cc_final: 0.7953 (tp) REVERT: F 866 TRP cc_start: 0.3579 (t-100) cc_final: 0.2467 (t-100) outliers start: 0 outliers final: 0 residues processed: 260 average time/residue: 0.1685 time to fit residues: 70.7148 Evaluate side-chains 198 residues out of total 2778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 198 time to evaluate : 1.007 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 121 optimal weight: 7.9990 chunk 139 optimal weight: 3.9990 chunk 48 optimal weight: 8.9990 chunk 27 optimal weight: 0.0050 chunk 41 optimal weight: 8.9990 chunk 192 optimal weight: 0.9980 chunk 205 optimal weight: 0.7980 chunk 161 optimal weight: 2.9990 chunk 308 optimal weight: 4.9990 chunk 200 optimal weight: 0.9990 chunk 269 optimal weight: 2.9990 overall best weight: 1.1598 ------------------------------------------------------------------------------- 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** ** C1366 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 532 GLN D 691 GLN ** E 815 HIS ** 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4271 r_free = 0.4271 target = 0.132385 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.106225 restraints weight = 125479.864| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.107069 restraints weight = 93363.845| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.107068 restraints weight = 77452.302| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.107520 restraints weight = 70179.721| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.107563 restraints weight = 60889.158| |-----------------------------------------------------------------------------| r_work (final): 0.3817 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7071 moved from start: 0.7455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 25831 Z= 0.127 Angle : 0.665 10.270 35014 Z= 0.327 Chirality : 0.044 0.209 3948 Planarity : 0.004 0.076 4488 Dihedral : 8.054 100.477 3581 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 9.83 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.56 % Favored : 93.41 % Rotamer: Outliers : 0.00 % Allowed : 0.68 % Favored : 99.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.00 % Cis-general : 0.34 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.03 (0.16), residues: 3109 helix: 0.78 (0.14), residues: 1437 sheet: 0.57 (0.27), residues: 366 loop : -1.07 (0.19), residues: 1306 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 478 TYR 0.011 0.001 TYR C1364 PHE 0.027 0.001 PHE F 877 TRP 0.023 0.001 TRP A 615 HIS 0.004 0.001 HIS A 900 Details of bonding type rmsd covalent geometry : bond 0.00282 (25829) covalent geometry : angle 0.66489 (35014) hydrogen bonds : bond 0.03439 ( 1008) hydrogen bonds : angle 4.67038 ( 2883) Misc. bond : bond 0.00227 ( 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 270 residues out of total 2778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 270 time to evaluate : 0.862 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 639 ILE cc_start: 0.6382 (mm) cc_final: 0.6161 (mm) REVERT: A 683 MET cc_start: -0.3548 (mmp) cc_final: -0.4291 (mtm) REVERT: A 825 LEU cc_start: 0.6722 (mt) cc_final: 0.5542 (tp) REVERT: A 1379 MET cc_start: -0.4293 (mmt) cc_final: -0.4618 (mmp) REVERT: B 495 MET cc_start: 0.7046 (tmm) cc_final: 0.6836 (tmm) REVERT: B 591 ASP cc_start: 0.7491 (m-30) cc_final: 0.7206 (m-30) REVERT: B 686 MET cc_start: 0.3438 (ppp) cc_final: 0.2827 (ppp) REVERT: B 932 PHE cc_start: 0.7327 (t80) cc_final: 0.6914 (t80) REVERT: C 631 CYS cc_start: 0.6525 (p) cc_final: 0.6155 (p) REVERT: C 876 THR cc_start: 0.8979 (m) cc_final: 0.8550 (p) REVERT: D 631 CYS cc_start: 0.7038 (p) cc_final: 0.6818 (p) REVERT: E 435 ILE cc_start: 0.8495 (mt) cc_final: 0.8225 (tt) REVERT: E 592 ARG cc_start: 0.6460 (mmm160) cc_final: 0.6087 (mmm160) REVERT: E 626 GLU cc_start: 0.8588 (mm-30) cc_final: 0.8132 (mm-30) REVERT: E 638 ASP cc_start: 0.9035 (m-30) cc_final: 0.8544 (m-30) REVERT: E 842 CYS cc_start: 0.8379 (t) cc_final: 0.7895 (t) REVERT: F 531 ASP cc_start: 0.8445 (t0) cc_final: 0.7956 (p0) REVERT: F 556 LEU cc_start: 0.8161 (pp) cc_final: 0.7785 (tp) REVERT: F 620 LEU cc_start: 0.6799 (mt) cc_final: 0.6470 (mt) REVERT: F 626 GLU cc_start: 0.7928 (tm-30) cc_final: 0.7512 (tm-30) REVERT: F 825 LEU cc_start: 0.8421 (tp) cc_final: 0.7879 (tp) outliers start: 0 outliers final: 0 residues processed: 270 average time/residue: 0.1456 time to fit residues: 63.1718 Evaluate side-chains 191 residues out of total 2778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 191 time to evaluate : 0.586 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 176 optimal weight: 0.2980 chunk 265 optimal weight: 10.0000 chunk 153 optimal weight: 0.8980 chunk 268 optimal weight: 3.9990 chunk 138 optimal weight: 4.9990 chunk 208 optimal weight: 5.9990 chunk 123 optimal weight: 5.9990 chunk 285 optimal weight: 0.9990 chunk 83 optimal weight: 6.9990 chunk 41 optimal weight: 1.9990 chunk 219 optimal weight: 7.9990 overall best weight: 1.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 699 GLN B 861 HIS C 611 HIS C 922 GLN C1361 GLN ** C1366 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 691 GLN ** E 815 HIS ** 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: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4216 r_free = 0.4216 target = 0.128620 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.102874 restraints weight = 125641.691| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.103427 restraints weight = 100462.910| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.103123 restraints weight = 79154.351| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.103272 restraints weight = 78606.683| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.103370 restraints weight = 69792.913| |-----------------------------------------------------------------------------| r_work (final): 0.3727 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7194 moved from start: 0.8243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 25831 Z= 0.151 Angle : 0.711 10.710 35014 Z= 0.352 Chirality : 0.045 0.243 3948 Planarity : 0.005 0.073 4488 Dihedral : 8.033 102.130 3581 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 10.81 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.01 % Favored : 92.96 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.09 (0.16), residues: 3109 helix: 0.71 (0.14), residues: 1438 sheet: 0.47 (0.27), residues: 377 loop : -1.07 (0.19), residues: 1294 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B1365 TYR 0.022 0.001 TYR F 448 PHE 0.019 0.002 PHE C 517 TRP 0.033 0.002 TRP A 615 HIS 0.005 0.001 HIS C 863 Details of bonding type rmsd covalent geometry : bond 0.00339 (25829) covalent geometry : angle 0.71145 (35014) hydrogen bonds : bond 0.03792 ( 1008) hydrogen bonds : angle 4.76633 ( 2883) Misc. bond : bond 0.00161 ( 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 268 residues out of total 2778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 266 time to evaluate : 0.987 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 789 MET cc_start: -0.0110 (ppp) cc_final: -0.0718 (mmm) REVERT: A 1379 MET cc_start: -0.4354 (mmt) cc_final: -0.4686 (mmp) REVERT: B 545 ASP cc_start: 0.8211 (m-30) cc_final: 0.7899 (m-30) REVERT: B 556 LEU cc_start: 0.7959 (mm) cc_final: 0.7346 (mm) REVERT: B 842 CYS cc_start: 0.8988 (t) cc_final: 0.8723 (t) REVERT: B 932 PHE cc_start: 0.7520 (t80) cc_final: 0.7067 (t80) REVERT: C 441 MET cc_start: 0.8214 (mmm) cc_final: 0.7931 (tpt) REVERT: C 631 CYS cc_start: 0.6730 (p) cc_final: 0.6413 (p) REVERT: E 435 ILE cc_start: 0.8591 (mt) cc_final: 0.8262 (tt) REVERT: E 592 ARG cc_start: 0.6749 (mmm160) cc_final: 0.6433 (mmm160) REVERT: E 638 ASP cc_start: 0.9061 (m-30) cc_final: 0.8679 (m-30) REVERT: F 531 ASP cc_start: 0.8406 (t0) cc_final: 0.7943 (p0) REVERT: F 556 LEU cc_start: 0.8223 (pp) cc_final: 0.7821 (tp) REVERT: F 825 LEU cc_start: 0.8503 (tp) cc_final: 0.8060 (tp) REVERT: F 866 TRP cc_start: 0.4707 (t-100) cc_final: 0.3040 (t-100) REVERT: F 1379 MET cc_start: 0.8882 (mpp) cc_final: 0.8584 (mmt) outliers start: 2 outliers final: 0 residues processed: 268 average time/residue: 0.1582 time to fit residues: 68.0049 Evaluate side-chains 182 residues out of total 2778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 182 time to evaluate : 1.030 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 238 optimal weight: 2.9990 chunk 177 optimal weight: 0.9990 chunk 232 optimal weight: 0.8980 chunk 138 optimal weight: 4.9990 chunk 68 optimal weight: 0.9990 chunk 237 optimal weight: 5.9990 chunk 98 optimal weight: 7.9990 chunk 141 optimal weight: 0.6980 chunk 271 optimal weight: 0.6980 chunk 2 optimal weight: 10.0000 chunk 84 optimal weight: 4.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 900 HIS C1361 GLN ** C1366 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 691 GLN ** E 815 HIS ** 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4231 r_free = 0.4231 target = 0.129277 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.103940 restraints weight = 124387.487| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.103588 restraints weight = 100104.191| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.104315 restraints weight = 83811.285| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.104393 restraints weight = 67907.199| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.104500 restraints weight = 64742.949| |-----------------------------------------------------------------------------| r_work (final): 0.3760 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7114 moved from start: 0.8390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 25831 Z= 0.121 Angle : 0.676 10.243 35014 Z= 0.331 Chirality : 0.044 0.200 3948 Planarity : 0.004 0.073 4488 Dihedral : 7.837 101.518 3581 Min Nonbonded Distance : 2.312 Molprobity Statistics. All-atom Clashscore : 9.65 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.30 % Favored : 93.66 % Rotamer: Outliers : 0.04 % Allowed : 0.32 % Favored : 99.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.00 % Cis-general : 0.34 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.01 (0.16), residues: 3109 helix: 0.85 (0.14), residues: 1426 sheet: 0.53 (0.27), residues: 371 loop : -1.06 (0.19), residues: 1312 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B1365 TYR 0.014 0.001 TYR E 634 PHE 0.024 0.001 PHE C 517 TRP 0.012 0.001 TRP E 865 HIS 0.003 0.001 HIS C 611 Details of bonding type rmsd covalent geometry : bond 0.00269 (25829) covalent geometry : angle 0.67583 (35014) hydrogen bonds : bond 0.03396 ( 1008) hydrogen bonds : angle 4.69800 ( 2883) Misc. bond : bond 0.00225 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4244.74 seconds wall clock time: 74 minutes 12.59 seconds (4452.59 seconds total)