Starting phenix.real_space_refine on Mon Sep 30 13:40:03 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8juz_36667/09_2024/8juz_36667_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8juz_36667/09_2024/8juz_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8juz_36667/09_2024/8juz_36667.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8juz_36667/09_2024/8juz_36667.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8juz_36667/09_2024/8juz_36667_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8juz_36667/09_2024/8juz_36667_neut.cif" } resolution = 4.29 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 17 5.49 5 S 110 5.16 5 C 16130 2.51 5 N 4361 2.21 5 O 4656 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 48 residue(s): 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 25274 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 4149 Number of conformers: 1 Conformer: "" Number of residues, atoms: 522, 4149 Classifications: {'peptide': 522} Link IDs: {'CIS': 3, 'PCIS': 2, 'PTRANS': 30, 'TRANS': 486} Chain breaks: 5 Chain: "B" Number of atoms: 4210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 529, 4210 Classifications: {'peptide': 529} Link IDs: {'CIS': 3, 'PCIS': 2, 'PTRANS': 32, 'TRANS': 491} Chain breaks: 2 Chain: "C" Number of atoms: 4199 Number of conformers: 1 Conformer: "" Number of residues, atoms: 528, 4199 Classifications: {'peptide': 528} Link IDs: {'PCIS': 2, 'PTRANS': 32, 'TRANS': 493} Chain breaks: 2 Chain: "D" Number of atoms: 4213 Number of conformers: 1 Conformer: "" Number of residues, atoms: 530, 4213 Classifications: {'peptide': 530} Link IDs: {'PCIS': 2, 'PTRANS': 32, 'TRANS': 495} Chain breaks: 2 Chain: "E" Number of atoms: 4202 Number of conformers: 1 Conformer: "" Number of residues, atoms: 528, 4202 Classifications: {'peptide': 528} Link IDs: {'CIS': 2, 'PCIS': 2, 'PTRANS': 32, 'TRANS': 491} Chain breaks: 2 Chain: "F" Number of atoms: 4119 Number of conformers: 1 Conformer: "" Number of residues, atoms: 518, 4119 Classifications: {'peptide': 518} Link IDs: {'CIS': 2, 'PCIS': 2, 'PTRANS': 30, 'TRANS': 483} Chain breaks: 4 Chain: "A" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 15.69, per 1000 atoms: 0.62 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: 7.42 Conformation dependent library (CDL) restraints added in 3.4 seconds 6218 Ramachandran restraints generated. 3109 Oldfield, 0 Emsley, 3109 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6022 Finding SS restraints... Secondary structure from input PDB file: 159 helices and 13 sheets defined 53.5% alpha, 7.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.74 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: 9.17 Time building geometry restraints manager: 7.67 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 7388 1.33 - 1.45: 3717 1.45 - 1.57: 14537 1.57 - 1.69: 28 1.69 - 1.81: 159 Bond restraints: 25829 Sorted by residual: bond pdb=" C4 ATP C1401 " pdb=" C5 ATP C1401 " ideal model delta sigma weight residual 1.388 1.472 -0.084 1.00e-02 1.00e+04 7.01e+01 bond pdb=" C4 ATP B1401 " pdb=" C5 ATP B1401 " ideal model delta sigma weight residual 1.388 1.471 -0.083 1.00e-02 1.00e+04 6.96e+01 bond pdb=" C4 ATP D1401 " pdb=" C5 ATP D1401 " ideal model delta sigma weight residual 1.388 1.470 -0.082 1.00e-02 1.00e+04 6.78e+01 bond pdb=" C5 ATP C1401 " pdb=" C6 ATP C1401 " ideal model delta sigma weight residual 1.409 1.482 -0.073 1.00e-02 1.00e+04 5.39e+01 bond pdb=" C5 ATP D1401 " pdb=" C6 ATP D1401 " ideal model delta sigma weight residual 1.409 1.482 -0.073 1.00e-02 1.00e+04 5.29e+01 ... (remaining 25824 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.90: 34847 3.90 - 7.81: 147 7.81 - 11.71: 14 11.71 - 15.62: 0 15.62 - 19.52: 6 Bond angle restraints: 35014 Sorted by residual: angle pdb=" PB ATP D1401 " pdb=" O3B ATP D1401 " pdb=" PG ATP D1401 " ideal model delta sigma weight residual 139.87 120.35 19.52 1.00e+00 1.00e+00 3.81e+02 angle pdb=" PB ATP C1401 " pdb=" O3B ATP C1401 " pdb=" PG ATP C1401 " ideal model delta sigma weight residual 139.87 120.53 19.34 1.00e+00 1.00e+00 3.74e+02 angle pdb=" PB ATP B1401 " pdb=" O3B ATP B1401 " pdb=" PG ATP B1401 " ideal model delta sigma weight residual 139.87 120.81 19.06 1.00e+00 1.00e+00 3.63e+02 angle pdb=" PA ATP C1401 " pdb=" O3A ATP C1401 " pdb=" PB ATP C1401 " ideal model delta sigma weight residual 136.83 120.42 16.41 1.00e+00 1.00e+00 2.69e+02 angle pdb=" PA ATP B1401 " pdb=" O3A ATP B1401 " pdb=" PB ATP B1401 " ideal model delta sigma weight residual 136.83 120.51 16.32 1.00e+00 1.00e+00 2.66e+02 ... (remaining 35009 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.53: 14599 21.53 - 43.07: 1119 43.07 - 64.60: 116 64.60 - 86.13: 63 86.13 - 107.66: 9 Dihedral angle restraints: 15906 sinusoidal: 6675 harmonic: 9231 Sorted by residual: dihedral pdb=" C5' ADP A1401 " pdb=" O5' ADP A1401 " pdb=" PA ADP A1401 " pdb=" O2A ADP A1401 " ideal model delta sinusoidal sigma weight residual -60.00 47.67 -107.66 1 2.00e+01 2.50e-03 3.13e+01 dihedral pdb=" O1B ADP A1401 " pdb=" O3A ADP A1401 " pdb=" PB ADP A1401 " pdb=" PA ADP A1401 " ideal model delta sinusoidal sigma weight residual -60.00 -149.55 89.55 1 2.00e+01 2.50e-03 2.38e+01 dihedral pdb=" CA PHE B 911 " pdb=" C PHE B 911 " pdb=" N ILE B 912 " pdb=" CA ILE B 912 " ideal model delta harmonic sigma weight residual -180.00 -158.07 -21.93 0 5.00e+00 4.00e-02 1.92e+01 ... (remaining 15903 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 2800 0.041 - 0.081: 862 0.081 - 0.122: 258 0.122 - 0.163: 24 0.163 - 0.204: 4 Chirality restraints: 3948 Sorted by residual: chirality pdb=" CA GLU E1382 " pdb=" N GLU E1382 " pdb=" C GLU E1382 " pdb=" CB GLU E1382 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 1.04e+00 chirality pdb=" CA ASN A 616 " pdb=" N ASN A 616 " pdb=" C ASN A 616 " pdb=" CB ASN A 616 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 9.36e-01 chirality pdb=" CB ILE B 672 " pdb=" CA ILE B 672 " pdb=" CG1 ILE B 672 " pdb=" CG2 ILE B 672 " both_signs ideal model delta sigma weight residual False 2.64 2.84 -0.19 2.00e-01 2.50e+01 9.26e-01 ... (remaining 3945 not shown) Planarity restraints: 4488 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG D 586 " -0.032 5.00e-02 4.00e+02 4.80e-02 3.69e+00 pdb=" N PRO D 587 " 0.083 5.00e-02 4.00e+02 pdb=" CA PRO D 587 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO D 587 " -0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG F 586 " -0.030 5.00e-02 4.00e+02 4.52e-02 3.27e+00 pdb=" N PRO F 587 " 0.078 5.00e-02 4.00e+02 pdb=" CA PRO F 587 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO F 587 " -0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP E 865 " -0.010 2.00e-02 2.50e+03 1.11e-02 3.09e+00 pdb=" CG TRP E 865 " 0.030 2.00e-02 2.50e+03 pdb=" CD1 TRP E 865 " -0.014 2.00e-02 2.50e+03 pdb=" CD2 TRP E 865 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP E 865 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP E 865 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP E 865 " -0.004 2.00e-02 2.50e+03 pdb=" CZ2 TRP E 865 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP E 865 " -0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP E 865 " -0.000 2.00e-02 2.50e+03 ... (remaining 4485 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.68: 458 2.68 - 3.24: 25087 3.24 - 3.79: 37111 3.79 - 4.35: 46992 4.35 - 4.90: 76572 Nonbonded interactions: 186220 Sorted by model distance: nonbonded pdb=" OE1 GLU D 440 " pdb=" OH TYR E 659 " model vdw 2.131 3.040 nonbonded pdb=" O GLN F 657 " pdb=" OG1 THR F 661 " model vdw 2.178 3.040 nonbonded pdb=" O ARG F 576 " pdb=" OG SER F 579 " model vdw 2.220 3.040 nonbonded pdb=" OD2 ASP C 668 " pdb=" OG SER C 670 " model vdw 2.221 3.040 nonbonded pdb=" O LYS C 706 " pdb=" NE2 GLN C 710 " model vdw 2.232 3.120 ... (remaining 186215 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 422 through 598 or resid 601 through 688 or resid 696 thro \ ugh 727 or resid 787 through 943 or resid 1331 through 1388)) selection = (chain 'B' and (resid 422 through 539 or resid 546 through 598 or resid 601 thro \ ugh 659 or resid 666 through 688 or resid 696 through 727 or resid 787 through 9 \ 23 or resid 925 through 943 or resid 1331 through 1388)) selection = (chain 'C' and (resid 422 through 539 or resid 546 through 598 or resid 601 thro \ ugh 659 or resid 666 through 688 or resid 696 through 727 or resid 787 through 9 \ 23 or resid 925 through 943 or resid 1331 through 1388)) selection = (chain 'D' and (resid 422 through 539 or resid 546 through 598 or resid 601 thro \ ugh 659 or resid 666 through 688 or resid 696 through 727 or resid 787 through 9 \ 23 or resid 925 through 943 or resid 1331 through 1388)) selection = (chain 'E' and (resid 422 through 539 or resid 546 through 598 or resid 601 thro \ ugh 659 or resid 666 through 688 or resid 696 through 727 or resid 787 through 9 \ 23 or resid 925 through 943 or resid 1331 through 1388)) selection = (chain 'F' and (resid 422 through 539 or resid 546 through 659 or resid 666 thro \ ugh 727 or resid 787 through 923 or resid 925 through 943 or resid 1331 through \ 1388)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.020 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.940 Check model and map are aligned: 0.200 Set scattering table: 0.250 Process input model: 56.380 Find NCS groups from input model: 1.960 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 64.750 ------------------------------------------------------------------------------- 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 : 0.003 0.084 25829 Z= 0.218 Angle : 0.723 19.522 35014 Z= 0.456 Chirality : 0.042 0.204 3948 Planarity : 0.004 0.052 4488 Dihedral : 15.177 107.663 9884 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 9.33 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.56 % Favored : 93.34 % Rotamer: Outliers : 0.07 % Allowed : 0.32 % Favored : 99.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.00 % Cis-general : 0.34 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.25 (0.16), residues: 3109 helix: 0.67 (0.15), residues: 1391 sheet: 0.46 (0.28), residues: 377 loop : -1.22 (0.18), residues: 1341 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP E 865 HIS 0.003 0.001 HIS C1366 PHE 0.010 0.001 PHE D 724 TYR 0.017 0.001 TYR C1364 ARG 0.006 0.000 ARG F 576 *********************** 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 fitting. rotamer outliers: 2 poor density : 633 time to evaluate : 2.799 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: 0.5626 (mm) REVERT: A 686 MET cc_start: 0.0558 (pmm) cc_final: 0.0348 (mtt) REVERT: A 1379 MET cc_start: -0.5244 (mmt) cc_final: -0.5847 (mmp) REVERT: B 686 MET cc_start: 0.3895 (ppp) cc_final: 0.3088 (ppp) REVERT: C 441 MET cc_start: 0.5248 (ttm) cc_final: 0.4284 (ttt) REVERT: C 642 ILE cc_start: 0.8023 (mm) cc_final: 0.7228 (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: 0.6992 (m-40) REVERT: D 789 MET cc_start: 0.6822 (ttp) cc_final: 0.6150 (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: 0.1248 (m-30) REVERT: E 789 MET cc_start: 0.7885 (tpt) cc_final: 0.7614 (tpt) REVERT: E 827 ILE cc_start: 0.7117 (mm) cc_final: 0.6866 (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: -0.1826 (ttt) REVERT: F 1355 LEU cc_start: 0.8742 (tp) cc_final: 0.8539 (tt) outliers start: 2 outliers final: 1 residues processed: 634 average time/residue: 0.4278 time to fit residues: 402.2720 Evaluate side-chains 294 residues out of total 2778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 293 time to evaluate : 3.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 263 optimal weight: 0.6980 chunk 236 optimal weight: 0.2980 chunk 131 optimal weight: 10.0000 chunk 80 optimal weight: 1.9990 chunk 159 optimal weight: 4.9990 chunk 126 optimal weight: 0.8980 chunk 244 optimal weight: 0.9990 chunk 94 optimal weight: 3.9990 chunk 148 optimal weight: 4.9990 chunk 182 optimal weight: 2.9990 chunk 283 optimal weight: 0.8980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 546 GLN ** A 861 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 512 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 548 HIS B 611 HIS B 882 GLN ** C 691 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 710 GLN C 882 GLN C1361 GLN D 532 GLN D 691 GLN D1361 GLN E 815 HIS E1330 HIS E1351 GLN ** F 544 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 611 HIS ** F 940 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5280 moved from start: 0.2813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 25829 Z= 0.198 Angle : 0.668 10.625 35014 Z= 0.333 Chirality : 0.044 0.191 3948 Planarity : 0.005 0.051 4488 Dihedral : 8.938 105.531 3581 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.69 % Favored : 93.21 % Rotamer: Outliers : 0.14 % Allowed : 4.82 % Favored : 95.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.00 % Cis-general : 0.34 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.17 (0.16), residues: 3109 helix: 0.64 (0.14), residues: 1422 sheet: 0.73 (0.28), residues: 375 loop : -1.17 (0.18), residues: 1312 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 505 HIS 0.016 0.001 HIS A 861 PHE 0.031 0.001 PHE C 517 TYR 0.024 0.002 TYR C 823 ARG 0.010 0.001 ARG A 589 *********************** 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 398 residues out of total 2778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 394 time to evaluate : 3.281 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: A 523 MET cc_start: 0.3444 (mmp) cc_final: 0.2521 (tpt) REVERT: A 686 MET cc_start: 0.0354 (pmm) cc_final: -0.0066 (mtt) REVERT: B 495 MET cc_start: 0.6419 (tpt) cc_final: 0.5864 (tmm) REVERT: B 1353 GLU cc_start: 0.4385 (OUTLIER) cc_final: 0.3586 (pt0) REVERT: C 876 THR cc_start: 0.8271 (m) cc_final: 0.7779 (p) REVERT: C 1382 GLU cc_start: 0.7161 (tt0) cc_final: 0.6910 (tt0) REVERT: C 1384 GLU cc_start: 0.6775 (OUTLIER) cc_final: 0.6428 (mp0) REVERT: D 424 ARG cc_start: 0.5231 (mmt180) cc_final: 0.4842 (tpp80) REVERT: D 857 VAL cc_start: 0.9197 (t) cc_final: 0.8899 (m) REVERT: E 620 LEU cc_start: 0.6997 (pt) cc_final: 0.6775 (mt) REVERT: F 559 MET cc_start: 0.4434 (tmm) cc_final: 0.3786 (tmm) REVERT: F 652 ARG cc_start: 0.8873 (tmm160) cc_final: 0.8220 (ttm-80) REVERT: F 789 MET cc_start: -0.1754 (ppp) cc_final: -0.2190 (ttt) outliers start: 4 outliers final: 1 residues processed: 398 average time/residue: 0.3867 time to fit residues: 240.2156 Evaluate side-chains 248 residues out of total 2778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 245 time to evaluate : 2.957 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 157 optimal weight: 6.9990 chunk 87 optimal weight: 6.9990 chunk 235 optimal weight: 2.9990 chunk 192 optimal weight: 0.5980 chunk 78 optimal weight: 0.9990 chunk 283 optimal weight: 0.9990 chunk 306 optimal weight: 7.9990 chunk 252 optimal weight: 2.9990 chunk 281 optimal weight: 2.9990 chunk 96 optimal weight: 3.9990 chunk 227 optimal weight: 0.5980 overall best weight: 1.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1351 GLN ** C 691 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 883 ASN C1361 GLN D 434 HIS ** D 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 611 HIS D 691 GLN D1361 GLN E 630 ASN E 726 HIS ** E 815 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 940 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5473 moved from start: 0.3818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 25829 Z= 0.205 Angle : 0.660 11.202 35014 Z= 0.328 Chirality : 0.044 0.215 3948 Planarity : 0.005 0.104 4488 Dihedral : 8.707 100.995 3581 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.18 % Favored : 93.76 % Rotamer: Outliers : 0.11 % Allowed : 4.86 % Favored : 95.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.00 % Cis-general : 0.34 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.13 (0.16), residues: 3109 helix: 0.65 (0.14), residues: 1428 sheet: 0.83 (0.28), residues: 378 loop : -1.17 (0.18), residues: 1303 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP E 865 HIS 0.008 0.001 HIS C 863 PHE 0.036 0.001 PHE E 529 TYR 0.016 0.001 TYR B 466 ARG 0.022 0.001 ARG E 847 *********************** 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 fitting. rotamer outliers: 3 poor density : 335 time to evaluate : 3.167 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: A 616 ASN cc_start: 0.2702 (p0) cc_final: 0.1767 (m-40) REVERT: A 639 ILE cc_start: 0.6130 (mm) cc_final: 0.5881 (mm) REVERT: A 789 MET cc_start: -0.0290 (ttt) cc_final: -0.1002 (ttt) REVERT: B 495 MET cc_start: 0.6479 (tpt) cc_final: 0.5932 (tmm) REVERT: B 686 MET cc_start: 0.4641 (ppp) cc_final: 0.3507 (ppp) REVERT: B 1353 GLU cc_start: 0.4663 (OUTLIER) cc_final: 0.2703 (pt0) REVERT: C 1379 MET cc_start: 0.7187 (mmm) cc_final: 0.6860 (mmp) REVERT: C 1382 GLU cc_start: 0.7243 (tt0) cc_final: 0.6826 (tt0) REVERT: D 789 MET cc_start: 0.7801 (ppp) cc_final: 0.7417 (ppp) REVERT: E 626 GLU cc_start: 0.8541 (mm-30) cc_final: 0.8260 (tt0) REVERT: E 1379 MET cc_start: 0.8737 (mpp) cc_final: 0.8213 (mpp) REVERT: F 626 GLU cc_start: 0.7344 (tm-30) cc_final: 0.6820 (tm-30) REVERT: F 652 ARG cc_start: 0.8976 (tmm160) cc_final: 0.8150 (ttm-80) REVERT: F 789 MET cc_start: -0.1178 (ppp) cc_final: -0.1683 (ttp) outliers start: 3 outliers final: 1 residues processed: 338 average time/residue: 0.4090 time to fit residues: 215.4542 Evaluate side-chains 224 residues out of total 2778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 222 time to evaluate : 3.004 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 280 optimal weight: 0.5980 chunk 213 optimal weight: 5.9990 chunk 147 optimal weight: 7.9990 chunk 31 optimal weight: 9.9990 chunk 135 optimal weight: 5.9990 chunk 190 optimal weight: 0.9980 chunk 284 optimal weight: 0.2980 chunk 301 optimal weight: 0.9980 chunk 148 optimal weight: 4.9990 chunk 269 optimal weight: 0.6980 chunk 81 optimal weight: 6.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 512 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 611 HIS C 691 GLN C 883 ASN D 458 GLN D 611 HIS D 691 GLN D 726 HIS D1361 GLN E 630 ASN E 815 HIS E1351 GLN ** F 940 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5514 moved from start: 0.4337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 25829 Z= 0.174 Angle : 0.630 11.055 35014 Z= 0.309 Chirality : 0.043 0.190 3948 Planarity : 0.005 0.101 4488 Dihedral : 8.503 99.895 3581 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 9.00 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.47 % Favored : 93.47 % Rotamer: Outliers : 0.11 % Allowed : 3.53 % Favored : 96.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.00 % Cis-general : 0.34 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.05 (0.16), residues: 3109 helix: 0.75 (0.14), residues: 1421 sheet: 0.75 (0.27), residues: 383 loop : -1.12 (0.18), residues: 1305 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 615 HIS 0.005 0.001 HIS B1366 PHE 0.027 0.001 PHE B 933 TYR 0.019 0.001 TYR B 858 ARG 0.022 0.000 ARG D 424 *********************** 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 310 residues out of total 2778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 307 time to evaluate : 3.261 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 441 MET cc_start: 0.2164 (tpp) cc_final: 0.1816 (tpp) REVERT: A 523 MET cc_start: 0.2781 (mmp) cc_final: 0.2474 (tpt) REVERT: A 616 ASN cc_start: 0.2154 (p0) cc_final: 0.1200 (m-40) REVERT: A 639 ILE cc_start: 0.6148 (mm) cc_final: 0.5858 (mm) REVERT: B 495 MET cc_start: 0.6561 (tpt) cc_final: 0.5982 (tmm) REVERT: B 686 MET cc_start: 0.4734 (ppp) cc_final: 0.3467 (ppp) REVERT: C 1356 TYR cc_start: 0.7421 (t80) cc_final: 0.7211 (t80) REVERT: C 1379 MET cc_start: 0.6984 (mmm) cc_final: 0.6716 (mmp) REVERT: C 1382 GLU cc_start: 0.7139 (tt0) cc_final: 0.6719 (tt0) REVERT: D 495 MET cc_start: 0.6933 (tmm) cc_final: 0.5917 (tmm) REVERT: D 789 MET cc_start: 0.7787 (ppp) cc_final: 0.7329 (ppp) REVERT: E 523 MET cc_start: 0.4956 (tpp) cc_final: 0.4682 (tpp) REVERT: E 686 MET cc_start: 0.8268 (ppp) cc_final: 0.7877 (ttm) REVERT: E 1379 MET cc_start: 0.8544 (mpp) cc_final: 0.8195 (mpp) REVERT: F 626 GLU cc_start: 0.7130 (tm-30) cc_final: 0.6801 (tm-30) REVERT: F 652 ARG cc_start: 0.8971 (tmm160) cc_final: 0.8074 (ttm-80) REVERT: F 1346 ASN cc_start: 0.6334 (t0) cc_final: 0.5908 (p0) outliers start: 3 outliers final: 1 residues processed: 310 average time/residue: 0.3561 time to fit residues: 174.5815 Evaluate side-chains 208 residues out of total 2778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 207 time to evaluate : 2.769 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 251 optimal weight: 0.4980 chunk 171 optimal weight: 0.0670 chunk 4 optimal weight: 0.0670 chunk 224 optimal weight: 0.9980 chunk 124 optimal weight: 6.9990 chunk 257 optimal weight: 0.8980 chunk 208 optimal weight: 4.9990 chunk 0 optimal weight: 20.0000 chunk 153 optimal weight: 0.9990 chunk 270 optimal weight: 8.9990 chunk 76 optimal weight: 2.9990 overall best weight: 0.5056 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 548 HIS ** C 691 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 883 ASN C1361 GLN C1366 HIS D 691 GLN D 726 HIS E 630 ASN ** E 815 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 863 HIS ** F 940 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5535 moved from start: 0.4620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 25829 Z= 0.164 Angle : 0.629 10.824 35014 Z= 0.305 Chirality : 0.043 0.195 3948 Planarity : 0.005 0.089 4488 Dihedral : 8.342 98.466 3581 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.30 % Favored : 93.63 % Rotamer: Outliers : 0.11 % Allowed : 2.99 % Favored : 96.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.00 % Cis-general : 0.34 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.04 (0.16), residues: 3109 helix: 0.78 (0.14), residues: 1434 sheet: 0.90 (0.27), residues: 386 loop : -1.08 (0.18), residues: 1289 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 505 HIS 0.006 0.001 HIS C1366 PHE 0.025 0.001 PHE C 517 TYR 0.016 0.001 TYR C1364 ARG 0.008 0.000 ARG D 692 *********************** 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 294 residues out of total 2778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 291 time to evaluate : 2.940 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 523 MET cc_start: 0.2997 (mmp) cc_final: 0.1892 (mtp) REVERT: A 616 ASN cc_start: 0.2242 (p0) cc_final: 0.1357 (m-40) REVERT: A 639 ILE cc_start: 0.6122 (mm) cc_final: 0.5843 (mm) REVERT: B 495 MET cc_start: 0.6480 (tpt) cc_final: 0.5897 (tmm) REVERT: B 686 MET cc_start: 0.4772 (ppp) cc_final: 0.3475 (ppp) REVERT: C 1379 MET cc_start: 0.7645 (mmm) cc_final: 0.7385 (mmp) REVERT: D 789 MET cc_start: 0.7917 (ppp) cc_final: 0.7471 (ppp) REVERT: E 523 MET cc_start: 0.4734 (tpp) cc_final: 0.4476 (tpp) REVERT: E 1379 MET cc_start: 0.8614 (mpp) cc_final: 0.8095 (mpp) REVERT: F 556 LEU cc_start: 0.7184 (pp) cc_final: 0.6582 (tp) REVERT: F 652 ARG cc_start: 0.8984 (tmm160) cc_final: 0.8104 (ttm-80) REVERT: F 1379 MET cc_start: 0.8545 (mpp) cc_final: 0.8322 (mmm) outliers start: 3 outliers final: 1 residues processed: 294 average time/residue: 0.3586 time to fit residues: 169.9762 Evaluate side-chains 214 residues out of total 2778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 213 time to evaluate : 3.102 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 101 optimal weight: 7.9990 chunk 271 optimal weight: 7.9990 chunk 59 optimal weight: 7.9990 chunk 177 optimal weight: 2.9990 chunk 74 optimal weight: 7.9990 chunk 301 optimal weight: 1.9990 chunk 250 optimal weight: 6.9990 chunk 139 optimal weight: 0.0070 chunk 25 optimal weight: 8.9990 chunk 99 optimal weight: 0.9980 chunk 158 optimal weight: 0.0980 overall best weight: 1.2202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 691 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 883 ASN C1361 GLN D 691 GLN D 726 HIS E 575 ASN E 630 ASN ** E 815 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 863 HIS F 900 HIS ** F 940 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5681 moved from start: 0.5170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.086 25829 Z= 0.192 Angle : 0.647 10.588 35014 Z= 0.319 Chirality : 0.044 0.231 3948 Planarity : 0.005 0.077 4488 Dihedral : 8.358 97.912 3581 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 9.63 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.56 % Favored : 93.41 % Rotamer: Outliers : 0.07 % Allowed : 2.48 % Favored : 97.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.00 % Cis-general : 0.34 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.04 (0.16), residues: 3109 helix: 0.73 (0.14), residues: 1453 sheet: 0.89 (0.27), residues: 384 loop : -1.03 (0.19), residues: 1272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 505 HIS 0.007 0.001 HIS C1366 PHE 0.031 0.001 PHE D 933 TYR 0.015 0.001 TYR B1356 ARG 0.010 0.000 ARG B1365 *********************** 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 fitting. rotamer outliers: 2 poor density : 286 time to evaluate : 3.268 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 441 MET cc_start: 0.1649 (tpp) cc_final: 0.1387 (tpp) REVERT: A 639 ILE cc_start: 0.6136 (mm) cc_final: 0.5862 (mm) REVERT: A 683 MET cc_start: -0.1959 (mmp) cc_final: -0.3134 (mtm) REVERT: B 686 MET cc_start: 0.4695 (ppp) cc_final: 0.3411 (ppp) REVERT: B 1353 GLU cc_start: 0.5058 (OUTLIER) cc_final: 0.3033 (pt0) REVERT: C 1379 MET cc_start: 0.7448 (mmm) cc_final: 0.7163 (mmp) REVERT: C 1382 GLU cc_start: 0.7238 (tt0) cc_final: 0.6895 (tt0) REVERT: D 789 MET cc_start: 0.8162 (ppp) cc_final: 0.7534 (ppp) REVERT: E 523 MET cc_start: 0.4753 (tpp) cc_final: 0.4519 (tpp) REVERT: E 1379 MET cc_start: 0.8586 (mpp) cc_final: 0.7958 (mpp) REVERT: F 556 LEU cc_start: 0.7150 (pp) cc_final: 0.6548 (tp) REVERT: F 652 ARG cc_start: 0.9027 (tmm160) cc_final: 0.8090 (ttm-80) outliers start: 2 outliers final: 0 residues processed: 288 average time/residue: 0.3427 time to fit residues: 160.2848 Evaluate side-chains 212 residues out of total 2778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 211 time to evaluate : 3.004 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 291 optimal weight: 1.9990 chunk 34 optimal weight: 0.0010 chunk 171 optimal weight: 6.9990 chunk 220 optimal weight: 0.8980 chunk 170 optimal weight: 6.9990 chunk 254 optimal weight: 1.9990 chunk 168 optimal weight: 2.9990 chunk 300 optimal weight: 5.9990 chunk 188 optimal weight: 0.9990 chunk 183 optimal weight: 0.0870 chunk 138 optimal weight: 3.9990 overall best weight: 0.7968 ------------------------------------------------------------------------------- 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** B1366 HIS ** C 691 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5710 moved from start: 0.5484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 25829 Z= 0.169 Angle : 0.634 10.472 35014 Z= 0.310 Chirality : 0.043 0.200 3948 Planarity : 0.004 0.074 4488 Dihedral : 8.242 98.379 3581 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.08 % Favored : 93.86 % Rotamer: Outliers : 0.04 % Allowed : 1.33 % Favored : 98.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.00 % Cis-general : 0.34 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.09 (0.16), residues: 3109 helix: 0.76 (0.14), residues: 1464 sheet: 0.82 (0.27), residues: 382 loop : -0.96 (0.19), residues: 1263 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 505 HIS 0.006 0.001 HIS C1366 PHE 0.028 0.001 PHE C 517 TYR 0.015 0.001 TYR C1364 ARG 0.006 0.000 ARG D 586 *********************** 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 287 residues out of total 2778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 286 time to evaluate : 2.990 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 639 ILE cc_start: 0.6149 (mm) cc_final: 0.5879 (mm) REVERT: A 683 MET cc_start: -0.2032 (mmt) cc_final: -0.3093 (mtm) REVERT: A 789 MET cc_start: -0.0704 (ttp) cc_final: -0.0941 (mmt) REVERT: C 555 LEU cc_start: 0.6656 (pp) cc_final: 0.6411 (pp) REVERT: C 581 ASP cc_start: 0.6801 (t0) cc_final: 0.6571 (t0) REVERT: E 523 MET cc_start: 0.4648 (tpp) cc_final: 0.4273 (tpp) REVERT: E 1379 MET cc_start: 0.8586 (mpp) cc_final: 0.8198 (mpp) REVERT: F 556 LEU cc_start: 0.7198 (pp) cc_final: 0.6615 (tp) REVERT: F 652 ARG cc_start: 0.9028 (tmm160) cc_final: 0.8083 (ttm-80) REVERT: F 856 ILE cc_start: 0.7161 (mm) cc_final: 0.6890 (mt) outliers start: 1 outliers final: 1 residues processed: 287 average time/residue: 0.3476 time to fit residues: 160.7552 Evaluate side-chains 210 residues out of total 2778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 209 time to evaluate : 2.989 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 186 optimal weight: 1.9990 chunk 120 optimal weight: 0.0970 chunk 179 optimal weight: 0.0970 chunk 90 optimal weight: 1.9990 chunk 59 optimal weight: 0.9980 chunk 58 optimal weight: 3.9990 chunk 191 optimal weight: 0.7980 chunk 204 optimal weight: 2.9990 chunk 148 optimal weight: 2.9990 chunk 28 optimal weight: 0.1980 chunk 236 optimal weight: 1.9990 overall best weight: 0.4376 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 699 GLN C 575 ASN ** C 691 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 883 ASN 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: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5711 moved from start: 0.5691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 25829 Z= 0.153 Angle : 0.625 10.416 35014 Z= 0.303 Chirality : 0.043 0.244 3948 Planarity : 0.004 0.075 4488 Dihedral : 8.116 98.241 3581 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.27 % Favored : 93.70 % Rotamer: Outliers : 0.04 % Allowed : 1.48 % Favored : 98.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.00 % Cis-general : 0.34 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.17 (0.16), residues: 3109 helix: 0.83 (0.14), residues: 1462 sheet: 0.95 (0.27), residues: 380 loop : -0.95 (0.19), residues: 1267 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP A 615 HIS 0.004 0.001 HIS C1366 PHE 0.022 0.001 PHE C 517 TYR 0.015 0.001 TYR F 858 ARG 0.005 0.000 ARG D 586 *********************** 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 280 residues out of total 2778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 279 time to evaluate : 3.005 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 639 ILE cc_start: 0.6151 (mm) cc_final: 0.5835 (mm) REVERT: A 683 MET cc_start: -0.2158 (mmt) cc_final: -0.3158 (mtm) REVERT: C 581 ASP cc_start: 0.6838 (t0) cc_final: 0.6611 (t0) REVERT: E 523 MET cc_start: 0.4593 (tpp) cc_final: 0.4250 (tpp) REVERT: F 556 LEU cc_start: 0.7392 (pp) cc_final: 0.6807 (tp) REVERT: F 1379 MET cc_start: 0.8631 (mpp) cc_final: 0.8203 (mmt) outliers start: 1 outliers final: 0 residues processed: 279 average time/residue: 0.3550 time to fit residues: 160.2793 Evaluate side-chains 195 residues out of total 2778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 195 time to evaluate : 3.021 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 273 optimal weight: 8.9990 chunk 288 optimal weight: 0.8980 chunk 262 optimal weight: 0.5980 chunk 280 optimal weight: 0.8980 chunk 168 optimal weight: 0.9980 chunk 122 optimal weight: 1.9990 chunk 220 optimal weight: 1.9990 chunk 85 optimal weight: 0.9990 chunk 253 optimal weight: 6.9990 chunk 265 optimal weight: 0.0570 chunk 279 optimal weight: 0.8980 overall best weight: 0.6698 ------------------------------------------------------------------------------- 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 900 HIS ** C 691 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 883 ASN D 482 ASN D 691 GLN ** E 630 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 815 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 548 HIS ** F 940 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F1354 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5756 moved from start: 0.5974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 25829 Z= 0.165 Angle : 0.645 10.409 35014 Z= 0.315 Chirality : 0.043 0.202 3948 Planarity : 0.004 0.075 4488 Dihedral : 8.158 98.417 3581 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.95 % Favored : 93.99 % Rotamer: Outliers : 0.00 % Allowed : 0.65 % Favored : 99.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.00 % Cis-general : 0.34 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.20 (0.16), residues: 3109 helix: 0.84 (0.14), residues: 1462 sheet: 1.00 (0.27), residues: 383 loop : -0.94 (0.19), residues: 1264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 615 HIS 0.003 0.001 HIS A 861 PHE 0.022 0.001 PHE C 517 TYR 0.013 0.001 TYR C1364 ARG 0.004 0.000 ARG D 586 *********************** 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 276 residues out of total 2778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 276 time to evaluate : 3.000 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: 0.6086 (mm) cc_final: 0.5784 (mm) REVERT: A 683 MET cc_start: -0.2235 (mmt) cc_final: -0.3196 (mtm) REVERT: B 560 ASP cc_start: 0.7636 (p0) cc_final: 0.7426 (p0) REVERT: B 686 MET cc_start: 0.4552 (ppp) cc_final: 0.3332 (ppp) REVERT: D 523 MET cc_start: 0.4310 (ptp) cc_final: 0.3664 (tpt) REVERT: E 523 MET cc_start: 0.4495 (tpp) cc_final: 0.4159 (tpp) REVERT: E 842 CYS cc_start: 0.7521 (t) cc_final: 0.6896 (t) REVERT: F 556 LEU cc_start: 0.7339 (pp) cc_final: 0.6732 (tp) REVERT: F 626 GLU cc_start: 0.7115 (tm-30) cc_final: 0.6597 (tm-30) REVERT: F 801 PRO cc_start: 0.6979 (Cg_exo) cc_final: 0.6734 (Cg_endo) REVERT: F 1379 MET cc_start: 0.8633 (mpp) cc_final: 0.8423 (mmm) outliers start: 0 outliers final: 0 residues processed: 276 average time/residue: 0.3502 time to fit residues: 154.4847 Evaluate side-chains 197 residues out of total 2778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 197 time to evaluate : 2.768 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 184 optimal weight: 2.9990 chunk 296 optimal weight: 9.9990 chunk 180 optimal weight: 0.2980 chunk 140 optimal weight: 1.9990 chunk 205 optimal weight: 0.9990 chunk 310 optimal weight: 0.2980 chunk 286 optimal weight: 2.9990 chunk 247 optimal weight: 1.9990 chunk 25 optimal weight: 6.9990 chunk 191 optimal weight: 0.0570 chunk 151 optimal weight: 3.9990 overall best weight: 0.7302 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 548 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 699 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 691 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 691 GLN ** E 630 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5800 moved from start: 0.6230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 25829 Z= 0.164 Angle : 0.655 10.394 35014 Z= 0.319 Chirality : 0.043 0.222 3948 Planarity : 0.004 0.074 4488 Dihedral : 8.017 98.986 3581 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.92 % Favored : 94.02 % Rotamer: Outliers : 0.00 % Allowed : 0.29 % Favored : 99.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.00 % Cis-general : 0.34 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.19 (0.16), residues: 3109 helix: 0.85 (0.14), residues: 1465 sheet: 0.94 (0.27), residues: 386 loop : -0.97 (0.19), residues: 1258 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.001 TRP E 615 HIS 0.003 0.001 HIS A 861 PHE 0.021 0.001 PHE C 517 TYR 0.017 0.001 TYR F 858 ARG 0.004 0.000 ARG D 929 ********************** 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 265 residues out of total 2778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 265 time to evaluate : 3.146 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 639 ILE cc_start: 0.6091 (mm) cc_final: 0.5848 (mm) REVERT: A 683 MET cc_start: -0.2269 (mmt) cc_final: -0.3233 (mtm) REVERT: B 686 MET cc_start: 0.4529 (ppp) cc_final: 0.3292 (ppp) REVERT: D 523 MET cc_start: 0.4480 (ptp) cc_final: 0.3828 (tpt) REVERT: E 576 ARG cc_start: 0.5713 (tpp-160) cc_final: 0.3149 (ttm170) REVERT: E 842 CYS cc_start: 0.7538 (t) cc_final: 0.6802 (t) REVERT: E 1379 MET cc_start: 0.8320 (mpp) cc_final: 0.7778 (mtm) REVERT: F 556 LEU cc_start: 0.7372 (pp) cc_final: 0.6745 (tp) REVERT: F 626 GLU cc_start: 0.7115 (tm-30) cc_final: 0.6437 (tm-30) REVERT: F 1379 MET cc_start: 0.8657 (mpp) cc_final: 0.8439 (mmm) outliers start: 0 outliers final: 0 residues processed: 265 average time/residue: 0.3537 time to fit residues: 152.7279 Evaluate side-chains 196 residues out of total 2778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 196 time to evaluate : 3.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 196 optimal weight: 4.9990 chunk 263 optimal weight: 8.9990 chunk 75 optimal weight: 0.9980 chunk 228 optimal weight: 3.9990 chunk 36 optimal weight: 6.9990 chunk 68 optimal weight: 0.0060 chunk 247 optimal weight: 5.9990 chunk 103 optimal weight: 5.9990 chunk 254 optimal weight: 0.8980 chunk 31 optimal weight: 4.9990 chunk 45 optimal weight: 0.8980 overall best weight: 1.3598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 548 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 699 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1354 ASN ** C 691 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 458 GLN D 691 GLN E 630 ASN ** E 815 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 548 HIS F 815 HIS ** F 940 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4305 r_free = 0.4305 target = 0.134473 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.105362 restraints weight = 120296.487| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.107150 restraints weight = 89445.853| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.107248 restraints weight = 66721.311| |-----------------------------------------------------------------------------| r_work (final): 0.3847 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7009 moved from start: 0.6960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 25829 Z= 0.209 Angle : 0.687 10.368 35014 Z= 0.337 Chirality : 0.045 0.294 3948 Planarity : 0.005 0.072 4488 Dihedral : 8.013 100.491 3581 Min Nonbonded Distance : 2.300 Molprobity Statistics. All-atom Clashscore : 9.94 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.66 % Favored : 93.28 % Rotamer: Outliers : 0.00 % Allowed : 0.36 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.16 (0.16), residues: 3109 helix: 0.83 (0.14), residues: 1456 sheet: 0.81 (0.27), residues: 386 loop : -0.91 (0.19), residues: 1267 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 505 HIS 0.009 0.001 HIS B 548 PHE 0.023 0.001 PHE C 517 TYR 0.023 0.002 TYR F1347 ARG 0.008 0.000 ARG E 576 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4975.21 seconds wall clock time: 91 minutes 21.09 seconds (5481.09 seconds total)