Starting phenix.real_space_refine on Tue Mar 19 22:09:00 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h3h_34468/03_2024/8h3h_34468_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h3h_34468/03_2024/8h3h_34468.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.15 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h3h_34468/03_2024/8h3h_34468.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h3h_34468/03_2024/8h3h_34468.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h3h_34468/03_2024/8h3h_34468_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h3h_34468/03_2024/8h3h_34468_neut_updated.pdb" } resolution = 3.15 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= 0.004 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 16215 2.51 5 N 4381 2.21 5 O 4685 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 461": "NH1" <-> "NH2" Residue "A ARG 511": "NH1" <-> "NH2" Residue "A ARG 514": "NH1" <-> "NH2" Residue "A ARG 585": "NH1" <-> "NH2" Residue "A ARG 586": "NH1" <-> "NH2" Residue "A GLU 602": "OE1" <-> "OE2" Residue "A GLU 626": "OE1" <-> "OE2" Residue "A GLU 629": "OE1" <-> "OE2" Residue "A GLU 645": "OE1" <-> "OE2" Residue "A ARG 654": "NH1" <-> "NH2" Residue "A GLU 800": "OE1" <-> "OE2" Residue "A GLU 1384": "OE1" <-> "OE2" Residue "B ARG 461": "NH1" <-> "NH2" Residue "B ARG 511": "NH1" <-> "NH2" Residue "B ARG 514": "NH1" <-> "NH2" Residue "B TYR 521": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 585": "NH1" <-> "NH2" Residue "B ARG 586": "NH1" <-> "NH2" Residue "B GLU 602": "OE1" <-> "OE2" Residue "B GLU 606": "OE1" <-> "OE2" Residue "B GLU 629": "OE1" <-> "OE2" Residue "B ARG 654": "NH1" <-> "NH2" Residue "B GLU 848": "OE1" <-> "OE2" Residue "B GLU 1331": "OE1" <-> "OE2" Residue "C GLU 453": "OE1" <-> "OE2" Residue "C ARG 461": "NH1" <-> "NH2" Residue "C ARG 511": "NH1" <-> "NH2" Residue "C ARG 514": "NH1" <-> "NH2" Residue "C ARG 585": "NH1" <-> "NH2" Residue "C GLU 602": "OE1" <-> "OE2" Residue "C GLU 606": "OE1" <-> "OE2" Residue "C ARG 654": "NH1" <-> "NH2" Residue "C GLU 680": "OE1" <-> "OE2" Residue "C GLU 1331": "OE1" <-> "OE2" Residue "C GLU 1380": "OE1" <-> "OE2" Residue "C GLU 1384": "OE1" <-> "OE2" Residue "D GLU 453": "OE1" <-> "OE2" Residue "D ARG 461": "NH1" <-> "NH2" Residue "D ARG 511": "NH1" <-> "NH2" Residue "D ARG 514": "NH1" <-> "NH2" Residue "D ARG 585": "NH1" <-> "NH2" Residue "D ARG 586": "NH1" <-> "NH2" Residue "D GLU 629": "OE1" <-> "OE2" Residue "D ARG 654": "NH1" <-> "NH2" Residue "D GLU 680": "OE1" <-> "OE2" Residue "D GLU 818": "OE1" <-> "OE2" Residue "D GLU 905": "OE1" <-> "OE2" Residue "D GLU 928": "OE1" <-> "OE2" Residue "D GLU 1380": "OE1" <-> "OE2" Residue "E ARG 461": "NH1" <-> "NH2" Residue "E ARG 511": "NH1" <-> "NH2" Residue "E ARG 514": "NH1" <-> "NH2" Residue "E TYR 521": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 585": "NH1" <-> "NH2" Residue "E ARG 586": "NH1" <-> "NH2" Residue "E GLU 593": "OE1" <-> "OE2" Residue "E GLU 602": "OE1" <-> "OE2" Residue "E GLU 626": "OE1" <-> "OE2" Residue "E GLU 629": "OE1" <-> "OE2" Residue "E ARG 654": "NH1" <-> "NH2" Residue "E GLU 663": "OE1" <-> "OE2" Residue "E GLU 728": "OE1" <-> "OE2" Residue "E GLU 818": "OE1" <-> "OE2" Residue "E GLU 906": "OE1" <-> "OE2" Residue "E GLU 928": "OE1" <-> "OE2" Residue "F GLU 453": "OE1" <-> "OE2" Residue "F ARG 461": "NH1" <-> "NH2" Residue "F ARG 490": "NH1" <-> "NH2" Residue "F GLU 510": "OE1" <-> "OE2" Residue "F ARG 511": "NH1" <-> "NH2" Residue "F ARG 514": "NH1" <-> "NH2" Residue "F ARG 585": "NH1" <-> "NH2" Residue "F ARG 586": "NH1" <-> "NH2" Residue "F ARG 654": "NH1" <-> "NH2" Residue "F GLU 905": "OE1" <-> "OE2" Residue "F GLU 928": "OE1" <-> "OE2" Residue "F GLU 1380": "OE1" <-> "OE2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 25408 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 4268 Number of conformers: 1 Conformer: "" Number of residues, atoms: 539, 4268 Classifications: {'peptide': 539} Link IDs: {'CIS': 3, 'PCIS': 2, 'PTRANS': 33, 'TRANS': 500} Chain breaks: 3 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: 4134 Number of conformers: 1 Conformer: "" Number of residues, atoms: 520, 4134 Classifications: {'peptide': 520} Link IDs: {'CIS': 2, 'PCIS': 2, 'PTRANS': 31, 'TRANS': 484} Chain breaks: 3 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: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 62 Unusual residues: {'ATP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 62 Unusual residues: {'ATP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 13.26, per 1000 atoms: 0.52 Number of scatterers: 25408 At special positions: 0 Unit cell: (152.15, 156.4, 98.6, 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 4685 8.00 N 4381 7.00 C 16215 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 - 3.50 Amino acid : False - 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=9, symmetry=0 Number of additional bonds: simple=9, symmetry=0 Coordination: Other bonds: Time building additional restraints: 10.63 Conformation dependent library (CDL) restraints added in 4.4 seconds 6268 Ramachandran restraints generated. 3134 Oldfield, 0 Emsley, 3134 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6058 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 148 helices and 13 sheets defined 41.1% alpha, 7.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.16 Creating SS restraints... Processing helix chain 'A' and resid 435 through 438 No H-bonds generated for 'chain 'A' and resid 435 through 438' Processing helix chain 'A' and resid 444 through 447 No H-bonds generated for 'chain 'A' and resid 444 through 447' Processing helix chain 'A' and resid 451 through 454 No H-bonds generated for 'chain 'A' and resid 451 through 454' Processing helix chain 'A' and resid 474 through 484 Processing helix chain 'A' and resid 508 through 523 Processing helix chain 'A' and resid 533 through 535 No H-bonds generated for 'chain 'A' and resid 533 through 535' Processing helix chain 'A' and resid 549 through 561 removed outlier: 3.571A pdb=" N THR A 554 " --> pdb=" O SER A 550 " (cutoff:3.500A) Processing helix chain 'A' and resid 577 through 579 No H-bonds generated for 'chain 'A' and resid 577 through 579' Processing helix chain 'A' and resid 601 through 611 removed outlier: 3.600A pdb=" N GLU A 606 " --> pdb=" O GLU A 602 " (cutoff:3.500A) Processing helix chain 'A' and resid 621 through 630 removed outlier: 3.763A pdb=" N GLU A 629 " --> pdb=" O GLU A 625 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ASN A 630 " --> pdb=" O GLU A 626 " (cutoff:3.500A) Processing helix chain 'A' and resid 637 through 654 removed outlier: 3.750A pdb=" N ALA A 647 " --> pdb=" O CYS A 643 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N LEU A 648 " --> pdb=" O ALA A 644 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ALA A 650 " --> pdb=" O ALA A 646 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LEU A 651 " --> pdb=" O ALA A 647 " (cutoff:3.500A) Processing helix chain 'A' and resid 680 through 684 Processing helix chain 'A' and resid 706 through 716 removed outlier: 6.234A pdb=" N ASN A 711 " --> pdb=" O PRO A 707 " (cutoff:3.500A) removed outlier: 5.487A pdb=" N THR A 712 " --> pdb=" O LEU A 708 " (cutoff:3.500A) Processing helix chain 'A' and resid 725 through 728 removed outlier: 3.976A pdb=" N GLU A 728 " --> pdb=" O PRO A 725 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 725 through 728' Processing helix chain 'A' and resid 809 through 816 Processing helix chain 'A' and resid 827 through 830 No H-bonds generated for 'chain 'A' and resid 827 through 830' Processing helix chain 'A' and resid 838 through 851 removed outlier: 3.773A pdb=" N CYS A 842 " --> pdb=" O PRO A 838 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ALA A 843 " --> pdb=" O GLU A 839 " (cutoff:3.500A) Processing helix chain 'A' and resid 862 through 865 No H-bonds generated for 'chain 'A' and resid 862 through 865' Processing helix chain 'A' and resid 871 through 880 removed outlier: 3.685A pdb=" N ALA A 875 " --> pdb=" O PRO A 871 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N THR A 879 " --> pdb=" O ALA A 875 " (cutoff:3.500A) Processing helix chain 'A' and resid 900 through 902 No H-bonds generated for 'chain 'A' and resid 900 through 902' Processing helix chain 'A' and resid 905 through 910 removed outlier: 4.545A pdb=" N LEU A 910 " --> pdb=" O GLU A 906 " (cutoff:3.500A) Processing helix chain 'A' and resid 913 through 915 No H-bonds generated for 'chain 'A' and resid 913 through 915' Processing helix chain 'A' and resid 926 through 937 removed outlier: 4.242A pdb=" N ASP A 935 " --> pdb=" O LYS A 931 " (cutoff:3.500A) removed outlier: 4.984A pdb=" N LEU A 936 " --> pdb=" O PHE A 932 " (cutoff:3.500A) Processing helix chain 'A' and resid 940 through 942 No H-bonds generated for 'chain 'A' and resid 940 through 942' Processing helix chain 'A' and resid 1332 through 1343 Processing helix chain 'A' and resid 1349 through 1352 No H-bonds generated for 'chain 'A' and resid 1349 through 1352' Processing helix chain 'A' and resid 1360 through 1365 Processing helix chain 'A' and resid 1376 through 1383 Processing helix chain 'B' and resid 433 through 442 removed outlier: 3.596A pdb=" N GLU B 440 " --> pdb=" O ALA B 436 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N MET B 441 " --> pdb=" O ALA B 437 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N VAL B 442 " --> pdb=" O LEU B 438 " (cutoff:3.500A) Processing helix chain 'B' and resid 451 through 454 No H-bonds generated for 'chain 'B' and resid 451 through 454' Processing helix chain 'B' and resid 473 through 484 removed outlier: 3.616A pdb=" N ALA B 477 " --> pdb=" O LYS B 473 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N CYS B 484 " --> pdb=" O LEU B 480 " (cutoff:3.500A) Processing helix chain 'B' and resid 511 through 522 removed outlier: 3.554A pdb=" N GLN B 522 " --> pdb=" O ASP B 518 " (cutoff:3.500A) Processing helix chain 'B' and resid 546 through 555 Processing helix chain 'B' and resid 577 through 579 No H-bonds generated for 'chain 'B' and resid 577 through 579' Processing helix chain 'B' and resid 601 through 611 removed outlier: 3.642A pdb=" N LYS B 605 " --> pdb=" O LYS B 601 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N GLU B 606 " --> pdb=" O GLU B 602 " (cutoff:3.500A) Processing helix chain 'B' and resid 621 through 630 removed outlier: 3.605A pdb=" N ASN B 630 " --> pdb=" O GLU B 626 " (cutoff:3.500A) Processing helix chain 'B' and resid 637 through 642 removed outlier: 3.517A pdb=" N ILE B 642 " --> pdb=" O ASP B 638 " (cutoff:3.500A) Processing helix chain 'B' and resid 648 through 654 Processing helix chain 'B' and resid 676 through 685 removed outlier: 3.905A pdb=" N GLU B 680 " --> pdb=" O LYS B 677 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N VAL B 681 " --> pdb=" O ASP B 678 " (cutoff:3.500A) Processing helix chain 'B' and resid 690 through 692 No H-bonds generated for 'chain 'B' and resid 690 through 692' Processing helix chain 'B' and resid 706 through 723 removed outlier: 6.731A pdb=" N ASN B 711 " --> pdb=" O PRO B 707 " (cutoff:3.500A) removed outlier: 5.642A pdb=" N THR B 712 " --> pdb=" O LEU B 708 " (cutoff:3.500A) Processing helix chain 'B' and resid 809 through 816 Processing helix chain 'B' and resid 827 through 830 No H-bonds generated for 'chain 'B' and resid 827 through 830' Processing helix chain 'B' and resid 838 through 851 removed outlier: 3.650A pdb=" N CYS B 842 " --> pdb=" O PRO B 838 " (cutoff:3.500A) Processing helix chain 'B' and resid 862 through 865 No H-bonds generated for 'chain 'B' and resid 862 through 865' Processing helix chain 'B' and resid 871 through 880 removed outlier: 3.708A pdb=" N ALA B 875 " --> pdb=" O PRO B 871 " (cutoff:3.500A) Processing helix chain 'B' and resid 900 through 902 No H-bonds generated for 'chain 'B' and resid 900 through 902' Processing helix chain 'B' and resid 905 through 910 removed outlier: 4.508A pdb=" N LEU B 910 " --> pdb=" O GLU B 906 " (cutoff:3.500A) Processing helix chain 'B' and resid 913 through 915 No H-bonds generated for 'chain 'B' and resid 913 through 915' Processing helix chain 'B' and resid 926 through 932 Processing helix chain 'B' and resid 1332 through 1343 Processing helix chain 'B' and resid 1349 through 1354 Processing helix chain 'B' and resid 1357 through 1366 removed outlier: 4.056A pdb=" N CYS B1362 " --> pdb=" O VAL B1358 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ILE B1363 " --> pdb=" O ILE B1359 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N HIS B1366 " --> pdb=" O CYS B1362 " (cutoff:3.500A) Processing helix chain 'B' and resid 1376 through 1383 Processing helix chain 'C' and resid 433 through 438 Processing helix chain 'C' and resid 444 through 447 No H-bonds generated for 'chain 'C' and resid 444 through 447' Processing helix chain 'C' and resid 451 through 454 No H-bonds generated for 'chain 'C' and resid 451 through 454' Processing helix chain 'C' and resid 473 through 485 removed outlier: 3.913A pdb=" N ALA C 477 " --> pdb=" O LYS C 473 " (cutoff:3.500A) Processing helix chain 'C' and resid 509 through 522 removed outlier: 3.742A pdb=" N LEU C 513 " --> pdb=" O SER C 509 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ARG C 514 " --> pdb=" O GLU C 510 " (cutoff:3.500A) Processing helix chain 'C' and resid 533 through 535 No H-bonds generated for 'chain 'C' and resid 533 through 535' Processing helix chain 'C' and resid 546 through 559 Processing helix chain 'C' and resid 577 through 579 No H-bonds generated for 'chain 'C' and resid 577 through 579' Processing helix chain 'C' and resid 601 through 611 removed outlier: 3.741A pdb=" N LYS C 605 " --> pdb=" O LYS C 601 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N GLU C 606 " --> pdb=" O GLU C 602 " (cutoff:3.500A) Processing helix chain 'C' and resid 621 through 628 removed outlier: 3.566A pdb=" N GLU C 626 " --> pdb=" O THR C 622 " (cutoff:3.500A) Processing helix chain 'C' and resid 636 through 654 removed outlier: 3.657A pdb=" N CYS C 643 " --> pdb=" O LYS C 640 " (cutoff:3.500A) removed outlier: 4.654A pdb=" N ALA C 646 " --> pdb=" O CYS C 643 " (cutoff:3.500A) Processing helix chain 'C' and resid 656 through 658 No H-bonds generated for 'chain 'C' and resid 656 through 658' Processing helix chain 'C' and resid 676 through 685 Processing helix chain 'C' and resid 706 through 723 removed outlier: 3.577A pdb=" N GLN C 710 " --> pdb=" O LYS C 706 " (cutoff:3.500A) removed outlier: 7.683A pdb=" N ASN C 711 " --> pdb=" O PRO C 707 " (cutoff:3.500A) removed outlier: 5.726A pdb=" N THR C 712 " --> pdb=" O LEU C 708 " (cutoff:3.500A) Processing helix chain 'C' and resid 810 through 816 Processing helix chain 'C' and resid 827 through 830 No H-bonds generated for 'chain 'C' and resid 827 through 830' Processing helix chain 'C' and resid 838 through 851 removed outlier: 3.528A pdb=" N GLN C 844 " --> pdb=" O GLU C 840 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N ILE C 846 " --> pdb=" O CYS C 842 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ARG C 847 " --> pdb=" O ALA C 843 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ALA C 849 " --> pdb=" O VAL C 845 " (cutoff:3.500A) Processing helix chain 'C' and resid 862 through 867 removed outlier: 4.610A pdb=" N GLU C 867 " --> pdb=" O HIS C 863 " (cutoff:3.500A) Processing helix chain 'C' and resid 871 through 880 removed outlier: 3.580A pdb=" N THR C 879 " --> pdb=" O ALA C 875 " (cutoff:3.500A) Processing helix chain 'C' and resid 913 through 915 No H-bonds generated for 'chain 'C' and resid 913 through 915' Processing helix chain 'C' and resid 926 through 938 removed outlier: 3.681A pdb=" N PHE C 933 " --> pdb=" O ARG C 929 " (cutoff:3.500A) removed outlier: 4.696A pdb=" N ASP C 935 " --> pdb=" O LYS C 931 " (cutoff:3.500A) removed outlier: 5.328A pdb=" N LEU C 936 " --> pdb=" O PHE C 932 " (cutoff:3.500A) Processing helix chain 'C' and resid 1333 through 1343 Processing helix chain 'C' and resid 1349 through 1366 removed outlier: 4.203A pdb=" N CYS C1362 " --> pdb=" O VAL C1358 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N ILE C1363 " --> pdb=" O ILE C1359 " (cutoff:3.500A) Processing helix chain 'C' and resid 1375 through 1384 Processing helix chain 'D' and resid 435 through 438 No H-bonds generated for 'chain 'D' and resid 435 through 438' Processing helix chain 'D' and resid 444 through 447 No H-bonds generated for 'chain 'D' and resid 444 through 447' Processing helix chain 'D' and resid 473 through 485 removed outlier: 3.612A pdb=" N ALA D 477 " --> pdb=" O LYS D 473 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ASN D 482 " --> pdb=" O ARG D 478 " (cutoff:3.500A) Processing helix chain 'D' and resid 506 through 521 removed outlier: 4.392A pdb=" N SER D 509 " --> pdb=" O VAL D 506 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N GLU D 510 " --> pdb=" O GLY D 507 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ARG D 511 " --> pdb=" O GLU D 508 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N GLN D 512 " --> pdb=" O SER D 509 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N GLN D 519 " --> pdb=" O LEU D 516 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ALA D 520 " --> pdb=" O PHE D 517 " (cutoff:3.500A) Processing helix chain 'D' and resid 533 through 535 No H-bonds generated for 'chain 'D' and resid 533 through 535' Processing helix chain 'D' and resid 546 through 555 removed outlier: 3.710A pdb=" N SER D 553 " --> pdb=" O SER D 549 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N THR D 554 " --> pdb=" O SER D 550 " (cutoff:3.500A) Processing helix chain 'D' and resid 601 through 611 removed outlier: 3.978A pdb=" N GLU D 606 " --> pdb=" O GLU D 602 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ILE D 607 " --> pdb=" O ALA D 603 " (cutoff:3.500A) removed outlier: 5.118A pdb=" N LYS D 609 " --> pdb=" O LYS D 605 " (cutoff:3.500A) Processing helix chain 'D' and resid 621 through 630 removed outlier: 3.696A pdb=" N ASN D 630 " --> pdb=" O GLU D 626 " (cutoff:3.500A) Processing helix chain 'D' and resid 637 through 654 removed outlier: 3.823A pdb=" N CYS D 643 " --> pdb=" O ILE D 639 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N ALA D 644 " --> pdb=" O LYS D 640 " (cutoff:3.500A) Processing helix chain 'D' and resid 679 through 682 No H-bonds generated for 'chain 'D' and resid 679 through 682' Processing helix chain 'D' and resid 690 through 692 No H-bonds generated for 'chain 'D' and resid 690 through 692' Processing helix chain 'D' and resid 706 through 723 removed outlier: 6.554A pdb=" N ASN D 711 " --> pdb=" O PRO D 707 " (cutoff:3.500A) removed outlier: 5.832A pdb=" N THR D 712 " --> pdb=" O LEU D 708 " (cutoff:3.500A) Processing helix chain 'D' and resid 810 through 816 Processing helix chain 'D' and resid 827 through 832 removed outlier: 3.858A pdb=" N GLY D 832 " --> pdb=" O PRO D 828 " (cutoff:3.500A) Processing helix chain 'D' and resid 838 through 851 removed outlier: 3.579A pdb=" N CYS D 842 " --> pdb=" O PRO D 838 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N ALA D 843 " --> pdb=" O GLU D 839 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ILE D 846 " --> pdb=" O CYS D 842 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ARG D 847 " --> pdb=" O ALA D 843 " (cutoff:3.500A) Processing helix chain 'D' and resid 862 through 867 removed outlier: 4.986A pdb=" N GLU D 867 " --> pdb=" O HIS D 863 " (cutoff:3.500A) Processing helix chain 'D' and resid 871 through 880 removed outlier: 3.638A pdb=" N THR D 879 " --> pdb=" O ALA D 875 " (cutoff:3.500A) Processing helix chain 'D' and resid 900 through 902 No H-bonds generated for 'chain 'D' and resid 900 through 902' Processing helix chain 'D' and resid 905 through 910 removed outlier: 4.600A pdb=" N LEU D 910 " --> pdb=" O GLU D 906 " (cutoff:3.500A) Processing helix chain 'D' and resid 913 through 915 No H-bonds generated for 'chain 'D' and resid 913 through 915' Processing helix chain 'D' and resid 926 through 937 removed outlier: 4.684A pdb=" N ASP D 935 " --> pdb=" O LYS D 931 " (cutoff:3.500A) removed outlier: 5.053A pdb=" N LEU D 936 " --> pdb=" O PHE D 932 " (cutoff:3.500A) Processing helix chain 'D' and resid 1333 through 1343 Processing helix chain 'D' and resid 1349 through 1365 removed outlier: 3.578A pdb=" N ALA D1357 " --> pdb=" O GLU D1353 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N CYS D1362 " --> pdb=" O VAL D1358 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ILE D1363 " --> pdb=" O ILE D1359 " (cutoff:3.500A) Processing helix chain 'D' and resid 1375 through 1385 Processing helix chain 'E' and resid 436 through 442 removed outlier: 3.817A pdb=" N GLU E 440 " --> pdb=" O ALA E 436 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N MET E 441 " --> pdb=" O ALA E 437 " (cutoff:3.500A) Processing helix chain 'E' and resid 444 through 447 No H-bonds generated for 'chain 'E' and resid 444 through 447' Processing helix chain 'E' and resid 451 through 454 No H-bonds generated for 'chain 'E' and resid 451 through 454' Processing helix chain 'E' and resid 474 through 486 Processing helix chain 'E' and resid 510 through 522 removed outlier: 3.608A pdb=" N ARG E 514 " --> pdb=" O GLU E 510 " (cutoff:3.500A) Processing helix chain 'E' and resid 533 through 535 No H-bonds generated for 'chain 'E' and resid 533 through 535' Processing helix chain 'E' and resid 546 through 558 removed outlier: 3.795A pdb=" N LEU E 558 " --> pdb=" O THR E 554 " (cutoff:3.500A) Processing helix chain 'E' and resid 560 through 562 No H-bonds generated for 'chain 'E' and resid 560 through 562' Processing helix chain 'E' and resid 577 through 579 No H-bonds generated for 'chain 'E' and resid 577 through 579' Processing helix chain 'E' and resid 601 through 611 removed outlier: 3.827A pdb=" N LYS E 605 " --> pdb=" O LYS E 601 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N GLU E 606 " --> pdb=" O GLU E 602 " (cutoff:3.500A) Processing helix chain 'E' and resid 621 through 630 removed outlier: 4.170A pdb=" N GLU E 629 " --> pdb=" O GLU E 625 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N ASN E 630 " --> pdb=" O GLU E 626 " (cutoff:3.500A) Processing helix chain 'E' and resid 636 through 654 removed outlier: 3.548A pdb=" N SER E 641 " --> pdb=" O ALA E 637 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ILE E 642 " --> pdb=" O ASP E 638 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N CYS E 643 " --> pdb=" O ILE E 639 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N ALA E 644 " --> pdb=" O LYS E 640 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N ALA E 647 " --> pdb=" O CYS E 643 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ARG E 652 " --> pdb=" O LEU E 648 " (cutoff:3.500A) Processing helix chain 'E' and resid 676 through 685 removed outlier: 3.661A pdb=" N LYS E 685 " --> pdb=" O VAL E 681 " (cutoff:3.500A) Processing helix chain 'E' and resid 706 through 723 removed outlier: 6.482A pdb=" N ASN E 711 " --> pdb=" O PRO E 707 " (cutoff:3.500A) removed outlier: 5.829A pdb=" N THR E 712 " --> pdb=" O LEU E 708 " (cutoff:3.500A) Processing helix chain 'E' and resid 809 through 816 Processing helix chain 'E' and resid 827 through 830 No H-bonds generated for 'chain 'E' and resid 827 through 830' Processing helix chain 'E' and resid 838 through 851 removed outlier: 3.613A pdb=" N ILE E 846 " --> pdb=" O CYS E 842 " (cutoff:3.500A) Processing helix chain 'E' and resid 862 through 865 No H-bonds generated for 'chain 'E' and resid 862 through 865' Processing helix chain 'E' and resid 871 through 881 removed outlier: 3.884A pdb=" N ALA E 875 " --> pdb=" O PRO E 871 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N LEU E 881 " --> pdb=" O PHE E 877 " (cutoff:3.500A) Processing helix chain 'E' and resid 905 through 908 No H-bonds generated for 'chain 'E' and resid 905 through 908' Processing helix chain 'E' and resid 926 through 933 removed outlier: 3.587A pdb=" N PHE E 933 " --> pdb=" O ARG E 929 " (cutoff:3.500A) Processing helix chain 'E' and resid 1331 through 1343 removed outlier: 3.612A pdb=" N LEU E1336 " --> pdb=" O ARG E1332 " (cutoff:3.500A) Processing helix chain 'E' and resid 1349 through 1366 removed outlier: 3.769A pdb=" N ASN E1354 " --> pdb=" O PHE E1350 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ALA E1357 " --> pdb=" O GLU E1353 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N HIS E1366 " --> pdb=" O CYS E1362 " (cutoff:3.500A) Processing helix chain 'E' and resid 1376 through 1385 Processing helix chain 'F' and resid 434 through 439 Processing helix chain 'F' and resid 444 through 447 No H-bonds generated for 'chain 'F' and resid 444 through 447' Processing helix chain 'F' and resid 449 through 452 No H-bonds generated for 'chain 'F' and resid 449 through 452' Processing helix chain 'F' and resid 473 through 485 removed outlier: 3.716A pdb=" N ALA F 477 " --> pdb=" O LYS F 473 " (cutoff:3.500A) Processing helix chain 'F' and resid 509 through 516 removed outlier: 3.610A pdb=" N LEU F 513 " --> pdb=" O SER F 509 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ARG F 514 " --> pdb=" O GLU F 510 " (cutoff:3.500A) Processing helix chain 'F' and resid 533 through 535 No H-bonds generated for 'chain 'F' and resid 533 through 535' Processing helix chain 'F' and resid 546 through 558 removed outlier: 3.714A pdb=" N ALA F 557 " --> pdb=" O SER F 553 " (cutoff:3.500A) Processing helix chain 'F' and resid 603 through 611 removed outlier: 3.677A pdb=" N LEU F 608 " --> pdb=" O ARG F 604 " (cutoff:3.500A) Processing helix chain 'F' and resid 621 through 630 Processing helix chain 'F' and resid 637 through 654 removed outlier: 3.828A pdb=" N CYS F 643 " --> pdb=" O ILE F 639 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N ALA F 644 " --> pdb=" O LYS F 640 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ALA F 647 " --> pdb=" O CYS F 643 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LEU F 651 " --> pdb=" O ALA F 647 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ARG F 652 " --> pdb=" O LEU F 648 " (cutoff:3.500A) Processing helix chain 'F' and resid 676 through 682 removed outlier: 3.939A pdb=" N GLU F 680 " --> pdb=" O ALA F 676 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N VAL F 681 " --> pdb=" O LYS F 677 " (cutoff:3.500A) Processing helix chain 'F' and resid 706 through 723 removed outlier: 6.695A pdb=" N ASN F 711 " --> pdb=" O PRO F 707 " (cutoff:3.500A) removed outlier: 5.588A pdb=" N THR F 712 " --> pdb=" O LEU F 708 " (cutoff:3.500A) Processing helix chain 'F' and resid 809 through 816 Processing helix chain 'F' and resid 827 through 830 No H-bonds generated for 'chain 'F' and resid 827 through 830' Processing helix chain 'F' and resid 840 through 851 removed outlier: 3.571A pdb=" N GLN F 844 " --> pdb=" O GLU F 840 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N VAL F 845 " --> pdb=" O THR F 841 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ILE F 846 " --> pdb=" O CYS F 842 " (cutoff:3.500A) Processing helix chain 'F' and resid 862 through 865 No H-bonds generated for 'chain 'F' and resid 862 through 865' Processing helix chain 'F' and resid 871 through 883 removed outlier: 3.872A pdb=" N ALA F 875 " --> pdb=" O PRO F 871 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N THR F 879 " --> pdb=" O ALA F 875 " (cutoff:3.500A) Processing helix chain 'F' and resid 905 through 910 removed outlier: 4.518A pdb=" N LEU F 910 " --> pdb=" O GLU F 906 " (cutoff:3.500A) Processing helix chain 'F' and resid 926 through 932 Processing helix chain 'F' and resid 1332 through 1346 removed outlier: 3.972A pdb=" N LYS F1343 " --> pdb=" O VAL F1340 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N SER F1344 " --> pdb=" O VAL F1341 " (cutoff:3.500A) removed outlier: 4.707A pdb=" N GLN F1345 " --> pdb=" O LYS F1342 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N ASN F1346 " --> pdb=" O LYS F1343 " (cutoff:3.500A) Processing helix chain 'F' and resid 1349 through 1365 removed outlier: 4.190A pdb=" N CYS F1362 " --> pdb=" O VAL F1358 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N ILE F1363 " --> pdb=" O ILE F1359 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N TYR F1364 " --> pdb=" O SER F1360 " (cutoff:3.500A) Processing helix chain 'F' and resid 1375 through 1383 Processing sheet with id= A, first strand: chain 'A' and resid 593 through 596 removed outlier: 8.368A pdb=" N PHE A 594 " --> pdb=" O GLY A 462 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N LEU A 464 " --> pdb=" O PHE A 594 " (cutoff:3.500A) removed outlier: 7.276A pdb=" N PHE A 596 " --> pdb=" O LEU A 464 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N TYR A 466 " --> pdb=" O PHE A 596 " (cutoff:3.500A) removed outlier: 8.971A pdb=" N CYS A 463 " --> pdb=" O ILE A 568 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N VAL A 570 " --> pdb=" O CYS A 463 " (cutoff:3.500A) removed outlier: 8.188A pdb=" N PHE A 465 " --> pdb=" O VAL A 570 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N GLY A 572 " --> pdb=" O PHE A 465 " (cutoff:3.500A) removed outlier: 8.293A pdb=" N GLY A 467 " --> pdb=" O GLY A 572 " (cutoff:3.500A) removed outlier: 6.098A pdb=" N THR A 574 " --> pdb=" O GLY A 467 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N SER A 526 " --> pdb=" O VAL A 569 " (cutoff:3.500A) removed outlier: 8.236A pdb=" N ILE A 571 " --> pdb=" O SER A 526 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N ILE A 528 " --> pdb=" O ILE A 571 " (cutoff:3.500A) removed outlier: 7.949A pdb=" N ALA A 573 " --> pdb=" O ILE A 528 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N PHE A 530 " --> pdb=" O ALA A 573 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N ALA A 492 " --> pdb=" O ILE A 527 " (cutoff:3.500A) removed outlier: 7.977A pdb=" N PHE A 529 " --> pdb=" O ALA A 492 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N PHE A 494 " --> pdb=" O PHE A 529 " (cutoff:3.500A) removed outlier: 7.385A pdb=" N ASP A 531 " --> pdb=" O PHE A 494 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N ARG A 496 " --> pdb=" O ASP A 531 " (cutoff:3.500A) No H-bonds generated for sheet with id= A Processing sheet with id= B, first strand: chain 'A' and resid 918 through 920 removed outlier: 8.121A pdb=" N PHE A 919 " --> pdb=" O ARG A 794 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N LEU A 796 " --> pdb=" O PHE A 919 " (cutoff:3.500A) removed outlier: 8.211A pdb=" N ILE A 795 " --> pdb=" O VAL A 890 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N LEU A 892 " --> pdb=" O ILE A 795 " (cutoff:3.500A) removed outlier: 7.782A pdb=" N ILE A 797 " --> pdb=" O LEU A 892 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N ALA A 894 " --> pdb=" O ILE A 797 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N SER A 855 " --> pdb=" O LEU A 891 " (cutoff:3.500A) removed outlier: 7.689A pdb=" N LEU A 893 " --> pdb=" O SER A 855 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N VAL A 857 " --> pdb=" O LEU A 893 " (cutoff:3.500A) removed outlier: 8.398A pdb=" N THR A 895 " --> pdb=" O VAL A 857 " (cutoff:3.500A) removed outlier: 7.528A pdb=" N VAL A 859 " --> pdb=" O THR A 895 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N THR A 821 " --> pdb=" O ILE A 856 " (cutoff:3.500A) removed outlier: 7.987A pdb=" N TYR A 858 " --> pdb=" O THR A 821 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N TYR A 823 " --> pdb=" O TYR A 858 " (cutoff:3.500A) No H-bonds generated for sheet with id= B Processing sheet with id= C, first strand: chain 'B' and resid 593 through 596 removed outlier: 8.256A pdb=" N PHE B 594 " --> pdb=" O GLY B 462 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N LEU B 464 " --> pdb=" O PHE B 594 " (cutoff:3.500A) removed outlier: 7.318A pdb=" N PHE B 596 " --> pdb=" O LEU B 464 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N TYR B 466 " --> pdb=" O PHE B 596 " (cutoff:3.500A) removed outlier: 8.607A pdb=" N CYS B 463 " --> pdb=" O ILE B 568 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N VAL B 570 " --> pdb=" O CYS B 463 " (cutoff:3.500A) removed outlier: 8.088A pdb=" N PHE B 465 " --> pdb=" O VAL B 570 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N GLY B 572 " --> pdb=" O PHE B 465 " (cutoff:3.500A) removed outlier: 8.499A pdb=" N GLY B 467 " --> pdb=" O GLY B 572 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N THR B 574 " --> pdb=" O GLY B 467 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N SER B 526 " --> pdb=" O VAL B 569 " (cutoff:3.500A) removed outlier: 8.257A pdb=" N ILE B 571 " --> pdb=" O SER B 526 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N ILE B 528 " --> pdb=" O ILE B 571 " (cutoff:3.500A) removed outlier: 8.140A pdb=" N ALA B 573 " --> pdb=" O ILE B 528 " (cutoff:3.500A) removed outlier: 7.271A pdb=" N PHE B 530 " --> pdb=" O ALA B 573 " (cutoff:3.500A) removed outlier: 6.994A pdb=" N PHE B 494 " --> pdb=" O PHE B 529 " (cutoff:3.500A) No H-bonds generated for sheet with id= C Processing sheet with id= D, first strand: chain 'B' and resid 918 through 920 removed outlier: 7.942A pdb=" N PHE B 919 " --> pdb=" O ARG B 794 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N LEU B 796 " --> pdb=" O PHE B 919 " (cutoff:3.500A) removed outlier: 8.308A pdb=" N ILE B 795 " --> pdb=" O VAL B 890 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N LEU B 892 " --> pdb=" O ILE B 795 " (cutoff:3.500A) removed outlier: 7.867A pdb=" N ILE B 797 " --> pdb=" O LEU B 892 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N ALA B 894 " --> pdb=" O ILE B 797 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N SER B 855 " --> pdb=" O LEU B 891 " (cutoff:3.500A) removed outlier: 7.820A pdb=" N LEU B 893 " --> pdb=" O SER B 855 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N VAL B 857 " --> pdb=" O LEU B 893 " (cutoff:3.500A) removed outlier: 8.466A pdb=" N THR B 895 " --> pdb=" O VAL B 857 " (cutoff:3.500A) removed outlier: 7.692A pdb=" N VAL B 859 " --> pdb=" O THR B 895 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N THR B 821 " --> pdb=" O ILE B 856 " (cutoff:3.500A) removed outlier: 7.638A pdb=" N TYR B 858 " --> pdb=" O THR B 821 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N TYR B 823 " --> pdb=" O TYR B 858 " (cutoff:3.500A) No H-bonds generated for sheet with id= D Processing sheet with id= E, first strand: chain 'C' and resid 592 through 596 removed outlier: 8.492A pdb=" N CYS C 463 " --> pdb=" O ILE C 568 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N VAL C 570 " --> pdb=" O CYS C 463 " (cutoff:3.500A) removed outlier: 7.951A pdb=" N PHE C 465 " --> pdb=" O VAL C 570 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N GLY C 572 " --> pdb=" O PHE C 465 " (cutoff:3.500A) removed outlier: 8.612A pdb=" N GLY C 467 " --> pdb=" O GLY C 572 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N THR C 574 " --> pdb=" O GLY C 467 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N SER C 526 " --> pdb=" O VAL C 569 " (cutoff:3.500A) removed outlier: 8.206A pdb=" N ILE C 571 " --> pdb=" O SER C 526 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N ILE C 528 " --> pdb=" O ILE C 571 " (cutoff:3.500A) removed outlier: 8.028A pdb=" N ALA C 573 " --> pdb=" O ILE C 528 " (cutoff:3.500A) removed outlier: 7.037A pdb=" N PHE C 530 " --> pdb=" O ALA C 573 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N PHE C 494 " --> pdb=" O PHE C 529 " (cutoff:3.500A) removed outlier: 7.580A pdb=" N ASP C 531 " --> pdb=" O PHE C 494 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N ARG C 496 " --> pdb=" O ASP C 531 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'C' and resid 918 through 920 removed outlier: 8.012A pdb=" N PHE C 919 " --> pdb=" O ARG C 794 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N LEU C 796 " --> pdb=" O PHE C 919 " (cutoff:3.500A) removed outlier: 8.131A pdb=" N ILE C 795 " --> pdb=" O VAL C 890 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N LEU C 892 " --> pdb=" O ILE C 795 " (cutoff:3.500A) removed outlier: 7.816A pdb=" N ILE C 797 " --> pdb=" O LEU C 892 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N ALA C 894 " --> pdb=" O ILE C 797 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N SER C 855 " --> pdb=" O LEU C 891 " (cutoff:3.500A) removed outlier: 7.624A pdb=" N LEU C 893 " --> pdb=" O SER C 855 " (cutoff:3.500A) removed outlier: 6.021A pdb=" N VAL C 857 " --> pdb=" O LEU C 893 " (cutoff:3.500A) removed outlier: 8.292A pdb=" N THR C 895 " --> pdb=" O VAL C 857 " (cutoff:3.500A) removed outlier: 7.605A pdb=" N VAL C 859 " --> pdb=" O THR C 895 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N THR C 821 " --> pdb=" O ILE C 856 " (cutoff:3.500A) removed outlier: 7.672A pdb=" N TYR C 858 " --> pdb=" O THR C 821 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N TYR C 823 " --> pdb=" O TYR C 858 " (cutoff:3.500A) No H-bonds generated for sheet with id= F Processing sheet with id= G, first strand: chain 'D' and resid 464 through 467 Processing sheet with id= H, first strand: chain 'D' and resid 492 through 496 Processing sheet with id= I, first strand: chain 'D' and resid 918 through 920 removed outlier: 7.966A pdb=" N PHE D 919 " --> pdb=" O ARG D 794 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N LEU D 796 " --> pdb=" O PHE D 919 " (cutoff:3.500A) removed outlier: 8.256A pdb=" N ILE D 795 " --> pdb=" O VAL D 890 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N LEU D 892 " --> pdb=" O ILE D 795 " (cutoff:3.500A) removed outlier: 7.814A pdb=" N ILE D 797 " --> pdb=" O LEU D 892 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N ALA D 894 " --> pdb=" O ILE D 797 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N SER D 855 " --> pdb=" O LEU D 891 " (cutoff:3.500A) removed outlier: 7.669A pdb=" N LEU D 893 " --> pdb=" O SER D 855 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N VAL D 857 " --> pdb=" O LEU D 893 " (cutoff:3.500A) removed outlier: 8.389A pdb=" N THR D 895 " --> pdb=" O VAL D 857 " (cutoff:3.500A) removed outlier: 7.663A pdb=" N VAL D 859 " --> pdb=" O THR D 895 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N THR D 821 " --> pdb=" O ILE D 856 " (cutoff:3.500A) removed outlier: 7.499A pdb=" N TYR D 858 " --> pdb=" O THR D 821 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N TYR D 823 " --> pdb=" O TYR D 858 " (cutoff:3.500A) No H-bonds generated for sheet with id= I Processing sheet with id= J, first strand: chain 'E' and resid 594 through 596 removed outlier: 8.728A pdb=" N CYS E 463 " --> pdb=" O ILE E 568 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N VAL E 570 " --> pdb=" O CYS E 463 " (cutoff:3.500A) removed outlier: 7.941A pdb=" N PHE E 465 " --> pdb=" O VAL E 570 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N GLY E 572 " --> pdb=" O PHE E 465 " (cutoff:3.500A) removed outlier: 8.615A pdb=" N GLY E 467 " --> pdb=" O GLY E 572 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N SER E 526 " --> pdb=" O VAL E 569 " (cutoff:3.500A) removed outlier: 8.123A pdb=" N ILE E 571 " --> pdb=" O SER E 526 " (cutoff:3.500A) removed outlier: 6.107A pdb=" N ILE E 528 " --> pdb=" O ILE E 571 " (cutoff:3.500A) removed outlier: 7.800A pdb=" N ALA E 573 " --> pdb=" O ILE E 528 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N PHE E 530 " --> pdb=" O ALA E 573 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N ALA E 492 " --> pdb=" O ILE E 527 " (cutoff:3.500A) removed outlier: 7.839A pdb=" N PHE E 529 " --> pdb=" O ALA E 492 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N PHE E 494 " --> pdb=" O PHE E 529 " (cutoff:3.500A) removed outlier: 7.671A pdb=" N ASP E 531 " --> pdb=" O PHE E 494 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N ARG E 496 " --> pdb=" O ASP E 531 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'E' and resid 918 through 920 removed outlier: 8.042A pdb=" N PHE E 919 " --> pdb=" O ARG E 794 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N LEU E 796 " --> pdb=" O PHE E 919 " (cutoff:3.500A) removed outlier: 8.061A pdb=" N ILE E 795 " --> pdb=" O VAL E 890 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N LEU E 892 " --> pdb=" O ILE E 795 " (cutoff:3.500A) removed outlier: 7.633A pdb=" N ILE E 797 " --> pdb=" O LEU E 892 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N ALA E 894 " --> pdb=" O ILE E 797 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N SER E 855 " --> pdb=" O LEU E 891 " (cutoff:3.500A) removed outlier: 7.728A pdb=" N LEU E 893 " --> pdb=" O SER E 855 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N VAL E 857 " --> pdb=" O LEU E 893 " (cutoff:3.500A) removed outlier: 8.382A pdb=" N THR E 895 " --> pdb=" O VAL E 857 " (cutoff:3.500A) removed outlier: 7.876A pdb=" N VAL E 859 " --> pdb=" O THR E 895 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'F' and resid 594 through 596 removed outlier: 8.765A pdb=" N CYS F 463 " --> pdb=" O ILE F 568 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N VAL F 570 " --> pdb=" O CYS F 463 " (cutoff:3.500A) removed outlier: 8.009A pdb=" N PHE F 465 " --> pdb=" O VAL F 570 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N GLY F 572 " --> pdb=" O PHE F 465 " (cutoff:3.500A) removed outlier: 8.615A pdb=" N GLY F 467 " --> pdb=" O GLY F 572 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N THR F 574 " --> pdb=" O GLY F 467 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N SER F 526 " --> pdb=" O VAL F 569 " (cutoff:3.500A) removed outlier: 7.798A pdb=" N ILE F 571 " --> pdb=" O SER F 526 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N ILE F 528 " --> pdb=" O ILE F 571 " (cutoff:3.500A) removed outlier: 8.061A pdb=" N ALA F 573 " --> pdb=" O ILE F 528 " (cutoff:3.500A) removed outlier: 7.107A pdb=" N PHE F 530 " --> pdb=" O ALA F 573 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N ALA F 492 " --> pdb=" O ILE F 527 " (cutoff:3.500A) removed outlier: 7.572A pdb=" N PHE F 529 " --> pdb=" O ALA F 492 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N PHE F 494 " --> pdb=" O PHE F 529 " (cutoff:3.500A) removed outlier: 7.314A pdb=" N ASP F 531 " --> pdb=" O PHE F 494 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N ARG F 496 " --> pdb=" O ASP F 531 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'F' and resid 918 through 920 removed outlier: 7.819A pdb=" N PHE F 919 " --> pdb=" O ARG F 794 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N LEU F 796 " --> pdb=" O PHE F 919 " (cutoff:3.500A) removed outlier: 8.260A pdb=" N ILE F 795 " --> pdb=" O VAL F 890 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N LEU F 892 " --> pdb=" O ILE F 795 " (cutoff:3.500A) removed outlier: 7.719A pdb=" N ILE F 797 " --> pdb=" O LEU F 892 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N ALA F 894 " --> pdb=" O ILE F 797 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N SER F 855 " --> pdb=" O LEU F 891 " (cutoff:3.500A) removed outlier: 7.513A pdb=" N LEU F 893 " --> pdb=" O SER F 855 " (cutoff:3.500A) removed outlier: 6.098A pdb=" N VAL F 857 " --> pdb=" O LEU F 893 " (cutoff:3.500A) removed outlier: 8.338A pdb=" N THR F 895 " --> pdb=" O VAL F 857 " (cutoff:3.500A) removed outlier: 7.620A pdb=" N VAL F 859 " --> pdb=" O THR F 895 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N THR F 821 " --> pdb=" O ILE F 856 " (cutoff:3.500A) removed outlier: 7.754A pdb=" N TYR F 858 " --> pdb=" O THR F 821 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N TYR F 823 " --> pdb=" O TYR F 858 " (cutoff:3.500A) No H-bonds generated for sheet with id= M 621 hydrogen bonds defined for protein. 1752 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 7.88 Time building geometry restraints manager: 11.37 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 8225 1.34 - 1.46: 4908 1.46 - 1.58: 12650 1.58 - 1.70: 28 1.70 - 1.82: 159 Bond restraints: 25970 Sorted by residual: bond pdb=" C4 ATP E1402 " pdb=" C5 ATP E1402 " ideal model delta sigma weight residual 1.388 1.463 -0.075 1.00e-02 1.00e+04 5.58e+01 bond pdb=" O1A ATP C1401 " pdb=" PA ATP C1401 " ideal model delta sigma weight residual 1.477 1.557 -0.080 1.10e-02 8.26e+03 5.31e+01 bond pdb=" C4 ATP B1401 " pdb=" C5 ATP B1401 " ideal model delta sigma weight residual 1.388 1.460 -0.072 1.00e-02 1.00e+04 5.24e+01 bond pdb=" C4 ATP C1401 " pdb=" C5 ATP C1401 " ideal model delta sigma weight residual 1.388 1.460 -0.072 1.00e-02 1.00e+04 5.17e+01 bond pdb=" C4 ATP C1402 " pdb=" C5 ATP C1402 " ideal model delta sigma weight residual 1.388 1.459 -0.071 1.00e-02 1.00e+04 5.05e+01 ... (remaining 25965 not shown) Histogram of bond angle deviations from ideal: 98.35 - 105.98: 781 105.98 - 113.61: 14626 113.61 - 121.25: 13350 121.25 - 128.88: 6289 128.88 - 136.51: 169 Bond angle restraints: 35215 Sorted by residual: angle pdb=" PB ATP C1402 " pdb=" O3B ATP C1402 " pdb=" PG ATP C1402 " ideal model delta sigma weight residual 139.87 113.46 26.41 1.00e+00 1.00e+00 6.98e+02 angle pdb=" PB ATP C1401 " pdb=" O3B ATP C1401 " pdb=" PG ATP C1401 " ideal model delta sigma weight residual 139.87 117.90 21.97 1.00e+00 1.00e+00 4.83e+02 angle pdb=" PB ATP E1402 " pdb=" O3B ATP E1402 " pdb=" PG ATP E1402 " ideal model delta sigma weight residual 139.87 118.76 21.11 1.00e+00 1.00e+00 4.45e+02 angle pdb=" PB ATP B1401 " pdb=" O3B ATP B1401 " pdb=" PG ATP B1401 " ideal model delta sigma weight residual 139.87 119.17 20.70 1.00e+00 1.00e+00 4.29e+02 angle pdb=" PA ATP C1401 " pdb=" O3A ATP C1401 " pdb=" PB ATP C1401 " ideal model delta sigma weight residual 136.83 117.40 19.43 1.00e+00 1.00e+00 3.78e+02 ... (remaining 35210 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.85: 13975 17.85 - 35.71: 1510 35.71 - 53.56: 393 53.56 - 71.41: 95 71.41 - 89.27: 26 Dihedral angle restraints: 15999 sinusoidal: 6710 harmonic: 9289 Sorted by residual: dihedral pdb=" CA ALA A 693 " pdb=" C ALA A 693 " pdb=" N VAL A 694 " pdb=" CA VAL A 694 " ideal model delta harmonic sigma weight residual -180.00 -154.25 -25.75 0 5.00e+00 4.00e-02 2.65e+01 dihedral pdb=" CA TRP C 505 " pdb=" C TRP C 505 " pdb=" N VAL C 506 " pdb=" CA VAL C 506 " ideal model delta harmonic sigma weight residual -180.00 -155.55 -24.45 0 5.00e+00 4.00e-02 2.39e+01 dihedral pdb=" CA TRP B 505 " pdb=" C TRP B 505 " pdb=" N VAL B 506 " pdb=" CA VAL B 506 " ideal model delta harmonic sigma weight residual -180.00 -155.56 -24.44 0 5.00e+00 4.00e-02 2.39e+01 ... (remaining 15996 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.094: 3675 0.094 - 0.188: 286 0.188 - 0.282: 9 0.282 - 0.376: 0 0.376 - 0.471: 2 Chirality restraints: 3972 Sorted by residual: chirality pdb=" CA PHE E 425 " pdb=" N PHE E 425 " pdb=" C PHE E 425 " pdb=" CB PHE E 425 " both_signs ideal model delta sigma weight residual False 2.51 2.04 0.47 2.00e-01 2.50e+01 5.54e+00 chirality pdb=" CA PHE F 425 " pdb=" N PHE F 425 " pdb=" C PHE F 425 " pdb=" CB PHE F 425 " both_signs ideal model delta sigma weight residual False 2.51 2.07 0.44 2.00e-01 2.50e+01 4.77e+00 chirality pdb=" CA ARG D 490 " pdb=" N ARG D 490 " pdb=" C ARG D 490 " pdb=" CB ARG D 490 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.55e+00 ... (remaining 3969 not shown) Planarity restraints: 4517 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS E 473 " -0.019 2.00e-02 2.50e+03 3.71e-02 1.38e+01 pdb=" C LYS E 473 " 0.064 2.00e-02 2.50e+03 pdb=" O LYS E 473 " -0.024 2.00e-02 2.50e+03 pdb=" N THR E 474 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR C 554 " 0.014 2.00e-02 2.50e+03 2.87e-02 8.25e+00 pdb=" C THR C 554 " -0.050 2.00e-02 2.50e+03 pdb=" O THR C 554 " 0.018 2.00e-02 2.50e+03 pdb=" N LEU C 555 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PRO D 468 " -0.044 5.00e-02 4.00e+02 6.68e-02 7.14e+00 pdb=" N PRO D 469 " 0.116 5.00e-02 4.00e+02 pdb=" CA PRO D 469 " -0.035 5.00e-02 4.00e+02 pdb=" CD PRO D 469 " -0.037 5.00e-02 4.00e+02 ... (remaining 4514 not shown) Histogram of nonbonded interaction distances: 1.85 - 2.46: 123 2.46 - 3.07: 16745 3.07 - 3.68: 35616 3.68 - 4.29: 54865 4.29 - 4.90: 92076 Nonbonded interactions: 199425 Sorted by model distance: nonbonded pdb=" NZ LYS A 454 " pdb=" ND2 ASN B 616 " model vdw 1.854 3.200 nonbonded pdb=" OD1 ASP C 534 " pdb=" OG1 THR C 574 " model vdw 2.032 2.440 nonbonded pdb=" OD1 ASN A 616 " pdb=" CD PRO A 617 " model vdw 2.045 3.440 nonbonded pdb=" OG SER E 837 " pdb=" OE1 GLU E 840 " model vdw 2.053 2.440 nonbonded pdb=" OH TYR D 786 " pdb=" OE1 GLN E 940 " model vdw 2.101 2.440 ... (remaining 199420 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 422 through 688 or resid 696 through 727 or resid 787 thro \ ugh 944 or resid 1331 through 1388)) selection = (chain 'B' and (resid 422 through 539 or resid 546 through 688 or resid 696 thro \ ugh 727 or resid 787 through 944 or resid 1331 through 1388)) selection = (chain 'C' and (resid 422 through 539 or resid 546 through 688 or resid 696 thro \ ugh 727 or resid 787 through 944 or resid 1331 through 1388)) selection = (chain 'D' and (resid 422 through 539 or resid 546 through 688 or resid 696 thro \ ugh 727 or resid 787 through 944 or resid 1331 through 1388)) selection = (chain 'E' and (resid 422 through 539 or resid 546 through 688 or resid 696 thro \ ugh 727 or resid 787 through 944 or resid 1331 through 1388)) selection = (chain 'F' and (resid 422 through 539 or resid 546 through 727 or resid 787 thro \ ugh 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.080 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: 6.840 Check model and map are aligned: 0.410 Set scattering table: 0.200 Process input model: 67.730 Find NCS groups from input model: 2.300 Set up NCS constraints: 0.110 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: 0.020 Load rotamer database and sin/cos tables:2.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 81.620 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8502 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 : 0.007 0.080 25970 Z= 0.442 Angle : 0.924 26.412 35215 Z= 0.615 Chirality : 0.051 0.471 3972 Planarity : 0.005 0.067 4517 Dihedral : 16.367 89.267 9941 Min Nonbonded Distance : 1.854 Molprobity Statistics. All-atom Clashscore : 12.44 Ramachandran Plot: Outliers : 0.45 % Allowed : 9.22 % Favored : 90.33 % Rotamer: Outliers : 3.65 % Allowed : 8.77 % Favored : 87.58 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 5.88 % 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: -4.15 (0.13), residues: 3134 helix: -2.72 (0.11), residues: 1431 sheet: -1.35 (0.25), residues: 391 loop : -3.13 (0.15), residues: 1312 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP E 505 HIS 0.006 0.001 HIS F 861 PHE 0.013 0.002 PHE B 724 TYR 0.008 0.001 TYR A 466 ARG 0.010 0.000 ARG C 576 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6268 Ramachandran restraints generated. 3134 Oldfield, 0 Emsley, 3134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6268 Ramachandran restraints generated. 3134 Oldfield, 0 Emsley, 3134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 450 residues out of total 2794 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 348 time to evaluate : 3.596 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 586 ARG cc_start: 0.7043 (mpt90) cc_final: 0.6219 (tmm160) REVERT: A 666 GLN cc_start: 0.5817 (OUTLIER) cc_final: 0.5481 (mt0) REVERT: A 792 ARG cc_start: 0.8907 (OUTLIER) cc_final: 0.8061 (mtt90) REVERT: B 867 GLU cc_start: 0.7849 (OUTLIER) cc_final: 0.7508 (mt-10) REVERT: B 1384 GLU cc_start: 0.7469 (OUTLIER) cc_final: 0.7190 (pp20) REVERT: C 658 ILE cc_start: 0.8314 (OUTLIER) cc_final: 0.8114 (tt) REVERT: C 1332 ARG cc_start: 0.7184 (ptm160) cc_final: 0.6968 (ptm160) REVERT: D 495 MET cc_start: 0.7655 (tmm) cc_final: 0.7416 (tmm) REVERT: D 677 LYS cc_start: 0.8085 (tppt) cc_final: 0.7844 (tppt) REVERT: D 867 GLU cc_start: 0.7650 (OUTLIER) cc_final: 0.7381 (mm-30) REVERT: D 1338 LYS cc_start: 0.8439 (tttt) cc_final: 0.8226 (tmtt) REVERT: E 559 MET cc_start: 0.8953 (ttm) cc_final: 0.8722 (ttp) REVERT: E 683 MET cc_start: 0.8658 (mtp) cc_final: 0.8341 (mtt) REVERT: F 489 LYS cc_start: 0.8177 (OUTLIER) cc_final: 0.7796 (mttt) REVERT: F 576 ARG cc_start: 0.7713 (mtt90) cc_final: 0.7024 (mtm-85) REVERT: F 789 MET cc_start: 0.8449 (OUTLIER) cc_final: 0.8142 (ttt) REVERT: F 867 GLU cc_start: 0.7952 (OUTLIER) cc_final: 0.7630 (mm-30) outliers start: 102 outliers final: 44 residues processed: 427 average time/residue: 0.4541 time to fit residues: 281.5071 Evaluate side-chains 310 residues out of total 2794 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 257 time to evaluate : 3.065 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 486 GLN Chi-restraints excluded: chain A residue 489 LYS Chi-restraints excluded: chain A residue 618 LYS Chi-restraints excluded: chain A residue 658 ILE Chi-restraints excluded: chain A residue 661 THR Chi-restraints excluded: chain A residue 665 LEU Chi-restraints excluded: chain A residue 666 GLN Chi-restraints excluded: chain A residue 792 ARG Chi-restraints excluded: chain A residue 926 LYS Chi-restraints excluded: chain A residue 943 LYS Chi-restraints excluded: chain A residue 1358 VAL Chi-restraints excluded: chain B residue 427 SER Chi-restraints excluded: chain B residue 533 ILE Chi-restraints excluded: chain B residue 556 LEU Chi-restraints excluded: chain B residue 616 ASN Chi-restraints excluded: chain B residue 618 LYS Chi-restraints excluded: chain B residue 659 TYR Chi-restraints excluded: chain B residue 786 TYR Chi-restraints excluded: chain B residue 789 MET Chi-restraints excluded: chain B residue 867 GLU Chi-restraints excluded: chain B residue 928 GLU Chi-restraints excluded: chain B residue 943 LYS Chi-restraints excluded: chain B residue 1358 VAL Chi-restraints excluded: chain B residue 1384 GLU Chi-restraints excluded: chain B residue 1385 ASN Chi-restraints excluded: chain C residue 427 SER Chi-restraints excluded: chain C residue 658 ILE Chi-restraints excluded: chain C residue 669 LEU Chi-restraints excluded: chain C residue 943 LYS Chi-restraints excluded: chain C residue 1361 GLN Chi-restraints excluded: chain D residue 427 SER Chi-restraints excluded: chain D residue 618 LYS Chi-restraints excluded: chain D residue 658 ILE Chi-restraints excluded: chain D residue 667 LEU Chi-restraints excluded: chain D residue 789 MET Chi-restraints excluded: chain D residue 867 GLU Chi-restraints excluded: chain D residue 1358 VAL Chi-restraints excluded: chain E residue 618 LYS Chi-restraints excluded: chain E residue 666 GLN Chi-restraints excluded: chain E residue 786 TYR Chi-restraints excluded: chain E residue 789 MET Chi-restraints excluded: chain E residue 867 GLU Chi-restraints excluded: chain E residue 1358 VAL Chi-restraints excluded: chain E residue 1388 CYS Chi-restraints excluded: chain F residue 426 ASP Chi-restraints excluded: chain F residue 488 ASP Chi-restraints excluded: chain F residue 489 LYS Chi-restraints excluded: chain F residue 661 THR Chi-restraints excluded: chain F residue 789 MET Chi-restraints excluded: chain F residue 867 GLU Chi-restraints excluded: chain F residue 928 GLU Chi-restraints excluded: chain F residue 1358 VAL Chi-restraints excluded: chain F residue 1361 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 265 optimal weight: 8.9990 chunk 237 optimal weight: 8.9990 chunk 132 optimal weight: 4.9990 chunk 81 optimal weight: 3.9990 chunk 160 optimal weight: 5.9990 chunk 127 optimal weight: 0.9990 chunk 246 optimal weight: 0.9990 chunk 95 optimal weight: 6.9990 chunk 149 optimal weight: 0.0980 chunk 183 optimal weight: 1.9990 chunk 285 optimal weight: 0.0010 overall best weight: 0.8192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 458 GLN A 691 GLN A 808 HIS A 844 GLN A1377 GLN B 512 GLN B 611 HIS B 808 HIS B 844 GLN C 673 ASN C 711 ASN C1346 ASN D 611 HIS D 657 GLN E 546 GLN E 575 ASN E 710 GLN ** E1335 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 544 GLN F 808 HIS F 920 ASN F 922 GLN F1345 GLN F1377 GLN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8455 moved from start: 0.1085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 25970 Z= 0.179 Angle : 0.611 12.675 35215 Z= 0.299 Chirality : 0.043 0.222 3972 Planarity : 0.005 0.059 4517 Dihedral : 10.578 92.535 3736 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.16 % Allowed : 7.24 % Favored : 92.60 % Rotamer: Outliers : 2.36 % Allowed : 12.24 % Favored : 85.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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: -2.75 (0.14), residues: 3134 helix: -1.45 (0.13), residues: 1415 sheet: -0.88 (0.25), residues: 393 loop : -2.46 (0.16), residues: 1326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP E 505 HIS 0.003 0.001 HIS B 548 PHE 0.021 0.001 PHE E 791 TYR 0.016 0.001 TYR A 448 ARG 0.006 0.000 ARG F 424 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6268 Ramachandran restraints generated. 3134 Oldfield, 0 Emsley, 3134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6268 Ramachandran restraints generated. 3134 Oldfield, 0 Emsley, 3134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 343 residues out of total 2794 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 277 time to evaluate : 2.893 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 586 ARG cc_start: 0.7060 (mpt90) cc_final: 0.6210 (tmm160) REVERT: A 666 GLN cc_start: 0.5998 (OUTLIER) cc_final: 0.5569 (mt0) REVERT: A 792 ARG cc_start: 0.9033 (OUTLIER) cc_final: 0.8070 (mtt90) REVERT: A 931 LYS cc_start: 0.8681 (tttt) cc_final: 0.8374 (ttmt) REVERT: B 683 MET cc_start: 0.8830 (mtp) cc_final: 0.8575 (mtt) REVERT: B 786 TYR cc_start: 0.6478 (OUTLIER) cc_final: 0.5667 (t80) REVERT: B 1384 GLU cc_start: 0.7511 (OUTLIER) cc_final: 0.7201 (pp20) REVERT: C 562 LEU cc_start: 0.8600 (OUTLIER) cc_final: 0.8316 (tt) REVERT: C 658 ILE cc_start: 0.8258 (tt) cc_final: 0.8039 (tt) REVERT: C 1332 ARG cc_start: 0.7013 (ptm160) cc_final: 0.6789 (ptm160) REVERT: D 867 GLU cc_start: 0.7807 (OUTLIER) cc_final: 0.7589 (mm-30) REVERT: E 558 LEU cc_start: 0.9170 (OUTLIER) cc_final: 0.8838 (pt) REVERT: E 683 MET cc_start: 0.8636 (mtp) cc_final: 0.8289 (mtt) REVERT: E 1372 LYS cc_start: 0.6327 (mmtt) cc_final: 0.4815 (pttp) REVERT: F 576 ARG cc_start: 0.7626 (mtt90) cc_final: 0.6973 (mtm-85) REVERT: F 867 GLU cc_start: 0.8076 (OUTLIER) cc_final: 0.7792 (mm-30) outliers start: 66 outliers final: 26 residues processed: 327 average time/residue: 0.4138 time to fit residues: 203.7263 Evaluate side-chains 280 residues out of total 2794 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 246 time to evaluate : 3.152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 455 PHE Chi-restraints excluded: chain A residue 661 THR Chi-restraints excluded: chain A residue 665 LEU Chi-restraints excluded: chain A residue 666 GLN Chi-restraints excluded: chain A residue 703 THR Chi-restraints excluded: chain A residue 792 ARG Chi-restraints excluded: chain A residue 821 THR Chi-restraints excluded: chain A residue 943 LYS Chi-restraints excluded: chain A residue 1358 VAL Chi-restraints excluded: chain A residue 1388 CYS Chi-restraints excluded: chain B residue 533 ILE Chi-restraints excluded: chain B residue 648 LEU Chi-restraints excluded: chain B residue 695 THR Chi-restraints excluded: chain B residue 786 TYR Chi-restraints excluded: chain B residue 867 GLU Chi-restraints excluded: chain B residue 937 ILE Chi-restraints excluded: chain B residue 1373 THR Chi-restraints excluded: chain B residue 1384 GLU Chi-restraints excluded: chain C residue 562 LEU Chi-restraints excluded: chain C residue 667 LEU Chi-restraints excluded: chain C residue 886 SER Chi-restraints excluded: chain C residue 1379 MET Chi-restraints excluded: chain D residue 618 LYS Chi-restraints excluded: chain D residue 867 GLU Chi-restraints excluded: chain E residue 558 LEU Chi-restraints excluded: chain E residue 662 SER Chi-restraints excluded: chain E residue 867 GLU Chi-restraints excluded: chain F residue 488 ASP Chi-restraints excluded: chain F residue 502 LEU Chi-restraints excluded: chain F residue 630 ASN Chi-restraints excluded: chain F residue 661 THR Chi-restraints excluded: chain F residue 720 LEU Chi-restraints excluded: chain F residue 867 GLU Chi-restraints excluded: chain F residue 938 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 158 optimal weight: 7.9990 chunk 88 optimal weight: 0.0470 chunk 237 optimal weight: 0.0370 chunk 194 optimal weight: 5.9990 chunk 78 optimal weight: 10.0000 chunk 285 optimal weight: 5.9990 chunk 308 optimal weight: 3.9990 chunk 254 optimal weight: 3.9990 chunk 283 optimal weight: 6.9990 chunk 97 optimal weight: 5.9990 chunk 229 optimal weight: 4.9990 overall best weight: 2.6162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C1346 ASN E 575 ASN ** E1335 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E1366 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8508 moved from start: 0.1204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 25970 Z= 0.308 Angle : 0.659 11.853 35215 Z= 0.319 Chirality : 0.045 0.354 3972 Planarity : 0.005 0.061 4517 Dihedral : 9.284 79.355 3644 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.16 % Allowed : 8.10 % Favored : 91.74 % Rotamer: Outliers : 3.08 % Allowed : 13.89 % Favored : 83.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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: -2.22 (0.15), residues: 3134 helix: -1.01 (0.13), residues: 1421 sheet: -0.62 (0.25), residues: 393 loop : -2.19 (0.17), residues: 1320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 505 HIS 0.005 0.001 HIS F 861 PHE 0.015 0.001 PHE E 791 TYR 0.012 0.001 TYR A 448 ARG 0.005 0.000 ARG D 851 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6268 Ramachandran restraints generated. 3134 Oldfield, 0 Emsley, 3134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6268 Ramachandran restraints generated. 3134 Oldfield, 0 Emsley, 3134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 333 residues out of total 2794 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 247 time to evaluate : 2.823 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 586 ARG cc_start: 0.7186 (mpt90) cc_final: 0.6263 (tmm160) REVERT: A 931 LYS cc_start: 0.8689 (tttt) cc_final: 0.8325 (ttmt) REVERT: A 943 LYS cc_start: 0.6966 (OUTLIER) cc_final: 0.5363 (mptt) REVERT: B 672 ILE cc_start: 0.7745 (OUTLIER) cc_final: 0.7523 (mt) REVERT: B 786 TYR cc_start: 0.6562 (OUTLIER) cc_final: 0.5693 (t80) REVERT: B 1384 GLU cc_start: 0.7512 (OUTLIER) cc_final: 0.7224 (pp20) REVERT: C 562 LEU cc_start: 0.8641 (OUTLIER) cc_final: 0.8329 (tt) REVERT: C 658 ILE cc_start: 0.8405 (tt) cc_final: 0.8166 (tt) REVERT: C 701 LEU cc_start: 0.9103 (OUTLIER) cc_final: 0.8858 (mm) REVERT: C 1346 ASN cc_start: 0.7993 (OUTLIER) cc_final: 0.7596 (t0) REVERT: C 1390 ARG cc_start: 0.7396 (OUTLIER) cc_final: 0.6807 (mmm160) REVERT: D 495 MET cc_start: 0.7605 (tpt) cc_final: 0.7244 (tpt) REVERT: D 683 MET cc_start: 0.8973 (mtm) cc_final: 0.8527 (mtt) REVERT: E 558 LEU cc_start: 0.9217 (OUTLIER) cc_final: 0.8830 (pt) REVERT: E 683 MET cc_start: 0.8675 (mtp) cc_final: 0.8329 (mtt) REVERT: E 1372 LYS cc_start: 0.6292 (mmtt) cc_final: 0.4856 (pttp) REVERT: F 576 ARG cc_start: 0.7632 (mtt90) cc_final: 0.7011 (mtm-85) REVERT: F 616 ASN cc_start: 0.6832 (OUTLIER) cc_final: 0.6382 (p0) outliers start: 86 outliers final: 48 residues processed: 313 average time/residue: 0.4034 time to fit residues: 190.5543 Evaluate side-chains 292 residues out of total 2794 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 234 time to evaluate : 3.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 451 VAL Chi-restraints excluded: chain A residue 455 PHE Chi-restraints excluded: chain A residue 534 ASP Chi-restraints excluded: chain A residue 661 THR Chi-restraints excluded: chain A residue 668 ASP Chi-restraints excluded: chain A residue 686 MET Chi-restraints excluded: chain A residue 703 THR Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 821 THR Chi-restraints excluded: chain A residue 937 ILE Chi-restraints excluded: chain A residue 943 LYS Chi-restraints excluded: chain A residue 1358 VAL Chi-restraints excluded: chain A residue 1360 SER Chi-restraints excluded: chain A residue 1388 CYS Chi-restraints excluded: chain B residue 447 LEU Chi-restraints excluded: chain B residue 475 LEU Chi-restraints excluded: chain B residue 533 ILE Chi-restraints excluded: chain B residue 554 THR Chi-restraints excluded: chain B residue 556 LEU Chi-restraints excluded: chain B residue 591 ASP Chi-restraints excluded: chain B residue 616 ASN Chi-restraints excluded: chain B residue 648 LEU Chi-restraints excluded: chain B residue 672 ILE Chi-restraints excluded: chain B residue 695 THR Chi-restraints excluded: chain B residue 786 TYR Chi-restraints excluded: chain B residue 821 THR Chi-restraints excluded: chain B residue 839 GLU Chi-restraints excluded: chain B residue 867 GLU Chi-restraints excluded: chain B residue 937 ILE Chi-restraints excluded: chain B residue 1373 THR Chi-restraints excluded: chain B residue 1384 GLU Chi-restraints excluded: chain C residue 562 LEU Chi-restraints excluded: chain C residue 667 LEU Chi-restraints excluded: chain C residue 701 LEU Chi-restraints excluded: chain C residue 821 THR Chi-restraints excluded: chain C residue 886 SER Chi-restraints excluded: chain C residue 1346 ASN Chi-restraints excluded: chain C residue 1379 MET Chi-restraints excluded: chain C residue 1390 ARG Chi-restraints excluded: chain D residue 591 ASP Chi-restraints excluded: chain D residue 618 LYS Chi-restraints excluded: chain E residue 495 MET Chi-restraints excluded: chain E residue 558 LEU Chi-restraints excluded: chain E residue 642 ILE Chi-restraints excluded: chain E residue 660 THR Chi-restraints excluded: chain E residue 662 SER Chi-restraints excluded: chain E residue 841 THR Chi-restraints excluded: chain E residue 852 THR Chi-restraints excluded: chain E residue 867 GLU Chi-restraints excluded: chain E residue 938 LEU Chi-restraints excluded: chain F residue 495 MET Chi-restraints excluded: chain F residue 502 LEU Chi-restraints excluded: chain F residue 616 ASN Chi-restraints excluded: chain F residue 630 ASN Chi-restraints excluded: chain F residue 661 THR Chi-restraints excluded: chain F residue 720 LEU Chi-restraints excluded: chain F residue 821 THR Chi-restraints excluded: chain F residue 938 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 282 optimal weight: 9.9990 chunk 214 optimal weight: 0.9990 chunk 148 optimal weight: 2.9990 chunk 31 optimal weight: 3.9990 chunk 136 optimal weight: 1.9990 chunk 191 optimal weight: 3.9990 chunk 286 optimal weight: 20.0000 chunk 303 optimal weight: 3.9990 chunk 149 optimal weight: 1.9990 chunk 271 optimal weight: 10.0000 chunk 81 optimal weight: 0.0040 overall best weight: 1.6000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 575 ASN ** E1335 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8483 moved from start: 0.1412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 25970 Z= 0.209 Angle : 0.596 10.845 35215 Z= 0.289 Chirality : 0.043 0.328 3972 Planarity : 0.005 0.059 4517 Dihedral : 8.779 83.815 3627 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.16 % Allowed : 7.15 % Favored : 92.69 % Rotamer: Outliers : 2.76 % Allowed : 15.64 % Favored : 81.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.34 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.81 (0.15), residues: 3134 helix: -0.65 (0.14), residues: 1410 sheet: -0.39 (0.26), residues: 390 loop : -2.01 (0.17), residues: 1334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 505 HIS 0.004 0.001 HIS F 861 PHE 0.014 0.001 PHE F 877 TYR 0.011 0.001 TYR A 448 ARG 0.005 0.000 ARG D 851 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6268 Ramachandran restraints generated. 3134 Oldfield, 0 Emsley, 3134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6268 Ramachandran restraints generated. 3134 Oldfield, 0 Emsley, 3134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 332 residues out of total 2794 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 255 time to evaluate : 3.349 Fit side-chains revert: symmetry clash REVERT: A 586 ARG cc_start: 0.7173 (mpt90) cc_final: 0.6257 (tmm160) REVERT: A 931 LYS cc_start: 0.8645 (tttt) cc_final: 0.8275 (ttmt) REVERT: B 672 ILE cc_start: 0.7744 (OUTLIER) cc_final: 0.7508 (mt) REVERT: B 683 MET cc_start: 0.8869 (mtp) cc_final: 0.8572 (mtt) REVERT: B 786 TYR cc_start: 0.6710 (OUTLIER) cc_final: 0.5705 (t80) REVERT: B 1384 GLU cc_start: 0.7483 (OUTLIER) cc_final: 0.7234 (pp20) REVERT: C 562 LEU cc_start: 0.8589 (OUTLIER) cc_final: 0.8345 (tt) REVERT: C 658 ILE cc_start: 0.8415 (tt) cc_final: 0.8145 (tt) REVERT: C 833 VAL cc_start: 0.8708 (t) cc_final: 0.8416 (m) REVERT: C 1390 ARG cc_start: 0.7289 (OUTLIER) cc_final: 0.6902 (mmm160) REVERT: D 683 MET cc_start: 0.8948 (mtm) cc_final: 0.8516 (mtt) REVERT: E 558 LEU cc_start: 0.9153 (OUTLIER) cc_final: 0.8801 (pt) REVERT: E 559 MET cc_start: 0.8686 (ttm) cc_final: 0.8111 (ttp) REVERT: E 683 MET cc_start: 0.8664 (mtp) cc_final: 0.8317 (mtt) REVERT: E 867 GLU cc_start: 0.7948 (OUTLIER) cc_final: 0.7267 (mm-30) REVERT: E 1372 LYS cc_start: 0.6398 (mmtt) cc_final: 0.4900 (pttp) REVERT: F 576 ARG cc_start: 0.7606 (mtt90) cc_final: 0.7001 (mtm-85) REVERT: F 820 PHE cc_start: 0.8144 (m-80) cc_final: 0.7871 (m-80) REVERT: F 1375 LEU cc_start: 0.8161 (OUTLIER) cc_final: 0.7959 (tt) outliers start: 77 outliers final: 51 residues processed: 311 average time/residue: 0.4174 time to fit residues: 195.9245 Evaluate side-chains 296 residues out of total 2794 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 237 time to evaluate : 2.818 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 451 VAL Chi-restraints excluded: chain A residue 455 PHE Chi-restraints excluded: chain A residue 534 ASP Chi-restraints excluded: chain A residue 618 LYS Chi-restraints excluded: chain A residue 632 VAL Chi-restraints excluded: chain A residue 668 ASP Chi-restraints excluded: chain A residue 686 MET Chi-restraints excluded: chain A residue 703 THR Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 821 THR Chi-restraints excluded: chain A residue 937 ILE Chi-restraints excluded: chain A residue 1358 VAL Chi-restraints excluded: chain A residue 1388 CYS Chi-restraints excluded: chain B residue 438 LEU Chi-restraints excluded: chain B residue 447 LEU Chi-restraints excluded: chain B residue 475 LEU Chi-restraints excluded: chain B residue 510 GLU Chi-restraints excluded: chain B residue 533 ILE Chi-restraints excluded: chain B residue 556 LEU Chi-restraints excluded: chain B residue 563 ASP Chi-restraints excluded: chain B residue 591 ASP Chi-restraints excluded: chain B residue 622 THR Chi-restraints excluded: chain B residue 648 LEU Chi-restraints excluded: chain B residue 672 ILE Chi-restraints excluded: chain B residue 694 VAL Chi-restraints excluded: chain B residue 695 THR Chi-restraints excluded: chain B residue 786 TYR Chi-restraints excluded: chain B residue 839 GLU Chi-restraints excluded: chain B residue 867 GLU Chi-restraints excluded: chain B residue 937 ILE Chi-restraints excluded: chain B residue 1384 GLU Chi-restraints excluded: chain C residue 486 GLN Chi-restraints excluded: chain C residue 562 LEU Chi-restraints excluded: chain C residue 886 SER Chi-restraints excluded: chain C residue 1390 ARG Chi-restraints excluded: chain D residue 591 ASP Chi-restraints excluded: chain D residue 618 LYS Chi-restraints excluded: chain E residue 463 CYS Chi-restraints excluded: chain E residue 473 LYS Chi-restraints excluded: chain E residue 495 MET Chi-restraints excluded: chain E residue 518 ASP Chi-restraints excluded: chain E residue 533 ILE Chi-restraints excluded: chain E residue 534 ASP Chi-restraints excluded: chain E residue 558 LEU Chi-restraints excluded: chain E residue 642 ILE Chi-restraints excluded: chain E residue 660 THR Chi-restraints excluded: chain E residue 662 SER Chi-restraints excluded: chain E residue 680 GLU Chi-restraints excluded: chain E residue 703 THR Chi-restraints excluded: chain E residue 867 GLU Chi-restraints excluded: chain E residue 938 LEU Chi-restraints excluded: chain F residue 495 MET Chi-restraints excluded: chain F residue 502 LEU Chi-restraints excluded: chain F residue 661 THR Chi-restraints excluded: chain F residue 720 LEU Chi-restraints excluded: chain F residue 928 GLU Chi-restraints excluded: chain F residue 938 LEU Chi-restraints excluded: chain F residue 1358 VAL Chi-restraints excluded: chain F residue 1375 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 252 optimal weight: 0.0070 chunk 172 optimal weight: 0.8980 chunk 4 optimal weight: 4.9990 chunk 225 optimal weight: 7.9990 chunk 125 optimal weight: 4.9990 chunk 259 optimal weight: 6.9990 chunk 209 optimal weight: 8.9990 chunk 0 optimal weight: 10.0000 chunk 154 optimal weight: 6.9990 chunk 272 optimal weight: 7.9990 chunk 76 optimal weight: 4.9990 overall best weight: 3.1804 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C1346 ASN D 721 GLN E 575 ASN ** E1335 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8526 moved from start: 0.1402 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.065 25970 Z= 0.361 Angle : 0.683 11.477 35215 Z= 0.329 Chirality : 0.047 0.313 3972 Planarity : 0.005 0.065 4517 Dihedral : 8.909 88.749 3622 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.16 % Allowed : 8.17 % Favored : 91.67 % Rotamer: Outliers : 3.40 % Allowed : 16.61 % Favored : 79.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.34 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.76 (0.15), residues: 3134 helix: -0.63 (0.14), residues: 1405 sheet: -0.34 (0.26), residues: 388 loop : -1.94 (0.17), residues: 1341 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 615 HIS 0.005 0.001 HIS F 861 PHE 0.010 0.002 PHE F 877 TYR 0.010 0.001 TYR B 655 ARG 0.005 0.000 ARG D 851 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6268 Ramachandran restraints generated. 3134 Oldfield, 0 Emsley, 3134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6268 Ramachandran restraints generated. 3134 Oldfield, 0 Emsley, 3134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 335 residues out of total 2794 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 240 time to evaluate : 3.056 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 586 ARG cc_start: 0.7179 (mpt90) cc_final: 0.6272 (tmm160) REVERT: A 931 LYS cc_start: 0.8665 (tttt) cc_final: 0.8287 (ttmt) REVERT: B 672 ILE cc_start: 0.7733 (OUTLIER) cc_final: 0.7520 (mt) REVERT: B 683 MET cc_start: 0.8869 (mtp) cc_final: 0.8597 (mtt) REVERT: B 1384 GLU cc_start: 0.7497 (OUTLIER) cc_final: 0.7236 (pp20) REVERT: C 562 LEU cc_start: 0.8648 (OUTLIER) cc_final: 0.8340 (tt) REVERT: C 616 ASN cc_start: 0.6468 (p0) cc_final: 0.6258 (p0) REVERT: C 658 ILE cc_start: 0.8451 (tt) cc_final: 0.8226 (tt) REVERT: C 701 LEU cc_start: 0.9128 (OUTLIER) cc_final: 0.8927 (mm) REVERT: C 833 VAL cc_start: 0.8753 (t) cc_final: 0.8444 (m) REVERT: C 1346 ASN cc_start: 0.8016 (OUTLIER) cc_final: 0.7649 (t0) REVERT: C 1390 ARG cc_start: 0.7327 (OUTLIER) cc_final: 0.6858 (mmm160) REVERT: D 495 MET cc_start: 0.7560 (tpt) cc_final: 0.7230 (tpt) REVERT: D 683 MET cc_start: 0.8973 (mtm) cc_final: 0.8537 (mtt) REVERT: E 473 LYS cc_start: 0.8181 (OUTLIER) cc_final: 0.7575 (pttp) REVERT: E 558 LEU cc_start: 0.9217 (OUTLIER) cc_final: 0.8840 (pt) REVERT: E 559 MET cc_start: 0.8700 (ttm) cc_final: 0.8120 (ttp) REVERT: E 683 MET cc_start: 0.8671 (mtp) cc_final: 0.8338 (mtt) REVERT: E 867 GLU cc_start: 0.8050 (OUTLIER) cc_final: 0.7605 (mm-30) REVERT: E 1372 LYS cc_start: 0.6420 (mmtt) cc_final: 0.4900 (pttp) REVERT: F 576 ARG cc_start: 0.7582 (mtt90) cc_final: 0.6939 (mtm-85) REVERT: F 820 PHE cc_start: 0.8163 (m-80) cc_final: 0.7883 (m-80) outliers start: 95 outliers final: 63 residues processed: 315 average time/residue: 0.4040 time to fit residues: 194.5576 Evaluate side-chains 303 residues out of total 2794 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 231 time to evaluate : 2.913 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 451 VAL Chi-restraints excluded: chain A residue 455 PHE Chi-restraints excluded: chain A residue 534 ASP Chi-restraints excluded: chain A residue 618 LYS Chi-restraints excluded: chain A residue 632 VAL Chi-restraints excluded: chain A residue 668 ASP Chi-restraints excluded: chain A residue 686 MET Chi-restraints excluded: chain A residue 703 THR Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 821 THR Chi-restraints excluded: chain A residue 878 THR Chi-restraints excluded: chain A residue 937 ILE Chi-restraints excluded: chain A residue 1358 VAL Chi-restraints excluded: chain A residue 1360 SER Chi-restraints excluded: chain A residue 1388 CYS Chi-restraints excluded: chain B residue 438 LEU Chi-restraints excluded: chain B residue 475 LEU Chi-restraints excluded: chain B residue 533 ILE Chi-restraints excluded: chain B residue 554 THR Chi-restraints excluded: chain B residue 556 LEU Chi-restraints excluded: chain B residue 563 ASP Chi-restraints excluded: chain B residue 591 ASP Chi-restraints excluded: chain B residue 616 ASN Chi-restraints excluded: chain B residue 622 THR Chi-restraints excluded: chain B residue 648 LEU Chi-restraints excluded: chain B residue 672 ILE Chi-restraints excluded: chain B residue 694 VAL Chi-restraints excluded: chain B residue 695 THR Chi-restraints excluded: chain B residue 821 THR Chi-restraints excluded: chain B residue 839 GLU Chi-restraints excluded: chain B residue 867 GLU Chi-restraints excluded: chain B residue 881 LEU Chi-restraints excluded: chain B residue 937 ILE Chi-restraints excluded: chain B residue 1358 VAL Chi-restraints excluded: chain B residue 1373 THR Chi-restraints excluded: chain B residue 1384 GLU Chi-restraints excluded: chain C residue 486 GLN Chi-restraints excluded: chain C residue 562 LEU Chi-restraints excluded: chain C residue 667 LEU Chi-restraints excluded: chain C residue 701 LEU Chi-restraints excluded: chain C residue 821 THR Chi-restraints excluded: chain C residue 886 SER Chi-restraints excluded: chain C residue 1346 ASN Chi-restraints excluded: chain C residue 1390 ARG Chi-restraints excluded: chain D residue 591 ASP Chi-restraints excluded: chain D residue 618 LYS Chi-restraints excluded: chain D residue 721 GLN Chi-restraints excluded: chain E residue 463 CYS Chi-restraints excluded: chain E residue 473 LYS Chi-restraints excluded: chain E residue 491 VAL Chi-restraints excluded: chain E residue 518 ASP Chi-restraints excluded: chain E residue 527 ILE Chi-restraints excluded: chain E residue 533 ILE Chi-restraints excluded: chain E residue 558 LEU Chi-restraints excluded: chain E residue 591 ASP Chi-restraints excluded: chain E residue 642 ILE Chi-restraints excluded: chain E residue 660 THR Chi-restraints excluded: chain E residue 662 SER Chi-restraints excluded: chain E residue 680 GLU Chi-restraints excluded: chain E residue 703 THR Chi-restraints excluded: chain E residue 841 THR Chi-restraints excluded: chain E residue 852 THR Chi-restraints excluded: chain E residue 867 GLU Chi-restraints excluded: chain E residue 938 LEU Chi-restraints excluded: chain F residue 502 LEU Chi-restraints excluded: chain F residue 661 THR Chi-restraints excluded: chain F residue 720 LEU Chi-restraints excluded: chain F residue 821 THR Chi-restraints excluded: chain F residue 826 ASP Chi-restraints excluded: chain F residue 928 GLU Chi-restraints excluded: chain F residue 938 LEU Chi-restraints excluded: chain F residue 1358 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 102 optimal weight: 0.9990 chunk 273 optimal weight: 5.9990 chunk 59 optimal weight: 9.9990 chunk 178 optimal weight: 4.9990 chunk 74 optimal weight: 2.9990 chunk 303 optimal weight: 8.9990 chunk 252 optimal weight: 0.2980 chunk 140 optimal weight: 2.9990 chunk 25 optimal weight: 6.9990 chunk 100 optimal weight: 2.9990 chunk 159 optimal weight: 3.9990 overall best weight: 2.0588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B1385 ASN D 721 GLN E 575 ASN ** E1335 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 805 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8505 moved from start: 0.1504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 25970 Z= 0.254 Angle : 0.635 13.683 35215 Z= 0.306 Chirality : 0.044 0.294 3972 Planarity : 0.005 0.066 4517 Dihedral : 8.620 85.187 3620 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.16 % Allowed : 7.34 % Favored : 92.50 % Rotamer: Outliers : 3.36 % Allowed : 17.25 % Favored : 79.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.34 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.55 (0.15), residues: 3134 helix: -0.46 (0.14), residues: 1407 sheet: -0.20 (0.26), residues: 390 loop : -1.85 (0.17), residues: 1337 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP E 505 HIS 0.004 0.001 HIS F 861 PHE 0.012 0.001 PHE F 877 TYR 0.010 0.001 TYR A 448 ARG 0.010 0.000 ARG B 543 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6268 Ramachandran restraints generated. 3134 Oldfield, 0 Emsley, 3134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6268 Ramachandran restraints generated. 3134 Oldfield, 0 Emsley, 3134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 336 residues out of total 2794 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 242 time to evaluate : 3.010 Fit side-chains revert: symmetry clash REVERT: A 586 ARG cc_start: 0.7197 (mpt90) cc_final: 0.6266 (tmm160) REVERT: A 931 LYS cc_start: 0.8640 (tttt) cc_final: 0.8419 (mmmm) REVERT: B 672 ILE cc_start: 0.7724 (OUTLIER) cc_final: 0.7510 (mt) REVERT: B 683 MET cc_start: 0.8857 (mtp) cc_final: 0.8578 (mtt) REVERT: B 1384 GLU cc_start: 0.7484 (OUTLIER) cc_final: 0.7224 (pp20) REVERT: C 562 LEU cc_start: 0.8615 (OUTLIER) cc_final: 0.8360 (tt) REVERT: C 616 ASN cc_start: 0.6553 (p0) cc_final: 0.6349 (p0) REVERT: C 658 ILE cc_start: 0.8439 (tt) cc_final: 0.8202 (tt) REVERT: C 701 LEU cc_start: 0.9111 (OUTLIER) cc_final: 0.8823 (mt) REVERT: C 833 VAL cc_start: 0.8698 (t) cc_final: 0.8413 (m) REVERT: C 1390 ARG cc_start: 0.7276 (OUTLIER) cc_final: 0.6995 (mmm160) REVERT: D 683 MET cc_start: 0.8960 (mtm) cc_final: 0.8529 (mtt) REVERT: E 473 LYS cc_start: 0.8118 (OUTLIER) cc_final: 0.7461 (pttp) REVERT: E 558 LEU cc_start: 0.9173 (OUTLIER) cc_final: 0.8811 (pt) REVERT: E 559 MET cc_start: 0.8655 (ttm) cc_final: 0.8091 (ttp) REVERT: E 683 MET cc_start: 0.8663 (mtp) cc_final: 0.8326 (mtt) REVERT: E 867 GLU cc_start: 0.8117 (OUTLIER) cc_final: 0.7695 (mm-30) REVERT: E 1372 LYS cc_start: 0.6381 (mmtt) cc_final: 0.4877 (pttp) REVERT: F 508 GLU cc_start: 0.7652 (mp0) cc_final: 0.7305 (pm20) REVERT: F 576 ARG cc_start: 0.7608 (mtt90) cc_final: 0.6963 (mtm-85) REVERT: F 820 PHE cc_start: 0.8094 (m-80) cc_final: 0.7808 (m-80) REVERT: F 1360 SER cc_start: 0.9008 (OUTLIER) cc_final: 0.8609 (p) outliers start: 94 outliers final: 66 residues processed: 317 average time/residue: 0.4055 time to fit residues: 197.1839 Evaluate side-chains 312 residues out of total 2794 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 237 time to evaluate : 3.091 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 451 VAL Chi-restraints excluded: chain A residue 455 PHE Chi-restraints excluded: chain A residue 534 ASP Chi-restraints excluded: chain A residue 632 VAL Chi-restraints excluded: chain A residue 668 ASP Chi-restraints excluded: chain A residue 686 MET Chi-restraints excluded: chain A residue 703 THR Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 821 THR Chi-restraints excluded: chain A residue 878 THR Chi-restraints excluded: chain A residue 937 ILE Chi-restraints excluded: chain A residue 1358 VAL Chi-restraints excluded: chain A residue 1360 SER Chi-restraints excluded: chain A residue 1375 LEU Chi-restraints excluded: chain A residue 1388 CYS Chi-restraints excluded: chain B residue 438 LEU Chi-restraints excluded: chain B residue 447 LEU Chi-restraints excluded: chain B residue 457 ILE Chi-restraints excluded: chain B residue 475 LEU Chi-restraints excluded: chain B residue 510 GLU Chi-restraints excluded: chain B residue 533 ILE Chi-restraints excluded: chain B residue 554 THR Chi-restraints excluded: chain B residue 556 LEU Chi-restraints excluded: chain B residue 563 ASP Chi-restraints excluded: chain B residue 591 ASP Chi-restraints excluded: chain B residue 622 THR Chi-restraints excluded: chain B residue 648 LEU Chi-restraints excluded: chain B residue 672 ILE Chi-restraints excluded: chain B residue 695 THR Chi-restraints excluded: chain B residue 821 THR Chi-restraints excluded: chain B residue 839 GLU Chi-restraints excluded: chain B residue 867 GLU Chi-restraints excluded: chain B residue 881 LEU Chi-restraints excluded: chain B residue 937 ILE Chi-restraints excluded: chain B residue 1373 THR Chi-restraints excluded: chain B residue 1375 LEU Chi-restraints excluded: chain B residue 1384 GLU Chi-restraints excluded: chain C residue 457 ILE Chi-restraints excluded: chain C residue 486 GLN Chi-restraints excluded: chain C residue 506 VAL Chi-restraints excluded: chain C residue 562 LEU Chi-restraints excluded: chain C residue 667 LEU Chi-restraints excluded: chain C residue 701 LEU Chi-restraints excluded: chain C residue 821 THR Chi-restraints excluded: chain C residue 886 SER Chi-restraints excluded: chain C residue 1390 ARG Chi-restraints excluded: chain D residue 500 ASP Chi-restraints excluded: chain D residue 591 ASP Chi-restraints excluded: chain D residue 618 LYS Chi-restraints excluded: chain D residue 721 GLN Chi-restraints excluded: chain E residue 473 LYS Chi-restraints excluded: chain E residue 491 VAL Chi-restraints excluded: chain E residue 533 ILE Chi-restraints excluded: chain E residue 534 ASP Chi-restraints excluded: chain E residue 558 LEU Chi-restraints excluded: chain E residue 591 ASP Chi-restraints excluded: chain E residue 642 ILE Chi-restraints excluded: chain E residue 660 THR Chi-restraints excluded: chain E residue 662 SER Chi-restraints excluded: chain E residue 669 LEU Chi-restraints excluded: chain E residue 680 GLU Chi-restraints excluded: chain E residue 703 THR Chi-restraints excluded: chain E residue 841 THR Chi-restraints excluded: chain E residue 852 THR Chi-restraints excluded: chain E residue 867 GLU Chi-restraints excluded: chain E residue 938 LEU Chi-restraints excluded: chain F residue 502 LEU Chi-restraints excluded: chain F residue 661 THR Chi-restraints excluded: chain F residue 720 LEU Chi-restraints excluded: chain F residue 821 THR Chi-restraints excluded: chain F residue 826 ASP Chi-restraints excluded: chain F residue 928 GLU Chi-restraints excluded: chain F residue 938 LEU Chi-restraints excluded: chain F residue 1358 VAL Chi-restraints excluded: chain F residue 1360 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 292 optimal weight: 10.0000 chunk 34 optimal weight: 0.4980 chunk 173 optimal weight: 3.9990 chunk 221 optimal weight: 7.9990 chunk 171 optimal weight: 0.0980 chunk 255 optimal weight: 5.9990 chunk 169 optimal weight: 2.9990 chunk 302 optimal weight: 6.9990 chunk 189 optimal weight: 4.9990 chunk 184 optimal weight: 0.8980 chunk 139 optimal weight: 3.9990 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 721 GLN E 575 ASN ** E1335 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 805 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8492 moved from start: 0.1598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 25970 Z= 0.222 Angle : 0.614 11.779 35215 Z= 0.297 Chirality : 0.044 0.384 3972 Planarity : 0.005 0.067 4517 Dihedral : 8.372 83.966 3620 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.16 % Allowed : 7.37 % Favored : 92.47 % Rotamer: Outliers : 3.04 % Allowed : 17.75 % Favored : 79.21 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.34 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.38 (0.15), residues: 3134 helix: -0.31 (0.14), residues: 1400 sheet: -0.07 (0.26), residues: 387 loop : -1.78 (0.17), residues: 1347 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 505 HIS 0.004 0.001 HIS E 611 PHE 0.013 0.001 PHE F 877 TYR 0.010 0.001 TYR A 448 ARG 0.009 0.000 ARG C 847 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6268 Ramachandran restraints generated. 3134 Oldfield, 0 Emsley, 3134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6268 Ramachandran restraints generated. 3134 Oldfield, 0 Emsley, 3134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 334 residues out of total 2794 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 249 time to evaluate : 3.058 Fit side-chains revert: symmetry clash REVERT: A 586 ARG cc_start: 0.7202 (mpt90) cc_final: 0.6266 (tmm160) REVERT: A 931 LYS cc_start: 0.8637 (tttt) cc_final: 0.8420 (mmmm) REVERT: B 453 GLU cc_start: 0.8005 (pp20) cc_final: 0.7671 (pp20) REVERT: B 672 ILE cc_start: 0.7720 (OUTLIER) cc_final: 0.7513 (mt) REVERT: B 683 MET cc_start: 0.8857 (mtp) cc_final: 0.8567 (mtt) REVERT: B 1384 GLU cc_start: 0.7498 (OUTLIER) cc_final: 0.7219 (pp20) REVERT: C 562 LEU cc_start: 0.8596 (OUTLIER) cc_final: 0.8325 (tt) REVERT: C 658 ILE cc_start: 0.8447 (tt) cc_final: 0.8215 (tt) REVERT: C 701 LEU cc_start: 0.9100 (OUTLIER) cc_final: 0.8811 (mt) REVERT: C 833 VAL cc_start: 0.8688 (t) cc_final: 0.8411 (m) REVERT: C 1390 ARG cc_start: 0.7236 (OUTLIER) cc_final: 0.6894 (mmm160) REVERT: D 495 MET cc_start: 0.7569 (tpt) cc_final: 0.7217 (tpt) REVERT: D 683 MET cc_start: 0.8944 (mtm) cc_final: 0.8517 (mtt) REVERT: E 558 LEU cc_start: 0.9132 (OUTLIER) cc_final: 0.8779 (pt) REVERT: E 559 MET cc_start: 0.8626 (ttm) cc_final: 0.8067 (ttp) REVERT: E 683 MET cc_start: 0.8659 (mtp) cc_final: 0.8323 (mtt) REVERT: E 867 GLU cc_start: 0.8100 (OUTLIER) cc_final: 0.7728 (mm-30) REVERT: E 1372 LYS cc_start: 0.6362 (mmtt) cc_final: 0.4829 (pttp) REVERT: F 508 GLU cc_start: 0.7472 (mp0) cc_final: 0.7185 (pm20) REVERT: F 576 ARG cc_start: 0.7610 (mtt90) cc_final: 0.6979 (mtm-85) REVERT: F 1360 SER cc_start: 0.9003 (OUTLIER) cc_final: 0.8590 (p) outliers start: 85 outliers final: 64 residues processed: 316 average time/residue: 0.3920 time to fit residues: 188.6546 Evaluate side-chains 309 residues out of total 2794 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 237 time to evaluate : 3.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 451 VAL Chi-restraints excluded: chain A residue 455 PHE Chi-restraints excluded: chain A residue 533 ILE Chi-restraints excluded: chain A residue 534 ASP Chi-restraints excluded: chain A residue 632 VAL Chi-restraints excluded: chain A residue 668 ASP Chi-restraints excluded: chain A residue 686 MET Chi-restraints excluded: chain A residue 703 THR Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 821 THR Chi-restraints excluded: chain A residue 878 THR Chi-restraints excluded: chain A residue 937 ILE Chi-restraints excluded: chain A residue 1358 VAL Chi-restraints excluded: chain A residue 1360 SER Chi-restraints excluded: chain A residue 1375 LEU Chi-restraints excluded: chain A residue 1388 CYS Chi-restraints excluded: chain B residue 438 LEU Chi-restraints excluded: chain B residue 475 LEU Chi-restraints excluded: chain B residue 510 GLU Chi-restraints excluded: chain B residue 533 ILE Chi-restraints excluded: chain B residue 554 THR Chi-restraints excluded: chain B residue 556 LEU Chi-restraints excluded: chain B residue 563 ASP Chi-restraints excluded: chain B residue 591 ASP Chi-restraints excluded: chain B residue 622 THR Chi-restraints excluded: chain B residue 648 LEU Chi-restraints excluded: chain B residue 672 ILE Chi-restraints excluded: chain B residue 694 VAL Chi-restraints excluded: chain B residue 695 THR Chi-restraints excluded: chain B residue 720 LEU Chi-restraints excluded: chain B residue 821 THR Chi-restraints excluded: chain B residue 839 GLU Chi-restraints excluded: chain B residue 867 GLU Chi-restraints excluded: chain B residue 881 LEU Chi-restraints excluded: chain B residue 937 ILE Chi-restraints excluded: chain B residue 1373 THR Chi-restraints excluded: chain B residue 1375 LEU Chi-restraints excluded: chain B residue 1384 GLU Chi-restraints excluded: chain C residue 486 GLN Chi-restraints excluded: chain C residue 506 VAL Chi-restraints excluded: chain C residue 562 LEU Chi-restraints excluded: chain C residue 667 LEU Chi-restraints excluded: chain C residue 701 LEU Chi-restraints excluded: chain C residue 821 THR Chi-restraints excluded: chain C residue 886 SER Chi-restraints excluded: chain C residue 1390 ARG Chi-restraints excluded: chain D residue 591 ASP Chi-restraints excluded: chain D residue 618 LYS Chi-restraints excluded: chain D residue 721 GLN Chi-restraints excluded: chain E residue 533 ILE Chi-restraints excluded: chain E residue 558 LEU Chi-restraints excluded: chain E residue 591 ASP Chi-restraints excluded: chain E residue 642 ILE Chi-restraints excluded: chain E residue 660 THR Chi-restraints excluded: chain E residue 662 SER Chi-restraints excluded: chain E residue 669 LEU Chi-restraints excluded: chain E residue 680 GLU Chi-restraints excluded: chain E residue 701 LEU Chi-restraints excluded: chain E residue 703 THR Chi-restraints excluded: chain E residue 841 THR Chi-restraints excluded: chain E residue 852 THR Chi-restraints excluded: chain E residue 867 GLU Chi-restraints excluded: chain E residue 938 LEU Chi-restraints excluded: chain F residue 502 LEU Chi-restraints excluded: chain F residue 661 THR Chi-restraints excluded: chain F residue 720 LEU Chi-restraints excluded: chain F residue 821 THR Chi-restraints excluded: chain F residue 826 ASP Chi-restraints excluded: chain F residue 928 GLU Chi-restraints excluded: chain F residue 938 LEU Chi-restraints excluded: chain F residue 1358 VAL Chi-restraints excluded: chain F residue 1360 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 187 optimal weight: 0.9990 chunk 120 optimal weight: 0.4980 chunk 180 optimal weight: 1.9990 chunk 91 optimal weight: 6.9990 chunk 59 optimal weight: 10.0000 chunk 58 optimal weight: 2.9990 chunk 192 optimal weight: 1.9990 chunk 206 optimal weight: 5.9990 chunk 149 optimal weight: 1.9990 chunk 28 optimal weight: 3.9990 chunk 237 optimal weight: 3.9990 overall best weight: 1.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 721 GLN E 575 ASN ** E1335 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 805 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8482 moved from start: 0.1687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 25970 Z= 0.204 Angle : 0.599 9.775 35215 Z= 0.289 Chirality : 0.043 0.313 3972 Planarity : 0.005 0.071 4517 Dihedral : 8.160 85.996 3620 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.16 % Allowed : 7.34 % Favored : 92.50 % Rotamer: Outliers : 3.11 % Allowed : 17.75 % Favored : 79.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.34 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.26 (0.15), residues: 3134 helix: -0.21 (0.14), residues: 1406 sheet: -0.01 (0.26), residues: 392 loop : -1.73 (0.17), residues: 1336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 865 HIS 0.003 0.001 HIS F 861 PHE 0.013 0.001 PHE F 877 TYR 0.013 0.001 TYR B 655 ARG 0.013 0.000 ARG B 543 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6268 Ramachandran restraints generated. 3134 Oldfield, 0 Emsley, 3134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6268 Ramachandran restraints generated. 3134 Oldfield, 0 Emsley, 3134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 340 residues out of total 2794 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 253 time to evaluate : 3.208 Fit side-chains revert: symmetry clash REVERT: A 586 ARG cc_start: 0.7231 (mpt90) cc_final: 0.6288 (tmm160) REVERT: B 453 GLU cc_start: 0.7992 (pp20) cc_final: 0.7699 (pp20) REVERT: B 672 ILE cc_start: 0.7692 (OUTLIER) cc_final: 0.7462 (mt) REVERT: B 683 MET cc_start: 0.8864 (mtp) cc_final: 0.8592 (mtt) REVERT: B 1384 GLU cc_start: 0.7489 (OUTLIER) cc_final: 0.7223 (pp20) REVERT: C 562 LEU cc_start: 0.8569 (OUTLIER) cc_final: 0.8337 (tt) REVERT: C 658 ILE cc_start: 0.8436 (tt) cc_final: 0.8207 (tt) REVERT: C 701 LEU cc_start: 0.9087 (OUTLIER) cc_final: 0.8796 (mt) REVERT: C 833 VAL cc_start: 0.8681 (t) cc_final: 0.8421 (m) REVERT: C 1390 ARG cc_start: 0.7181 (OUTLIER) cc_final: 0.6949 (mmm160) REVERT: D 826 ASP cc_start: 0.7488 (p0) cc_final: 0.7042 (t0) REVERT: E 473 LYS cc_start: 0.8118 (OUTLIER) cc_final: 0.6387 (ttpt) REVERT: E 558 LEU cc_start: 0.9096 (OUTLIER) cc_final: 0.8748 (pt) REVERT: E 559 MET cc_start: 0.8617 (ttm) cc_final: 0.8060 (ttp) REVERT: E 683 MET cc_start: 0.8658 (mtp) cc_final: 0.8315 (mtt) REVERT: E 935 ASP cc_start: 0.7427 (t0) cc_final: 0.7061 (p0) REVERT: E 1372 LYS cc_start: 0.6314 (mmtt) cc_final: 0.4774 (pttp) REVERT: F 576 ARG cc_start: 0.7592 (mtt90) cc_final: 0.6972 (mtm-85) REVERT: F 1360 SER cc_start: 0.8994 (OUTLIER) cc_final: 0.8602 (p) outliers start: 87 outliers final: 66 residues processed: 324 average time/residue: 0.4022 time to fit residues: 199.2293 Evaluate side-chains 311 residues out of total 2794 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 237 time to evaluate : 2.755 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 451 VAL Chi-restraints excluded: chain A residue 455 PHE Chi-restraints excluded: chain A residue 533 ILE Chi-restraints excluded: chain A residue 534 ASP Chi-restraints excluded: chain A residue 632 VAL Chi-restraints excluded: chain A residue 661 THR Chi-restraints excluded: chain A residue 668 ASP Chi-restraints excluded: chain A residue 686 MET Chi-restraints excluded: chain A residue 703 THR Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 821 THR Chi-restraints excluded: chain A residue 878 THR Chi-restraints excluded: chain A residue 937 ILE Chi-restraints excluded: chain A residue 1360 SER Chi-restraints excluded: chain A residue 1375 LEU Chi-restraints excluded: chain A residue 1388 CYS Chi-restraints excluded: chain B residue 438 LEU Chi-restraints excluded: chain B residue 475 LEU Chi-restraints excluded: chain B residue 510 GLU Chi-restraints excluded: chain B residue 533 ILE Chi-restraints excluded: chain B residue 554 THR Chi-restraints excluded: chain B residue 563 ASP Chi-restraints excluded: chain B residue 591 ASP Chi-restraints excluded: chain B residue 622 THR Chi-restraints excluded: chain B residue 648 LEU Chi-restraints excluded: chain B residue 672 ILE Chi-restraints excluded: chain B residue 694 VAL Chi-restraints excluded: chain B residue 695 THR Chi-restraints excluded: chain B residue 720 LEU Chi-restraints excluded: chain B residue 821 THR Chi-restraints excluded: chain B residue 839 GLU Chi-restraints excluded: chain B residue 867 GLU Chi-restraints excluded: chain B residue 881 LEU Chi-restraints excluded: chain B residue 937 ILE Chi-restraints excluded: chain B residue 1373 THR Chi-restraints excluded: chain B residue 1375 LEU Chi-restraints excluded: chain B residue 1384 GLU Chi-restraints excluded: chain C residue 486 GLN Chi-restraints excluded: chain C residue 506 VAL Chi-restraints excluded: chain C residue 533 ILE Chi-restraints excluded: chain C residue 562 LEU Chi-restraints excluded: chain C residue 667 LEU Chi-restraints excluded: chain C residue 701 LEU Chi-restraints excluded: chain C residue 821 THR Chi-restraints excluded: chain C residue 886 SER Chi-restraints excluded: chain C residue 1390 ARG Chi-restraints excluded: chain D residue 427 SER Chi-restraints excluded: chain D residue 441 MET Chi-restraints excluded: chain D residue 591 ASP Chi-restraints excluded: chain D residue 721 GLN Chi-restraints excluded: chain E residue 473 LYS Chi-restraints excluded: chain E residue 491 VAL Chi-restraints excluded: chain E residue 533 ILE Chi-restraints excluded: chain E residue 558 LEU Chi-restraints excluded: chain E residue 562 LEU Chi-restraints excluded: chain E residue 591 ASP Chi-restraints excluded: chain E residue 642 ILE Chi-restraints excluded: chain E residue 660 THR Chi-restraints excluded: chain E residue 662 SER Chi-restraints excluded: chain E residue 669 LEU Chi-restraints excluded: chain E residue 680 GLU Chi-restraints excluded: chain E residue 703 THR Chi-restraints excluded: chain E residue 841 THR Chi-restraints excluded: chain E residue 852 THR Chi-restraints excluded: chain E residue 938 LEU Chi-restraints excluded: chain F residue 502 LEU Chi-restraints excluded: chain F residue 661 THR Chi-restraints excluded: chain F residue 720 LEU Chi-restraints excluded: chain F residue 821 THR Chi-restraints excluded: chain F residue 826 ASP Chi-restraints excluded: chain F residue 928 GLU Chi-restraints excluded: chain F residue 938 LEU Chi-restraints excluded: chain F residue 1358 VAL Chi-restraints excluded: chain F residue 1360 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 275 optimal weight: 3.9990 chunk 289 optimal weight: 0.9990 chunk 264 optimal weight: 0.9980 chunk 282 optimal weight: 1.9990 chunk 169 optimal weight: 4.9990 chunk 122 optimal weight: 0.9980 chunk 221 optimal weight: 0.0670 chunk 86 optimal weight: 0.6980 chunk 254 optimal weight: 0.9980 chunk 266 optimal weight: 0.1980 chunk 281 optimal weight: 0.8980 overall best weight: 0.5718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 691 GLN D 721 GLN E 575 ASN ** E1335 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E1385 ASN ** F 805 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8443 moved from start: 0.1887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.051 25970 Z= 0.150 Angle : 0.575 10.083 35215 Z= 0.279 Chirality : 0.043 0.515 3972 Planarity : 0.004 0.074 4517 Dihedral : 7.809 88.930 3612 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.83 % Favored : 93.01 % Rotamer: Outliers : 2.33 % Allowed : 18.54 % Favored : 79.13 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.34 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.00 (0.15), residues: 3134 helix: 0.00 (0.14), residues: 1414 sheet: 0.18 (0.26), residues: 392 loop : -1.62 (0.18), residues: 1328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 505 HIS 0.005 0.001 HIS A 611 PHE 0.018 0.001 PHE A 729 TYR 0.011 0.001 TYR B 655 ARG 0.007 0.000 ARG C 847 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6268 Ramachandran restraints generated. 3134 Oldfield, 0 Emsley, 3134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6268 Ramachandran restraints generated. 3134 Oldfield, 0 Emsley, 3134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 2794 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 254 time to evaluate : 3.125 Fit side-chains revert: symmetry clash REVERT: A 461 ARG cc_start: 0.7832 (mmp-170) cc_final: 0.7198 (mmp-170) REVERT: A 586 ARG cc_start: 0.7186 (mpt90) cc_final: 0.6213 (tmm160) REVERT: B 453 GLU cc_start: 0.7974 (pp20) cc_final: 0.7710 (pp20) REVERT: B 683 MET cc_start: 0.8817 (mtp) cc_final: 0.8561 (mtt) REVERT: B 1384 GLU cc_start: 0.7483 (OUTLIER) cc_final: 0.7213 (pp20) REVERT: C 562 LEU cc_start: 0.8485 (OUTLIER) cc_final: 0.8261 (tt) REVERT: C 658 ILE cc_start: 0.8419 (tt) cc_final: 0.8172 (tt) REVERT: C 701 LEU cc_start: 0.9050 (OUTLIER) cc_final: 0.8763 (mt) REVERT: C 833 VAL cc_start: 0.8642 (t) cc_final: 0.8394 (m) REVERT: D 683 MET cc_start: 0.8917 (mtm) cc_final: 0.8645 (mtt) REVERT: D 721 GLN cc_start: 0.7930 (OUTLIER) cc_final: 0.7660 (tt0) REVERT: E 558 LEU cc_start: 0.9009 (OUTLIER) cc_final: 0.8662 (pt) REVERT: E 559 MET cc_start: 0.8567 (ttm) cc_final: 0.8011 (ttp) REVERT: E 683 MET cc_start: 0.8653 (mtp) cc_final: 0.8294 (mtt) REVERT: E 935 ASP cc_start: 0.7353 (t0) cc_final: 0.7037 (p0) REVERT: E 1372 LYS cc_start: 0.6301 (mmtt) cc_final: 0.4755 (pttp) REVERT: F 576 ARG cc_start: 0.7569 (mtt90) cc_final: 0.6943 (mtm-85) REVERT: F 1334 LYS cc_start: 0.7792 (pttm) cc_final: 0.7124 (ptmm) REVERT: F 1360 SER cc_start: 0.8955 (OUTLIER) cc_final: 0.8568 (p) outliers start: 65 outliers final: 46 residues processed: 304 average time/residue: 0.4149 time to fit residues: 191.8050 Evaluate side-chains 290 residues out of total 2794 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 238 time to evaluate : 3.050 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 451 VAL Chi-restraints excluded: chain A residue 455 PHE Chi-restraints excluded: chain A residue 534 ASP Chi-restraints excluded: chain A residue 632 VAL Chi-restraints excluded: chain A residue 668 ASP Chi-restraints excluded: chain A residue 686 MET Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 821 THR Chi-restraints excluded: chain A residue 878 THR Chi-restraints excluded: chain A residue 1375 LEU Chi-restraints excluded: chain A residue 1388 CYS Chi-restraints excluded: chain B residue 533 ILE Chi-restraints excluded: chain B residue 563 ASP Chi-restraints excluded: chain B residue 591 ASP Chi-restraints excluded: chain B residue 648 LEU Chi-restraints excluded: chain B residue 694 VAL Chi-restraints excluded: chain B residue 695 THR Chi-restraints excluded: chain B residue 821 THR Chi-restraints excluded: chain B residue 867 GLU Chi-restraints excluded: chain B residue 937 ILE Chi-restraints excluded: chain B residue 1373 THR Chi-restraints excluded: chain B residue 1375 LEU Chi-restraints excluded: chain B residue 1384 GLU Chi-restraints excluded: chain C residue 486 GLN Chi-restraints excluded: chain C residue 506 VAL Chi-restraints excluded: chain C residue 533 ILE Chi-restraints excluded: chain C residue 562 LEU Chi-restraints excluded: chain C residue 667 LEU Chi-restraints excluded: chain C residue 701 LEU Chi-restraints excluded: chain C residue 886 SER Chi-restraints excluded: chain D residue 591 ASP Chi-restraints excluded: chain D residue 721 GLN Chi-restraints excluded: chain E residue 473 LYS Chi-restraints excluded: chain E residue 491 VAL Chi-restraints excluded: chain E residue 518 ASP Chi-restraints excluded: chain E residue 533 ILE Chi-restraints excluded: chain E residue 558 LEU Chi-restraints excluded: chain E residue 591 ASP Chi-restraints excluded: chain E residue 660 THR Chi-restraints excluded: chain E residue 669 LEU Chi-restraints excluded: chain E residue 680 GLU Chi-restraints excluded: chain E residue 841 THR Chi-restraints excluded: chain E residue 938 LEU Chi-restraints excluded: chain F residue 495 MET Chi-restraints excluded: chain F residue 502 LEU Chi-restraints excluded: chain F residue 661 THR Chi-restraints excluded: chain F residue 720 LEU Chi-restraints excluded: chain F residue 821 THR Chi-restraints excluded: chain F residue 826 ASP Chi-restraints excluded: chain F residue 928 GLU Chi-restraints excluded: chain F residue 938 LEU Chi-restraints excluded: chain F residue 1360 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 185 optimal weight: 3.9990 chunk 298 optimal weight: 0.6980 chunk 182 optimal weight: 0.9990 chunk 141 optimal weight: 0.9980 chunk 207 optimal weight: 8.9990 chunk 312 optimal weight: 9.9990 chunk 287 optimal weight: 8.9990 chunk 249 optimal weight: 3.9990 chunk 25 optimal weight: 2.9990 chunk 192 optimal weight: 1.9990 chunk 152 optimal weight: 5.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 616 ASN D 721 GLN E 575 ASN ** E1335 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8466 moved from start: 0.1869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 25970 Z= 0.211 Angle : 0.608 11.318 35215 Z= 0.292 Chirality : 0.044 0.439 3972 Planarity : 0.005 0.071 4517 Dihedral : 7.883 89.492 3612 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.76 % Favored : 93.08 % Rotamer: Outliers : 2.08 % Allowed : 18.86 % Favored : 79.06 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 5.88 % 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: -0.96 (0.15), residues: 3134 helix: 0.03 (0.14), residues: 1415 sheet: 0.21 (0.26), residues: 389 loop : -1.58 (0.18), residues: 1330 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 865 HIS 0.006 0.001 HIS A 611 PHE 0.014 0.001 PHE A 729 TYR 0.022 0.001 TYR B 655 ARG 0.006 0.000 ARG D 851 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6268 Ramachandran restraints generated. 3134 Oldfield, 0 Emsley, 3134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6268 Ramachandran restraints generated. 3134 Oldfield, 0 Emsley, 3134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 2794 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 244 time to evaluate : 3.383 Fit side-chains revert: symmetry clash REVERT: A 461 ARG cc_start: 0.7831 (mmp-170) cc_final: 0.7186 (mmp-170) REVERT: A 586 ARG cc_start: 0.7222 (mpt90) cc_final: 0.6276 (tmm160) REVERT: B 453 GLU cc_start: 0.8003 (pp20) cc_final: 0.7743 (pp20) REVERT: B 683 MET cc_start: 0.8826 (mtp) cc_final: 0.8560 (mtt) REVERT: B 1384 GLU cc_start: 0.7478 (OUTLIER) cc_final: 0.7202 (pp20) REVERT: C 562 LEU cc_start: 0.8518 (OUTLIER) cc_final: 0.8312 (tt) REVERT: C 658 ILE cc_start: 0.8436 (tt) cc_final: 0.8205 (tt) REVERT: C 701 LEU cc_start: 0.9075 (OUTLIER) cc_final: 0.8768 (mt) REVERT: C 833 VAL cc_start: 0.8657 (t) cc_final: 0.8411 (m) REVERT: D 683 MET cc_start: 0.8922 (mtm) cc_final: 0.8658 (mtt) REVERT: E 473 LYS cc_start: 0.8120 (OUTLIER) cc_final: 0.6320 (ttpt) REVERT: E 558 LEU cc_start: 0.9041 (OUTLIER) cc_final: 0.8677 (pt) REVERT: E 559 MET cc_start: 0.8613 (ttm) cc_final: 0.8067 (ttp) REVERT: E 683 MET cc_start: 0.8677 (mtp) cc_final: 0.8315 (mtt) REVERT: E 935 ASP cc_start: 0.7367 (t0) cc_final: 0.7057 (p0) REVERT: E 1372 LYS cc_start: 0.6305 (mmtt) cc_final: 0.4757 (pttp) REVERT: F 576 ARG cc_start: 0.7557 (mtt90) cc_final: 0.6928 (mtm-85) REVERT: F 1334 LYS cc_start: 0.7813 (pttm) cc_final: 0.7244 (ptmm) REVERT: F 1360 SER cc_start: 0.8963 (OUTLIER) cc_final: 0.8587 (p) outliers start: 58 outliers final: 48 residues processed: 290 average time/residue: 0.4118 time to fit residues: 181.0473 Evaluate side-chains 290 residues out of total 2794 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 236 time to evaluate : 2.736 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 451 VAL Chi-restraints excluded: chain A residue 455 PHE Chi-restraints excluded: chain A residue 534 ASP Chi-restraints excluded: chain A residue 632 VAL Chi-restraints excluded: chain A residue 661 THR Chi-restraints excluded: chain A residue 668 ASP Chi-restraints excluded: chain A residue 686 MET Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 821 THR Chi-restraints excluded: chain A residue 878 THR Chi-restraints excluded: chain A residue 1375 LEU Chi-restraints excluded: chain A residue 1388 CYS Chi-restraints excluded: chain B residue 533 ILE Chi-restraints excluded: chain B residue 563 ASP Chi-restraints excluded: chain B residue 591 ASP Chi-restraints excluded: chain B residue 648 LEU Chi-restraints excluded: chain B residue 694 VAL Chi-restraints excluded: chain B residue 695 THR Chi-restraints excluded: chain B residue 720 LEU Chi-restraints excluded: chain B residue 821 THR Chi-restraints excluded: chain B residue 867 GLU Chi-restraints excluded: chain B residue 881 LEU Chi-restraints excluded: chain B residue 937 ILE Chi-restraints excluded: chain B residue 1373 THR Chi-restraints excluded: chain B residue 1375 LEU Chi-restraints excluded: chain B residue 1384 GLU Chi-restraints excluded: chain C residue 486 GLN Chi-restraints excluded: chain C residue 506 VAL Chi-restraints excluded: chain C residue 533 ILE Chi-restraints excluded: chain C residue 562 LEU Chi-restraints excluded: chain C residue 667 LEU Chi-restraints excluded: chain C residue 701 LEU Chi-restraints excluded: chain C residue 821 THR Chi-restraints excluded: chain C residue 886 SER Chi-restraints excluded: chain D residue 591 ASP Chi-restraints excluded: chain E residue 473 LYS Chi-restraints excluded: chain E residue 491 VAL Chi-restraints excluded: chain E residue 533 ILE Chi-restraints excluded: chain E residue 558 LEU Chi-restraints excluded: chain E residue 591 ASP Chi-restraints excluded: chain E residue 660 THR Chi-restraints excluded: chain E residue 669 LEU Chi-restraints excluded: chain E residue 680 GLU Chi-restraints excluded: chain E residue 841 THR Chi-restraints excluded: chain E residue 938 LEU Chi-restraints excluded: chain F residue 495 MET Chi-restraints excluded: chain F residue 502 LEU Chi-restraints excluded: chain F residue 661 THR Chi-restraints excluded: chain F residue 720 LEU Chi-restraints excluded: chain F residue 821 THR Chi-restraints excluded: chain F residue 826 ASP Chi-restraints excluded: chain F residue 928 GLU Chi-restraints excluded: chain F residue 938 LEU Chi-restraints excluded: chain F residue 1360 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 197 optimal weight: 0.7980 chunk 265 optimal weight: 1.9990 chunk 76 optimal weight: 0.5980 chunk 229 optimal weight: 0.0040 chunk 36 optimal weight: 5.9990 chunk 69 optimal weight: 0.8980 chunk 249 optimal weight: 5.9990 chunk 104 optimal weight: 3.9990 chunk 256 optimal weight: 10.0000 chunk 31 optimal weight: 0.8980 chunk 45 optimal weight: 3.9990 overall best weight: 0.6392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 458 GLN A 630 ASN E 575 ASN ** E1335 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 710 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.139419 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.114504 restraints weight = 33917.511| |-----------------------------------------------------------------------------| r_work (start): 0.3292 rms_B_bonded: 1.74 r_work: 0.3120 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2996 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.2996 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8705 moved from start: 0.2095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.060 25970 Z= 0.148 Angle : 0.573 11.431 35215 Z= 0.276 Chirality : 0.043 0.398 3972 Planarity : 0.004 0.068 4517 Dihedral : 7.488 86.239 3612 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.73 % Favored : 93.11 % Rotamer: Outliers : 1.90 % Allowed : 18.90 % Favored : 79.21 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 5.88 % 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: -0.72 (0.15), residues: 3134 helix: 0.23 (0.14), residues: 1424 sheet: 0.39 (0.26), residues: 391 loop : -1.51 (0.18), residues: 1319 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 865 HIS 0.009 0.001 HIS A 611 PHE 0.014 0.001 PHE A 729 TYR 0.015 0.001 TYR B 655 ARG 0.022 0.000 ARG B 543 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5503.99 seconds wall clock time: 99 minutes 32.25 seconds (5972.25 seconds total)