Starting phenix.real_space_refine on Tue Mar 19 20:28:35 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8juz_36667/03_2024/8juz_36667_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8juz_36667/03_2024/8juz_36667.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.29 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8juz_36667/03_2024/8juz_36667.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8juz_36667/03_2024/8juz_36667.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8juz_36667/03_2024/8juz_36667_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8juz_36667/03_2024/8juz_36667_neut_updated.pdb" } resolution = 4.29 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 17 5.49 5 S 110 5.16 5 C 16130 2.51 5 N 4361 2.21 5 O 4656 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 508": "OE1" <-> "OE2" Residue "A ASP 518": "OD1" <-> "OD2" Residue "A GLU 602": "OE1" <-> "OE2" Residue "A ASP 638": "OD1" <-> "OD2" Residue "A PHE 729": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 867": "OE1" <-> "OE2" Residue "A GLU 909": "OE1" <-> "OE2" Residue "A GLU 1331": "OE1" <-> "OE2" Residue "A GLU 1380": "OE1" <-> "OE2" Residue "B PHE 530": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 606": "OE1" <-> "OE2" Residue "B GLU 680": "OE1" <-> "OE2" Residue "B PHE 831": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 493": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 530": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 545": "OD1" <-> "OD2" Residue "C ASP 560": "OD1" <-> "OD2" Residue "C GLU 567": "OE1" <-> "OE2" Residue "C GLU 645": "OE1" <-> "OE2" Residue "C GLU 909": "OE1" <-> "OE2" Residue "C GLU 1353": "OE1" <-> "OE2" Residue "C TYR 1356": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 483": "OE1" <-> "OE2" Residue "D PHE 517": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 518": "OD1" <-> "OD2" Residue "D ASP 578": "OD1" <-> "OD2" Residue "D ASP 581": "OD1" <-> "OD2" Residue "D GLU 626": "OE1" <-> "OE2" Residue "D GLU 645": "OE1" <-> "OE2" Residue "D GLU 848": "OE1" <-> "OE2" Residue "E GLU 440": "OE1" <-> "OE2" Residue "E ASP 500": "OD1" <-> "OD2" Residue "E PHE 530": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 590": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 659": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 679": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 820": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 867": "OE1" <-> "OE2" Residue "E TYR 1364": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 426": "OD1" <-> "OD2" Residue "F TYR 448": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 455": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 645": "OE1" <-> "OE2" Residue "F GLU 718": "OE1" <-> "OE2" Residue "F GLU 867": "OE1" <-> "OE2" Residue "F GLU 909": "OE1" <-> "OE2" Residue "F GLU 927": "OE1" <-> "OE2" Residue "F PHE 1350": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 25274 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 4149 Number of conformers: 1 Conformer: "" Number of residues, atoms: 522, 4149 Classifications: {'peptide': 522} Link IDs: {'CIS': 3, 'PCIS': 2, 'PTRANS': 30, 'TRANS': 486} Chain breaks: 5 Chain: "B" Number of atoms: 4210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 529, 4210 Classifications: {'peptide': 529} Link IDs: {'CIS': 3, 'PCIS': 2, 'PTRANS': 32, 'TRANS': 491} Chain breaks: 2 Chain: "C" Number of atoms: 4199 Number of conformers: 1 Conformer: "" Number of residues, atoms: 528, 4199 Classifications: {'peptide': 528} Link IDs: {'PCIS': 2, 'PTRANS': 32, 'TRANS': 493} Chain breaks: 2 Chain: "D" Number of atoms: 4213 Number of conformers: 1 Conformer: "" Number of residues, atoms: 530, 4213 Classifications: {'peptide': 530} Link IDs: {'PCIS': 2, 'PTRANS': 32, 'TRANS': 495} Chain breaks: 2 Chain: "E" Number of atoms: 4202 Number of conformers: 1 Conformer: "" Number of residues, atoms: 528, 4202 Classifications: {'peptide': 528} Link IDs: {'CIS': 2, 'PCIS': 2, 'PTRANS': 32, 'TRANS': 491} Chain breaks: 2 Chain: "F" Number of atoms: 4119 Number of conformers: 1 Conformer: "" Number of residues, atoms: 518, 4119 Classifications: {'peptide': 518} Link IDs: {'CIS': 2, 'PCIS': 2, 'PTRANS': 30, 'TRANS': 483} Chain breaks: 4 Chain: "A" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 12.41, per 1000 atoms: 0.49 Number of scatterers: 25274 At special positions: 0 Unit cell: (148.5, 152.9, 146.3, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 110 16.00 P 17 15.00 O 4656 8.00 N 4361 7.00 C 16130 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 9.31 Conformation dependent library (CDL) restraints added in 4.2 seconds 6218 Ramachandran restraints generated. 3109 Oldfield, 0 Emsley, 3109 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6022 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 154 helices and 14 sheets defined 45.6% alpha, 7.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.20 Creating SS restraints... Processing helix chain 'A' and resid 433 through 439 Processing helix chain 'A' and resid 443 through 447 Processing helix chain 'A' and resid 473 through 484 removed outlier: 4.007A pdb=" N ALA A 477 " --> pdb=" O LYS A 473 " (cutoff:3.500A) 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 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 582 through 584 No H-bonds generated for 'chain 'A' and resid 582 through 584' Processing helix chain 'A' and resid 601 through 612 Processing helix chain 'A' and resid 621 through 630 Processing helix chain 'A' and resid 637 through 654 removed outlier: 3.743A pdb=" N ALA A 647 " --> pdb=" O CYS A 643 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N LEU A 648 " --> pdb=" O ALA A 644 " (cutoff:3.500A) Processing helix chain 'A' and resid 656 through 658 No H-bonds generated for 'chain 'A' and resid 656 through 658' Processing helix chain 'A' and resid 680 through 685 removed outlier: 3.915A pdb=" N LYS A 685 " --> pdb=" O VAL A 681 " (cutoff:3.500A) Processing helix chain 'A' and resid 703 through 721 Proline residue: A 707 - end of helix removed outlier: 6.048A pdb=" N ASN A 711 " --> pdb=" O PRO A 707 " (cutoff:3.500A) removed outlier: 5.557A pdb=" N THR A 712 " --> pdb=" O LEU A 708 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N LEU A 717 " --> pdb=" O VAL A 713 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N GLU A 718 " --> pdb=" O ASP A 714 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ALA A 719 " --> pdb=" O LYS A 715 " (cutoff:3.500A) Processing helix chain 'A' and resid 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: 4.031A pdb=" N CYS A 842 " --> pdb=" O PRO A 838 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N ALA A 843 " --> pdb=" O GLU A 839 " (cutoff:3.500A) Processing helix chain 'A' and resid 862 through 867 removed outlier: 4.854A pdb=" N GLU A 867 " --> pdb=" O HIS A 863 " (cutoff:3.500A) Processing helix chain 'A' and resid 871 through 881 removed outlier: 3.620A pdb=" N LEU A 881 " --> pdb=" O PHE A 877 " (cutoff:3.500A) Processing helix chain 'A' and resid 905 through 910 removed outlier: 4.441A 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: 4.519A pdb=" N ASP A 935 " --> pdb=" O LYS A 931 " (cutoff:3.500A) removed outlier: 4.650A pdb=" N LEU A 936 " --> pdb=" O PHE A 932 " (cutoff:3.500A) Processing helix chain 'A' and resid 1332 through 1344 Processing helix chain 'A' and resid 1349 through 1366 removed outlier: 3.504A pdb=" N LEU A1355 " --> pdb=" O GLN A1351 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N TYR A1356 " --> pdb=" O LEU A1352 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N GLN A1361 " --> pdb=" O ALA A1357 " (cutoff:3.500A) Processing helix chain 'A' and resid 1376 through 1385 removed outlier: 3.506A pdb=" N GLU A1384 " --> pdb=" O GLU A1380 " (cutoff:3.500A) Processing helix chain 'B' and resid 433 through 442 removed outlier: 3.559A pdb=" N VAL B 442 " --> pdb=" O LEU B 438 " (cutoff:3.500A) Processing helix chain 'B' and resid 444 through 446 No H-bonds generated for 'chain 'B' and resid 444 through 446' Processing helix chain 'B' and resid 451 through 455 removed outlier: 3.636A pdb=" N PHE B 455 " --> pdb=" O VAL B 451 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 451 through 455' Processing helix chain 'B' and resid 473 through 484 removed outlier: 4.452A pdb=" N ALA B 477 " --> pdb=" O LYS B 473 " (cutoff:3.500A) Processing helix chain 'B' and resid 509 through 522 removed outlier: 4.041A pdb=" N LEU B 513 " --> pdb=" O SER B 509 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N ARG B 514 " --> pdb=" O GLU B 510 " (cutoff:3.500A) Processing helix chain 'B' and resid 533 through 535 No H-bonds generated for 'chain 'B' and resid 533 through 535' Processing helix chain 'B' and resid 546 through 559 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: 4.281A pdb=" N LYS B 605 " --> pdb=" O LYS B 601 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N GLU B 606 " --> pdb=" O GLU B 602 " (cutoff:3.500A) Processing helix chain 'B' and resid 621 through 630 removed outlier: 4.026A pdb=" N ASN B 630 " --> pdb=" O GLU B 626 " (cutoff:3.500A) Processing helix chain 'B' and resid 637 through 654 removed outlier: 3.847A pdb=" N ALA B 647 " --> pdb=" O CYS B 643 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N LEU B 648 " --> pdb=" O ALA B 644 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N CYS B 649 " --> pdb=" O GLU B 645 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ALA B 650 " --> pdb=" O ALA B 646 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LEU B 651 " --> pdb=" O ALA B 647 " (cutoff:3.500A) Processing helix chain 'B' and resid 676 through 685 removed outlier: 3.958A pdb=" N GLU B 680 " --> pdb=" O ALA B 676 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N VAL B 681 " --> pdb=" O LYS B 677 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ALA B 682 " --> pdb=" O ASP B 678 " (cutoff:3.500A) Processing helix chain 'B' and resid 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: 7.044A pdb=" N ASN B 711 " --> pdb=" O PRO B 707 " (cutoff:3.500A) removed outlier: 5.851A pdb=" N THR B 712 " --> pdb=" O LEU B 708 " (cutoff:3.500A) Processing helix chain 'B' and resid 725 through 727 No H-bonds generated for 'chain 'B' and resid 725 through 727' Processing helix chain 'B' and resid 805 through 816 removed outlier: 3.550A pdb=" N LEU B 809 " --> pdb=" O GLN B 805 " (cutoff:3.500A) removed outlier: 6.089A pdb=" N ALA B 810 " --> pdb=" O GLY B 806 " (cutoff:3.500A) Proline residue: B 811 - end of helix Processing helix chain 'B' and resid 827 through 830 No H-bonds generated for 'chain 'B' and resid 827 through 830' Processing helix chain 'B' and resid 838 through 851 Processing helix chain 'B' and resid 862 through 868 removed outlier: 5.194A pdb=" N GLU B 867 " --> pdb=" O HIS B 863 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N ILE B 868 " --> pdb=" O VAL B 864 " (cutoff:3.500A) Processing helix chain 'B' and resid 871 through 883 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: 4.529A 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 936 through 939 No H-bonds generated for 'chain 'B' and resid 936 through 939' Processing helix chain 'B' and resid 1332 through 1343 Processing helix chain 'B' and resid 1349 through 1366 removed outlier: 3.600A pdb=" N ILE B1359 " --> pdb=" O LEU B1355 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N HIS B1366 " --> pdb=" O CYS B1362 " (cutoff:3.500A) Processing helix chain 'B' and resid 1376 through 1385 removed outlier: 3.563A pdb=" N GLU B1384 " --> pdb=" O GLU B1380 " (cutoff:3.500A) Processing helix chain 'C' and resid 433 through 442 removed outlier: 4.038A pdb=" N GLU C 440 " --> pdb=" O ALA C 436 " (cutoff:3.500A) removed outlier: 4.782A pdb=" N MET C 441 " --> pdb=" O ALA C 437 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N VAL C 442 " --> pdb=" O LEU C 438 " (cutoff:3.500A) Processing helix chain 'C' and resid 444 through 447 No H-bonds generated for 'chain 'C' and resid 444 through 447' Processing helix chain 'C' and resid 449 through 455 removed outlier: 4.495A pdb=" N GLU C 453 " --> pdb=" O PRO C 449 " (cutoff:3.500A) removed outlier: 4.872A pdb=" N LYS C 454 " --> pdb=" O GLU C 450 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N PHE C 455 " --> pdb=" O VAL C 451 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 449 through 455' Processing helix chain 'C' and resid 474 through 485 Processing helix chain 'C' and resid 511 through 523 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 547 through 558 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 582 through 584 No H-bonds generated for 'chain 'C' and resid 582 through 584' Processing helix chain 'C' and resid 601 through 611 Processing helix chain 'C' and resid 621 through 630 removed outlier: 3.875A pdb=" N GLU C 629 " --> pdb=" O GLU C 625 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N ASN C 630 " --> pdb=" O GLU C 626 " (cutoff:3.500A) Processing helix chain 'C' and resid 636 through 654 removed outlier: 4.311A pdb=" N ALA C 646 " --> pdb=" O CYS C 643 " (cutoff:3.500A) Processing helix chain 'C' and resid 676 through 685 Processing helix chain 'C' and resid 690 through 692 No H-bonds generated for 'chain 'C' and resid 690 through 692' Processing helix chain 'C' and resid 703 through 708 Proline residue: C 707 - end of helix No H-bonds generated for 'chain 'C' and resid 703 through 708' Processing helix chain 'C' and resid 710 through 723 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 Processing helix chain 'C' and resid 862 through 865 No H-bonds generated for 'chain 'C' and resid 862 through 865' Processing helix chain 'C' and resid 871 through 882 removed outlier: 3.574A pdb=" N LEU C 881 " --> pdb=" O PHE C 877 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N GLN C 882 " --> pdb=" O THR C 878 " (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: 3.518A pdb=" N PHE C 933 " --> pdb=" O ARG C 929 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N ASP C 935 " --> pdb=" O LYS C 931 " (cutoff:3.500A) removed outlier: 4.759A pdb=" N LEU C 936 " --> pdb=" O PHE C 932 " (cutoff:3.500A) Processing helix chain 'C' and resid 1331 through 1343 removed outlier: 3.548A pdb=" N ASN C1335 " --> pdb=" O GLU C1331 " (cutoff:3.500A) Processing helix chain 'C' and resid 1349 through 1365 removed outlier: 4.028A pdb=" N CYS C1362 " --> pdb=" O VAL C1358 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ILE C1363 " --> pdb=" O ILE C1359 " (cutoff:3.500A) Processing helix chain 'C' and resid 1375 through 1385 Processing helix chain 'D' and resid 433 through 447 removed outlier: 3.523A pdb=" N GLU D 440 " --> pdb=" O ALA D 436 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N MET D 441 " --> pdb=" O ALA D 437 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N VAL D 442 " --> pdb=" O LEU D 438 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N PHE D 444 " --> pdb=" O GLU D 440 " (cutoff:3.500A) Proline residue: D 445 - end of helix Processing helix chain 'D' and resid 452 through 455 No H-bonds generated for 'chain 'D' and resid 452 through 455' Processing helix chain 'D' and resid 473 through 485 removed outlier: 3.718A pdb=" N ALA D 477 " --> pdb=" O LYS D 473 " (cutoff:3.500A) Processing helix chain 'D' and resid 508 through 522 removed outlier: 3.602A pdb=" N LEU D 513 " --> pdb=" O SER D 509 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ARG D 514 " --> pdb=" O GLU D 510 " (cutoff:3.500A) 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 547 through 556 Processing helix chain 'D' and resid 601 through 611 Processing helix chain 'D' and resid 621 through 630 removed outlier: 4.007A pdb=" N ASN D 630 " --> pdb=" O GLU D 626 " (cutoff:3.500A) Processing helix chain 'D' and resid 637 through 654 removed outlier: 3.815A pdb=" N CYS D 643 " --> pdb=" O ILE D 639 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N ALA D 644 " --> pdb=" O LYS D 640 " (cutoff:3.500A) Processing helix chain 'D' and resid 678 through 685 removed outlier: 3.974A pdb=" N LYS D 685 " --> pdb=" O VAL D 681 " (cutoff:3.500A) 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 703 through 723 Proline residue: D 707 - end of helix removed outlier: 5.677A pdb=" N ASN D 711 " --> pdb=" O PRO D 707 " (cutoff:3.500A) removed outlier: 5.670A pdb=" N THR D 712 " --> pdb=" O LEU D 708 " (cutoff:3.500A) Processing helix chain 'D' and resid 810 through 816 Processing helix chain 'D' and resid 827 through 832 Processing helix chain 'D' and resid 838 through 851 Processing helix chain 'D' and resid 862 through 865 No H-bonds generated for 'chain 'D' and resid 862 through 865' Processing helix chain 'D' and resid 871 through 883 removed outlier: 3.801A pdb=" N GLN D 882 " --> pdb=" O THR D 878 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ASN D 883 " --> pdb=" O THR D 879 " (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: 3.794A 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: 4.312A pdb=" N ASP D 935 " --> pdb=" O LYS D 931 " (cutoff:3.500A) removed outlier: 5.003A pdb=" N LEU D 936 " --> pdb=" O PHE D 932 " (cutoff:3.500A) Processing helix chain 'D' and resid 1332 through 1343 Processing helix chain 'D' and resid 1349 through 1366 removed outlier: 4.032A pdb=" N HIS D1366 " --> pdb=" O CYS D1362 " (cutoff:3.500A) Processing helix chain 'D' and resid 1376 through 1384 Processing helix chain 'E' and resid 434 through 442 Processing helix chain 'E' and resid 444 through 446 No H-bonds generated for 'chain 'E' and resid 444 through 446' 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 475 through 485 Processing helix chain 'E' and resid 511 through 523 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 560 removed outlier: 3.739A pdb=" N LEU E 558 " --> pdb=" O THR E 554 " (cutoff:3.500A) Processing helix chain 'E' and resid 601 through 611 Processing helix chain 'E' and resid 621 through 630 removed outlier: 4.256A pdb=" N ASN E 630 " --> pdb=" O GLU E 626 " (cutoff:3.500A) Processing helix chain 'E' and resid 636 through 654 removed outlier: 3.692A pdb=" N ALA E 644 " --> pdb=" O LYS E 640 " (cutoff:3.500A) Processing helix chain 'E' and resid 676 through 685 removed outlier: 3.605A pdb=" N LYS E 685 " --> pdb=" O VAL E 681 " (cutoff:3.500A) Processing helix chain 'E' and resid 703 through 723 Proline residue: E 707 - end of helix removed outlier: 6.717A pdb=" N ASN E 711 " --> pdb=" O PRO E 707 " (cutoff:3.500A) removed outlier: 5.479A pdb=" N THR E 712 " --> pdb=" O LEU E 708 " (cutoff:3.500A) Processing helix chain 'E' and resid 725 through 727 No H-bonds generated for 'chain 'E' and resid 725 through 727' Processing helix chain 'E' and resid 801 through 803 No H-bonds generated for 'chain 'E' and resid 801 through 803' 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 Processing helix chain 'E' and resid 862 through 867 removed outlier: 4.732A pdb=" N GLU E 867 " --> pdb=" O HIS E 863 " (cutoff:3.500A) Processing helix chain 'E' and resid 871 through 883 removed outlier: 3.836A pdb=" N LEU E 881 " --> pdb=" O PHE E 877 " (cutoff:3.500A) removed outlier: 4.740A pdb=" N GLN E 882 " --> pdb=" O THR E 878 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N ASN E 883 " --> pdb=" O THR E 879 " (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 913 through 915 No H-bonds generated for 'chain 'E' and resid 913 through 915' Processing helix chain 'E' and resid 926 through 934 Processing helix chain 'E' and resid 1331 through 1344 Processing helix chain 'E' and resid 1349 through 1366 removed outlier: 3.804A 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 432 through 447 removed outlier: 3.642A pdb=" N ALA F 436 " --> pdb=" O SER F 432 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N MET F 441 " --> pdb=" O ALA F 437 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N VAL F 442 " --> pdb=" O LEU F 438 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N PHE F 444 " --> pdb=" O GLU F 440 " (cutoff:3.500A) Proline residue: F 445 - end of helix Processing helix chain 'F' and resid 449 through 451 No H-bonds generated for 'chain 'F' and resid 449 through 451' Processing helix chain 'F' and resid 473 through 485 Processing helix chain 'F' and resid 510 through 519 removed outlier: 3.901A pdb=" N ARG F 514 " --> pdb=" O GLU F 510 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N ASP F 518 " --> pdb=" O ARG F 514 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLN F 519 " --> pdb=" O LEU F 515 " (cutoff:3.500A) Processing helix chain 'F' and resid 533 through 536 No H-bonds generated for 'chain 'F' and resid 533 through 536' Processing helix chain 'F' and resid 546 through 561 removed outlier: 3.928A pdb=" N ASP F 560 " --> pdb=" O LEU F 556 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N GLY F 561 " --> pdb=" O ALA F 557 " (cutoff:3.500A) Processing helix chain 'F' and resid 577 through 579 No H-bonds generated for 'chain 'F' and resid 577 through 579' Processing helix chain 'F' and resid 582 through 584 No H-bonds generated for 'chain 'F' and resid 582 through 584' Processing helix chain 'F' and resid 603 through 611 Processing helix chain 'F' and resid 621 through 630 Processing helix chain 'F' and resid 637 through 653 removed outlier: 3.651A pdb=" N CYS F 643 " --> pdb=" O ILE F 639 " (cutoff:3.500A) Processing helix chain 'F' and resid 656 through 658 No H-bonds generated for 'chain 'F' and resid 656 through 658' Processing helix chain 'F' and resid 676 through 684 removed outlier: 4.109A pdb=" N GLU F 680 " --> pdb=" O ALA F 676 " (cutoff:3.500A) Processing helix chain 'F' and resid 706 through 723 removed outlier: 6.588A pdb=" N ASN F 711 " --> pdb=" O PRO F 707 " (cutoff:3.500A) removed outlier: 5.348A pdb=" N THR F 712 " --> pdb=" O LEU F 708 " (cutoff:3.500A) Processing helix chain 'F' and resid 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 838 through 851 removed outlier: 3.776A pdb=" N GLN F 844 " --> pdb=" O GLU F 840 " (cutoff:3.500A) Processing helix chain 'F' and resid 862 through 867 removed outlier: 3.590A pdb=" N TRP F 866 " --> pdb=" O ILE F 862 " (cutoff:3.500A) removed outlier: 5.125A pdb=" N GLU F 867 " --> pdb=" O HIS F 863 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 862 through 867' Processing helix chain 'F' and resid 871 through 882 removed outlier: 3.571A pdb=" N ALA F 875 " --> pdb=" O PRO F 871 " (cutoff:3.500A) Processing helix chain 'F' and resid 900 through 902 No H-bonds generated for 'chain 'F' and resid 900 through 902' Processing helix chain 'F' and resid 905 through 910 removed outlier: 3.601A 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 1343 Processing helix chain 'F' and resid 1349 through 1366 removed outlier: 3.520A pdb=" N ILE F1363 " --> pdb=" O ILE F1359 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N TYR F1364 " --> pdb=" O SER F1360 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N HIS F1366 " --> pdb=" O CYS F1362 " (cutoff:3.500A) Processing helix chain 'F' and resid 1375 through 1385 removed outlier: 3.633A pdb=" N GLU F1384 " --> pdb=" O GLU F1380 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 592 through 596 removed outlier: 4.245A pdb=" N ARG A 592 " --> pdb=" O GLY A 462 " (cutoff:3.500A) removed outlier: 8.512A pdb=" N CYS A 463 " --> pdb=" O ILE A 568 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N VAL A 570 " --> pdb=" O CYS A 463 " (cutoff:3.500A) removed outlier: 7.732A pdb=" N PHE A 465 " --> pdb=" O VAL A 570 " (cutoff:3.500A) removed outlier: 6.144A pdb=" N GLY A 572 " --> pdb=" O PHE A 465 " (cutoff:3.500A) removed outlier: 8.090A pdb=" N GLY A 467 " --> pdb=" O GLY A 572 " (cutoff:3.500A) removed outlier: 5.900A pdb=" N THR A 574 " --> pdb=" O GLY A 467 " (cutoff:3.500A) removed outlier: 7.228A pdb=" N SER A 526 " --> pdb=" O VAL A 569 " (cutoff:3.500A) removed outlier: 8.471A pdb=" N ILE A 571 " --> pdb=" O SER A 526 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N ILE A 528 " --> pdb=" O ILE A 571 " (cutoff:3.500A) removed outlier: 8.035A pdb=" N ALA A 573 " --> pdb=" O ILE A 528 " (cutoff:3.500A) removed outlier: 7.050A pdb=" N PHE A 530 " --> pdb=" O ALA A 573 " (cutoff:3.500A) removed outlier: 6.110A pdb=" N ALA A 492 " --> pdb=" O ILE A 527 " (cutoff:3.500A) removed outlier: 7.420A pdb=" N PHE A 529 " --> pdb=" O ALA A 492 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N PHE A 494 " --> pdb=" O PHE A 529 " (cutoff:3.500A) removed outlier: 7.177A pdb=" N ASP A 531 " --> pdb=" O PHE A 494 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N ARG A 496 " --> pdb=" O ASP A 531 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 918 through 920 removed outlier: 8.203A pdb=" N PHE A 919 " --> pdb=" O ARG A 794 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N LEU A 796 " --> pdb=" O PHE A 919 " (cutoff:3.500A) removed outlier: 8.144A pdb=" N ILE A 795 " --> pdb=" O VAL A 890 " (cutoff:3.500A) removed outlier: 6.289A pdb=" N LEU A 892 " --> pdb=" O ILE A 795 " (cutoff:3.500A) removed outlier: 8.057A pdb=" N ILE A 797 " --> pdb=" O LEU A 892 " (cutoff:3.500A) removed outlier: 6.995A pdb=" N ALA A 894 " --> pdb=" O ILE A 797 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N SER A 855 " --> pdb=" O LEU A 891 " (cutoff:3.500A) removed outlier: 7.848A pdb=" N LEU A 893 " --> pdb=" O SER A 855 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N VAL A 857 " --> pdb=" O LEU A 893 " (cutoff:3.500A) removed outlier: 8.374A pdb=" N THR A 895 " --> pdb=" O VAL A 857 " (cutoff:3.500A) removed outlier: 7.593A pdb=" N VAL A 859 " --> pdb=" O THR A 895 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N THR A 821 " --> pdb=" O ILE A 856 " (cutoff:3.500A) removed outlier: 7.810A pdb=" N TYR A 858 " --> pdb=" O THR A 821 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N TYR A 823 " --> pdb=" O TYR A 858 " (cutoff:3.500A) 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: 8.195A pdb=" N PHE B 594 " --> pdb=" O GLY B 462 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N LEU B 464 " --> pdb=" O PHE B 594 " (cutoff:3.500A) removed outlier: 7.341A pdb=" N PHE B 596 " --> pdb=" O LEU B 464 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N TYR B 466 " --> pdb=" O PHE B 596 " (cutoff:3.500A) removed outlier: 8.820A pdb=" N CYS B 463 " --> pdb=" O ILE B 568 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N VAL B 570 " --> pdb=" O CYS B 463 " (cutoff:3.500A) removed outlier: 8.036A pdb=" N PHE B 465 " --> pdb=" O VAL B 570 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N GLY B 572 " --> pdb=" O PHE B 465 " (cutoff:3.500A) removed outlier: 8.592A pdb=" N GLY B 467 " --> pdb=" O GLY B 572 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N THR B 574 " --> pdb=" O GLY B 467 " (cutoff:3.500A) removed outlier: 7.175A pdb=" N SER B 526 " --> pdb=" O VAL B 569 " (cutoff:3.500A) removed outlier: 8.600A pdb=" N ILE B 571 " --> pdb=" O SER B 526 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N ILE B 528 " --> pdb=" O ILE B 571 " (cutoff:3.500A) removed outlier: 8.660A pdb=" N ALA B 573 " --> pdb=" O ILE B 528 " (cutoff:3.500A) removed outlier: 7.690A pdb=" N PHE B 530 " --> pdb=" O ALA B 573 " (cutoff:3.500A) removed outlier: 6.963A 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: 8.236A pdb=" N PHE B 919 " --> pdb=" O ARG B 794 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N LEU B 796 " --> pdb=" O PHE B 919 " (cutoff:3.500A) removed outlier: 8.011A pdb=" N ILE B 795 " --> pdb=" O VAL B 890 " (cutoff:3.500A) removed outlier: 6.078A pdb=" N LEU B 892 " --> pdb=" O ILE B 795 " (cutoff:3.500A) removed outlier: 7.768A pdb=" N ILE B 797 " --> pdb=" O LEU B 892 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N ALA B 894 " --> pdb=" O ILE B 797 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N SER B 855 " --> pdb=" O LEU B 891 " (cutoff:3.500A) removed outlier: 7.809A pdb=" N LEU B 893 " --> pdb=" O SER B 855 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N VAL B 857 " --> pdb=" O LEU B 893 " (cutoff:3.500A) removed outlier: 8.438A pdb=" N THR B 895 " --> pdb=" O VAL B 857 " (cutoff:3.500A) removed outlier: 7.903A pdb=" N VAL B 859 " --> pdb=" O THR B 895 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N THR B 821 " --> pdb=" O ILE B 856 " (cutoff:3.500A) removed outlier: 7.596A pdb=" N TYR B 858 " --> pdb=" O THR B 821 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N TYR B 823 " --> pdb=" O TYR B 858 " (cutoff:3.500A) 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: 3.561A pdb=" N TYR C 466 " --> pdb=" O PHE C 594 " (cutoff:3.500A) removed outlier: 8.486A pdb=" N CYS C 463 " --> pdb=" O ILE C 568 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N VAL C 570 " --> pdb=" O CYS C 463 " (cutoff:3.500A) removed outlier: 7.896A pdb=" N PHE C 465 " --> pdb=" O VAL C 570 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N GLY C 572 " --> pdb=" O PHE C 465 " (cutoff:3.500A) removed outlier: 8.716A pdb=" N GLY C 467 " --> pdb=" O GLY C 572 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N THR C 574 " --> pdb=" O GLY C 467 " (cutoff:3.500A) removed outlier: 7.227A pdb=" N SER C 526 " --> pdb=" O VAL C 569 " (cutoff:3.500A) removed outlier: 8.609A pdb=" N ILE C 571 " --> pdb=" O SER C 526 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N ILE C 528 " --> pdb=" O ILE C 571 " (cutoff:3.500A) removed outlier: 8.654A pdb=" N ALA C 573 " --> pdb=" O ILE C 528 " (cutoff:3.500A) removed outlier: 7.362A pdb=" N PHE C 530 " --> pdb=" O ALA C 573 " (cutoff:3.500A) removed outlier: 7.101A pdb=" N PHE C 494 " --> pdb=" O PHE C 529 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'C' and resid 794 through 798 removed outlier: 8.359A pdb=" N ILE C 795 " --> pdb=" O VAL C 890 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N LEU C 892 " --> pdb=" O ILE C 795 " (cutoff:3.500A) removed outlier: 8.090A pdb=" N ILE C 797 " --> pdb=" O LEU C 892 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N ALA C 894 " --> pdb=" O ILE C 797 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N SER C 855 " --> pdb=" O LEU C 891 " (cutoff:3.500A) removed outlier: 7.925A pdb=" N LEU C 893 " --> pdb=" O SER C 855 " (cutoff:3.500A) removed outlier: 6.177A pdb=" N VAL C 857 " --> pdb=" O LEU C 893 " (cutoff:3.500A) removed outlier: 8.266A pdb=" N THR C 895 " --> pdb=" O VAL C 857 " (cutoff:3.500A) removed outlier: 7.535A pdb=" N VAL C 859 " --> pdb=" O THR C 895 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'D' and resid 593 through 596 removed outlier: 8.161A pdb=" N PHE D 594 " --> pdb=" O GLY D 462 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N LEU D 464 " --> pdb=" O PHE D 594 " (cutoff:3.500A) removed outlier: 7.557A pdb=" N PHE D 596 " --> pdb=" O LEU D 464 " (cutoff:3.500A) removed outlier: 7.035A pdb=" N TYR D 466 " --> pdb=" O PHE D 596 " (cutoff:3.500A) removed outlier: 8.739A pdb=" N CYS D 463 " --> pdb=" O ILE D 568 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N VAL D 570 " --> pdb=" O CYS D 463 " (cutoff:3.500A) removed outlier: 8.023A pdb=" N PHE D 465 " --> pdb=" O VAL D 570 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N GLY D 572 " --> pdb=" O PHE D 465 " (cutoff:3.500A) removed outlier: 8.708A pdb=" N GLY D 467 " --> pdb=" O GLY D 572 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N SER D 526 " --> pdb=" O VAL D 569 " (cutoff:3.500A) removed outlier: 8.039A pdb=" N ILE D 571 " --> pdb=" O SER D 526 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N ILE D 528 " --> pdb=" O ILE D 571 " (cutoff:3.500A) removed outlier: 8.063A pdb=" N ALA D 573 " --> pdb=" O ILE D 528 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N PHE D 530 " --> pdb=" O ALA D 573 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N ALA D 492 " --> pdb=" O ILE D 527 " (cutoff:3.500A) removed outlier: 8.218A pdb=" N PHE D 529 " --> pdb=" O ALA D 492 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N PHE D 494 " --> pdb=" O PHE D 529 " (cutoff:3.500A) removed outlier: 7.884A pdb=" N ASP D 531 " --> pdb=" O PHE D 494 " (cutoff:3.500A) removed outlier: 7.039A pdb=" N ARG D 496 " --> pdb=" O ASP D 531 " (cutoff:3.500A) No H-bonds generated for sheet with id= G Processing sheet with id= H, first strand: chain 'D' and resid 796 through 798 Processing sheet with id= I, first strand: chain 'D' and resid 821 through 824 removed outlier: 3.775A pdb=" N THR D 895 " --> pdb=" O VAL D 859 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'E' and resid 463 through 467 removed outlier: 6.925A pdb=" N ARG E 592 " --> pdb=" O LEU E 464 " (cutoff:3.500A) removed outlier: 7.985A pdb=" N TYR E 466 " --> pdb=" O ARG E 592 " (cutoff:3.500A) removed outlier: 5.905A pdb=" N PHE E 594 " --> pdb=" O TYR E 466 " (cutoff:3.500A) No H-bonds generated for sheet with id= J Processing sheet with id= K, first strand: chain 'E' and resid 492 through 495 removed outlier: 3.554A pdb=" N ILE E 527 " --> pdb=" O ALA E 492 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N VAL E 569 " --> pdb=" O SER E 526 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'E' and resid 918 through 920 removed outlier: 8.619A pdb=" N PHE E 919 " --> pdb=" O ARG E 794 " (cutoff:3.500A) removed outlier: 6.977A pdb=" N LEU E 796 " --> pdb=" O PHE E 919 " (cutoff:3.500A) removed outlier: 8.005A pdb=" N ILE E 795 " --> pdb=" O VAL E 890 " (cutoff:3.500A) removed outlier: 5.963A pdb=" N LEU E 892 " --> pdb=" O ILE E 795 " (cutoff:3.500A) removed outlier: 7.529A pdb=" N ILE E 797 " --> pdb=" O LEU E 892 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N ALA E 894 " --> pdb=" O ILE E 797 " (cutoff:3.500A) removed outlier: 7.105A pdb=" N SER E 855 " --> pdb=" O LEU E 891 " (cutoff:3.500A) removed outlier: 8.079A pdb=" N LEU E 893 " --> pdb=" O SER E 855 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N VAL E 857 " --> pdb=" O LEU E 893 " (cutoff:3.500A) removed outlier: 8.438A pdb=" N THR E 895 " --> pdb=" O VAL E 857 " (cutoff:3.500A) removed outlier: 7.671A pdb=" N VAL E 859 " --> pdb=" O THR E 895 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N THR E 821 " --> pdb=" O ILE E 856 " (cutoff:3.500A) removed outlier: 8.113A pdb=" N TYR E 858 " --> pdb=" O THR E 821 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N TYR E 823 " --> pdb=" O TYR E 858 " (cutoff:3.500A) No H-bonds generated for sheet with id= L Processing sheet with id= M, first strand: chain 'F' and resid 463 through 465 removed outlier: 3.997A pdb=" N CYS F 463 " --> pdb=" O VAL F 570 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N GLY F 572 " --> pdb=" O CYS F 463 " (cutoff:3.500A) removed outlier: 7.421A pdb=" N SER F 526 " --> pdb=" O VAL F 569 " (cutoff:3.500A) removed outlier: 8.183A pdb=" N ILE F 571 " --> pdb=" O SER F 526 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N ILE F 528 " --> pdb=" O ILE F 571 " (cutoff:3.500A) removed outlier: 8.189A pdb=" N ALA F 573 " --> pdb=" O ILE F 528 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N PHE F 530 " --> pdb=" O ALA F 573 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N ALA F 492 " --> pdb=" O ILE F 527 " (cutoff:3.500A) removed outlier: 8.027A pdb=" N PHE F 529 " --> pdb=" O ALA F 492 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N PHE F 494 " --> pdb=" O PHE F 529 " (cutoff:3.500A) removed outlier: 8.184A pdb=" N ASP F 531 " --> pdb=" O PHE F 494 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'F' and resid 918 through 920 removed outlier: 8.332A pdb=" N PHE F 919 " --> pdb=" O ARG F 794 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N LEU F 796 " --> pdb=" O PHE F 919 " (cutoff:3.500A) removed outlier: 5.817A pdb=" N LEU F 892 " --> pdb=" O ILE F 795 " (cutoff:3.500A) removed outlier: 7.272A pdb=" N ILE F 797 " --> pdb=" O LEU F 892 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N ALA F 894 " --> pdb=" O ILE F 797 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N THR F 895 " --> pdb=" O VAL F 859 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N THR F 821 " --> pdb=" O ILE F 856 " (cutoff:3.500A) removed outlier: 7.803A pdb=" N TYR F 858 " --> pdb=" O THR F 821 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N TYR F 823 " --> pdb=" O TYR F 858 " (cutoff:3.500A) 750 hydrogen bonds defined for protein. 2196 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: 7.93 Time building geometry restraints manager: 10.13 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 7388 1.33 - 1.45: 3717 1.45 - 1.57: 14537 1.57 - 1.69: 28 1.69 - 1.81: 159 Bond restraints: 25829 Sorted by residual: bond pdb=" C4 ATP C1401 " pdb=" C5 ATP C1401 " ideal model delta sigma weight residual 1.388 1.472 -0.084 1.00e-02 1.00e+04 7.01e+01 bond pdb=" C4 ATP B1401 " pdb=" C5 ATP B1401 " ideal model delta sigma weight residual 1.388 1.471 -0.083 1.00e-02 1.00e+04 6.96e+01 bond pdb=" C4 ATP D1401 " pdb=" C5 ATP D1401 " ideal model delta sigma weight residual 1.388 1.470 -0.082 1.00e-02 1.00e+04 6.78e+01 bond pdb=" C5 ATP C1401 " pdb=" C6 ATP C1401 " ideal model delta sigma weight residual 1.409 1.482 -0.073 1.00e-02 1.00e+04 5.39e+01 bond pdb=" C5 ATP D1401 " pdb=" C6 ATP D1401 " ideal model delta sigma weight residual 1.409 1.482 -0.073 1.00e-02 1.00e+04 5.29e+01 ... (remaining 25824 not shown) Histogram of bond angle deviations from ideal: 98.90 - 107.08: 1000 107.08 - 115.26: 15720 115.26 - 123.44: 17539 123.44 - 131.62: 715 131.62 - 139.81: 40 Bond angle restraints: 35014 Sorted by residual: angle pdb=" PB ATP D1401 " pdb=" O3B ATP D1401 " pdb=" PG ATP D1401 " ideal model delta sigma weight residual 139.87 120.35 19.52 1.00e+00 1.00e+00 3.81e+02 angle pdb=" PB ATP C1401 " pdb=" O3B ATP C1401 " pdb=" PG ATP C1401 " ideal model delta sigma weight residual 139.87 120.53 19.34 1.00e+00 1.00e+00 3.74e+02 angle pdb=" PB ATP B1401 " pdb=" O3B ATP B1401 " pdb=" PG ATP B1401 " ideal model delta sigma weight residual 139.87 120.81 19.06 1.00e+00 1.00e+00 3.63e+02 angle pdb=" PA ATP C1401 " pdb=" O3A ATP C1401 " pdb=" PB ATP C1401 " ideal model delta sigma weight residual 136.83 120.42 16.41 1.00e+00 1.00e+00 2.69e+02 angle pdb=" PA ATP B1401 " pdb=" O3A ATP B1401 " pdb=" PB ATP B1401 " ideal model delta sigma weight residual 136.83 120.51 16.32 1.00e+00 1.00e+00 2.66e+02 ... (remaining 35009 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.53: 14599 21.53 - 43.07: 1119 43.07 - 64.60: 116 64.60 - 86.13: 63 86.13 - 107.66: 9 Dihedral angle restraints: 15906 sinusoidal: 6675 harmonic: 9231 Sorted by residual: dihedral pdb=" C5' ADP A1401 " pdb=" O5' ADP A1401 " pdb=" PA ADP A1401 " pdb=" O2A ADP A1401 " ideal model delta sinusoidal sigma weight residual -60.00 47.67 -107.66 1 2.00e+01 2.50e-03 3.13e+01 dihedral pdb=" O1B ADP A1401 " pdb=" O3A ADP A1401 " pdb=" PB ADP A1401 " pdb=" PA ADP A1401 " ideal model delta sinusoidal sigma weight residual -60.00 -149.55 89.55 1 2.00e+01 2.50e-03 2.38e+01 dihedral pdb=" CA PHE B 911 " pdb=" C PHE B 911 " pdb=" N ILE B 912 " pdb=" CA ILE B 912 " ideal model delta harmonic sigma weight residual -180.00 -158.07 -21.93 0 5.00e+00 4.00e-02 1.92e+01 ... (remaining 15903 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 2800 0.041 - 0.081: 862 0.081 - 0.122: 258 0.122 - 0.163: 24 0.163 - 0.204: 4 Chirality restraints: 3948 Sorted by residual: chirality pdb=" CA GLU E1382 " pdb=" N GLU E1382 " pdb=" C GLU E1382 " pdb=" CB GLU E1382 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 1.04e+00 chirality pdb=" CA ASN A 616 " pdb=" N ASN A 616 " pdb=" C ASN A 616 " pdb=" CB ASN A 616 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 9.36e-01 chirality pdb=" CB ILE B 672 " pdb=" CA ILE B 672 " pdb=" CG1 ILE B 672 " pdb=" CG2 ILE B 672 " both_signs ideal model delta sigma weight residual False 2.64 2.84 -0.19 2.00e-01 2.50e+01 9.26e-01 ... (remaining 3945 not shown) Planarity restraints: 4488 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG D 586 " -0.032 5.00e-02 4.00e+02 4.80e-02 3.69e+00 pdb=" N PRO D 587 " 0.083 5.00e-02 4.00e+02 pdb=" CA PRO D 587 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO D 587 " -0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG F 586 " -0.030 5.00e-02 4.00e+02 4.52e-02 3.27e+00 pdb=" N PRO F 587 " 0.078 5.00e-02 4.00e+02 pdb=" CA PRO F 587 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO F 587 " -0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP E 865 " -0.010 2.00e-02 2.50e+03 1.11e-02 3.09e+00 pdb=" CG TRP E 865 " 0.030 2.00e-02 2.50e+03 pdb=" CD1 TRP E 865 " -0.014 2.00e-02 2.50e+03 pdb=" CD2 TRP E 865 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP E 865 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP E 865 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP E 865 " -0.004 2.00e-02 2.50e+03 pdb=" CZ2 TRP E 865 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP E 865 " -0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP E 865 " -0.000 2.00e-02 2.50e+03 ... (remaining 4485 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.68: 482 2.68 - 3.24: 25255 3.24 - 3.79: 37376 3.79 - 4.35: 47457 4.35 - 4.90: 76682 Nonbonded interactions: 187252 Sorted by model distance: nonbonded pdb=" OE1 GLU D 440 " pdb=" OH TYR E 659 " model vdw 2.131 2.440 nonbonded pdb=" O GLN F 657 " pdb=" OG1 THR F 661 " model vdw 2.178 2.440 nonbonded pdb=" O ARG F 576 " pdb=" OG SER F 579 " model vdw 2.220 2.440 nonbonded pdb=" OD2 ASP C 668 " pdb=" OG SER C 670 " model vdw 2.221 2.440 nonbonded pdb=" O LYS C 706 " pdb=" NE2 GLN C 710 " model vdw 2.232 2.520 ... (remaining 187247 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 598 or resid 601 through 688 or resid 696 thro \ ugh 727 or resid 787 through 943 or resid 1331 through 1388)) selection = (chain 'B' and (resid 422 through 539 or resid 546 through 598 or resid 601 thro \ ugh 659 or resid 666 through 688 or resid 696 through 727 or resid 787 through 9 \ 23 or resid 925 through 943 or resid 1331 through 1388)) selection = (chain 'C' and (resid 422 through 539 or resid 546 through 598 or resid 601 thro \ ugh 659 or resid 666 through 688 or resid 696 through 727 or resid 787 through 9 \ 23 or resid 925 through 943 or resid 1331 through 1388)) selection = (chain 'D' and (resid 422 through 539 or resid 546 through 598 or resid 601 thro \ ugh 659 or resid 666 through 688 or resid 696 through 727 or resid 787 through 9 \ 23 or resid 925 through 943 or resid 1331 through 1388)) selection = (chain 'E' and (resid 422 through 539 or resid 546 through 598 or resid 601 thro \ ugh 659 or resid 666 through 688 or resid 696 through 727 or resid 787 through 9 \ 23 or resid 925 through 943 or resid 1331 through 1388)) selection = (chain 'F' and (resid 422 through 539 or resid 546 through 659 or resid 666 thro \ ugh 727 or resid 787 through 923 or resid 925 through 943 or resid 1331 through \ 1388)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.520 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 7.100 Check model and map are aligned: 0.420 Set scattering table: 0.260 Process input model: 62.120 Find NCS groups from input model: 1.860 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 76.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4999 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.084 25829 Z= 0.217 Angle : 0.723 19.522 35014 Z= 0.456 Chirality : 0.042 0.204 3948 Planarity : 0.004 0.052 4488 Dihedral : 15.177 107.663 9884 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 9.33 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.56 % Favored : 93.34 % Rotamer: Outliers : 0.07 % Allowed : 0.32 % Favored : 99.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.00 % Cis-general : 0.34 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.25 (0.16), residues: 3109 helix: 0.67 (0.15), residues: 1391 sheet: 0.46 (0.28), residues: 377 loop : -1.22 (0.18), residues: 1341 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP E 865 HIS 0.003 0.001 HIS C1366 PHE 0.010 0.001 PHE D 724 TYR 0.017 0.001 TYR C1364 ARG 0.006 0.000 ARG F 576 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6218 Ramachandran restraints generated. 3109 Oldfield, 0 Emsley, 3109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6218 Ramachandran restraints generated. 3109 Oldfield, 0 Emsley, 3109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 635 residues out of total 2778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 633 time to evaluate : 2.911 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 639 ILE cc_start: 0.5841 (mm) cc_final: 0.5626 (mm) REVERT: A 686 MET cc_start: 0.0558 (pmm) cc_final: 0.0348 (mtt) REVERT: A 1379 MET cc_start: -0.5244 (mmt) cc_final: -0.5847 (mmp) REVERT: B 686 MET cc_start: 0.3895 (ppp) cc_final: 0.3088 (ppp) REVERT: C 441 MET cc_start: 0.5248 (ttm) cc_final: 0.4284 (ttt) REVERT: C 642 ILE cc_start: 0.8023 (mm) cc_final: 0.7228 (tp) REVERT: C 876 THR cc_start: 0.8155 (m) cc_final: 0.7449 (p) REVERT: C 883 ASN cc_start: 0.7292 (m110) cc_final: 0.6992 (m-40) REVERT: D 789 MET cc_start: 0.6822 (ttp) cc_final: 0.6150 (ppp) REVERT: D 857 VAL cc_start: 0.9198 (t) cc_final: 0.8976 (m) REVERT: E 578 ASP cc_start: 0.1467 (m-30) cc_final: 0.1248 (m-30) REVERT: E 789 MET cc_start: 0.7885 (tpt) cc_final: 0.7614 (tpt) REVERT: E 827 ILE cc_start: 0.7117 (mm) cc_final: 0.6866 (mm) REVERT: F 548 HIS cc_start: 0.7333 (m90) cc_final: 0.6979 (m170) REVERT: F 789 MET cc_start: -0.1316 (ppp) cc_final: -0.1826 (ttt) REVERT: F 1355 LEU cc_start: 0.8742 (tp) cc_final: 0.8539 (tt) outliers start: 2 outliers final: 1 residues processed: 634 average time/residue: 0.4223 time to fit residues: 400.3217 Evaluate side-chains 294 residues out of total 2778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 293 time to evaluate : 2.933 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 263 optimal weight: 5.9990 chunk 236 optimal weight: 0.0050 chunk 131 optimal weight: 4.9990 chunk 80 optimal weight: 0.3980 chunk 159 optimal weight: 1.9990 chunk 126 optimal weight: 0.7980 chunk 244 optimal weight: 4.9990 chunk 94 optimal weight: 0.7980 chunk 148 optimal weight: 3.9990 chunk 182 optimal weight: 0.1980 chunk 283 optimal weight: 0.4980 overall best weight: 0.3794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 546 GLN A1351 GLN ** A1381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 548 HIS B 611 HIS B 882 GLN ** C 691 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 882 GLN ** C1345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1361 GLN ** D 532 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 691 GLN D1361 GLN E 815 HIS E1330 HIS E1351 GLN ** F 544 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 611 HIS ** F 940 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5223 moved from start: 0.2537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 25829 Z= 0.177 Angle : 0.618 10.317 35014 Z= 0.302 Chirality : 0.042 0.193 3948 Planarity : 0.004 0.051 4488 Dihedral : 8.946 104.865 3581 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 9.98 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.24 % Favored : 93.66 % Rotamer: Outliers : 0.07 % Allowed : 4.72 % Favored : 95.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.00 % Cis-general : 0.34 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.16 (0.16), residues: 3109 helix: 0.66 (0.14), residues: 1398 sheet: 0.67 (0.28), residues: 379 loop : -1.14 (0.18), residues: 1332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 505 HIS 0.014 0.001 HIS A 861 PHE 0.029 0.001 PHE C 517 TYR 0.030 0.001 TYR C 823 ARG 0.008 0.000 ARG B 524 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6218 Ramachandran restraints generated. 3109 Oldfield, 0 Emsley, 3109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6218 Ramachandran restraints generated. 3109 Oldfield, 0 Emsley, 3109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 395 residues out of total 2778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 393 time to evaluate : 3.301 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 523 MET cc_start: 0.4233 (mmp) cc_final: 0.2960 (tpt) REVERT: A 639 ILE cc_start: 0.5926 (mm) cc_final: 0.5698 (mm) REVERT: A 686 MET cc_start: 0.0402 (pmm) cc_final: -0.0071 (mtt) REVERT: A 1379 MET cc_start: -0.5105 (mmt) cc_final: -0.5609 (mmp) REVERT: B 686 MET cc_start: 0.4125 (ppp) cc_final: 0.3698 (ppp) REVERT: C 527 ILE cc_start: 0.5334 (mp) cc_final: 0.5102 (mp) REVERT: C 851 ARG cc_start: 0.7782 (mtp-110) cc_final: 0.7490 (ttp80) REVERT: C 876 THR cc_start: 0.8315 (m) cc_final: 0.8066 (p) REVERT: C 1384 GLU cc_start: 0.6366 (OUTLIER) cc_final: 0.5978 (mp0) REVERT: D 424 ARG cc_start: 0.5042 (mmt180) cc_final: 0.4786 (tpp80) REVERT: D 444 PHE cc_start: 0.5004 (m-10) cc_final: 0.4553 (m-10) REVERT: D 857 VAL cc_start: 0.9189 (t) cc_final: 0.8965 (m) REVERT: E 670 SER cc_start: 0.6487 (m) cc_final: 0.6240 (p) REVERT: F 789 MET cc_start: -0.1329 (ppp) cc_final: -0.1550 (ttp) REVERT: F 891 LEU cc_start: 0.6147 (tp) cc_final: 0.5896 (tp) outliers start: 2 outliers final: 1 residues processed: 395 average time/residue: 0.3692 time to fit residues: 227.8570 Evaluate side-chains 253 residues out of total 2778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 251 time to evaluate : 2.765 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 157 optimal weight: 7.9990 chunk 87 optimal weight: 0.0470 chunk 235 optimal weight: 0.8980 chunk 192 optimal weight: 0.5980 chunk 78 optimal weight: 9.9990 chunk 283 optimal weight: 0.7980 chunk 306 optimal weight: 6.9990 chunk 252 optimal weight: 6.9990 chunk 281 optimal weight: 0.8980 chunk 96 optimal weight: 0.0670 chunk 227 optimal weight: 0.0970 overall best weight: 0.3214 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 691 GLN C 883 ASN ** C1345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 434 HIS D 532 GLN D 691 GLN D1361 GLN E 630 ASN E 815 HIS ** E1351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 940 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5262 moved from start: 0.3086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 25829 Z= 0.156 Angle : 0.593 11.412 35014 Z= 0.287 Chirality : 0.042 0.182 3948 Planarity : 0.004 0.061 4488 Dihedral : 8.791 98.560 3581 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 9.57 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.14 % Favored : 93.79 % Rotamer: Outliers : 0.04 % Allowed : 3.38 % Favored : 96.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.00 % Cis-general : 0.34 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.08 (0.16), residues: 3109 helix: 0.67 (0.14), residues: 1403 sheet: 0.87 (0.28), residues: 372 loop : -1.07 (0.18), residues: 1334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP E 865 HIS 0.006 0.001 HIS A 900 PHE 0.043 0.001 PHE E 529 TYR 0.021 0.001 TYR B1356 ARG 0.018 0.000 ARG E 847 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6218 Ramachandran restraints generated. 3109 Oldfield, 0 Emsley, 3109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6218 Ramachandran restraints generated. 3109 Oldfield, 0 Emsley, 3109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 345 residues out of total 2778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 344 time to evaluate : 2.820 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 523 MET cc_start: 0.4385 (mmp) cc_final: 0.3290 (tpt) REVERT: A 639 ILE cc_start: 0.5932 (mm) cc_final: 0.5708 (mm) REVERT: A 686 MET cc_start: 0.0299 (pmm) cc_final: -0.0052 (mtt) REVERT: A 789 MET cc_start: -0.0317 (ttt) cc_final: -0.0786 (ttt) REVERT: A 892 LEU cc_start: 0.0671 (pt) cc_final: 0.0371 (pp) REVERT: A 1379 MET cc_start: -0.4997 (mmt) cc_final: -0.5429 (mmp) REVERT: B 686 MET cc_start: 0.4050 (ppp) cc_final: 0.3749 (ppp) REVERT: C 851 ARG cc_start: 0.7842 (mtp-110) cc_final: 0.7587 (ttp80) REVERT: C 876 THR cc_start: 0.8400 (m) cc_final: 0.8122 (p) REVERT: C 1382 GLU cc_start: 0.6937 (tt0) cc_final: 0.6701 (tt0) REVERT: D 424 ARG cc_start: 0.5169 (mmt180) cc_final: 0.4578 (tpp80) REVERT: D 444 PHE cc_start: 0.4813 (m-10) cc_final: 0.4568 (m-10) REVERT: D 789 MET cc_start: 0.7475 (ppp) cc_final: 0.7234 (ppp) REVERT: D 857 VAL cc_start: 0.9236 (t) cc_final: 0.8979 (m) REVERT: E 670 SER cc_start: 0.6583 (m) cc_final: 0.6306 (p) REVERT: F 652 ARG cc_start: 0.8802 (tmm160) cc_final: 0.8313 (tpp-160) REVERT: F 1382 GLU cc_start: 0.8288 (tm-30) cc_final: 0.7775 (tp30) outliers start: 1 outliers final: 0 residues processed: 345 average time/residue: 0.3554 time to fit residues: 194.2438 Evaluate side-chains 236 residues out of total 2778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 236 time to evaluate : 2.852 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 280 optimal weight: 4.9990 chunk 213 optimal weight: 5.9990 chunk 147 optimal weight: 4.9990 chunk 31 optimal weight: 10.0000 chunk 135 optimal weight: 5.9990 chunk 190 optimal weight: 5.9990 chunk 284 optimal weight: 7.9990 chunk 301 optimal weight: 0.0980 chunk 148 optimal weight: 7.9990 chunk 269 optimal weight: 3.9990 chunk 81 optimal weight: 6.9990 overall best weight: 4.0188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1381 GLN ** B 544 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 630 ASN B 844 GLN C 611 HIS C 630 ASN C 699 GLN C 883 ASN C 922 GLN C1361 GLN ** C1366 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1385 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 691 GLN E 482 ASN E 787 GLN ** E 815 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 900 HIS E 908 GLN ** E1351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E1361 GLN ** F 544 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 815 HIS ** F 900 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 940 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6142 moved from start: 0.6520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.092 25829 Z= 0.440 Angle : 1.012 12.878 35014 Z= 0.517 Chirality : 0.055 0.311 3948 Planarity : 0.009 0.141 4488 Dihedral : 9.881 97.957 3581 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 21.36 Ramachandran Plot: Outliers : 0.10 % Allowed : 8.91 % Favored : 90.99 % Rotamer: Outliers : 0.54 % Allowed : 7.34 % Favored : 92.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.00 % Cis-general : 0.34 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -1.49 (0.15), residues: 3109 helix: -0.64 (0.13), residues: 1429 sheet: -0.06 (0.28), residues: 362 loop : -1.55 (0.17), residues: 1318 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.058 0.004 TRP A 505 HIS 0.051 0.003 HIS A 863 PHE 0.033 0.003 PHE D 517 TYR 0.061 0.004 TYR B 466 ARG 0.018 0.001 ARG C 543 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6218 Ramachandran restraints generated. 3109 Oldfield, 0 Emsley, 3109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6218 Ramachandran restraints generated. 3109 Oldfield, 0 Emsley, 3109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 324 residues out of total 2778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 309 time to evaluate : 2.909 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 616 ASN cc_start: 0.2694 (p0) cc_final: 0.1521 (m-40) REVERT: A 639 ILE cc_start: 0.6606 (mm) cc_final: 0.6357 (mm) REVERT: A 789 MET cc_start: -0.0098 (ttt) cc_final: -0.0646 (ttt) REVERT: A 863 HIS cc_start: 0.3116 (p-80) cc_final: 0.2859 (p90) REVERT: B 495 MET cc_start: 0.6644 (tpt) cc_final: 0.4726 (ttm) REVERT: B 686 MET cc_start: 0.4622 (ppp) cc_final: 0.4178 (ppp) REVERT: C 459 PRO cc_start: 0.8042 (Cg_endo) cc_final: 0.7817 (Cg_exo) REVERT: C 536 LEU cc_start: 0.7212 (tt) cc_final: 0.6970 (tt) REVERT: D 451 VAL cc_start: 0.8477 (p) cc_final: 0.8186 (t) REVERT: D 471 THR cc_start: 0.9113 (OUTLIER) cc_final: 0.8896 (m) REVERT: D 495 MET cc_start: 0.6131 (tpt) cc_final: 0.5448 (tpt) REVERT: D 496 ARG cc_start: 0.6794 (mtm-85) cc_final: 0.6071 (ttt90) REVERT: D 533 ILE cc_start: 0.7073 (mp) cc_final: 0.6747 (tp) REVERT: D 571 ILE cc_start: 0.7972 (mm) cc_final: 0.6792 (mm) REVERT: F 1379 MET cc_start: 0.8614 (mpp) cc_final: 0.8252 (mpp) outliers start: 15 outliers final: 4 residues processed: 323 average time/residue: 0.3696 time to fit residues: 184.2120 Evaluate side-chains 206 residues out of total 2778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 201 time to evaluate : 2.605 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 251 optimal weight: 7.9990 chunk 171 optimal weight: 0.9990 chunk 4 optimal weight: 0.0670 chunk 224 optimal weight: 2.9990 chunk 124 optimal weight: 0.9990 chunk 257 optimal weight: 5.9990 chunk 208 optimal weight: 7.9990 chunk 0 optimal weight: 20.0000 chunk 153 optimal weight: 0.9990 chunk 270 optimal weight: 4.9990 chunk 76 optimal weight: 6.9990 overall best weight: 1.2126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 575 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 630 ASN C 908 GLN ** C1345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1346 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1361 GLN C1385 ASN D 691 GLN D1361 GLN ** E 815 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 863 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 908 GLN ** E1351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 548 HIS F 900 HIS ** F 940 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6054 moved from start: 0.6762 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 25829 Z= 0.198 Angle : 0.675 10.759 35014 Z= 0.332 Chirality : 0.045 0.192 3948 Planarity : 0.005 0.082 4488 Dihedral : 9.125 98.242 3581 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 12.03 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.95 % Favored : 93.95 % Rotamer: Outliers : 0.04 % Allowed : 2.38 % Favored : 97.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.00 % Cis-general : 0.34 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.84 (0.15), residues: 3109 helix: 0.02 (0.14), residues: 1411 sheet: 0.12 (0.28), residues: 365 loop : -1.31 (0.18), residues: 1333 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A 505 HIS 0.008 0.001 HIS C 548 PHE 0.045 0.002 PHE C 517 TYR 0.017 0.002 TYR C 634 ARG 0.009 0.001 ARG C 592 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6218 Ramachandran restraints generated. 3109 Oldfield, 0 Emsley, 3109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6218 Ramachandran restraints generated. 3109 Oldfield, 0 Emsley, 3109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 2778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 300 time to evaluate : 2.745 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 639 ILE cc_start: 0.6221 (mm) cc_final: 0.5986 (mm) REVERT: A 825 LEU cc_start: 0.1698 (tt) cc_final: 0.0946 (tp) REVERT: B 686 MET cc_start: 0.4262 (ppp) cc_final: 0.3889 (ppp) REVERT: C 459 PRO cc_start: 0.8049 (Cg_endo) cc_final: 0.7765 (Cg_exo) REVERT: C 530 PHE cc_start: 0.7523 (t80) cc_final: 0.7236 (t80) REVERT: D 444 PHE cc_start: 0.7006 (m-10) cc_final: 0.6710 (m-10) REVERT: D 451 VAL cc_start: 0.8190 (p) cc_final: 0.7953 (t) REVERT: D 495 MET cc_start: 0.5866 (tpt) cc_final: 0.5348 (tpt) REVERT: D 496 ARG cc_start: 0.6627 (mtm-85) cc_final: 0.6044 (ttt90) REVERT: E 478 ARG cc_start: 0.7509 (mtm180) cc_final: 0.6028 (tpt170) REVERT: E 523 MET cc_start: 0.5421 (tpp) cc_final: 0.5214 (tpp) REVERT: E 683 MET cc_start: 0.7821 (tmm) cc_final: 0.7583 (tmm) REVERT: F 626 GLU cc_start: 0.7274 (tm-30) cc_final: 0.6752 (tm-30) REVERT: F 801 PRO cc_start: 0.7360 (Cg_exo) cc_final: 0.7159 (Cg_endo) REVERT: F 1382 GLU cc_start: 0.8320 (tm-30) cc_final: 0.8057 (tp30) outliers start: 1 outliers final: 0 residues processed: 301 average time/residue: 0.3801 time to fit residues: 177.6182 Evaluate side-chains 201 residues out of total 2778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 201 time to evaluate : 2.689 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 101 optimal weight: 10.0000 chunk 271 optimal weight: 0.9990 chunk 59 optimal weight: 9.9990 chunk 177 optimal weight: 3.9990 chunk 74 optimal weight: 20.0000 chunk 301 optimal weight: 4.9990 chunk 250 optimal weight: 0.7980 chunk 139 optimal weight: 8.9990 chunk 25 optimal weight: 20.0000 chunk 99 optimal weight: 0.9990 chunk 158 optimal weight: 0.2980 overall best weight: 1.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1351 GLN A1354 ASN C 548 HIS C 575 ASN C 908 GLN ** C1345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1346 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1361 GLN ** C1366 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 519 GLN D 532 GLN D 691 GLN E 815 HIS ** E1351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 548 HIS ** F 630 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 940 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6134 moved from start: 0.7191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 25829 Z= 0.196 Angle : 0.649 11.289 35014 Z= 0.317 Chirality : 0.043 0.260 3948 Planarity : 0.005 0.074 4488 Dihedral : 8.737 96.646 3581 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 12.76 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.30 % Favored : 92.63 % Rotamer: Outliers : 0.11 % Allowed : 2.84 % Favored : 97.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.00 % Cis-general : 0.34 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.58 (0.16), residues: 3109 helix: 0.25 (0.14), residues: 1409 sheet: 0.11 (0.27), residues: 372 loop : -1.17 (0.18), residues: 1328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 615 HIS 0.008 0.001 HIS A 861 PHE 0.023 0.001 PHE C 517 TYR 0.019 0.002 TYR E 634 ARG 0.009 0.001 ARG C 424 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6218 Ramachandran restraints generated. 3109 Oldfield, 0 Emsley, 3109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6218 Ramachandran restraints generated. 3109 Oldfield, 0 Emsley, 3109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 2778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 268 time to evaluate : 3.216 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 639 ILE cc_start: 0.6357 (mm) cc_final: 0.6104 (mm) REVERT: A 683 MET cc_start: -0.1838 (mmt) cc_final: -0.2446 (mtm) REVERT: A 789 MET cc_start: -0.0322 (ttt) cc_final: -0.0574 (ttt) REVERT: A 825 LEU cc_start: 0.2045 (tt) cc_final: 0.1372 (tp) REVERT: B 686 MET cc_start: 0.4329 (ppp) cc_final: 0.3875 (ppp) REVERT: C 459 PRO cc_start: 0.7968 (Cg_endo) cc_final: 0.7759 (Cg_exo) REVERT: C 932 PHE cc_start: 0.6065 (t80) cc_final: 0.5753 (t80) REVERT: D 451 VAL cc_start: 0.8260 (p) cc_final: 0.8033 (t) REVERT: D 495 MET cc_start: 0.6324 (tpt) cc_final: 0.5760 (tpt) REVERT: D 496 ARG cc_start: 0.7035 (mtm-85) cc_final: 0.6535 (ttt90) REVERT: E 683 MET cc_start: 0.7882 (tmm) cc_final: 0.7548 (tmm) REVERT: F 626 GLU cc_start: 0.7419 (tm-30) cc_final: 0.6594 (tm-30) REVERT: F 801 PRO cc_start: 0.7331 (Cg_exo) cc_final: 0.7065 (Cg_endo) REVERT: F 1382 GLU cc_start: 0.8351 (tm-30) cc_final: 0.8114 (tp30) outliers start: 3 outliers final: 0 residues processed: 271 average time/residue: 0.3673 time to fit residues: 156.9188 Evaluate side-chains 189 residues out of total 2778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 189 time to evaluate : 2.699 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 291 optimal weight: 2.9990 chunk 34 optimal weight: 0.4980 chunk 171 optimal weight: 3.9990 chunk 220 optimal weight: 0.5980 chunk 170 optimal weight: 3.9990 chunk 254 optimal weight: 8.9990 chunk 168 optimal weight: 6.9990 chunk 300 optimal weight: 0.9980 chunk 188 optimal weight: 0.8980 chunk 183 optimal weight: 0.0970 chunk 138 optimal weight: 1.9990 overall best weight: 0.6178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 863 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 630 ASN B1361 GLN ** B1381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 486 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 575 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 883 ASN ** C1345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1346 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 691 GLN E 630 ASN ** E1351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 548 HIS ** F 630 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 940 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6102 moved from start: 0.7347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 25829 Z= 0.163 Angle : 0.627 10.385 35014 Z= 0.305 Chirality : 0.043 0.196 3948 Planarity : 0.005 0.092 4488 Dihedral : 8.484 97.875 3581 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 11.64 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.89 % Favored : 94.05 % Rotamer: Outliers : 0.04 % Allowed : 1.19 % Favored : 98.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.00 % Cis-general : 0.34 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.44 (0.16), residues: 3109 helix: 0.35 (0.14), residues: 1413 sheet: 0.28 (0.27), residues: 372 loop : -1.11 (0.18), residues: 1324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 615 HIS 0.006 0.001 HIS A 900 PHE 0.026 0.001 PHE D 590 TYR 0.014 0.001 TYR B 858 ARG 0.011 0.000 ARG D 514 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6218 Ramachandran restraints generated. 3109 Oldfield, 0 Emsley, 3109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6218 Ramachandran restraints generated. 3109 Oldfield, 0 Emsley, 3109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 2778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 267 time to evaluate : 2.712 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 639 ILE cc_start: 0.6282 (mm) cc_final: 0.6017 (mm) REVERT: A 683 MET cc_start: -0.1982 (mmt) cc_final: -0.2555 (mtm) REVERT: A 825 LEU cc_start: 0.1769 (tt) cc_final: 0.1116 (tp) REVERT: B 686 MET cc_start: 0.4361 (ppp) cc_final: 0.4092 (ppp) REVERT: B 1377 GLN cc_start: 0.5277 (pm20) cc_final: 0.4854 (pm20) REVERT: C 530 PHE cc_start: 0.7525 (t80) cc_final: 0.7307 (t80) REVERT: E 435 ILE cc_start: 0.8403 (mt) cc_final: 0.8190 (tt) REVERT: E 792 ARG cc_start: 0.6684 (mtt180) cc_final: 0.6410 (mtt180) REVERT: F 626 GLU cc_start: 0.7270 (tm-30) cc_final: 0.6593 (tm-30) REVERT: F 801 PRO cc_start: 0.7230 (Cg_exo) cc_final: 0.6999 (Cg_endo) REVERT: F 1379 MET cc_start: 0.8829 (mpp) cc_final: 0.8597 (mmm) REVERT: F 1382 GLU cc_start: 0.8331 (tm-30) cc_final: 0.8101 (tp30) outliers start: 1 outliers final: 1 residues processed: 268 average time/residue: 0.3695 time to fit residues: 154.1937 Evaluate side-chains 191 residues out of total 2778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 190 time to evaluate : 2.920 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 186 optimal weight: 2.9990 chunk 120 optimal weight: 0.0980 chunk 179 optimal weight: 2.9990 chunk 90 optimal weight: 3.9990 chunk 59 optimal weight: 8.9990 chunk 58 optimal weight: 8.9990 chunk 191 optimal weight: 0.7980 chunk 204 optimal weight: 0.9990 chunk 148 optimal weight: 7.9990 chunk 28 optimal weight: 2.9990 chunk 236 optimal weight: 6.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 863 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 575 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 611 HIS C 883 ASN C 908 GLN ** C1345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1346 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 532 GLN D 691 GLN ** E 544 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 630 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 548 HIS ** F 630 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 940 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6226 moved from start: 0.7891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 25829 Z= 0.208 Angle : 0.652 10.234 35014 Z= 0.320 Chirality : 0.043 0.207 3948 Planarity : 0.005 0.075 4488 Dihedral : 8.460 98.830 3581 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 13.15 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.43 % Favored : 92.51 % Rotamer: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.00 % Cis-general : 0.34 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.44 (0.16), residues: 3109 helix: 0.36 (0.14), residues: 1417 sheet: 0.30 (0.27), residues: 387 loop : -1.14 (0.18), residues: 1305 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP A 615 HIS 0.005 0.001 HIS C1366 PHE 0.020 0.002 PHE C 517 TYR 0.014 0.001 TYR E 634 ARG 0.008 0.001 ARG C 424 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6218 Ramachandran restraints generated. 3109 Oldfield, 0 Emsley, 3109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6218 Ramachandran restraints generated. 3109 Oldfield, 0 Emsley, 3109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 2778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 266 time to evaluate : 2.650 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 639 ILE cc_start: 0.6056 (mm) cc_final: 0.5757 (mm) REVERT: C 530 PHE cc_start: 0.7642 (t80) cc_final: 0.7382 (t80) REVERT: E 792 ARG cc_start: 0.6988 (mtt180) cc_final: 0.6534 (mtt180) REVERT: F 556 LEU cc_start: 0.7373 (pp) cc_final: 0.6870 (tp) REVERT: F 801 PRO cc_start: 0.7596 (Cg_exo) cc_final: 0.7358 (Cg_endo) REVERT: F 1379 MET cc_start: 0.8822 (mpp) cc_final: 0.7887 (mpp) outliers start: 0 outliers final: 0 residues processed: 266 average time/residue: 0.3582 time to fit residues: 150.2178 Evaluate side-chains 180 residues out of total 2778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 180 time to evaluate : 2.842 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 273 optimal weight: 9.9990 chunk 288 optimal weight: 1.9990 chunk 262 optimal weight: 5.9990 chunk 280 optimal weight: 0.6980 chunk 168 optimal weight: 10.0000 chunk 122 optimal weight: 3.9990 chunk 220 optimal weight: 3.9990 chunk 85 optimal weight: 0.1980 chunk 253 optimal weight: 1.9990 chunk 265 optimal weight: 5.9990 chunk 279 optimal weight: 6.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 863 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 575 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 710 GLN C 908 GLN ** C1345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1346 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 544 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 630 ASN ** E1351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 548 HIS ** F 940 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1385 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6300 moved from start: 0.8502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 25829 Z= 0.211 Angle : 0.655 10.208 35014 Z= 0.323 Chirality : 0.044 0.156 3948 Planarity : 0.005 0.074 4488 Dihedral : 8.489 99.931 3581 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 13.41 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.69 % Favored : 93.25 % Rotamer: Outliers : 0.00 % Allowed : 0.47 % Favored : 99.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.00 % Cis-general : 0.34 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.45 (0.16), residues: 3109 helix: 0.37 (0.14), residues: 1396 sheet: 0.30 (0.27), residues: 385 loop : -1.14 (0.18), residues: 1328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP A 615 HIS 0.011 0.001 HIS A 611 PHE 0.023 0.002 PHE C 517 TYR 0.014 0.001 TYR E 634 ARG 0.010 0.001 ARG E 524 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6218 Ramachandran restraints generated. 3109 Oldfield, 0 Emsley, 3109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6218 Ramachandran restraints generated. 3109 Oldfield, 0 Emsley, 3109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 2778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 259 time to evaluate : 3.024 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 616 ASN cc_start: 0.2562 (p0) cc_final: 0.1495 (m-40) REVERT: A 639 ILE cc_start: 0.6114 (mm) cc_final: 0.5796 (mm) REVERT: E 638 ASP cc_start: 0.8614 (m-30) cc_final: 0.8324 (m-30) REVERT: F 523 MET cc_start: -0.1458 (ppp) cc_final: -0.2408 (ptp) REVERT: F 556 LEU cc_start: 0.7390 (pp) cc_final: 0.6890 (tp) REVERT: F 801 PRO cc_start: 0.7568 (Cg_exo) cc_final: 0.7354 (Cg_endo) outliers start: 0 outliers final: 0 residues processed: 259 average time/residue: 0.3612 time to fit residues: 148.3057 Evaluate side-chains 178 residues out of total 2778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 178 time to evaluate : 3.068 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 184 optimal weight: 0.9990 chunk 296 optimal weight: 0.0870 chunk 180 optimal weight: 2.9990 chunk 140 optimal weight: 0.6980 chunk 205 optimal weight: 0.6980 chunk 310 optimal weight: 9.9990 chunk 286 optimal weight: 7.9990 chunk 247 optimal weight: 3.9990 chunk 25 optimal weight: 0.7980 chunk 191 optimal weight: 1.9990 chunk 151 optimal weight: 1.9990 overall best weight: 0.6560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B1381 GLN ** C 575 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1346 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 691 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 544 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 548 HIS ** F 940 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1385 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6270 moved from start: 0.8590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.050 25829 Z= 0.158 Angle : 0.626 10.238 35014 Z= 0.305 Chirality : 0.043 0.264 3948 Planarity : 0.004 0.078 4488 Dihedral : 8.243 100.076 3581 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 11.18 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.40 % Favored : 93.53 % Rotamer: Outliers : 0.04 % Allowed : 0.25 % Favored : 99.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.00 % Cis-general : 0.34 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.34 (0.16), residues: 3109 helix: 0.42 (0.14), residues: 1398 sheet: 0.42 (0.27), residues: 386 loop : -1.06 (0.18), residues: 1325 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 615 HIS 0.003 0.000 HIS C 611 PHE 0.027 0.001 PHE C 791 TYR 0.011 0.001 TYR E 634 ARG 0.008 0.000 ARG D 514 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6218 Ramachandran restraints generated. 3109 Oldfield, 0 Emsley, 3109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6218 Ramachandran restraints generated. 3109 Oldfield, 0 Emsley, 3109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 2778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 250 time to evaluate : 5.015 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 639 ILE cc_start: 0.6106 (mm) cc_final: 0.5773 (mm) REVERT: B 556 LEU cc_start: 0.7276 (mm) cc_final: 0.6812 (mm) REVERT: C 592 ARG cc_start: 0.7369 (mtm-85) cc_final: 0.7045 (mtm-85) REVERT: D 691 GLN cc_start: 0.7780 (pp30) cc_final: 0.7541 (pp30) REVERT: E 638 ASP cc_start: 0.8611 (m-30) cc_final: 0.8272 (m-30) REVERT: F 523 MET cc_start: -0.1320 (ppp) cc_final: -0.1640 (ptt) REVERT: F 556 LEU cc_start: 0.7415 (pp) cc_final: 0.6963 (tp) REVERT: F 801 PRO cc_start: 0.7395 (Cg_exo) cc_final: 0.7185 (Cg_endo) REVERT: F 1379 MET cc_start: 0.8789 (mpp) cc_final: 0.7946 (mpp) outliers start: 1 outliers final: 0 residues processed: 251 average time/residue: 0.3742 time to fit residues: 150.7802 Evaluate side-chains 177 residues out of total 2778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 177 time to evaluate : 3.114 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 196 optimal weight: 5.9990 chunk 263 optimal weight: 0.8980 chunk 75 optimal weight: 0.0670 chunk 228 optimal weight: 0.9990 chunk 36 optimal weight: 2.9990 chunk 68 optimal weight: 2.9990 chunk 247 optimal weight: 4.9990 chunk 103 optimal weight: 0.0770 chunk 254 optimal weight: 0.9990 chunk 31 optimal weight: 0.8980 chunk 45 optimal weight: 4.9990 overall best weight: 0.5878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B1381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 575 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1346 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 691 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 544 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 548 HIS ** F 940 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1385 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4201 r_free = 0.4201 target = 0.126926 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.097148 restraints weight = 118663.179| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.098214 restraints weight = 88121.730| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.098219 restraints weight = 72858.838| |-----------------------------------------------------------------------------| r_work (final): 0.3708 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7280 moved from start: 0.8706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 25829 Z= 0.156 Angle : 0.619 10.215 35014 Z= 0.300 Chirality : 0.042 0.250 3948 Planarity : 0.004 0.079 4488 Dihedral : 8.066 99.906 3581 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 10.44 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.21 % Favored : 93.73 % Rotamer: Outliers : 0.00 % Allowed : 0.32 % Favored : 99.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.00 % Cis-general : 0.34 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.25 (0.16), residues: 3109 helix: 0.48 (0.14), residues: 1399 sheet: 0.51 (0.27), residues: 387 loop : -1.01 (0.19), residues: 1323 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 615 HIS 0.003 0.000 HIS C 611 PHE 0.026 0.001 PHE C 517 TYR 0.013 0.001 TYR C 448 ARG 0.008 0.000 ARG D 496 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4835.08 seconds wall clock time: 88 minutes 37.19 seconds (5317.19 seconds total)