Starting phenix.real_space_refine on Thu May 16 06:04:45 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wya_37921/05_2024/8wya_37921_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wya_37921/05_2024/8wya_37921.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.62 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wya_37921/05_2024/8wya_37921.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wya_37921/05_2024/8wya_37921.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wya_37921/05_2024/8wya_37921_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wya_37921/05_2024/8wya_37921_neut.pdb" } resolution = 3.62 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= 0.044 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: 4 Type Number sf(0) Gaussians S 124 5.16 5 C 21149 2.51 5 N 5240 2.21 5 O 6108 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 68": "OE1" <-> "OE2" Residue "A GLU 262": "OE1" <-> "OE2" Residue "A GLU 284": "OE1" <-> "OE2" Residue "A GLU 365": "OE1" <-> "OE2" Residue "A GLU 450": "OE1" <-> "OE2" Residue "A GLU 510": "OE1" <-> "OE2" Residue "A GLU 534": "OE1" <-> "OE2" Residue "A GLU 682": "OE1" <-> "OE2" Residue "A GLU 715": "OE1" <-> "OE2" Residue "A GLU 731": "OE1" <-> "OE2" Residue "A GLU 812": "OE1" <-> "OE2" Residue "A GLU 882": "OE1" <-> "OE2" Residue "B GLU 335": "OE1" <-> "OE2" Residue "B GLU 379": "OE1" <-> "OE2" Residue "B GLU 510": "OE1" <-> "OE2" Residue "B GLU 621": "OE1" <-> "OE2" Residue "B GLU 685": "OE1" <-> "OE2" Residue "B GLU 860": "OE1" <-> "OE2" Residue "C GLU 71": "OE1" <-> "OE2" Residue "C GLU 221": "OE1" <-> "OE2" Residue "D GLU 68": "OE1" <-> "OE2" Residue "D GLU 69": "OE1" <-> "OE2" Residue "D GLU 187": "OE1" <-> "OE2" Residue "D GLU 362": "OE1" <-> "OE2" Residue "D GLU 369": "OE1" <-> "OE2" Residue "D TYR 472": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 607": "OE1" <-> "OE2" Residue "D GLU 746": "OE1" <-> "OE2" Residue "E GLU 28": "OE1" <-> "OE2" Residue "E GLU 32": "OE1" <-> "OE2" Residue "E GLU 35": "OE1" <-> "OE2" Residue "E GLU 254": "OE1" <-> "OE2" Residue "E GLU 262": "OE1" <-> "OE2" Residue "E GLU 335": "OE1" <-> "OE2" Residue "E GLU 543": "OE1" <-> "OE2" Residue "E GLU 686": "OE1" <-> "OE2" Residue "F TYR 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5322/modules/chem_data/mon_lib" Total number of atoms: 32621 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 7655 Number of conformers: 1 Conformer: "" Number of residues, atoms: 915, 7655 Classifications: {'peptide': 915} Link IDs: {'PTRANS': 19, 'TRANS': 895} Chain breaks: 10 Chain: "B" Number of atoms: 7706 Number of conformers: 1 Conformer: "" Number of residues, atoms: 923, 7706 Classifications: {'peptide': 923} Link IDs: {'PTRANS': 19, 'TRANS': 903} Chain breaks: 9 Chain: "C" Number of atoms: 939 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 939 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 4, 'TRANS': 111} Chain breaks: 4 Chain: "D" Number of atoms: 7705 Number of conformers: 1 Conformer: "" Number of residues, atoms: 921, 7705 Classifications: {'peptide': 921} Link IDs: {'PTRANS': 19, 'TRANS': 901} Chain breaks: 9 Chain: "E" Number of atoms: 7677 Number of conformers: 1 Conformer: "" Number of residues, atoms: 919, 7677 Classifications: {'peptide': 919} Link IDs: {'PTRANS': 18, 'TRANS': 900} Chain breaks: 9 Chain: "F" Number of atoms: 939 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 939 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 4, 'TRANS': 111} Chain breaks: 4 Time building chain proxies: 16.25, per 1000 atoms: 0.50 Number of scatterers: 32621 At special positions: 0 Unit cell: (100.776, 131.404, 276.64, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 124 16.00 O 6108 8.00 N 5240 7.00 C 21149 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=0, symmetry=0 Time building additional restraints: 13.53 Conformation dependent library (CDL) restraints added in 5.7 seconds 7616 Ramachandran restraints generated. 3808 Oldfield, 0 Emsley, 3808 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7484 Finding SS restraints... Secondary structure from input PDB file: 227 helices and 13 sheets defined 68.1% alpha, 5.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.85 Creating SS restraints... Processing helix chain 'A' and resid 23 through 40 removed outlier: 3.625A pdb=" N VAL A 27 " --> pdb=" O ASP A 23 " (cutoff:3.500A) Processing helix chain 'A' and resid 48 through 54 removed outlier: 3.668A pdb=" N SER A 54 " --> pdb=" O VAL A 50 " (cutoff:3.500A) Processing helix chain 'A' and resid 58 through 72 removed outlier: 3.570A pdb=" N LEU A 62 " --> pdb=" O GLN A 58 " (cutoff:3.500A) Processing helix chain 'A' and resid 80 through 95 Proline residue: A 88 - end of helix Processing helix chain 'A' and resid 96 through 109 removed outlier: 3.648A pdb=" N PHE A 100 " --> pdb=" O GLY A 96 " (cutoff:3.500A) Processing helix chain 'A' and resid 115 through 124 removed outlier: 3.871A pdb=" N ASP A 119 " --> pdb=" O ASN A 115 " (cutoff:3.500A) Processing helix chain 'A' and resid 136 through 144 removed outlier: 3.534A pdb=" N THR A 140 " --> pdb=" O ASN A 136 " (cutoff:3.500A) Processing helix chain 'A' and resid 155 through 160 removed outlier: 4.343A pdb=" N ALA A 159 " --> pdb=" O GLU A 155 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N ASN A 160 " --> pdb=" O GLU A 156 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 155 through 160' Processing helix chain 'A' and resid 179 through 183 removed outlier: 3.763A pdb=" N ASN A 182 " --> pdb=" O LYS A 179 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N VAL A 183 " --> pdb=" O GLY A 180 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 179 through 183' Processing helix chain 'A' and resid 186 through 192 Processing helix chain 'A' and resid 192 through 197 Processing helix chain 'A' and resid 197 through 210 Processing helix chain 'A' and resid 222 through 235 removed outlier: 3.604A pdb=" N ASN A 226 " --> pdb=" O ASP A 222 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LYS A 234 " --> pdb=" O ASN A 230 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N LEU A 235 " --> pdb=" O TRP A 231 " (cutoff:3.500A) Processing helix chain 'A' and resid 254 through 265 removed outlier: 3.768A pdb=" N GLY A 265 " --> pdb=" O TYR A 261 " (cutoff:3.500A) Processing helix chain 'A' and resid 271 through 275 Processing helix chain 'A' and resid 281 through 294 removed outlier: 3.812A pdb=" N VAL A 289 " --> pdb=" O ARG A 285 " (cutoff:3.500A) Processing helix chain 'A' and resid 304 through 317 Processing helix chain 'A' and resid 318 through 322 removed outlier: 3.630A pdb=" N ALA A 321 " --> pdb=" O PRO A 318 " (cutoff:3.500A) Processing helix chain 'A' and resid 326 through 328 No H-bonds generated for 'chain 'A' and resid 326 through 328' Processing helix chain 'A' and resid 329 through 334 removed outlier: 3.529A pdb=" N VAL A 333 " --> pdb=" O ASP A 329 " (cutoff:3.500A) Processing helix chain 'A' and resid 355 through 366 Processing helix chain 'A' and resid 367 through 372 removed outlier: 3.904A pdb=" N LYS A 372 " --> pdb=" O ASP A 368 " (cutoff:3.500A) Processing helix chain 'A' and resid 374 through 391 Processing helix chain 'A' and resid 411 through 416 Processing helix chain 'A' and resid 417 through 427 Processing helix chain 'A' and resid 431 through 445 Processing helix chain 'A' and resid 447 through 462 removed outlier: 3.553A pdb=" N SER A 451 " --> pdb=" O ARG A 447 " (cutoff:3.500A) Processing helix chain 'A' and resid 469 through 494 Processing helix chain 'A' and resid 508 through 520 Processing helix chain 'A' and resid 532 through 539 Processing helix chain 'A' and resid 542 through 546 Processing helix chain 'A' and resid 551 through 572 Processing helix chain 'A' and resid 579 through 598 removed outlier: 3.580A pdb=" N ASN A 598 " --> pdb=" O PHE A 594 " (cutoff:3.500A) Processing helix chain 'A' and resid 600 through 604 removed outlier: 3.525A pdb=" N VAL A 603 " --> pdb=" O LEU A 600 " (cutoff:3.500A) Processing helix chain 'A' and resid 605 through 628 removed outlier: 3.613A pdb=" N HIS A 609 " --> pdb=" O PHE A 605 " (cutoff:3.500A) Processing helix chain 'A' and resid 648 through 658 Processing helix chain 'A' and resid 660 through 671 Processing helix chain 'A' and resid 680 through 699 removed outlier: 3.545A pdb=" N ILE A 684 " --> pdb=" O GLU A 680 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N PHE A 699 " --> pdb=" O ILE A 695 " (cutoff:3.500A) Processing helix chain 'A' and resid 706 through 723 removed outlier: 4.092A pdb=" N GLN A 711 " --> pdb=" O VAL A 707 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N SER A 714 " --> pdb=" O THR A 710 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N GLU A 715 " --> pdb=" O GLN A 711 " (cutoff:3.500A) Processing helix chain 'A' and resid 724 through 726 No H-bonds generated for 'chain 'A' and resid 724 through 726' Processing helix chain 'A' and resid 729 through 742 Processing helix chain 'A' and resid 750 through 765 removed outlier: 4.177A pdb=" N CYS A 764 " --> pdb=" O ARG A 760 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N ASN A 765 " --> pdb=" O LEU A 761 " (cutoff:3.500A) Processing helix chain 'A' and resid 768 through 786 removed outlier: 3.639A pdb=" N ILE A 772 " --> pdb=" O PRO A 768 " (cutoff:3.500A) Processing helix chain 'A' and resid 800 through 811 removed outlier: 3.779A pdb=" N PHE A 811 " --> pdb=" O LEU A 807 " (cutoff:3.500A) Processing helix chain 'A' and resid 817 through 826 Processing helix chain 'A' and resid 831 through 841 removed outlier: 3.790A pdb=" N ILE A 835 " --> pdb=" O LYS A 831 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LYS A 840 " --> pdb=" O ASP A 836 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N LEU A 841 " --> pdb=" O PHE A 837 " (cutoff:3.500A) Processing helix chain 'A' and resid 846 through 857 removed outlier: 4.120A pdb=" N HIS A 852 " --> pdb=" O ASN A 848 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N LEU A 853 " --> pdb=" O ALA A 849 " (cutoff:3.500A) Processing helix chain 'A' and resid 863 through 872 Processing helix chain 'A' and resid 878 through 897 Processing helix chain 'A' and resid 913 through 922 removed outlier: 3.785A pdb=" N GLY A 917 " --> pdb=" O MET A 913 " (cutoff:3.500A) Processing helix chain 'A' and resid 929 through 933 Processing helix chain 'A' and resid 937 through 945 Processing helix chain 'A' and resid 950 through 955 removed outlier: 3.969A pdb=" N LYS A 953 " --> pdb=" O ASP A 950 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N PHE A 954 " --> pdb=" O TYR A 951 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N ILE A 955 " --> pdb=" O LYS A 952 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 950 through 955' Processing helix chain 'A' and resid 956 through 962 removed outlier: 3.636A pdb=" N LYS A 960 " --> pdb=" O PRO A 956 " (cutoff:3.500A) Processing helix chain 'A' and resid 963 through 974 removed outlier: 3.817A pdb=" N LYS A 974 " --> pdb=" O ILE A 970 " (cutoff:3.500A) Processing helix chain 'A' and resid 976 through 991 Processing helix chain 'A' and resid 994 through 1004 removed outlier: 3.503A pdb=" N GLU A 998 " --> pdb=" O LYS A 994 " (cutoff:3.500A) Processing helix chain 'B' and resid 24 through 39 removed outlier: 3.597A pdb=" N ASN B 39 " --> pdb=" O GLU B 35 " (cutoff:3.500A) Processing helix chain 'B' and resid 48 through 54 Processing helix chain 'B' and resid 58 through 72 removed outlier: 3.710A pdb=" N LEU B 62 " --> pdb=" O GLN B 58 " (cutoff:3.500A) Processing helix chain 'B' and resid 80 through 96 removed outlier: 3.708A pdb=" N LEU B 85 " --> pdb=" O SER B 81 " (cutoff:3.500A) Proline residue: B 88 - end of helix Processing helix chain 'B' and resid 96 through 109 removed outlier: 3.567A pdb=" N PHE B 100 " --> pdb=" O GLY B 96 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N PHE B 107 " --> pdb=" O ILE B 103 " (cutoff:3.500A) Processing helix chain 'B' and resid 115 through 124 removed outlier: 3.714A pdb=" N ASP B 119 " --> pdb=" O ASN B 115 " (cutoff:3.500A) Processing helix chain 'B' and resid 136 through 146 Processing helix chain 'B' and resid 155 through 159 removed outlier: 3.710A pdb=" N VAL B 158 " --> pdb=" O GLU B 155 " (cutoff:3.500A) Processing helix chain 'B' and resid 186 through 192 Processing helix chain 'B' and resid 192 through 197 Processing helix chain 'B' and resid 197 through 211 Processing helix chain 'B' and resid 222 through 235 removed outlier: 3.521A pdb=" N LEU B 235 " --> pdb=" O TRP B 231 " (cutoff:3.500A) Processing helix chain 'B' and resid 254 through 263 Processing helix chain 'B' and resid 282 through 299 Processing helix chain 'B' and resid 304 through 317 Processing helix chain 'B' and resid 318 through 322 Processing helix chain 'B' and resid 328 through 334 removed outlier: 4.098A pdb=" N HIS B 332 " --> pdb=" O ILE B 328 " (cutoff:3.500A) Processing helix chain 'B' and resid 355 through 366 removed outlier: 3.753A pdb=" N ARG B 359 " --> pdb=" O GLY B 355 " (cutoff:3.500A) Processing helix chain 'B' and resid 374 through 391 Processing helix chain 'B' and resid 411 through 416 Processing helix chain 'B' and resid 417 through 427 removed outlier: 3.780A pdb=" N MET B 421 " --> pdb=" O LYS B 417 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N LYS B 422 " --> pdb=" O TYR B 418 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N GLU B 427 " --> pdb=" O LYS B 423 " (cutoff:3.500A) Processing helix chain 'B' and resid 431 through 445 Processing helix chain 'B' and resid 447 through 462 Processing helix chain 'B' and resid 468 through 495 Processing helix chain 'B' and resid 495 through 501 removed outlier: 3.866A pdb=" N THR B 499 " --> pdb=" O LEU B 495 " (cutoff:3.500A) Processing helix chain 'B' and resid 508 through 520 Processing helix chain 'B' and resid 532 through 539 Processing helix chain 'B' and resid 540 through 546 removed outlier: 3.984A pdb=" N PHE B 544 " --> pdb=" O ILE B 541 " (cutoff:3.500A) Processing helix chain 'B' and resid 552 through 561 Processing helix chain 'B' and resid 580 through 598 removed outlier: 3.528A pdb=" N GLU B 597 " --> pdb=" O ARG B 593 " (cutoff:3.500A) Processing helix chain 'B' and resid 600 through 604 Processing helix chain 'B' and resid 605 through 628 Processing helix chain 'B' and resid 648 through 659 Processing helix chain 'B' and resid 660 through 671 Processing helix chain 'B' and resid 672 through 676 removed outlier: 3.602A pdb=" N ILE B 676 " --> pdb=" O ILE B 673 " (cutoff:3.500A) Processing helix chain 'B' and resid 680 through 701 removed outlier: 3.684A pdb=" N ILE B 684 " --> pdb=" O GLU B 680 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ALA B 701 " --> pdb=" O LYS B 697 " (cutoff:3.500A) Processing helix chain 'B' and resid 705 through 723 removed outlier: 4.924A pdb=" N SER B 714 " --> pdb=" O THR B 710 " (cutoff:3.500A) removed outlier: 4.760A pdb=" N GLU B 715 " --> pdb=" O GLN B 711 " (cutoff:3.500A) Processing helix chain 'B' and resid 724 through 726 No H-bonds generated for 'chain 'B' and resid 724 through 726' Processing helix chain 'B' and resid 729 through 742 Processing helix chain 'B' and resid 750 through 765 removed outlier: 4.292A pdb=" N CYS B 764 " --> pdb=" O ARG B 760 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N ASN B 765 " --> pdb=" O LEU B 761 " (cutoff:3.500A) Processing helix chain 'B' and resid 768 through 786 removed outlier: 3.556A pdb=" N ILE B 772 " --> pdb=" O PRO B 768 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N HIS B 786 " --> pdb=" O GLN B 782 " (cutoff:3.500A) Processing helix chain 'B' and resid 800 through 813 removed outlier: 3.572A pdb=" N TYR B 804 " --> pdb=" O TYR B 800 " (cutoff:3.500A) Processing helix chain 'B' and resid 818 through 826 Processing helix chain 'B' and resid 831 through 840 removed outlier: 4.015A pdb=" N LYS B 840 " --> pdb=" O ASP B 836 " (cutoff:3.500A) Processing helix chain 'B' and resid 841 through 845 Processing helix chain 'B' and resid 846 through 856 removed outlier: 4.046A pdb=" N PHE B 856 " --> pdb=" O HIS B 852 " (cutoff:3.500A) Processing helix chain 'B' and resid 861 through 871 Processing helix chain 'B' and resid 878 through 897 removed outlier: 3.866A pdb=" N ILE B 897 " --> pdb=" O LYS B 893 " (cutoff:3.500A) Processing helix chain 'B' and resid 912 through 922 Processing helix chain 'B' and resid 929 through 934 removed outlier: 4.043A pdb=" N GLU B 932 " --> pdb=" O LYS B 929 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ILE B 934 " --> pdb=" O GLU B 931 " (cutoff:3.500A) Processing helix chain 'B' and resid 940 through 945 removed outlier: 3.712A pdb=" N VAL B 944 " --> pdb=" O TYR B 940 " (cutoff:3.500A) Processing helix chain 'B' and resid 946 through 949 Processing helix chain 'B' and resid 950 through 954 Processing helix chain 'B' and resid 955 through 956 No H-bonds generated for 'chain 'B' and resid 955 through 956' Processing helix chain 'B' and resid 957 through 962 removed outlier: 3.751A pdb=" N ASN B 961 " --> pdb=" O SER B 957 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N TYR B 962 " --> pdb=" O TRP B 958 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 957 through 962' Processing helix chain 'B' and resid 963 through 974 removed outlier: 4.081A pdb=" N LYS B 974 " --> pdb=" O ILE B 970 " (cutoff:3.500A) Processing helix chain 'B' and resid 976 through 991 Processing helix chain 'B' and resid 995 through 1004 removed outlier: 4.157A pdb=" N TYR B1003 " --> pdb=" O ILE B 999 " (cutoff:3.500A) Processing helix chain 'C' and resid 69 through 76 removed outlier: 3.751A pdb=" N LEU C 73 " --> pdb=" O ASP C 69 " (cutoff:3.500A) Processing helix chain 'D' and resid 26 through 40 Processing helix chain 'D' and resid 48 through 54 removed outlier: 3.864A pdb=" N SER D 54 " --> pdb=" O VAL D 50 " (cutoff:3.500A) Processing helix chain 'D' and resid 58 through 71 removed outlier: 3.701A pdb=" N LEU D 62 " --> pdb=" O GLN D 58 " (cutoff:3.500A) Processing helix chain 'D' and resid 80 through 96 Proline residue: D 88 - end of helix Processing helix chain 'D' and resid 97 through 108 Processing helix chain 'D' and resid 115 through 124 removed outlier: 3.943A pdb=" N ASP D 119 " --> pdb=" O ASN D 115 " (cutoff:3.500A) Processing helix chain 'D' and resid 137 through 146 Processing helix chain 'D' and resid 155 through 159 removed outlier: 3.583A pdb=" N VAL D 158 " --> pdb=" O GLU D 155 " (cutoff:3.500A) Processing helix chain 'D' and resid 179 through 183 Processing helix chain 'D' and resid 186 through 192 Processing helix chain 'D' and resid 192 through 197 Processing helix chain 'D' and resid 197 through 211 Processing helix chain 'D' and resid 222 through 235 Processing helix chain 'D' and resid 254 through 263 Processing helix chain 'D' and resid 271 through 275 Processing helix chain 'D' and resid 282 through 296 removed outlier: 3.535A pdb=" N VAL D 289 " --> pdb=" O ARG D 285 " (cutoff:3.500A) Processing helix chain 'D' and resid 304 through 317 removed outlier: 3.761A pdb=" N GLY D 314 " --> pdb=" O ASP D 310 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N LYS D 315 " --> pdb=" O TYR D 311 " (cutoff:3.500A) Processing helix chain 'D' and resid 318 through 322 Processing helix chain 'D' and resid 326 through 328 No H-bonds generated for 'chain 'D' and resid 326 through 328' Processing helix chain 'D' and resid 329 through 334 removed outlier: 3.544A pdb=" N PHE D 334 " --> pdb=" O LEU D 330 " (cutoff:3.500A) Processing helix chain 'D' and resid 355 through 366 Processing helix chain 'D' and resid 366 through 372 removed outlier: 3.710A pdb=" N ARG D 370 " --> pdb=" O SER D 366 " (cutoff:3.500A) Processing helix chain 'D' and resid 374 through 391 removed outlier: 3.985A pdb=" N ALA D 383 " --> pdb=" O GLU D 379 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N GLU D 389 " --> pdb=" O PHE D 385 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N LYS D 390 " --> pdb=" O ASN D 386 " (cutoff:3.500A) Processing helix chain 'D' and resid 411 through 416 Processing helix chain 'D' and resid 419 through 427 removed outlier: 3.778A pdb=" N GLU D 427 " --> pdb=" O LYS D 423 " (cutoff:3.500A) Processing helix chain 'D' and resid 431 through 445 Processing helix chain 'D' and resid 447 through 462 removed outlier: 3.666A pdb=" N ASN D 457 " --> pdb=" O ASP D 453 " (cutoff:3.500A) Processing helix chain 'D' and resid 469 through 494 Processing helix chain 'D' and resid 508 through 521 removed outlier: 3.509A pdb=" N GLU D 516 " --> pdb=" O LEU D 512 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N GLU D 518 " --> pdb=" O ARG D 514 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N ASN D 521 " --> pdb=" O ARG D 517 " (cutoff:3.500A) Processing helix chain 'D' and resid 532 through 539 Processing helix chain 'D' and resid 551 through 572 removed outlier: 3.581A pdb=" N VAL D 556 " --> pdb=" O TYR D 552 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LEU D 561 " --> pdb=" O LYS D 557 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N SER D 570 " --> pdb=" O ARG D 566 " (cutoff:3.500A) Processing helix chain 'D' and resid 579 through 598 Processing helix chain 'D' and resid 600 through 604 Processing helix chain 'D' and resid 605 through 628 removed outlier: 3.665A pdb=" N LEU D 618 " --> pdb=" O ASN D 614 " (cutoff:3.500A) Processing helix chain 'D' and resid 648 through 659 removed outlier: 4.007A pdb=" N ASN D 654 " --> pdb=" O TYR D 650 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N PHE D 659 " --> pdb=" O ILE D 655 " (cutoff:3.500A) Processing helix chain 'D' and resid 660 through 671 Processing helix chain 'D' and resid 680 through 699 removed outlier: 3.844A pdb=" N GLU D 694 " --> pdb=" O GLY D 690 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N PHE D 699 " --> pdb=" O ILE D 695 " (cutoff:3.500A) Processing helix chain 'D' and resid 706 through 722 removed outlier: 3.584A pdb=" N GLN D 711 " --> pdb=" O VAL D 707 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N SER D 714 " --> pdb=" O THR D 710 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N GLU D 715 " --> pdb=" O GLN D 711 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N LEU D 720 " --> pdb=" O ALA D 716 " (cutoff:3.500A) Processing helix chain 'D' and resid 723 through 726 Processing helix chain 'D' and resid 729 through 743 Processing helix chain 'D' and resid 750 through 765 removed outlier: 3.602A pdb=" N LEU D 761 " --> pdb=" O TRP D 757 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N CYS D 764 " --> pdb=" O ARG D 760 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ASN D 765 " --> pdb=" O LEU D 761 " (cutoff:3.500A) Processing helix chain 'D' and resid 768 through 786 removed outlier: 3.649A pdb=" N LYS D 785 " --> pdb=" O LEU D 781 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N HIS D 786 " --> pdb=" O GLN D 782 " (cutoff:3.500A) Processing helix chain 'D' and resid 800 through 811 removed outlier: 4.011A pdb=" N ILE D 808 " --> pdb=" O TYR D 804 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N PHE D 811 " --> pdb=" O LEU D 807 " (cutoff:3.500A) Processing helix chain 'D' and resid 817 through 826 removed outlier: 3.633A pdb=" N CYS D 826 " --> pdb=" O GLU D 822 " (cutoff:3.500A) Processing helix chain 'D' and resid 831 through 841 removed outlier: 3.562A pdb=" N ILE D 835 " --> pdb=" O LYS D 831 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LEU D 841 " --> pdb=" O PHE D 837 " (cutoff:3.500A) Processing helix chain 'D' and resid 846 through 857 removed outlier: 4.142A pdb=" N HIS D 852 " --> pdb=" O ASN D 848 " (cutoff:3.500A) Processing helix chain 'D' and resid 863 through 872 removed outlier: 3.552A pdb=" N ASN D 867 " --> pdb=" O ASN D 863 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLY D 868 " --> pdb=" O ASP D 864 " (cutoff:3.500A) Processing helix chain 'D' and resid 878 through 897 removed outlier: 3.640A pdb=" N LEU D 889 " --> pdb=" O ILE D 885 " (cutoff:3.500A) Processing helix chain 'D' and resid 911 through 914 removed outlier: 4.177A pdb=" N SER D 914 " --> pdb=" O ASP D 911 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 911 through 914' Processing helix chain 'D' and resid 915 through 922 removed outlier: 3.564A pdb=" N TRP D 919 " --> pdb=" O THR D 915 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N TYR D 920 " --> pdb=" O PHE D 916 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N LEU D 922 " --> pdb=" O ILE D 918 " (cutoff:3.500A) Processing helix chain 'D' and resid 929 through 934 removed outlier: 3.867A pdb=" N PHE D 933 " --> pdb=" O MET D 930 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N ILE D 934 " --> pdb=" O GLU D 931 " (cutoff:3.500A) Processing helix chain 'D' and resid 937 through 945 Processing helix chain 'D' and resid 956 through 962 removed outlier: 4.062A pdb=" N LYS D 960 " --> pdb=" O PRO D 956 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ASN D 961 " --> pdb=" O SER D 957 " (cutoff:3.500A) Processing helix chain 'D' and resid 963 through 974 removed outlier: 4.516A pdb=" N LYS D 974 " --> pdb=" O ILE D 970 " (cutoff:3.500A) Processing helix chain 'D' and resid 976 through 991 removed outlier: 3.908A pdb=" N VAL D 980 " --> pdb=" O MET D 976 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ILE D 981 " --> pdb=" O LYS D 977 " (cutoff:3.500A) Processing helix chain 'D' and resid 994 through 1004 Processing helix chain 'E' and resid 23 through 39 Processing helix chain 'E' and resid 47 through 52 removed outlier: 4.415A pdb=" N SER E 51 " --> pdb=" O GLY E 47 " (cutoff:3.500A) Processing helix chain 'E' and resid 58 through 70 removed outlier: 3.827A pdb=" N LEU E 62 " --> pdb=" O GLN E 58 " (cutoff:3.500A) Processing helix chain 'E' and resid 80 through 108 removed outlier: 3.884A pdb=" N TYR E 84 " --> pdb=" O SER E 80 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N LEU E 85 " --> pdb=" O SER E 81 " (cutoff:3.500A) Proline residue: E 88 - end of helix removed outlier: 7.441A pdb=" N GLU E 97 " --> pdb=" O ASN E 93 " (cutoff:3.500A) removed outlier: 8.854A pdb=" N MET E 98 " --> pdb=" O VAL E 94 " (cutoff:3.500A) Processing helix chain 'E' and resid 115 through 123 removed outlier: 3.825A pdb=" N ASP E 119 " --> pdb=" O ASN E 115 " (cutoff:3.500A) Processing helix chain 'E' and resid 136 through 146 Processing helix chain 'E' and resid 179 through 183 Processing helix chain 'E' and resid 186 through 192 Processing helix chain 'E' and resid 192 through 197 Processing helix chain 'E' and resid 197 through 211 Processing helix chain 'E' and resid 222 through 235 removed outlier: 3.594A pdb=" N ARG E 233 " --> pdb=" O LEU E 229 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N LYS E 234 " --> pdb=" O ASN E 230 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N LEU E 235 " --> pdb=" O TRP E 231 " (cutoff:3.500A) Processing helix chain 'E' and resid 254 through 265 removed outlier: 3.842A pdb=" N GLY E 265 " --> pdb=" O TYR E 261 " (cutoff:3.500A) Processing helix chain 'E' and resid 271 through 275 Processing helix chain 'E' and resid 281 through 298 removed outlier: 3.624A pdb=" N ARG E 285 " --> pdb=" O ASP E 281 " (cutoff:3.500A) Processing helix chain 'E' and resid 304 through 317 removed outlier: 3.586A pdb=" N LYS E 315 " --> pdb=" O TYR E 311 " (cutoff:3.500A) Processing helix chain 'E' and resid 318 through 322 Processing helix chain 'E' and resid 329 through 334 Processing helix chain 'E' and resid 355 through 366 removed outlier: 3.593A pdb=" N ARG E 359 " --> pdb=" O GLY E 355 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N GLU E 362 " --> pdb=" O GLU E 358 " (cutoff:3.500A) Processing helix chain 'E' and resid 374 through 391 removed outlier: 3.668A pdb=" N PHE E 387 " --> pdb=" O ALA E 383 " (cutoff:3.500A) Processing helix chain 'E' and resid 419 through 427 removed outlier: 3.706A pdb=" N LYS E 423 " --> pdb=" O ASP E 419 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N PHE E 424 " --> pdb=" O VAL E 420 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N GLU E 426 " --> pdb=" O LYS E 422 " (cutoff:3.500A) Processing helix chain 'E' and resid 431 through 445 removed outlier: 3.577A pdb=" N CYS E 444 " --> pdb=" O PHE E 440 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N LEU E 445 " --> pdb=" O PHE E 441 " (cutoff:3.500A) Processing helix chain 'E' and resid 447 through 462 Processing helix chain 'E' and resid 468 through 495 removed outlier: 3.740A pdb=" N TYR E 472 " --> pdb=" O GLY E 468 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LEU E 473 " --> pdb=" O CYS E 469 " (cutoff:3.500A) Processing helix chain 'E' and resid 495 through 501 Processing helix chain 'E' and resid 508 through 520 removed outlier: 3.579A pdb=" N ARG E 517 " --> pdb=" O ALA E 513 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N GLU E 518 " --> pdb=" O ARG E 514 " (cutoff:3.500A) Processing helix chain 'E' and resid 532 through 539 Processing helix chain 'E' and resid 541 through 546 removed outlier: 3.717A pdb=" N PHE E 544 " --> pdb=" O ILE E 541 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LEU E 545 " --> pdb=" O LEU E 542 " (cutoff:3.500A) Processing helix chain 'E' and resid 552 through 561 removed outlier: 3.734A pdb=" N VAL E 556 " --> pdb=" O TYR E 552 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N LYS E 557 " --> pdb=" O ASP E 553 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N LEU E 561 " --> pdb=" O LYS E 557 " (cutoff:3.500A) Processing helix chain 'E' and resid 580 through 596 removed outlier: 4.031A pdb=" N ARG E 587 " --> pdb=" O VAL E 583 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N TYR E 589 " --> pdb=" O LEU E 585 " (cutoff:3.500A) Processing helix chain 'E' and resid 600 through 604 Processing helix chain 'E' and resid 605 through 628 Processing helix chain 'E' and resid 649 through 659 removed outlier: 3.655A pdb=" N VAL E 653 " --> pdb=" O TYR E 649 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N ASN E 654 " --> pdb=" O TYR E 650 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N ILE E 655 " --> pdb=" O ASP E 651 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N PHE E 659 " --> pdb=" O ILE E 655 " (cutoff:3.500A) Processing helix chain 'E' and resid 660 through 671 Processing helix chain 'E' and resid 680 through 700 removed outlier: 3.617A pdb=" N GLU E 686 " --> pdb=" O GLU E 682 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ILE E 695 " --> pdb=" O ILE E 691 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N THR E 696 " --> pdb=" O ALA E 692 " (cutoff:3.500A) Processing helix chain 'E' and resid 705 through 723 removed outlier: 3.642A pdb=" N THR E 710 " --> pdb=" O VAL E 706 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N GLN E 711 " --> pdb=" O VAL E 707 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N SER E 714 " --> pdb=" O THR E 710 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N GLU E 715 " --> pdb=" O GLN E 711 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ALA E 718 " --> pdb=" O SER E 714 " (cutoff:3.500A) Processing helix chain 'E' and resid 724 through 726 No H-bonds generated for 'chain 'E' and resid 724 through 726' Processing helix chain 'E' and resid 729 through 742 Processing helix chain 'E' and resid 750 through 762 removed outlier: 3.626A pdb=" N LEU E 761 " --> pdb=" O TRP E 757 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N THR E 762 " --> pdb=" O LEU E 758 " (cutoff:3.500A) Processing helix chain 'E' and resid 768 through 786 Processing helix chain 'E' and resid 800 through 813 removed outlier: 3.987A pdb=" N TYR E 804 " --> pdb=" O TYR E 800 " (cutoff:3.500A) Processing helix chain 'E' and resid 817 through 826 Processing helix chain 'E' and resid 831 through 841 removed outlier: 3.567A pdb=" N ASP E 836 " --> pdb=" O GLN E 832 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N PHE E 837 " --> pdb=" O LYS E 833 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LYS E 840 " --> pdb=" O ASP E 836 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N LEU E 841 " --> pdb=" O PHE E 837 " (cutoff:3.500A) Processing helix chain 'E' and resid 846 through 856 removed outlier: 4.314A pdb=" N PHE E 856 " --> pdb=" O HIS E 852 " (cutoff:3.500A) Processing helix chain 'E' and resid 861 through 872 removed outlier: 3.808A pdb=" N LEU E 865 " --> pdb=" O ASN E 861 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N MET E 866 " --> pdb=" O ILE E 862 " (cutoff:3.500A) Processing helix chain 'E' and resid 880 through 897 removed outlier: 3.708A pdb=" N LEU E 884 " --> pdb=" O GLU E 880 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ILE E 885 " --> pdb=" O HIS E 881 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ILE E 886 " --> pdb=" O GLU E 882 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ILE E 897 " --> pdb=" O LYS E 893 " (cutoff:3.500A) Processing helix chain 'E' and resid 911 through 922 removed outlier: 3.794A pdb=" N THR E 915 " --> pdb=" O ASP E 911 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N TYR E 920 " --> pdb=" O PHE E 916 " (cutoff:3.500A) Processing helix chain 'E' and resid 929 through 934 removed outlier: 4.104A pdb=" N GLU E 932 " --> pdb=" O LYS E 929 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ILE E 934 " --> pdb=" O GLU E 931 " (cutoff:3.500A) Processing helix chain 'E' and resid 940 through 945 Processing helix chain 'E' and resid 946 through 949 Processing helix chain 'E' and resid 950 through 954 Processing helix chain 'E' and resid 955 through 962 removed outlier: 3.703A pdb=" N LEU E 959 " --> pdb=" O PRO E 956 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N LYS E 960 " --> pdb=" O SER E 957 " (cutoff:3.500A) Processing helix chain 'E' and resid 963 through 974 removed outlier: 4.030A pdb=" N LYS E 974 " --> pdb=" O ILE E 970 " (cutoff:3.500A) Processing helix chain 'E' and resid 976 through 991 removed outlier: 3.908A pdb=" N ARG E 987 " --> pdb=" O VAL E 983 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N VAL E 988 " --> pdb=" O LEU E 984 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N LYS E 989 " --> pdb=" O LYS E 985 " (cutoff:3.500A) Processing helix chain 'E' and resid 994 through 1003 removed outlier: 3.603A pdb=" N GLU E 998 " --> pdb=" O LYS E 994 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N TYR E1003 " --> pdb=" O ILE E 999 " (cutoff:3.500A) Processing helix chain 'F' and resid 69 through 76 Processing sheet with id=AA1, first strand: chain 'A' and resid 150 through 152 removed outlier: 4.083A pdb=" N HIS A 128 " --> pdb=" O LEU A 42 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N PHE A 44 " --> pdb=" O HIS A 128 " (cutoff:3.500A) removed outlier: 6.037A pdb=" N PHE A 245 " --> pdb=" O ILE A 269 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 338 through 340 Processing sheet with id=AA3, first strand: chain 'A' and resid 574 through 575 removed outlier: 6.900A pdb=" N PHE C 23 " --> pdb=" O PHE C 68 " (cutoff:3.500A) removed outlier: 7.079A pdb=" N PHE C 68 " --> pdb=" O PHE C 23 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N ALA C 25 " --> pdb=" O ALA C 66 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N ALA C 66 " --> pdb=" O ALA C 25 " (cutoff:3.500A) removed outlier: 8.186A pdb=" N ALA C 27 " --> pdb=" O LYS C 64 " (cutoff:3.500A) removed outlier: 5.991A pdb=" N LYS C 64 " --> pdb=" O ALA C 27 " (cutoff:3.500A) removed outlier: 4.839A pdb=" N LYS C 219 " --> pdb=" O SER C 201 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N TYR C 171 " --> pdb=" O ASN C 197 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N ARG C 15 " --> pdb=" O LEU C 21 " (cutoff:3.500A) removed outlier: 6.982A pdb=" N LEU C 21 " --> pdb=" O ARG C 15 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 150 through 152 removed outlier: 6.070A pdb=" N SER B 150 " --> pdb=" O LEU B 167 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N LYS B 169 " --> pdb=" O SER B 150 " (cutoff:3.500A) removed outlier: 6.104A pdb=" N ILE B 152 " --> pdb=" O LYS B 169 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N HIS B 128 " --> pdb=" O LEU B 42 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N PHE B 44 " --> pdb=" O HIS B 128 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N VAL B 43 " --> pdb=" O VAL B 214 " (cutoff:3.500A) removed outlier: 7.494A pdb=" N ILE B 216 " --> pdb=" O VAL B 43 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N PHE B 45 " --> pdb=" O ILE B 216 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N PHE B 244 " --> pdb=" O ILE B 213 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N PHE B 245 " --> pdb=" O ILE B 269 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 338 through 340 Processing sheet with id=AA6, first strand: chain 'B' and resid 794 through 795 Processing sheet with id=AA7, first strand: chain 'D' and resid 150 through 152 removed outlier: 3.570A pdb=" N PHE D 44 " --> pdb=" O HIS D 128 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N VAL D 43 " --> pdb=" O VAL D 214 " (cutoff:3.500A) removed outlier: 7.491A pdb=" N ILE D 216 " --> pdb=" O VAL D 43 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N PHE D 45 " --> pdb=" O ILE D 216 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 338 through 340 Processing sheet with id=AA9, first strand: chain 'E' and resid 150 through 152 removed outlier: 6.175A pdb=" N SER E 150 " --> pdb=" O LEU E 167 " (cutoff:3.500A) removed outlier: 7.265A pdb=" N LYS E 169 " --> pdb=" O SER E 150 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N ILE E 152 " --> pdb=" O LYS E 169 " (cutoff:3.500A) removed outlier: 7.051A pdb=" N LEU E 42 " --> pdb=" O HIS E 128 " (cutoff:3.500A) removed outlier: 8.538A pdb=" N ILE E 130 " --> pdb=" O LEU E 42 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N PHE E 44 " --> pdb=" O ILE E 130 " (cutoff:3.500A) removed outlier: 5.991A pdb=" N PHE E 245 " --> pdb=" O ILE E 269 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 338 through 340 Processing sheet with id=AB2, first strand: chain 'E' and resid 646 through 647 removed outlier: 3.941A pdb=" N MET E 647 " --> pdb=" O ARG E 677 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'E' and resid 794 through 795 Processing sheet with id=AB4, first strand: chain 'E' and resid 906 through 907 removed outlier: 4.052A pdb=" N VAL F 233 " --> pdb=" O GLN F 194 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N ILE F 235 " --> pdb=" O TYR F 192 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N TYR F 192 " --> pdb=" O ILE F 235 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ASP F 10 " --> pdb=" O ARG F 176 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N ARG F 15 " --> pdb=" O LEU F 21 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N LEU F 21 " --> pdb=" O ARG F 15 " (cutoff:3.500A) removed outlier: 8.447A pdb=" N VAL F 22 " --> pdb=" O PHE F 68 " (cutoff:3.500A) removed outlier: 5.149A pdb=" N PHE F 68 " --> pdb=" O VAL F 22 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N THR F 24 " --> pdb=" O ALA F 66 " (cutoff:3.500A) removed outlier: 4.723A pdb=" N ALA F 66 " --> pdb=" O THR F 24 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N GLU F 26 " --> pdb=" O LYS F 64 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N THR F 62 " --> pdb=" O GLN F 28 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N ALA F 30 " --> pdb=" O ASN F 60 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N ASN F 60 " --> pdb=" O ALA F 30 " (cutoff:3.500A) 1689 hydrogen bonds defined for protein. 4902 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: 13.29 Time building geometry restraints manager: 14.56 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 10167 1.34 - 1.46: 7415 1.46 - 1.58: 15557 1.58 - 1.70: 1 1.70 - 1.83: 208 Bond restraints: 33348 Sorted by residual: bond pdb=" CB PRO B 956 " pdb=" CG PRO B 956 " ideal model delta sigma weight residual 1.492 1.631 -0.139 5.00e-02 4.00e+02 7.72e+00 bond pdb=" CA ASN B 160 " pdb=" CB ASN B 160 " ideal model delta sigma weight residual 1.526 1.552 -0.026 1.53e-02 4.27e+03 2.84e+00 bond pdb=" CB LYS D 540 " pdb=" CG LYS D 540 " ideal model delta sigma weight residual 1.520 1.565 -0.045 3.00e-02 1.11e+03 2.24e+00 bond pdb=" CB GLN B 832 " pdb=" CG GLN B 832 " ideal model delta sigma weight residual 1.520 1.563 -0.043 3.00e-02 1.11e+03 2.07e+00 bond pdb=" CG1 ILE B 808 " pdb=" CD1 ILE B 808 " ideal model delta sigma weight residual 1.513 1.461 0.052 3.90e-02 6.57e+02 1.77e+00 ... (remaining 33343 not shown) Histogram of bond angle deviations from ideal: 96.12 - 103.72: 231 103.72 - 111.33: 13039 111.33 - 118.93: 13195 118.93 - 126.54: 18128 126.54 - 134.15: 308 Bond angle restraints: 44901 Sorted by residual: angle pdb=" CA PRO B 956 " pdb=" N PRO B 956 " pdb=" CD PRO B 956 " ideal model delta sigma weight residual 112.00 98.32 13.68 1.40e+00 5.10e-01 9.55e+01 angle pdb=" N VAL A 706 " pdb=" CA VAL A 706 " pdb=" C VAL A 706 " ideal model delta sigma weight residual 113.53 109.25 4.28 9.80e-01 1.04e+00 1.90e+01 angle pdb=" CB LYS D 540 " pdb=" CG LYS D 540 " pdb=" CD LYS D 540 " ideal model delta sigma weight residual 111.30 121.07 -9.77 2.30e+00 1.89e-01 1.80e+01 angle pdb=" CA MET B 866 " pdb=" CB MET B 866 " pdb=" CG MET B 866 " ideal model delta sigma weight residual 114.10 122.56 -8.46 2.00e+00 2.50e-01 1.79e+01 angle pdb=" CB MET E 616 " pdb=" CG MET E 616 " pdb=" SD MET E 616 " ideal model delta sigma weight residual 112.70 125.16 -12.46 3.00e+00 1.11e-01 1.72e+01 ... (remaining 44896 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.92: 16558 17.92 - 35.85: 2527 35.85 - 53.77: 607 53.77 - 71.69: 113 71.69 - 89.62: 48 Dihedral angle restraints: 19853 sinusoidal: 8253 harmonic: 11600 Sorted by residual: dihedral pdb=" CA ARG E 267 " pdb=" C ARG E 267 " pdb=" N ILE E 268 " pdb=" CA ILE E 268 " ideal model delta harmonic sigma weight residual -180.00 -157.97 -22.03 0 5.00e+00 4.00e-02 1.94e+01 dihedral pdb=" CA ASP A 803 " pdb=" C ASP A 803 " pdb=" N TYR A 804 " pdb=" CA TYR A 804 " ideal model delta harmonic sigma weight residual 180.00 159.27 20.73 0 5.00e+00 4.00e-02 1.72e+01 dihedral pdb=" CA ARG D 267 " pdb=" C ARG D 267 " pdb=" N ILE D 268 " pdb=" CA ILE D 268 " ideal model delta harmonic sigma weight residual -180.00 -159.54 -20.46 0 5.00e+00 4.00e-02 1.68e+01 ... (remaining 19850 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.075: 4446 0.075 - 0.151: 342 0.151 - 0.226: 7 0.226 - 0.301: 0 0.301 - 0.377: 1 Chirality restraints: 4796 Sorted by residual: chirality pdb=" CG LEU B 781 " pdb=" CB LEU B 781 " pdb=" CD1 LEU B 781 " pdb=" CD2 LEU B 781 " both_signs ideal model delta sigma weight residual False -2.59 -2.21 -0.38 2.00e-01 2.50e+01 3.55e+00 chirality pdb=" CB ILE B 808 " pdb=" CA ILE B 808 " pdb=" CG1 ILE B 808 " pdb=" CG2 ILE B 808 " both_signs ideal model delta sigma weight residual False 2.64 2.45 0.19 2.00e-01 2.50e+01 9.16e-01 chirality pdb=" CG LEU A 363 " pdb=" CB LEU A 363 " pdb=" CD1 LEU A 363 " pdb=" CD2 LEU A 363 " both_signs ideal model delta sigma weight residual False -2.59 -2.40 -0.19 2.00e-01 2.50e+01 8.62e-01 ... (remaining 4793 not shown) Planarity restraints: 5697 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE B 955 " -0.119 5.00e-02 4.00e+02 1.68e-01 4.54e+01 pdb=" N PRO B 956 " 0.291 5.00e-02 4.00e+02 pdb=" CA PRO B 956 " -0.089 5.00e-02 4.00e+02 pdb=" CD PRO B 956 " -0.083 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA SER B 287 " 0.013 2.00e-02 2.50e+03 2.63e-02 6.90e+00 pdb=" C SER B 287 " -0.045 2.00e-02 2.50e+03 pdb=" O SER B 287 " 0.017 2.00e-02 2.50e+03 pdb=" N ALA B 288 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASP E 291 " 0.012 2.00e-02 2.50e+03 2.42e-02 5.88e+00 pdb=" CG ASP E 291 " -0.042 2.00e-02 2.50e+03 pdb=" OD1 ASP E 291 " 0.015 2.00e-02 2.50e+03 pdb=" OD2 ASP E 291 " 0.015 2.00e-02 2.50e+03 ... (remaining 5694 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.60: 434 2.60 - 3.18: 30101 3.18 - 3.75: 54061 3.75 - 4.33: 71260 4.33 - 4.90: 113493 Nonbonded interactions: 269349 Sorted by model distance: nonbonded pdb=" O TRP C 72 " pdb=" OG1 THR C 76 " model vdw 2.026 2.440 nonbonded pdb=" OG SER D 80 " pdb=" OD1 ASP D 82 " model vdw 2.094 2.440 nonbonded pdb=" O TYR A 912 " pdb=" OG1 THR A 915 " model vdw 2.132 2.440 nonbonded pdb=" O MET D 930 " pdb=" OH TYR D 940 " model vdw 2.136 2.440 nonbonded pdb=" OH TYR D 324 " pdb=" OD1 ASP D 590 " model vdw 2.138 2.440 ... (remaining 269344 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 23 through 71 or resid 80 through 367 or resid 373 through \ 399 or resid 406 through 546 or resid 551 through 562 or resid 579 through 628 \ or resid 645 through 1005)) selection = (chain 'B' and (resid 23 through 71 or resid 80 through 144 or resid 148 through \ 296 or resid 303 through 462 or resid 468 through 494 or resid 504 through 628 \ or resid 645 through 699 or resid 705 through 788 or resid 793 through 857 or re \ sid 862 through 897 or resid 911 through 1005)) selection = (chain 'D' and (resid 23 through 71 or resid 80 through 144 or resid 148 through \ 296 or resid 303 through 367 or resid 373 through 399 or resid 406 through 546 \ or resid 551 through 562 or resid 579 through 628 or resid 645 through 1005)) selection = (chain 'E' and (resid 23 through 144 or resid 148 through 296 or resid 303 throu \ gh 462 or resid 468 through 494 or resid 504 through 628 or resid 645 through 69 \ 9 or resid 705 through 788 or resid 793 through 857 or resid 862 through 897 or \ resid 911 through 1005)) } ncs_group { reference = chain 'C' selection = chain 'F' } 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: 4.640 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 21.840 Check model and map are aligned: 0.240 Set scattering table: 0.270 Process input model: 87.280 Find NCS groups from input model: 2.350 Set up NCS constraints: 0.170 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:3.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 119.830 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1583 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 0.139 33348 Z= 0.205 Angle : 0.711 13.848 44901 Z= 0.365 Chirality : 0.041 0.377 4796 Planarity : 0.004 0.168 5697 Dihedral : 18.133 89.618 12369 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 16.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 1.67 % Allowed : 33.83 % Favored : 64.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.20 (0.13), residues: 3808 helix: 0.39 (0.11), residues: 2287 sheet: -0.61 (0.45), residues: 120 loop : -0.82 (0.16), residues: 1401 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP D 601 HIS 0.005 0.001 HIS A 118 PHE 0.032 0.001 PHE D 742 TYR 0.027 0.001 TYR E 709 ARG 0.005 0.000 ARG A 359 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7616 Ramachandran restraints generated. 3808 Oldfield, 0 Emsley, 3808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7616 Ramachandran restraints generated. 3808 Oldfield, 0 Emsley, 3808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 630 residues out of total 3592 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 570 time to evaluate : 3.701 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: A 111 ASP cc_start: 0.5828 (p0) cc_final: 0.5619 (t70) REVERT: A 551 LEU cc_start: 0.1752 (mt) cc_final: 0.1401 (tp) REVERT: A 758 LEU cc_start: 0.6029 (pp) cc_final: 0.5053 (tp) REVERT: A 804 TYR cc_start: 0.7452 (m-10) cc_final: 0.7017 (m-80) REVERT: A 930 MET cc_start: 0.5168 (mpt) cc_final: 0.3299 (ppp) REVERT: A 940 TYR cc_start: 0.6534 (t80) cc_final: 0.5501 (t80) REVERT: A 996 TYR cc_start: 0.4947 (m-80) cc_final: 0.4288 (m-80) REVERT: B 124 MET cc_start: 0.2646 (mmt) cc_final: 0.2239 (mmt) REVERT: B 160 ASN cc_start: 0.1739 (OUTLIER) cc_final: 0.1298 (m110) REVERT: B 476 ILE cc_start: 0.5317 (mm) cc_final: 0.5036 (pt) REVERT: B 491 GLN cc_start: 0.7998 (tt0) cc_final: 0.7770 (tm-30) REVERT: B 757 TRP cc_start: -0.1791 (OUTLIER) cc_final: -0.2291 (m-90) REVERT: B 930 MET cc_start: 0.1446 (ppp) cc_final: 0.1000 (ptp) REVERT: C 8 THR cc_start: -0.1232 (OUTLIER) cc_final: -0.2004 (t) REVERT: C 231 MET cc_start: 0.1256 (tpt) cc_final: -0.0002 (ppp) REVERT: D 240 PHE cc_start: -0.1098 (p90) cc_final: -0.1842 (p90) REVERT: D 409 ILE cc_start: 0.1396 (mm) cc_final: 0.1179 (mt) REVERT: D 418 TYR cc_start: 0.3611 (m-80) cc_final: 0.2556 (m-80) REVERT: D 507 PHE cc_start: 0.2218 (OUTLIER) cc_final: 0.1075 (m-80) REVERT: D 592 LEU cc_start: 0.8623 (tm) cc_final: 0.8085 (tt) REVERT: D 837 PHE cc_start: 0.2808 (t80) cc_final: 0.2282 (t80) REVERT: D 930 MET cc_start: 0.4379 (tpt) cc_final: 0.1996 (tpt) REVERT: D 933 PHE cc_start: 0.3241 (m-10) cc_final: 0.2760 (m-10) REVERT: D 936 MET cc_start: 0.0945 (ptt) cc_final: -0.0198 (tpp) REVERT: E 114 THR cc_start: -0.0328 (OUTLIER) cc_final: -0.0800 (p) REVERT: E 419 ASP cc_start: -0.1567 (OUTLIER) cc_final: -0.1987 (m-30) REVERT: E 445 LEU cc_start: 0.4106 (mt) cc_final: 0.3522 (mp) REVERT: E 553 ASP cc_start: 0.2938 (m-30) cc_final: 0.2555 (t70) REVERT: E 764 CYS cc_start: 0.5259 (m) cc_final: 0.5026 (t) REVERT: E 861 ASN cc_start: 0.2761 (p0) cc_final: 0.2530 (p0) REVERT: E 936 MET cc_start: 0.3289 (mmp) cc_final: 0.2509 (tpp) REVERT: E 975 HIS cc_start: 0.5488 (m90) cc_final: 0.5269 (m90) REVERT: E 1001 MET cc_start: 0.4369 (mtt) cc_final: 0.3833 (mmt) REVERT: E 1004 PHE cc_start: 0.3472 (t80) cc_final: 0.3037 (m-10) REVERT: F 172 GLU cc_start: 0.6499 (tt0) cc_final: 0.5942 (pp20) outliers start: 60 outliers final: 13 residues processed: 622 average time/residue: 0.4920 time to fit residues: 474.3048 Evaluate side-chains 355 residues out of total 3592 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 336 time to evaluate : 3.669 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 SER Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 697 LYS Chi-restraints excluded: chain A residue 740 LEU Chi-restraints excluded: chain A residue 938 ASP Chi-restraints excluded: chain B residue 160 ASN Chi-restraints excluded: chain B residue 757 TRP Chi-restraints excluded: chain B residue 859 VAL Chi-restraints excluded: chain C residue 8 THR Chi-restraints excluded: chain C residue 192 TYR Chi-restraints excluded: chain D residue 222 ASP Chi-restraints excluded: chain D residue 257 THR Chi-restraints excluded: chain D residue 507 PHE Chi-restraints excluded: chain E residue 114 THR Chi-restraints excluded: chain E residue 134 TYR Chi-restraints excluded: chain E residue 213 ILE Chi-restraints excluded: chain E residue 378 TYR Chi-restraints excluded: chain E residue 419 ASP Chi-restraints excluded: chain E residue 498 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 388 random chunks: chunk 327 optimal weight: 0.7980 chunk 294 optimal weight: 0.0060 chunk 163 optimal weight: 9.9990 chunk 100 optimal weight: 2.9990 chunk 198 optimal weight: 2.9990 chunk 157 optimal weight: 3.9990 chunk 304 optimal weight: 5.9990 chunk 117 optimal weight: 0.8980 chunk 184 optimal weight: 2.9990 chunk 226 optimal weight: 8.9990 chunk 352 optimal weight: 7.9990 overall best weight: 1.5400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 202 ASN ** A 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 351 ASN A 483 GLN A 654 ASN A 829 GLN A 863 ASN ** B 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 133 ASN ** B 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 332 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 477 ASN ** B 702 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 786 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 34 GLN D 58 GLN D 133 ASN D 332 HIS D 475 GLN D 591 ASN D 765 ASN D 786 HIS ** D 867 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 973 ASN ** D 975 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 978 HIS ** E 391 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 483 GLN E 536 GLN E 666 ASN E 698 GLN E 834 GLN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2150 moved from start: 0.3260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 33348 Z= 0.237 Angle : 0.719 13.451 44901 Z= 0.371 Chirality : 0.044 0.282 4796 Planarity : 0.005 0.081 5697 Dihedral : 5.279 53.334 4305 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 19.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 5.12 % Allowed : 28.45 % Favored : 66.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -0.28 (0.13), residues: 3808 helix: 0.33 (0.10), residues: 2368 sheet: -0.77 (0.62), residues: 54 loop : -0.92 (0.16), residues: 1386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP B 448 HIS 0.021 0.002 HIS E 118 PHE 0.028 0.002 PHE E 107 TYR 0.032 0.002 TYR A 223 ARG 0.014 0.001 ARG D 760 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7616 Ramachandran restraints generated. 3808 Oldfield, 0 Emsley, 3808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7616 Ramachandran restraints generated. 3808 Oldfield, 0 Emsley, 3808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 558 residues out of total 3592 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 184 poor density : 374 time to evaluate : 4.127 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: A 98 MET cc_start: 0.4093 (pmm) cc_final: 0.3495 (pmm) REVERT: A 267 ARG cc_start: 0.2643 (OUTLIER) cc_final: 0.2289 (mtm180) REVERT: A 493 ASN cc_start: 0.5666 (OUTLIER) cc_final: 0.4466 (t0) REVERT: A 551 LEU cc_start: 0.1352 (mt) cc_final: 0.1000 (tp) REVERT: A 683 LYS cc_start: 0.4393 (tttp) cc_final: 0.3601 (tttt) REVERT: A 735 LYS cc_start: 0.5724 (tptp) cc_final: 0.5377 (tptt) REVERT: A 785 LYS cc_start: 0.3062 (OUTLIER) cc_final: 0.2809 (tttt) REVERT: A 842 LEU cc_start: 0.7274 (OUTLIER) cc_final: 0.6846 (mt) REVERT: A 930 MET cc_start: 0.4918 (mpt) cc_final: 0.2347 (ppp) REVERT: B 124 MET cc_start: 0.3441 (mmt) cc_final: 0.3002 (mmt) REVERT: B 160 ASN cc_start: 0.1622 (OUTLIER) cc_final: -0.0181 (p0) REVERT: B 447 ARG cc_start: 0.5465 (mmp-170) cc_final: 0.4963 (mmp-170) REVERT: B 476 ILE cc_start: 0.5486 (OUTLIER) cc_final: 0.5010 (tp) REVERT: B 491 GLN cc_start: 0.8072 (tt0) cc_final: 0.7692 (tm-30) REVERT: B 524 ILE cc_start: 0.5751 (tp) cc_final: 0.5224 (pt) REVERT: B 647 MET cc_start: -0.3504 (ptm) cc_final: -0.3997 (ptp) REVERT: B 930 MET cc_start: 0.1821 (ppp) cc_final: 0.0628 (ptp) REVERT: C 34 GLN cc_start: -0.1132 (OUTLIER) cc_final: -0.1683 (mt0) REVERT: C 173 VAL cc_start: -0.2137 (OUTLIER) cc_final: -0.2413 (m) REVERT: C 206 MET cc_start: 0.3890 (pmm) cc_final: 0.3225 (mpp) REVERT: C 231 MET cc_start: 0.1418 (tpt) cc_final: -0.0446 (ppp) REVERT: D 124 MET cc_start: -0.1780 (tpt) cc_final: -0.2024 (tpt) REVERT: D 204 MET cc_start: -0.0970 (OUTLIER) cc_final: -0.3144 (mmm) REVERT: D 240 PHE cc_start: -0.1335 (p90) cc_final: -0.2550 (p90) REVERT: D 507 PHE cc_start: 0.2109 (m-80) cc_final: 0.1454 (m-10) REVERT: D 621 GLU cc_start: 0.6356 (tp30) cc_final: 0.6116 (mm-30) REVERT: D 651 ASP cc_start: -0.2605 (OUTLIER) cc_final: -0.3068 (t70) REVERT: D 837 PHE cc_start: 0.3158 (t80) cc_final: 0.2712 (t80) REVERT: D 930 MET cc_start: 0.2776 (tpt) cc_final: 0.1952 (tpt) REVERT: D 933 PHE cc_start: 0.3332 (m-10) cc_final: 0.2998 (m-10) REVERT: D 936 MET cc_start: 0.0785 (ptt) cc_final: -0.0374 (tpp) REVERT: D 941 ASP cc_start: 0.8328 (m-30) cc_final: 0.8077 (t0) REVERT: E 97 GLU cc_start: 0.1166 (OUTLIER) cc_final: 0.0108 (mm-30) REVERT: E 133 ASN cc_start: 0.5949 (m-40) cc_final: 0.5302 (t0) REVERT: E 290 MET cc_start: 0.7016 (tpp) cc_final: 0.6357 (tpt) REVERT: E 396 MET cc_start: -0.4781 (mmm) cc_final: -0.5469 (mtp) REVERT: E 553 ASP cc_start: 0.2963 (m-30) cc_final: 0.2696 (t70) REVERT: E 554 ASP cc_start: -0.3987 (OUTLIER) cc_final: -0.4246 (t0) REVERT: E 646 PHE cc_start: 0.4094 (OUTLIER) cc_final: 0.3797 (p90) REVERT: E 647 MET cc_start: 0.3465 (OUTLIER) cc_final: 0.3109 (ppp) REVERT: E 824 THR cc_start: -0.1596 (OUTLIER) cc_final: -0.1884 (m) REVERT: E 936 MET cc_start: 0.3390 (mmp) cc_final: 0.2344 (tpp) REVERT: F 231 MET cc_start: 0.1030 (pmm) cc_final: 0.0778 (mtp) outliers start: 184 outliers final: 69 residues processed: 524 average time/residue: 0.4591 time to fit residues: 388.6357 Evaluate side-chains 389 residues out of total 3592 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 305 time to evaluate : 3.693 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 80 SER Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 227 MET Chi-restraints excluded: chain A residue 267 ARG Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 337 ASP Chi-restraints excluded: chain A residue 420 VAL Chi-restraints excluded: chain A residue 427 GLU Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 493 ASN Chi-restraints excluded: chain A residue 555 THR Chi-restraints excluded: chain A residue 615 SER Chi-restraints excluded: chain A residue 645 PHE Chi-restraints excluded: chain A residue 697 LYS Chi-restraints excluded: chain A residue 785 LYS Chi-restraints excluded: chain A residue 836 ASP Chi-restraints excluded: chain A residue 842 LEU Chi-restraints excluded: chain A residue 938 ASP Chi-restraints excluded: chain B residue 37 SER Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain B residue 139 ASP Chi-restraints excluded: chain B residue 160 ASN Chi-restraints excluded: chain B residue 357 MET Chi-restraints excluded: chain B residue 476 ILE Chi-restraints excluded: chain B residue 526 ASP Chi-restraints excluded: chain B residue 597 GLU Chi-restraints excluded: chain B residue 625 TYR Chi-restraints excluded: chain B residue 709 TYR Chi-restraints excluded: chain B residue 744 PHE Chi-restraints excluded: chain B residue 828 THR Chi-restraints excluded: chain B residue 847 THR Chi-restraints excluded: chain B residue 859 VAL Chi-restraints excluded: chain B residue 936 MET Chi-restraints excluded: chain B residue 970 ILE Chi-restraints excluded: chain C residue 34 GLN Chi-restraints excluded: chain C residue 173 VAL Chi-restraints excluded: chain C residue 192 TYR Chi-restraints excluded: chain C residue 198 VAL Chi-restraints excluded: chain C residue 220 PHE Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain D residue 26 VAL Chi-restraints excluded: chain D residue 45 PHE Chi-restraints excluded: chain D residue 62 LEU Chi-restraints excluded: chain D residue 121 ILE Chi-restraints excluded: chain D residue 204 MET Chi-restraints excluded: chain D residue 227 MET Chi-restraints excluded: chain D residue 234 LYS Chi-restraints excluded: chain D residue 368 ASP Chi-restraints excluded: chain D residue 458 ILE Chi-restraints excluded: chain D residue 546 SER Chi-restraints excluded: chain D residue 651 ASP Chi-restraints excluded: chain D residue 654 ASN Chi-restraints excluded: chain D residue 765 ASN Chi-restraints excluded: chain D residue 776 ASP Chi-restraints excluded: chain D residue 780 VAL Chi-restraints excluded: chain D residue 794 VAL Chi-restraints excluded: chain D residue 912 TYR Chi-restraints excluded: chain E residue 97 GLU Chi-restraints excluded: chain E residue 107 PHE Chi-restraints excluded: chain E residue 129 VAL Chi-restraints excluded: chain E residue 131 THR Chi-restraints excluded: chain E residue 134 TYR Chi-restraints excluded: chain E residue 142 CYS Chi-restraints excluded: chain E residue 203 LEU Chi-restraints excluded: chain E residue 222 ASP Chi-restraints excluded: chain E residue 228 LEU Chi-restraints excluded: chain E residue 378 TYR Chi-restraints excluded: chain E residue 554 ASP Chi-restraints excluded: chain E residue 646 PHE Chi-restraints excluded: chain E residue 647 MET Chi-restraints excluded: chain E residue 661 ILE Chi-restraints excluded: chain E residue 684 ILE Chi-restraints excluded: chain E residue 707 VAL Chi-restraints excluded: chain E residue 730 GLU Chi-restraints excluded: chain E residue 740 LEU Chi-restraints excluded: chain E residue 778 PHE Chi-restraints excluded: chain E residue 824 THR Chi-restraints excluded: chain E residue 862 ILE Chi-restraints excluded: chain E residue 1005 ILE Chi-restraints excluded: chain F residue 21 LEU Chi-restraints excluded: chain F residue 193 ILE Chi-restraints excluded: chain F residue 197 ASN Chi-restraints excluded: chain F residue 234 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 388 random chunks: chunk 195 optimal weight: 3.9990 chunk 109 optimal weight: 0.7980 chunk 293 optimal weight: 0.4980 chunk 239 optimal weight: 5.9990 chunk 97 optimal weight: 0.7980 chunk 352 optimal weight: 5.9990 chunk 381 optimal weight: 7.9990 chunk 314 optimal weight: 4.9990 chunk 350 optimal weight: 5.9990 chunk 120 optimal weight: 3.9990 chunk 283 optimal weight: 20.0000 overall best weight: 2.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 58 GLN ** A 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 136 ASN A 202 ASN A 224 ASN A 386 ASN A 475 GLN ** A 563 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 591 ASN A 654 ASN ** B 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 211 HIS ** B 332 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 339 HIS B 477 ASN ** B 598 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 609 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 702 ASN ** B 786 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 852 HIS D 39 ASN D 58 GLN D 89 GLN D 211 HIS D 698 GLN ** D 867 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 975 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 39 ASN ** E 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 263 ASN E 339 HIS ** E 377 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2547 moved from start: 0.4914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 33348 Z= 0.273 Angle : 0.728 17.041 44901 Z= 0.379 Chirality : 0.044 0.235 4796 Planarity : 0.005 0.072 5697 Dihedral : 5.249 51.918 4287 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 22.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 5.68 % Allowed : 27.31 % Favored : 67.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -0.55 (0.13), residues: 3808 helix: 0.15 (0.10), residues: 2360 sheet: -0.91 (0.48), residues: 114 loop : -1.10 (0.16), residues: 1334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.003 TRP E 231 HIS 0.016 0.002 HIS B 332 PHE 0.028 0.002 PHE B 45 TYR 0.035 0.002 TYR A 223 ARG 0.015 0.001 ARG D 613 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7616 Ramachandran restraints generated. 3808 Oldfield, 0 Emsley, 3808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7616 Ramachandran restraints generated. 3808 Oldfield, 0 Emsley, 3808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 549 residues out of total 3592 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 204 poor density : 345 time to evaluate : 3.708 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 45 PHE cc_start: 0.1964 (OUTLIER) cc_final: 0.0433 (t80) REVERT: A 202 ASN cc_start: 0.3224 (OUTLIER) cc_final: 0.2746 (t0) REVERT: A 223 TYR cc_start: 0.1065 (t80) cc_final: -0.0224 (p90) REVERT: A 391 ASN cc_start: -0.0650 (OUTLIER) cc_final: -0.2081 (m-40) REVERT: A 475 GLN cc_start: -0.2719 (OUTLIER) cc_final: -0.3257 (tt0) REVERT: A 616 MET cc_start: 0.5258 (mmt) cc_final: 0.4860 (mmt) REVERT: A 785 LYS cc_start: 0.3498 (OUTLIER) cc_final: 0.3252 (tttt) REVERT: A 842 LEU cc_start: 0.7284 (OUTLIER) cc_final: 0.7036 (mt) REVERT: A 930 MET cc_start: 0.5356 (mpt) cc_final: 0.2702 (ptm) REVERT: B 124 MET cc_start: 0.3754 (OUTLIER) cc_final: 0.3104 (mmt) REVERT: B 339 HIS cc_start: -0.0981 (OUTLIER) cc_final: -0.1262 (p90) REVERT: B 447 ARG cc_start: 0.5556 (mmp-170) cc_final: 0.5125 (mmp-170) REVERT: B 476 ILE cc_start: 0.5860 (OUTLIER) cc_final: 0.5446 (tp) REVERT: B 491 GLN cc_start: 0.8244 (tt0) cc_final: 0.7966 (tp-100) REVERT: B 611 TYR cc_start: 0.2796 (t80) cc_final: 0.1833 (m-80) REVERT: B 652 PHE cc_start: 0.2438 (t80) cc_final: 0.1869 (t80) REVERT: B 781 LEU cc_start: 0.6342 (OUTLIER) cc_final: 0.6047 (tp) REVERT: B 822 GLU cc_start: 0.8150 (mm-30) cc_final: 0.7865 (mm-30) REVERT: B 930 MET cc_start: 0.2003 (ppp) cc_final: 0.0637 (ptp) REVERT: C 206 MET cc_start: 0.4039 (pmm) cc_final: 0.2693 (tpt) REVERT: C 231 MET cc_start: 0.2377 (tpt) cc_final: -0.1123 (ptp) REVERT: D 71 TYR cc_start: -0.2382 (OUTLIER) cc_final: -0.3222 (m-80) REVERT: D 204 MET cc_start: -0.1614 (tpp) cc_final: -0.4105 (mmm) REVERT: D 326 ARG cc_start: -0.0405 (mtm180) cc_final: -0.0676 (mtm180) REVERT: D 361 PHE cc_start: -0.2989 (OUTLIER) cc_final: -0.4240 (m-80) REVERT: D 507 PHE cc_start: 0.2034 (m-80) cc_final: 0.1495 (m-80) REVERT: D 765 ASN cc_start: 0.1720 (OUTLIER) cc_final: 0.1069 (p0) REVERT: D 837 PHE cc_start: 0.3081 (t80) cc_final: 0.2495 (t80) REVERT: D 866 MET cc_start: -0.1960 (mtt) cc_final: -0.2303 (mpp) REVERT: D 930 MET cc_start: 0.2317 (tpt) cc_final: 0.1904 (tpt) REVERT: D 933 PHE cc_start: 0.3294 (m-10) cc_final: 0.2881 (m-10) REVERT: D 936 MET cc_start: 0.0657 (ptt) cc_final: -0.0427 (tpp) REVERT: D 1005 ILE cc_start: 0.2702 (OUTLIER) cc_final: 0.2071 (mp) REVERT: E 184 VAL cc_start: 0.0396 (OUTLIER) cc_final: 0.0126 (p) REVERT: E 290 MET cc_start: 0.7159 (tpp) cc_final: 0.6808 (tpt) REVERT: E 523 ASN cc_start: -0.0038 (OUTLIER) cc_final: -0.0981 (m-40) REVERT: E 553 ASP cc_start: 0.2675 (m-30) cc_final: 0.2448 (t70) REVERT: E 554 ASP cc_start: -0.3829 (OUTLIER) cc_final: -0.4116 (t0) REVERT: E 647 MET cc_start: 0.4225 (OUTLIER) cc_final: 0.3949 (ppp) REVERT: E 913 MET cc_start: -0.2116 (mmt) cc_final: -0.2338 (mmt) REVERT: E 930 MET cc_start: 0.2694 (ptt) cc_final: 0.2274 (ppp) REVERT: E 936 MET cc_start: 0.3334 (mmp) cc_final: 0.2284 (tpp) REVERT: E 977 LYS cc_start: 0.5443 (OUTLIER) cc_final: 0.5229 (mmmm) REVERT: E 1004 PHE cc_start: 0.6707 (t80) cc_final: 0.5782 (m-10) REVERT: F 62 THR cc_start: -0.0687 (OUTLIER) cc_final: -0.1009 (p) REVERT: F 219 LYS cc_start: 0.1180 (OUTLIER) cc_final: 0.0964 (mttt) REVERT: F 231 MET cc_start: 0.0972 (pmm) cc_final: 0.0697 (mtp) outliers start: 204 outliers final: 89 residues processed: 511 average time/residue: 0.4493 time to fit residues: 368.0376 Evaluate side-chains 411 residues out of total 3592 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 110 poor density : 301 time to evaluate : 3.716 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 45 PHE Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 200 ILE Chi-restraints excluded: chain A residue 202 ASN Chi-restraints excluded: chain A residue 257 THR Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 391 ASN Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 475 GLN Chi-restraints excluded: chain A residue 508 THR Chi-restraints excluded: chain A residue 555 THR Chi-restraints excluded: chain A residue 615 SER Chi-restraints excluded: chain A residue 645 PHE Chi-restraints excluded: chain A residue 651 ASP Chi-restraints excluded: chain A residue 708 PHE Chi-restraints excluded: chain A residue 785 LYS Chi-restraints excluded: chain A residue 836 ASP Chi-restraints excluded: chain A residue 841 LEU Chi-restraints excluded: chain A residue 842 LEU Chi-restraints excluded: chain A residue 1001 MET Chi-restraints excluded: chain B residue 37 SER Chi-restraints excluded: chain B residue 52 THR Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain B residue 110 VAL Chi-restraints excluded: chain B residue 124 MET Chi-restraints excluded: chain B residue 139 ASP Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 208 ILE Chi-restraints excluded: chain B residue 282 TYR Chi-restraints excluded: chain B residue 339 HIS Chi-restraints excluded: chain B residue 378 TYR Chi-restraints excluded: chain B residue 395 CYS Chi-restraints excluded: chain B residue 407 ILE Chi-restraints excluded: chain B residue 476 ILE Chi-restraints excluded: chain B residue 481 ILE Chi-restraints excluded: chain B residue 597 GLU Chi-restraints excluded: chain B residue 620 ILE Chi-restraints excluded: chain B residue 625 TYR Chi-restraints excluded: chain B residue 670 SER Chi-restraints excluded: chain B residue 707 VAL Chi-restraints excluded: chain B residue 709 TYR Chi-restraints excluded: chain B residue 744 PHE Chi-restraints excluded: chain B residue 781 LEU Chi-restraints excluded: chain B residue 828 THR Chi-restraints excluded: chain B residue 846 SER Chi-restraints excluded: chain B residue 859 VAL Chi-restraints excluded: chain B residue 948 ASN Chi-restraints excluded: chain C residue 192 TYR Chi-restraints excluded: chain C residue 198 VAL Chi-restraints excluded: chain C residue 220 PHE Chi-restraints excluded: chain C residue 228 THR Chi-restraints excluded: chain D residue 26 VAL Chi-restraints excluded: chain D residue 45 PHE Chi-restraints excluded: chain D residue 71 TYR Chi-restraints excluded: chain D residue 114 THR Chi-restraints excluded: chain D residue 121 ILE Chi-restraints excluded: chain D residue 138 ILE Chi-restraints excluded: chain D residue 192 ASN Chi-restraints excluded: chain D residue 227 MET Chi-restraints excluded: chain D residue 241 HIS Chi-restraints excluded: chain D residue 257 THR Chi-restraints excluded: chain D residue 361 PHE Chi-restraints excluded: chain D residue 388 PHE Chi-restraints excluded: chain D residue 458 ILE Chi-restraints excluded: chain D residue 550 PHE Chi-restraints excluded: chain D residue 592 LEU Chi-restraints excluded: chain D residue 654 ASN Chi-restraints excluded: chain D residue 765 ASN Chi-restraints excluded: chain D residue 776 ASP Chi-restraints excluded: chain D residue 794 VAL Chi-restraints excluded: chain D residue 816 ILE Chi-restraints excluded: chain D residue 839 PHE Chi-restraints excluded: chain D residue 912 TYR Chi-restraints excluded: chain D residue 1005 ILE Chi-restraints excluded: chain E residue 129 VAL Chi-restraints excluded: chain E residue 131 THR Chi-restraints excluded: chain E residue 134 TYR Chi-restraints excluded: chain E residue 142 CYS Chi-restraints excluded: chain E residue 144 LYS Chi-restraints excluded: chain E residue 184 VAL Chi-restraints excluded: chain E residue 203 LEU Chi-restraints excluded: chain E residue 222 ASP Chi-restraints excluded: chain E residue 228 LEU Chi-restraints excluded: chain E residue 276 ASP Chi-restraints excluded: chain E residue 282 TYR Chi-restraints excluded: chain E residue 285 ARG Chi-restraints excluded: chain E residue 356 TYR Chi-restraints excluded: chain E residue 378 TYR Chi-restraints excluded: chain E residue 523 ASN Chi-restraints excluded: chain E residue 554 ASP Chi-restraints excluded: chain E residue 647 MET Chi-restraints excluded: chain E residue 661 ILE Chi-restraints excluded: chain E residue 672 SER Chi-restraints excluded: chain E residue 707 VAL Chi-restraints excluded: chain E residue 713 ILE Chi-restraints excluded: chain E residue 726 VAL Chi-restraints excluded: chain E residue 730 GLU Chi-restraints excluded: chain E residue 740 LEU Chi-restraints excluded: chain E residue 778 PHE Chi-restraints excluded: chain E residue 862 ILE Chi-restraints excluded: chain E residue 977 LYS Chi-restraints excluded: chain E residue 1005 ILE Chi-restraints excluded: chain F residue 11 VAL Chi-restraints excluded: chain F residue 21 LEU Chi-restraints excluded: chain F residue 62 THR Chi-restraints excluded: chain F residue 193 ILE Chi-restraints excluded: chain F residue 197 ASN Chi-restraints excluded: chain F residue 219 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 388 random chunks: chunk 348 optimal weight: 20.0000 chunk 265 optimal weight: 5.9990 chunk 183 optimal weight: 8.9990 chunk 39 optimal weight: 0.2980 chunk 168 optimal weight: 0.5980 chunk 237 optimal weight: 0.9990 chunk 354 optimal weight: 2.9990 chunk 375 optimal weight: 7.9990 chunk 185 optimal weight: 0.4980 chunk 335 optimal weight: 0.9980 chunk 101 optimal weight: 5.9990 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 563 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 711 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 89 GLN ** B 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 224 ASN B 332 HIS ** B 339 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 377 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 487 GLN ** B 493 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 598 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 609 HIS B 711 GLN ** B 786 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 196 ASN D 765 ASN ** D 867 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 975 HIS D1002 ASN E 133 ASN ** E 377 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 391 ASN E 457 ASN ** E 491 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 948 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2468 moved from start: 0.5287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 33348 Z= 0.174 Angle : 0.631 15.058 44901 Z= 0.324 Chirality : 0.041 0.210 4796 Planarity : 0.004 0.058 5697 Dihedral : 4.815 51.299 4279 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 17.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 3.93 % Allowed : 28.93 % Favored : 67.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -0.28 (0.13), residues: 3808 helix: 0.40 (0.11), residues: 2368 sheet: -1.41 (0.50), residues: 96 loop : -1.01 (0.16), residues: 1344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP B 601 HIS 0.009 0.001 HIS B 332 PHE 0.018 0.002 PHE B 385 TYR 0.041 0.001 TYR A 223 ARG 0.010 0.000 ARG B 502 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7616 Ramachandran restraints generated. 3808 Oldfield, 0 Emsley, 3808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7616 Ramachandran restraints generated. 3808 Oldfield, 0 Emsley, 3808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 460 residues out of total 3592 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 141 poor density : 319 time to evaluate : 3.781 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 45 PHE cc_start: 0.1756 (OUTLIER) cc_final: 0.0771 (t80) REVERT: A 223 TYR cc_start: 0.0152 (OUTLIER) cc_final: -0.2043 (t80) REVERT: A 493 ASN cc_start: 0.6346 (OUTLIER) cc_final: 0.5159 (t0) REVERT: A 551 LEU cc_start: 0.2412 (OUTLIER) cc_final: 0.1381 (tp) REVERT: A 765 ASN cc_start: 0.5767 (t0) cc_final: 0.5551 (t0) REVERT: A 842 LEU cc_start: 0.7313 (OUTLIER) cc_final: 0.6983 (mt) REVERT: A 930 MET cc_start: 0.5427 (mpt) cc_final: 0.2817 (ptm) REVERT: A 936 MET cc_start: 0.3202 (mmm) cc_final: 0.2833 (mtt) REVERT: B 32 GLU cc_start: 0.8357 (OUTLIER) cc_final: 0.7296 (pp20) REVERT: B 275 ILE cc_start: -0.3155 (OUTLIER) cc_final: -0.3400 (mp) REVERT: B 447 ARG cc_start: 0.5484 (mmp-170) cc_final: 0.5004 (mmp80) REVERT: B 476 ILE cc_start: 0.5744 (OUTLIER) cc_final: 0.5197 (tp) REVERT: B 491 GLN cc_start: 0.8274 (tt0) cc_final: 0.7917 (tp-100) REVERT: B 611 TYR cc_start: 0.2685 (t80) cc_final: 0.2063 (m-80) REVERT: B 647 MET cc_start: -0.3052 (ptp) cc_final: -0.3561 (ptm) REVERT: B 781 LEU cc_start: 0.6059 (OUTLIER) cc_final: 0.5835 (tp) REVERT: B 930 MET cc_start: 0.2244 (ppp) cc_final: 0.0575 (ptp) REVERT: B 936 MET cc_start: 0.4571 (OUTLIER) cc_final: 0.3770 (pmm) REVERT: C 206 MET cc_start: 0.3600 (pmm) cc_final: 0.2561 (mpp) REVERT: C 231 MET cc_start: 0.2136 (tpt) cc_final: -0.0878 (ptp) REVERT: D 124 MET cc_start: -0.1884 (tpt) cc_final: -0.2155 (tpt) REVERT: D 204 MET cc_start: -0.1418 (tpp) cc_final: -0.4686 (mtp) REVERT: D 241 HIS cc_start: -0.1584 (OUTLIER) cc_final: -0.2655 (m90) REVERT: D 589 TYR cc_start: 0.7210 (m-10) cc_final: 0.6966 (m-10) REVERT: D 592 LEU cc_start: 0.7966 (OUTLIER) cc_final: 0.7301 (mt) REVERT: D 625 TYR cc_start: 0.5945 (t80) cc_final: 0.5673 (t80) REVERT: D 677 ARG cc_start: 0.7415 (ptt90) cc_final: 0.7008 (ptt-90) REVERT: D 709 TYR cc_start: 0.7457 (t80) cc_final: 0.7254 (t80) REVERT: D 761 LEU cc_start: -0.5424 (OUTLIER) cc_final: -0.5651 (mt) REVERT: D 837 PHE cc_start: 0.2925 (t80) cc_final: 0.2513 (t80) REVERT: D 889 LEU cc_start: -0.3006 (OUTLIER) cc_final: -0.3610 (mt) REVERT: D 930 MET cc_start: 0.2264 (tpt) cc_final: 0.1155 (tpp) REVERT: D 933 PHE cc_start: 0.3222 (m-10) cc_final: 0.2919 (m-10) REVERT: D 936 MET cc_start: 0.0868 (ptt) cc_final: -0.0789 (tpp) REVERT: D 981 ILE cc_start: 0.2052 (OUTLIER) cc_final: 0.1820 (mm) REVERT: E 124 MET cc_start: -0.2333 (tmm) cc_final: -0.4192 (mtm) REVERT: E 202 ASN cc_start: -0.4126 (OUTLIER) cc_final: -0.4867 (m-40) REVERT: E 290 MET cc_start: 0.7153 (tpp) cc_final: 0.6507 (tpp) REVERT: E 554 ASP cc_start: -0.3839 (OUTLIER) cc_final: -0.4155 (t0) REVERT: E 647 MET cc_start: 0.4723 (OUTLIER) cc_final: 0.3892 (ppp) REVERT: E 913 MET cc_start: -0.2382 (mmt) cc_final: -0.2620 (mmt) REVERT: E 930 MET cc_start: 0.2703 (ptt) cc_final: 0.2341 (ppp) REVERT: E 936 MET cc_start: 0.3244 (mmp) cc_final: 0.2237 (tpp) REVERT: E 947 GLU cc_start: 0.5599 (OUTLIER) cc_final: 0.5306 (pm20) REVERT: E 1004 PHE cc_start: 0.6602 (t80) cc_final: 0.5633 (m-10) REVERT: F 219 LYS cc_start: 0.1204 (OUTLIER) cc_final: 0.0913 (mttt) REVERT: F 231 MET cc_start: 0.0734 (pmm) cc_final: 0.0213 (ttm) outliers start: 141 outliers final: 79 residues processed: 433 average time/residue: 0.4600 time to fit residues: 324.1524 Evaluate side-chains 390 residues out of total 3592 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 291 time to evaluate : 4.175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 PHE Chi-restraints excluded: chain A residue 136 ASN Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 223 TYR Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 493 ASN Chi-restraints excluded: chain A residue 508 THR Chi-restraints excluded: chain A residue 551 LEU Chi-restraints excluded: chain A residue 554 ASP Chi-restraints excluded: chain A residue 579 SER Chi-restraints excluded: chain A residue 611 TYR Chi-restraints excluded: chain A residue 615 SER Chi-restraints excluded: chain A residue 645 PHE Chi-restraints excluded: chain A residue 763 LYS Chi-restraints excluded: chain A residue 773 SER Chi-restraints excluded: chain A residue 836 ASP Chi-restraints excluded: chain A residue 841 LEU Chi-restraints excluded: chain A residue 842 LEU Chi-restraints excluded: chain A residue 996 TYR Chi-restraints excluded: chain A residue 1001 MET Chi-restraints excluded: chain B residue 32 GLU Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain B residue 110 VAL Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 208 ILE Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain B residue 275 ILE Chi-restraints excluded: chain B residue 282 TYR Chi-restraints excluded: chain B residue 294 ILE Chi-restraints excluded: chain B residue 332 HIS Chi-restraints excluded: chain B residue 378 TYR Chi-restraints excluded: chain B residue 407 ILE Chi-restraints excluded: chain B residue 476 ILE Chi-restraints excluded: chain B residue 493 ASN Chi-restraints excluded: chain B residue 524 ILE Chi-restraints excluded: chain B residue 526 ASP Chi-restraints excluded: chain B residue 597 GLU Chi-restraints excluded: chain B residue 620 ILE Chi-restraints excluded: chain B residue 670 SER Chi-restraints excluded: chain B residue 709 TYR Chi-restraints excluded: chain B residue 744 PHE Chi-restraints excluded: chain B residue 781 LEU Chi-restraints excluded: chain B residue 859 VAL Chi-restraints excluded: chain B residue 925 ILE Chi-restraints excluded: chain B residue 936 MET Chi-restraints excluded: chain B residue 948 ASN Chi-restraints excluded: chain C residue 192 TYR Chi-restraints excluded: chain C residue 220 PHE Chi-restraints excluded: chain D residue 26 VAL Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 121 ILE Chi-restraints excluded: chain D residue 139 ASP Chi-restraints excluded: chain D residue 227 MET Chi-restraints excluded: chain D residue 234 LYS Chi-restraints excluded: chain D residue 241 HIS Chi-restraints excluded: chain D residue 257 THR Chi-restraints excluded: chain D residue 368 ASP Chi-restraints excluded: chain D residue 550 PHE Chi-restraints excluded: chain D residue 592 LEU Chi-restraints excluded: chain D residue 654 ASN Chi-restraints excluded: chain D residue 761 LEU Chi-restraints excluded: chain D residue 765 ASN Chi-restraints excluded: chain D residue 776 ASP Chi-restraints excluded: chain D residue 794 VAL Chi-restraints excluded: chain D residue 889 LEU Chi-restraints excluded: chain D residue 912 TYR Chi-restraints excluded: chain D residue 981 ILE Chi-restraints excluded: chain E residue 129 VAL Chi-restraints excluded: chain E residue 131 THR Chi-restraints excluded: chain E residue 133 ASN Chi-restraints excluded: chain E residue 134 TYR Chi-restraints excluded: chain E residue 142 CYS Chi-restraints excluded: chain E residue 144 LYS Chi-restraints excluded: chain E residue 183 VAL Chi-restraints excluded: chain E residue 202 ASN Chi-restraints excluded: chain E residue 203 LEU Chi-restraints excluded: chain E residue 204 MET Chi-restraints excluded: chain E residue 222 ASP Chi-restraints excluded: chain E residue 228 LEU Chi-restraints excluded: chain E residue 282 TYR Chi-restraints excluded: chain E residue 356 TYR Chi-restraints excluded: chain E residue 378 TYR Chi-restraints excluded: chain E residue 554 ASP Chi-restraints excluded: chain E residue 647 MET Chi-restraints excluded: chain E residue 661 ILE Chi-restraints excluded: chain E residue 672 SER Chi-restraints excluded: chain E residue 713 ILE Chi-restraints excluded: chain E residue 730 GLU Chi-restraints excluded: chain E residue 740 LEU Chi-restraints excluded: chain E residue 778 PHE Chi-restraints excluded: chain E residue 862 ILE Chi-restraints excluded: chain E residue 947 GLU Chi-restraints excluded: chain E residue 948 ASN Chi-restraints excluded: chain E residue 1005 ILE Chi-restraints excluded: chain F residue 11 VAL Chi-restraints excluded: chain F residue 21 LEU Chi-restraints excluded: chain F residue 193 ILE Chi-restraints excluded: chain F residue 197 ASN Chi-restraints excluded: chain F residue 219 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 388 random chunks: chunk 312 optimal weight: 3.9990 chunk 212 optimal weight: 0.5980 chunk 5 optimal weight: 0.0060 chunk 279 optimal weight: 0.8980 chunk 154 optimal weight: 4.9990 chunk 320 optimal weight: 6.9990 chunk 259 optimal weight: 0.9990 chunk 0 optimal weight: 7.9990 chunk 191 optimal weight: 6.9990 chunk 336 optimal weight: 8.9990 chunk 94 optimal weight: 0.3980 overall best weight: 0.5798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 202 ASN A 332 HIS ** A 563 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 711 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 211 HIS B 339 HIS ** B 377 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 487 GLN ** B 493 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 598 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 786 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 196 ASN ** D 765 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 867 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 133 ASN ** E 377 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 491 GLN ** E 975 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2471 moved from start: 0.5563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 33348 Z= 0.168 Angle : 0.613 12.926 44901 Z= 0.311 Chirality : 0.041 0.221 4796 Planarity : 0.004 0.082 5697 Dihedral : 4.689 50.706 4279 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 17.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 4.23 % Allowed : 28.62 % Favored : 67.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.19 (0.13), residues: 3808 helix: 0.52 (0.11), residues: 2367 sheet: -1.93 (0.41), residues: 134 loop : -0.99 (0.17), residues: 1307 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP B 601 HIS 0.027 0.001 HIS E 975 PHE 0.019 0.001 PHE D 608 TYR 0.031 0.001 TYR E 282 ARG 0.005 0.000 ARG B 819 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7616 Ramachandran restraints generated. 3808 Oldfield, 0 Emsley, 3808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7616 Ramachandran restraints generated. 3808 Oldfield, 0 Emsley, 3808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 464 residues out of total 3592 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 152 poor density : 312 time to evaluate : 3.797 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 45 PHE cc_start: 0.1749 (OUTLIER) cc_final: 0.0788 (t80) REVERT: A 223 TYR cc_start: 0.0477 (OUTLIER) cc_final: -0.1443 (t80) REVERT: A 493 ASN cc_start: 0.6385 (OUTLIER) cc_final: 0.5226 (t0) REVERT: A 551 LEU cc_start: 0.2271 (OUTLIER) cc_final: 0.1395 (tp) REVERT: A 665 LYS cc_start: 0.8674 (ptpp) cc_final: 0.8458 (tppt) REVERT: A 735 LYS cc_start: 0.6007 (tptp) cc_final: 0.5725 (tptt) REVERT: A 765 ASN cc_start: 0.5887 (t0) cc_final: 0.5607 (t0) REVERT: A 842 LEU cc_start: 0.7327 (OUTLIER) cc_final: 0.6997 (mt) REVERT: A 930 MET cc_start: 0.5360 (mpt) cc_final: 0.2715 (ptp) REVERT: A 936 MET cc_start: 0.3095 (mmm) cc_final: 0.2751 (mtt) REVERT: B 447 ARG cc_start: 0.5821 (mmp-170) cc_final: 0.5330 (mmp80) REVERT: B 476 ILE cc_start: 0.5803 (OUTLIER) cc_final: 0.5266 (tp) REVERT: B 491 GLN cc_start: 0.8243 (tt0) cc_final: 0.7824 (tp-100) REVERT: B 611 TYR cc_start: 0.2785 (t80) cc_final: 0.2072 (m-80) REVERT: B 647 MET cc_start: -0.3042 (ptp) cc_final: -0.3557 (ptm) REVERT: B 930 MET cc_start: 0.1772 (ppp) cc_final: 0.0198 (ptp) REVERT: C 206 MET cc_start: 0.3649 (pmm) cc_final: 0.2697 (mpp) REVERT: C 231 MET cc_start: 0.2014 (tpt) cc_final: -0.0971 (ptp) REVERT: D 41 LYS cc_start: 0.0561 (OUTLIER) cc_final: -0.0729 (mtmm) REVERT: D 204 MET cc_start: -0.1395 (tpp) cc_final: -0.4670 (mtp) REVERT: D 241 HIS cc_start: -0.1604 (OUTLIER) cc_final: -0.2611 (m90) REVERT: D 361 PHE cc_start: -0.2778 (OUTLIER) cc_final: -0.3930 (m-80) REVERT: D 589 TYR cc_start: 0.7334 (m-10) cc_final: 0.7059 (m-10) REVERT: D 592 LEU cc_start: 0.8051 (OUTLIER) cc_final: 0.7385 (mt) REVERT: D 837 PHE cc_start: 0.2932 (t80) cc_final: 0.2535 (t80) REVERT: D 866 MET cc_start: -0.1800 (mtt) cc_final: -0.2117 (mpp) REVERT: D 889 LEU cc_start: -0.3052 (OUTLIER) cc_final: -0.3683 (mt) REVERT: D 936 MET cc_start: 0.0657 (ptt) cc_final: -0.0922 (tpp) REVERT: D 1005 ILE cc_start: 0.2471 (OUTLIER) cc_final: 0.2064 (mp) REVERT: E 124 MET cc_start: -0.2386 (tmm) cc_final: -0.4213 (mtm) REVERT: E 202 ASN cc_start: -0.4202 (OUTLIER) cc_final: -0.4997 (m-40) REVERT: E 205 LYS cc_start: 0.2157 (OUTLIER) cc_final: 0.1543 (mmtp) REVERT: E 290 MET cc_start: 0.7331 (tpp) cc_final: 0.6744 (tpp) REVERT: E 647 MET cc_start: 0.4575 (OUTLIER) cc_final: 0.3819 (ppp) REVERT: E 930 MET cc_start: 0.2704 (ptt) cc_final: 0.2389 (ppp) REVERT: E 936 MET cc_start: 0.3234 (mmp) cc_final: 0.2240 (tpp) REVERT: E 1004 PHE cc_start: 0.6317 (t80) cc_final: 0.5442 (m-10) REVERT: F 219 LYS cc_start: 0.1247 (OUTLIER) cc_final: 0.0949 (mttt) outliers start: 152 outliers final: 93 residues processed: 434 average time/residue: 0.4701 time to fit residues: 328.2693 Evaluate side-chains 395 residues out of total 3592 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 109 poor density : 286 time to evaluate : 3.740 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 VAL Chi-restraints excluded: chain A residue 45 PHE Chi-restraints excluded: chain A residue 80 SER Chi-restraints excluded: chain A residue 136 ASN Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 202 ASN Chi-restraints excluded: chain A residue 218 TYR Chi-restraints excluded: chain A residue 223 TYR Chi-restraints excluded: chain A residue 275 ILE Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 493 ASN Chi-restraints excluded: chain A residue 508 THR Chi-restraints excluded: chain A residue 551 LEU Chi-restraints excluded: chain A residue 554 ASP Chi-restraints excluded: chain A residue 579 SER Chi-restraints excluded: chain A residue 611 TYR Chi-restraints excluded: chain A residue 615 SER Chi-restraints excluded: chain A residue 645 PHE Chi-restraints excluded: chain A residue 651 ASP Chi-restraints excluded: chain A residue 773 SER Chi-restraints excluded: chain A residue 836 ASP Chi-restraints excluded: chain A residue 841 LEU Chi-restraints excluded: chain A residue 842 LEU Chi-restraints excluded: chain A residue 996 TYR Chi-restraints excluded: chain B residue 37 SER Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 208 ILE Chi-restraints excluded: chain B residue 214 VAL Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain B residue 282 TYR Chi-restraints excluded: chain B residue 378 TYR Chi-restraints excluded: chain B residue 395 CYS Chi-restraints excluded: chain B residue 407 ILE Chi-restraints excluded: chain B residue 476 ILE Chi-restraints excluded: chain B residue 493 ASN Chi-restraints excluded: chain B residue 495 LEU Chi-restraints excluded: chain B residue 524 ILE Chi-restraints excluded: chain B residue 526 ASP Chi-restraints excluded: chain B residue 597 GLU Chi-restraints excluded: chain B residue 620 ILE Chi-restraints excluded: chain B residue 625 TYR Chi-restraints excluded: chain B residue 661 ILE Chi-restraints excluded: chain B residue 709 TYR Chi-restraints excluded: chain B residue 744 PHE Chi-restraints excluded: chain B residue 828 THR Chi-restraints excluded: chain B residue 859 VAL Chi-restraints excluded: chain B residue 891 THR Chi-restraints excluded: chain B residue 925 ILE Chi-restraints excluded: chain B residue 948 ASN Chi-restraints excluded: chain C residue 192 TYR Chi-restraints excluded: chain C residue 220 PHE Chi-restraints excluded: chain C residue 228 THR Chi-restraints excluded: chain D residue 26 VAL Chi-restraints excluded: chain D residue 29 CYS Chi-restraints excluded: chain D residue 41 LYS Chi-restraints excluded: chain D residue 45 PHE Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 114 THR Chi-restraints excluded: chain D residue 121 ILE Chi-restraints excluded: chain D residue 227 MET Chi-restraints excluded: chain D residue 234 LYS Chi-restraints excluded: chain D residue 241 HIS Chi-restraints excluded: chain D residue 257 THR Chi-restraints excluded: chain D residue 361 PHE Chi-restraints excluded: chain D residue 368 ASP Chi-restraints excluded: chain D residue 455 TYR Chi-restraints excluded: chain D residue 550 PHE Chi-restraints excluded: chain D residue 592 LEU Chi-restraints excluded: chain D residue 654 ASN Chi-restraints excluded: chain D residue 776 ASP Chi-restraints excluded: chain D residue 889 LEU Chi-restraints excluded: chain D residue 912 TYR Chi-restraints excluded: chain D residue 979 HIS Chi-restraints excluded: chain D residue 1005 ILE Chi-restraints excluded: chain E residue 129 VAL Chi-restraints excluded: chain E residue 131 THR Chi-restraints excluded: chain E residue 134 TYR Chi-restraints excluded: chain E residue 142 CYS Chi-restraints excluded: chain E residue 144 LYS Chi-restraints excluded: chain E residue 183 VAL Chi-restraints excluded: chain E residue 202 ASN Chi-restraints excluded: chain E residue 203 LEU Chi-restraints excluded: chain E residue 204 MET Chi-restraints excluded: chain E residue 205 LYS Chi-restraints excluded: chain E residue 222 ASP Chi-restraints excluded: chain E residue 228 LEU Chi-restraints excluded: chain E residue 257 THR Chi-restraints excluded: chain E residue 282 TYR Chi-restraints excluded: chain E residue 356 TYR Chi-restraints excluded: chain E residue 363 LEU Chi-restraints excluded: chain E residue 378 TYR Chi-restraints excluded: chain E residue 647 MET Chi-restraints excluded: chain E residue 661 ILE Chi-restraints excluded: chain E residue 713 ILE Chi-restraints excluded: chain E residue 730 GLU Chi-restraints excluded: chain E residue 740 LEU Chi-restraints excluded: chain E residue 778 PHE Chi-restraints excluded: chain E residue 862 ILE Chi-restraints excluded: chain E residue 884 LEU Chi-restraints excluded: chain F residue 11 VAL Chi-restraints excluded: chain F residue 21 LEU Chi-restraints excluded: chain F residue 193 ILE Chi-restraints excluded: chain F residue 197 ASN Chi-restraints excluded: chain F residue 219 LYS Chi-restraints excluded: chain F residue 234 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 388 random chunks: chunk 126 optimal weight: 0.6980 chunk 337 optimal weight: 3.9990 chunk 74 optimal weight: 10.0000 chunk 220 optimal weight: 0.9980 chunk 92 optimal weight: 0.9990 chunk 375 optimal weight: 20.0000 chunk 311 optimal weight: 0.8980 chunk 173 optimal weight: 9.9990 chunk 31 optimal weight: 0.7980 chunk 124 optimal weight: 0.9980 chunk 197 optimal weight: 1.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 118 HIS A 133 ASN A 475 GLN ** A 563 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 711 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 332 HIS ** B 598 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 786 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 606 HIS D 609 HIS D 765 ASN D 852 HIS ** D 867 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 160 ASN ** E 377 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 948 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2551 moved from start: 0.5991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 33348 Z= 0.173 Angle : 0.625 15.687 44901 Z= 0.317 Chirality : 0.041 0.202 4796 Planarity : 0.004 0.075 5697 Dihedral : 4.680 49.263 4279 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 18.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 4.15 % Allowed : 28.26 % Favored : 67.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -0.18 (0.13), residues: 3808 helix: 0.55 (0.11), residues: 2365 sheet: -1.70 (0.43), residues: 126 loop : -1.05 (0.16), residues: 1317 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP B 601 HIS 0.012 0.001 HIS B 339 PHE 0.019 0.002 PHE E 646 TYR 0.032 0.001 TYR A 223 ARG 0.007 0.000 ARG A 380 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7616 Ramachandran restraints generated. 3808 Oldfield, 0 Emsley, 3808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7616 Ramachandran restraints generated. 3808 Oldfield, 0 Emsley, 3808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 455 residues out of total 3592 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 149 poor density : 306 time to evaluate : 3.864 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: A 45 PHE cc_start: 0.1770 (OUTLIER) cc_final: 0.0619 (t80) REVERT: A 223 TYR cc_start: 0.0305 (OUTLIER) cc_final: -0.0019 (p90) REVERT: A 475 GLN cc_start: -0.2856 (OUTLIER) cc_final: -0.3627 (tt0) REVERT: A 493 ASN cc_start: 0.6557 (OUTLIER) cc_final: 0.5487 (t0) REVERT: A 551 LEU cc_start: 0.2546 (OUTLIER) cc_final: 0.1664 (tp) REVERT: A 665 LYS cc_start: 0.8698 (ptpp) cc_final: 0.8457 (tppt) REVERT: A 683 LYS cc_start: 0.2063 (tttt) cc_final: 0.1451 (tttt) REVERT: A 735 LYS cc_start: 0.5744 (tptp) cc_final: 0.5339 (tptt) REVERT: A 765 ASN cc_start: 0.5892 (t0) cc_final: 0.5684 (t0) REVERT: A 842 LEU cc_start: 0.7296 (OUTLIER) cc_final: 0.6960 (mt) REVERT: A 930 MET cc_start: 0.5427 (mpt) cc_final: 0.2753 (ptp) REVERT: A 936 MET cc_start: 0.2739 (mmm) cc_final: 0.2376 (mtt) REVERT: B 32 GLU cc_start: 0.8470 (OUTLIER) cc_final: 0.7357 (pp20) REVERT: B 98 MET cc_start: 0.0480 (tpp) cc_final: 0.0128 (tpp) REVERT: B 447 ARG cc_start: 0.6010 (mmp-170) cc_final: 0.5737 (mmp80) REVERT: B 476 ILE cc_start: 0.5899 (OUTLIER) cc_final: 0.5413 (tp) REVERT: B 491 GLN cc_start: 0.8154 (tt0) cc_final: 0.7778 (tp-100) REVERT: B 930 MET cc_start: 0.1881 (ppp) cc_final: 0.0479 (ptp) REVERT: C 206 MET cc_start: 0.3609 (pmm) cc_final: 0.2618 (mpp) REVERT: C 231 MET cc_start: 0.2154 (tpt) cc_final: -0.1026 (ptp) REVERT: D 41 LYS cc_start: 0.0219 (OUTLIER) cc_final: -0.0895 (mtmt) REVERT: D 204 MET cc_start: -0.1686 (tpp) cc_final: -0.2689 (tpp) REVERT: D 241 HIS cc_start: -0.1680 (OUTLIER) cc_final: -0.3312 (m-70) REVERT: D 361 PHE cc_start: -0.2771 (OUTLIER) cc_final: -0.3888 (m-80) REVERT: D 709 TYR cc_start: 0.7487 (t80) cc_final: 0.7031 (t80) REVERT: D 837 PHE cc_start: 0.2928 (t80) cc_final: 0.2539 (t80) REVERT: D 936 MET cc_start: 0.1018 (ptt) cc_final: -0.0712 (tpp) REVERT: D 1005 ILE cc_start: 0.2655 (OUTLIER) cc_final: 0.2330 (mp) REVERT: E 124 MET cc_start: -0.2841 (tmm) cc_final: -0.4241 (mtm) REVERT: E 140 THR cc_start: 0.1887 (p) cc_final: 0.0638 (m) REVERT: E 202 ASN cc_start: -0.4062 (OUTLIER) cc_final: -0.4860 (m-40) REVERT: E 205 LYS cc_start: 0.2174 (OUTLIER) cc_final: 0.1427 (mmtp) REVERT: E 290 MET cc_start: 0.7066 (tpp) cc_final: 0.6478 (tpp) REVERT: E 647 MET cc_start: 0.4769 (OUTLIER) cc_final: 0.4068 (ppp) REVERT: E 936 MET cc_start: 0.3229 (mmp) cc_final: 0.2250 (tpp) REVERT: E 1004 PHE cc_start: 0.6273 (t80) cc_final: 0.5254 (m-10) REVERT: F 219 LYS cc_start: 0.1573 (OUTLIER) cc_final: 0.1249 (mttt) outliers start: 149 outliers final: 103 residues processed: 424 average time/residue: 0.4481 time to fit residues: 306.8865 Evaluate side-chains 405 residues out of total 3592 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 119 poor density : 286 time to evaluate : 3.797 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 VAL Chi-restraints excluded: chain A residue 45 PHE Chi-restraints excluded: chain A residue 80 SER Chi-restraints excluded: chain A residue 82 ASP Chi-restraints excluded: chain A residue 136 ASN Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 218 TYR Chi-restraints excluded: chain A residue 223 TYR Chi-restraints excluded: chain A residue 275 ILE Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 475 GLN Chi-restraints excluded: chain A residue 493 ASN Chi-restraints excluded: chain A residue 508 THR Chi-restraints excluded: chain A residue 551 LEU Chi-restraints excluded: chain A residue 554 ASP Chi-restraints excluded: chain A residue 579 SER Chi-restraints excluded: chain A residue 611 TYR Chi-restraints excluded: chain A residue 615 SER Chi-restraints excluded: chain A residue 645 PHE Chi-restraints excluded: chain A residue 651 ASP Chi-restraints excluded: chain A residue 763 LYS Chi-restraints excluded: chain A residue 785 LYS Chi-restraints excluded: chain A residue 836 ASP Chi-restraints excluded: chain A residue 841 LEU Chi-restraints excluded: chain A residue 842 LEU Chi-restraints excluded: chain A residue 996 TYR Chi-restraints excluded: chain B residue 32 GLU Chi-restraints excluded: chain B residue 37 SER Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 150 SER Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 208 ILE Chi-restraints excluded: chain B residue 214 VAL Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain B residue 282 TYR Chi-restraints excluded: chain B residue 378 TYR Chi-restraints excluded: chain B residue 407 ILE Chi-restraints excluded: chain B residue 476 ILE Chi-restraints excluded: chain B residue 493 ASN Chi-restraints excluded: chain B residue 495 LEU Chi-restraints excluded: chain B residue 524 ILE Chi-restraints excluded: chain B residue 597 GLU Chi-restraints excluded: chain B residue 620 ILE Chi-restraints excluded: chain B residue 625 TYR Chi-restraints excluded: chain B residue 661 ILE Chi-restraints excluded: chain B residue 707 VAL Chi-restraints excluded: chain B residue 709 TYR Chi-restraints excluded: chain B residue 764 CYS Chi-restraints excluded: chain B residue 828 THR Chi-restraints excluded: chain B residue 830 ASP Chi-restraints excluded: chain B residue 846 SER Chi-restraints excluded: chain B residue 859 VAL Chi-restraints excluded: chain B residue 869 ILE Chi-restraints excluded: chain B residue 891 THR Chi-restraints excluded: chain B residue 925 ILE Chi-restraints excluded: chain B residue 936 MET Chi-restraints excluded: chain B residue 948 ASN Chi-restraints excluded: chain C residue 192 TYR Chi-restraints excluded: chain C residue 220 PHE Chi-restraints excluded: chain C residue 228 THR Chi-restraints excluded: chain D residue 26 VAL Chi-restraints excluded: chain D residue 29 CYS Chi-restraints excluded: chain D residue 41 LYS Chi-restraints excluded: chain D residue 45 PHE Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 114 THR Chi-restraints excluded: chain D residue 121 ILE Chi-restraints excluded: chain D residue 139 ASP Chi-restraints excluded: chain D residue 227 MET Chi-restraints excluded: chain D residue 234 LYS Chi-restraints excluded: chain D residue 241 HIS Chi-restraints excluded: chain D residue 285 ARG Chi-restraints excluded: chain D residue 361 PHE Chi-restraints excluded: chain D residue 368 ASP Chi-restraints excluded: chain D residue 455 TYR Chi-restraints excluded: chain D residue 550 PHE Chi-restraints excluded: chain D residue 592 LEU Chi-restraints excluded: chain D residue 613 ARG Chi-restraints excluded: chain D residue 765 ASN Chi-restraints excluded: chain D residue 776 ASP Chi-restraints excluded: chain D residue 979 HIS Chi-restraints excluded: chain D residue 1005 ILE Chi-restraints excluded: chain E residue 129 VAL Chi-restraints excluded: chain E residue 131 THR Chi-restraints excluded: chain E residue 133 ASN Chi-restraints excluded: chain E residue 134 TYR Chi-restraints excluded: chain E residue 142 CYS Chi-restraints excluded: chain E residue 144 LYS Chi-restraints excluded: chain E residue 183 VAL Chi-restraints excluded: chain E residue 202 ASN Chi-restraints excluded: chain E residue 203 LEU Chi-restraints excluded: chain E residue 204 MET Chi-restraints excluded: chain E residue 205 LYS Chi-restraints excluded: chain E residue 222 ASP Chi-restraints excluded: chain E residue 228 LEU Chi-restraints excluded: chain E residue 257 THR Chi-restraints excluded: chain E residue 282 TYR Chi-restraints excluded: chain E residue 339 HIS Chi-restraints excluded: chain E residue 356 TYR Chi-restraints excluded: chain E residue 363 LEU Chi-restraints excluded: chain E residue 378 TYR Chi-restraints excluded: chain E residue 647 MET Chi-restraints excluded: chain E residue 661 ILE Chi-restraints excluded: chain E residue 672 SER Chi-restraints excluded: chain E residue 713 ILE Chi-restraints excluded: chain E residue 730 GLU Chi-restraints excluded: chain E residue 740 LEU Chi-restraints excluded: chain E residue 778 PHE Chi-restraints excluded: chain E residue 862 ILE Chi-restraints excluded: chain E residue 884 LEU Chi-restraints excluded: chain F residue 11 VAL Chi-restraints excluded: chain F residue 21 LEU Chi-restraints excluded: chain F residue 193 ILE Chi-restraints excluded: chain F residue 197 ASN Chi-restraints excluded: chain F residue 219 LYS Chi-restraints excluded: chain F residue 234 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 388 random chunks: chunk 361 optimal weight: 9.9990 chunk 42 optimal weight: 5.9990 chunk 213 optimal weight: 0.0670 chunk 274 optimal weight: 20.0000 chunk 212 optimal weight: 0.9990 chunk 316 optimal weight: 0.7980 chunk 209 optimal weight: 1.9990 chunk 373 optimal weight: 7.9990 chunk 234 optimal weight: 0.7980 chunk 227 optimal weight: 0.8980 chunk 172 optimal weight: 3.9990 overall best weight: 0.7120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 475 GLN ** A 563 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 606 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 711 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 377 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 598 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 786 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 961 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 606 HIS ** D 765 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 867 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 241 HIS ** E 377 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 410 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2560 moved from start: 0.6237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 33348 Z= 0.163 Angle : 0.606 13.851 44901 Z= 0.308 Chirality : 0.041 0.267 4796 Planarity : 0.004 0.070 5697 Dihedral : 4.621 48.714 4279 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 17.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 3.67 % Allowed : 28.81 % Favored : 67.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -0.11 (0.13), residues: 3808 helix: 0.62 (0.11), residues: 2363 sheet: -1.74 (0.42), residues: 135 loop : -1.05 (0.16), residues: 1310 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 601 HIS 0.010 0.001 HIS B 339 PHE 0.033 0.001 PHE A 778 TYR 0.029 0.001 TYR A 223 ARG 0.007 0.000 ARG D 613 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7616 Ramachandran restraints generated. 3808 Oldfield, 0 Emsley, 3808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7616 Ramachandran restraints generated. 3808 Oldfield, 0 Emsley, 3808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 438 residues out of total 3592 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 132 poor density : 306 time to evaluate : 3.742 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 45 PHE cc_start: 0.1802 (OUTLIER) cc_final: 0.0681 (t80) REVERT: A 223 TYR cc_start: 0.0304 (OUTLIER) cc_final: -0.1473 (t80) REVERT: A 475 GLN cc_start: -0.2640 (OUTLIER) cc_final: -0.3584 (tt0) REVERT: A 665 LYS cc_start: 0.8686 (ptpp) cc_final: 0.8447 (tppt) REVERT: A 683 LYS cc_start: 0.2178 (tttt) cc_final: 0.1316 (tttt) REVERT: A 735 LYS cc_start: 0.5938 (tptp) cc_final: 0.5535 (tptt) REVERT: A 765 ASN cc_start: 0.5840 (t0) cc_final: 0.5634 (t0) REVERT: A 842 LEU cc_start: 0.7284 (OUTLIER) cc_final: 0.6956 (mt) REVERT: A 930 MET cc_start: 0.5421 (mpt) cc_final: 0.2839 (ptm) REVERT: A 936 MET cc_start: 0.2717 (mmm) cc_final: 0.2325 (mtt) REVERT: B 32 GLU cc_start: 0.8520 (OUTLIER) cc_final: 0.7329 (pp20) REVERT: B 98 MET cc_start: 0.0171 (tpp) cc_final: -0.0159 (tpp) REVERT: B 447 ARG cc_start: 0.5955 (mmp-170) cc_final: 0.5581 (mmp80) REVERT: B 476 ILE cc_start: 0.5918 (OUTLIER) cc_final: 0.5418 (tp) REVERT: B 491 GLN cc_start: 0.8104 (tt0) cc_final: 0.7773 (tm-30) REVERT: B 611 TYR cc_start: 0.2668 (t80) cc_final: 0.1796 (m-80) REVERT: B 923 GLU cc_start: 0.6709 (tp30) cc_final: 0.6241 (mp0) REVERT: B 930 MET cc_start: 0.1743 (ppp) cc_final: 0.0469 (ptp) REVERT: C 206 MET cc_start: 0.3410 (pmm) cc_final: 0.2493 (mpp) REVERT: C 231 MET cc_start: 0.2072 (tpt) cc_final: -0.1040 (ptp) REVERT: D 41 LYS cc_start: 0.0432 (OUTLIER) cc_final: -0.0728 (mtmt) REVERT: D 79 TYR cc_start: 0.0826 (OUTLIER) cc_final: 0.0000 (t80) REVERT: D 204 MET cc_start: -0.1789 (tpp) cc_final: -0.2817 (tpp) REVERT: D 241 HIS cc_start: -0.1626 (OUTLIER) cc_final: -0.3288 (m-70) REVERT: D 361 PHE cc_start: -0.2729 (OUTLIER) cc_final: -0.3821 (m-80) REVERT: D 589 TYR cc_start: 0.7386 (m-10) cc_final: 0.7168 (m-10) REVERT: D 592 LEU cc_start: 0.8120 (OUTLIER) cc_final: 0.7511 (mp) REVERT: D 837 PHE cc_start: 0.3027 (t80) cc_final: 0.2555 (t80) REVERT: D 936 MET cc_start: 0.0904 (ptt) cc_final: -0.0892 (tpp) REVERT: D 1005 ILE cc_start: 0.2604 (OUTLIER) cc_final: 0.2250 (mp) REVERT: E 124 MET cc_start: -0.2938 (tmm) cc_final: -0.4267 (mtt) REVERT: E 140 THR cc_start: 0.2008 (p) cc_final: 0.0780 (m) REVERT: E 202 ASN cc_start: -0.4093 (OUTLIER) cc_final: -0.4868 (m-40) REVERT: E 205 LYS cc_start: 0.2060 (OUTLIER) cc_final: 0.1282 (mmtp) REVERT: E 290 MET cc_start: 0.6903 (tpp) cc_final: 0.6693 (tpt) REVERT: E 616 MET cc_start: -0.2403 (mtp) cc_final: -0.2610 (mtm) REVERT: E 647 MET cc_start: 0.4719 (OUTLIER) cc_final: 0.4050 (ppp) REVERT: E 866 MET cc_start: 0.0459 (tmm) cc_final: -0.0617 (mmt) REVERT: E 936 MET cc_start: 0.3172 (mmp) cc_final: 0.2260 (tpp) REVERT: F 219 LYS cc_start: 0.1553 (OUTLIER) cc_final: 0.1169 (ptpt) outliers start: 132 outliers final: 97 residues processed: 409 average time/residue: 0.4577 time to fit residues: 302.0706 Evaluate side-chains 402 residues out of total 3592 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 113 poor density : 289 time to evaluate : 3.814 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 VAL Chi-restraints excluded: chain A residue 45 PHE Chi-restraints excluded: chain A residue 80 SER Chi-restraints excluded: chain A residue 82 ASP Chi-restraints excluded: chain A residue 136 ASN Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 218 TYR Chi-restraints excluded: chain A residue 223 TYR Chi-restraints excluded: chain A residue 275 ILE Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 475 GLN Chi-restraints excluded: chain A residue 493 ASN Chi-restraints excluded: chain A residue 508 THR Chi-restraints excluded: chain A residue 554 ASP Chi-restraints excluded: chain A residue 579 SER Chi-restraints excluded: chain A residue 611 TYR Chi-restraints excluded: chain A residue 645 PHE Chi-restraints excluded: chain A residue 651 ASP Chi-restraints excluded: chain A residue 740 LEU Chi-restraints excluded: chain A residue 836 ASP Chi-restraints excluded: chain A residue 841 LEU Chi-restraints excluded: chain A residue 842 LEU Chi-restraints excluded: chain A residue 996 TYR Chi-restraints excluded: chain B residue 32 GLU Chi-restraints excluded: chain B residue 37 SER Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain B residue 112 LYS Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 208 ILE Chi-restraints excluded: chain B residue 214 VAL Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain B residue 378 TYR Chi-restraints excluded: chain B residue 395 CYS Chi-restraints excluded: chain B residue 407 ILE Chi-restraints excluded: chain B residue 476 ILE Chi-restraints excluded: chain B residue 493 ASN Chi-restraints excluded: chain B residue 495 LEU Chi-restraints excluded: chain B residue 524 ILE Chi-restraints excluded: chain B residue 597 GLU Chi-restraints excluded: chain B residue 620 ILE Chi-restraints excluded: chain B residue 625 TYR Chi-restraints excluded: chain B residue 661 ILE Chi-restraints excluded: chain B residue 670 SER Chi-restraints excluded: chain B residue 707 VAL Chi-restraints excluded: chain B residue 709 TYR Chi-restraints excluded: chain B residue 764 CYS Chi-restraints excluded: chain B residue 828 THR Chi-restraints excluded: chain B residue 830 ASP Chi-restraints excluded: chain B residue 846 SER Chi-restraints excluded: chain B residue 869 ILE Chi-restraints excluded: chain B residue 925 ILE Chi-restraints excluded: chain B residue 936 MET Chi-restraints excluded: chain B residue 948 ASN Chi-restraints excluded: chain C residue 192 TYR Chi-restraints excluded: chain C residue 220 PHE Chi-restraints excluded: chain C residue 228 THR Chi-restraints excluded: chain D residue 26 VAL Chi-restraints excluded: chain D residue 41 LYS Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 79 TYR Chi-restraints excluded: chain D residue 114 THR Chi-restraints excluded: chain D residue 121 ILE Chi-restraints excluded: chain D residue 139 ASP Chi-restraints excluded: chain D residue 227 MET Chi-restraints excluded: chain D residue 228 LEU Chi-restraints excluded: chain D residue 234 LYS Chi-restraints excluded: chain D residue 241 HIS Chi-restraints excluded: chain D residue 253 ILE Chi-restraints excluded: chain D residue 285 ARG Chi-restraints excluded: chain D residue 361 PHE Chi-restraints excluded: chain D residue 368 ASP Chi-restraints excluded: chain D residue 455 TYR Chi-restraints excluded: chain D residue 550 PHE Chi-restraints excluded: chain D residue 592 LEU Chi-restraints excluded: chain D residue 695 ILE Chi-restraints excluded: chain D residue 776 ASP Chi-restraints excluded: chain D residue 979 HIS Chi-restraints excluded: chain D residue 1005 ILE Chi-restraints excluded: chain E residue 129 VAL Chi-restraints excluded: chain E residue 133 ASN Chi-restraints excluded: chain E residue 134 TYR Chi-restraints excluded: chain E residue 142 CYS Chi-restraints excluded: chain E residue 144 LYS Chi-restraints excluded: chain E residue 183 VAL Chi-restraints excluded: chain E residue 202 ASN Chi-restraints excluded: chain E residue 203 LEU Chi-restraints excluded: chain E residue 204 MET Chi-restraints excluded: chain E residue 205 LYS Chi-restraints excluded: chain E residue 228 LEU Chi-restraints excluded: chain E residue 257 THR Chi-restraints excluded: chain E residue 282 TYR Chi-restraints excluded: chain E residue 356 TYR Chi-restraints excluded: chain E residue 363 LEU Chi-restraints excluded: chain E residue 378 TYR Chi-restraints excluded: chain E residue 647 MET Chi-restraints excluded: chain E residue 661 ILE Chi-restraints excluded: chain E residue 672 SER Chi-restraints excluded: chain E residue 707 VAL Chi-restraints excluded: chain E residue 713 ILE Chi-restraints excluded: chain E residue 730 GLU Chi-restraints excluded: chain E residue 740 LEU Chi-restraints excluded: chain E residue 778 PHE Chi-restraints excluded: chain E residue 862 ILE Chi-restraints excluded: chain E residue 884 LEU Chi-restraints excluded: chain F residue 11 VAL Chi-restraints excluded: chain F residue 21 LEU Chi-restraints excluded: chain F residue 193 ILE Chi-restraints excluded: chain F residue 197 ASN Chi-restraints excluded: chain F residue 219 LYS Chi-restraints excluded: chain F residue 234 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 388 random chunks: chunk 231 optimal weight: 0.0870 chunk 149 optimal weight: 0.8980 chunk 223 optimal weight: 1.9990 chunk 112 optimal weight: 0.5980 chunk 73 optimal weight: 3.9990 chunk 72 optimal weight: 6.9990 chunk 237 optimal weight: 0.7980 chunk 254 optimal weight: 0.9990 chunk 184 optimal weight: 6.9990 chunk 34 optimal weight: 3.9990 chunk 293 optimal weight: 3.9990 overall best weight: 0.6760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 475 GLN ** A 563 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 711 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 230 ASN B 339 HIS ** B 377 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 391 ASN ** B 598 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 786 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 961 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 606 HIS D 765 ASN ** D 867 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 241 HIS ** E 377 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 948 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2582 moved from start: 0.6499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 33348 Z= 0.166 Angle : 0.618 16.401 44901 Z= 0.314 Chirality : 0.041 0.290 4796 Planarity : 0.004 0.096 5697 Dihedral : 4.590 49.247 4278 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 16.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 3.90 % Allowed : 28.93 % Favored : 67.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -0.06 (0.14), residues: 3808 helix: 0.65 (0.11), residues: 2353 sheet: -1.62 (0.43), residues: 125 loop : -1.03 (0.16), residues: 1330 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP D 757 HIS 0.026 0.001 HIS A 810 PHE 0.051 0.002 PHE A 722 TYR 0.044 0.001 TYR A 313 ARG 0.008 0.000 ARG E 819 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7616 Ramachandran restraints generated. 3808 Oldfield, 0 Emsley, 3808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7616 Ramachandran restraints generated. 3808 Oldfield, 0 Emsley, 3808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 444 residues out of total 3592 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 140 poor density : 304 time to evaluate : 3.837 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 73 SER cc_start: 0.6373 (t) cc_final: 0.6120 (p) REVERT: A 312 ILE cc_start: 0.1167 (OUTLIER) cc_final: 0.0718 (pt) REVERT: A 475 GLN cc_start: -0.2512 (OUTLIER) cc_final: -0.3360 (tt0) REVERT: A 647 MET cc_start: 0.0802 (tpt) cc_final: 0.0266 (tpt) REVERT: A 665 LYS cc_start: 0.8738 (ptpp) cc_final: 0.8489 (tppt) REVERT: A 683 LYS cc_start: 0.2983 (tttt) cc_final: 0.2313 (tttt) REVERT: A 735 LYS cc_start: 0.6328 (tptp) cc_final: 0.5894 (tptt) REVERT: A 765 ASN cc_start: 0.5299 (t0) cc_final: 0.4813 (t0) REVERT: A 842 LEU cc_start: 0.7281 (OUTLIER) cc_final: 0.6959 (mt) REVERT: A 930 MET cc_start: 0.5390 (mpt) cc_final: 0.2960 (ppp) REVERT: A 936 MET cc_start: 0.2680 (mmm) cc_final: 0.2258 (mtt) REVERT: B 32 GLU cc_start: 0.8571 (OUTLIER) cc_final: 0.7426 (pp20) REVERT: B 98 MET cc_start: 0.0098 (tpp) cc_final: -0.0221 (tpp) REVERT: B 447 ARG cc_start: 0.6080 (mmp-170) cc_final: 0.5654 (mmp80) REVERT: B 476 ILE cc_start: 0.5944 (OUTLIER) cc_final: 0.5460 (tp) REVERT: B 491 GLN cc_start: 0.8076 (tt0) cc_final: 0.7755 (tm-30) REVERT: B 828 THR cc_start: 0.5536 (OUTLIER) cc_final: 0.5285 (t) REVERT: B 923 GLU cc_start: 0.6640 (tp30) cc_final: 0.6214 (mp0) REVERT: B 930 MET cc_start: 0.1653 (ppp) cc_final: 0.0375 (ptp) REVERT: C 206 MET cc_start: 0.3403 (pmm) cc_final: 0.2740 (mpp) REVERT: C 231 MET cc_start: 0.2060 (tpt) cc_final: -0.0275 (mtm) REVERT: D 41 LYS cc_start: 0.0617 (OUTLIER) cc_final: -0.0564 (mtmt) REVERT: D 204 MET cc_start: -0.1790 (tpp) cc_final: -0.2778 (tpp) REVERT: D 241 HIS cc_start: -0.1757 (OUTLIER) cc_final: -0.3427 (m-70) REVERT: D 361 PHE cc_start: -0.2663 (OUTLIER) cc_final: -0.3893 (m-10) REVERT: D 709 TYR cc_start: 0.7376 (t80) cc_final: 0.6997 (m-80) REVERT: D 837 PHE cc_start: 0.3015 (t80) cc_final: 0.2543 (t80) REVERT: D 936 MET cc_start: 0.1034 (ptt) cc_final: 0.0278 (ttp) REVERT: D 1005 ILE cc_start: 0.2434 (OUTLIER) cc_final: 0.2105 (mp) REVERT: E 124 MET cc_start: -0.3217 (tmm) cc_final: -0.4387 (mtm) REVERT: E 202 ASN cc_start: -0.4125 (OUTLIER) cc_final: -0.4879 (m-40) REVERT: E 205 LYS cc_start: 0.1950 (OUTLIER) cc_final: 0.1154 (mmtp) REVERT: E 290 MET cc_start: 0.6918 (tpp) cc_final: 0.6458 (tpp) REVERT: E 647 MET cc_start: 0.4319 (OUTLIER) cc_final: 0.3641 (ppp) REVERT: E 819 ARG cc_start: 0.4016 (OUTLIER) cc_final: 0.3790 (ptt-90) REVERT: E 930 MET cc_start: 0.3039 (ptt) cc_final: 0.1282 (mtm) REVERT: E 936 MET cc_start: 0.3077 (mmp) cc_final: 0.2316 (tpp) REVERT: F 219 LYS cc_start: 0.1417 (OUTLIER) cc_final: 0.1049 (ptpt) outliers start: 140 outliers final: 103 residues processed: 416 average time/residue: 0.5089 time to fit residues: 342.9951 Evaluate side-chains 409 residues out of total 3592 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 118 poor density : 291 time to evaluate : 3.770 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 VAL Chi-restraints excluded: chain A residue 80 SER Chi-restraints excluded: chain A residue 136 ASN Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 218 TYR Chi-restraints excluded: chain A residue 275 ILE Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 451 SER Chi-restraints excluded: chain A residue 475 GLN Chi-restraints excluded: chain A residue 493 ASN Chi-restraints excluded: chain A residue 508 THR Chi-restraints excluded: chain A residue 554 ASP Chi-restraints excluded: chain A residue 579 SER Chi-restraints excluded: chain A residue 611 TYR Chi-restraints excluded: chain A residue 615 SER Chi-restraints excluded: chain A residue 645 PHE Chi-restraints excluded: chain A residue 740 LEU Chi-restraints excluded: chain A residue 836 ASP Chi-restraints excluded: chain A residue 841 LEU Chi-restraints excluded: chain A residue 842 LEU Chi-restraints excluded: chain A residue 937 ASP Chi-restraints excluded: chain A residue 996 TYR Chi-restraints excluded: chain B residue 32 GLU Chi-restraints excluded: chain B residue 37 SER Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain B residue 112 LYS Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 150 SER Chi-restraints excluded: chain B residue 168 LEU Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 208 ILE Chi-restraints excluded: chain B residue 214 VAL Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain B residue 263 ASN Chi-restraints excluded: chain B residue 378 TYR Chi-restraints excluded: chain B residue 395 CYS Chi-restraints excluded: chain B residue 407 ILE Chi-restraints excluded: chain B residue 476 ILE Chi-restraints excluded: chain B residue 477 ASN Chi-restraints excluded: chain B residue 495 LEU Chi-restraints excluded: chain B residue 497 LEU Chi-restraints excluded: chain B residue 524 ILE Chi-restraints excluded: chain B residue 597 GLU Chi-restraints excluded: chain B residue 625 TYR Chi-restraints excluded: chain B residue 661 ILE Chi-restraints excluded: chain B residue 670 SER Chi-restraints excluded: chain B residue 707 VAL Chi-restraints excluded: chain B residue 709 TYR Chi-restraints excluded: chain B residue 764 CYS Chi-restraints excluded: chain B residue 828 THR Chi-restraints excluded: chain B residue 830 ASP Chi-restraints excluded: chain B residue 846 SER Chi-restraints excluded: chain B residue 869 ILE Chi-restraints excluded: chain B residue 891 THR Chi-restraints excluded: chain B residue 925 ILE Chi-restraints excluded: chain B residue 936 MET Chi-restraints excluded: chain B residue 948 ASN Chi-restraints excluded: chain C residue 192 TYR Chi-restraints excluded: chain C residue 220 PHE Chi-restraints excluded: chain C residue 228 THR Chi-restraints excluded: chain D residue 26 VAL Chi-restraints excluded: chain D residue 41 LYS Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 79 TYR Chi-restraints excluded: chain D residue 114 THR Chi-restraints excluded: chain D residue 121 ILE Chi-restraints excluded: chain D residue 139 ASP Chi-restraints excluded: chain D residue 227 MET Chi-restraints excluded: chain D residue 228 LEU Chi-restraints excluded: chain D residue 241 HIS Chi-restraints excluded: chain D residue 253 ILE Chi-restraints excluded: chain D residue 257 THR Chi-restraints excluded: chain D residue 285 ARG Chi-restraints excluded: chain D residue 361 PHE Chi-restraints excluded: chain D residue 368 ASP Chi-restraints excluded: chain D residue 455 TYR Chi-restraints excluded: chain D residue 550 PHE Chi-restraints excluded: chain D residue 592 LEU Chi-restraints excluded: chain D residue 695 ILE Chi-restraints excluded: chain D residue 765 ASN Chi-restraints excluded: chain D residue 776 ASP Chi-restraints excluded: chain D residue 979 HIS Chi-restraints excluded: chain D residue 1005 ILE Chi-restraints excluded: chain E residue 129 VAL Chi-restraints excluded: chain E residue 133 ASN Chi-restraints excluded: chain E residue 134 TYR Chi-restraints excluded: chain E residue 142 CYS Chi-restraints excluded: chain E residue 144 LYS Chi-restraints excluded: chain E residue 183 VAL Chi-restraints excluded: chain E residue 202 ASN Chi-restraints excluded: chain E residue 203 LEU Chi-restraints excluded: chain E residue 204 MET Chi-restraints excluded: chain E residue 205 LYS Chi-restraints excluded: chain E residue 228 LEU Chi-restraints excluded: chain E residue 257 THR Chi-restraints excluded: chain E residue 282 TYR Chi-restraints excluded: chain E residue 339 HIS Chi-restraints excluded: chain E residue 356 TYR Chi-restraints excluded: chain E residue 363 LEU Chi-restraints excluded: chain E residue 378 TYR Chi-restraints excluded: chain E residue 647 MET Chi-restraints excluded: chain E residue 661 ILE Chi-restraints excluded: chain E residue 672 SER Chi-restraints excluded: chain E residue 713 ILE Chi-restraints excluded: chain E residue 730 GLU Chi-restraints excluded: chain E residue 778 PHE Chi-restraints excluded: chain E residue 819 ARG Chi-restraints excluded: chain E residue 862 ILE Chi-restraints excluded: chain E residue 884 LEU Chi-restraints excluded: chain F residue 11 VAL Chi-restraints excluded: chain F residue 21 LEU Chi-restraints excluded: chain F residue 193 ILE Chi-restraints excluded: chain F residue 197 ASN Chi-restraints excluded: chain F residue 219 LYS Chi-restraints excluded: chain F residue 234 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 388 random chunks: chunk 340 optimal weight: 10.0000 chunk 358 optimal weight: 5.9990 chunk 326 optimal weight: 6.9990 chunk 348 optimal weight: 9.9990 chunk 209 optimal weight: 0.0980 chunk 151 optimal weight: 7.9990 chunk 273 optimal weight: 5.9990 chunk 106 optimal weight: 5.9990 chunk 314 optimal weight: 0.9980 chunk 329 optimal weight: 5.9990 chunk 347 optimal weight: 1.9990 overall best weight: 3.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 549 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 563 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 711 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 810 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 832 GLN ** A 834 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 377 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 391 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 536 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 598 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 614 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 786 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 171 HIS ** D 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 226 ASN ** D 598 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 867 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 978 HIS ** E 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 377 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 610 GLN E 614 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3185 moved from start: 0.8348 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.150 33348 Z= 0.367 Angle : 0.939 21.172 44901 Z= 0.489 Chirality : 0.052 0.326 4796 Planarity : 0.006 0.077 5697 Dihedral : 6.140 57.334 4278 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 31.80 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.44 % Favored : 94.51 % Rotamer: Outliers : 4.06 % Allowed : 29.26 % Favored : 66.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -1.40 (0.13), residues: 3808 helix: -0.43 (0.10), residues: 2354 sheet: -1.96 (0.37), residues: 167 loop : -1.49 (0.16), residues: 1287 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.004 TRP A 60 HIS 0.025 0.002 HIS D 171 PHE 0.055 0.004 PHE A 722 TYR 0.044 0.003 TYR A 223 ARG 0.015 0.001 ARG A 86 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7616 Ramachandran restraints generated. 3808 Oldfield, 0 Emsley, 3808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7616 Ramachandran restraints generated. 3808 Oldfield, 0 Emsley, 3808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 492 residues out of total 3592 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 146 poor density : 346 time to evaluate : 3.732 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 190 TYR cc_start: 0.2653 (m-80) cc_final: 0.2327 (m-80) REVERT: A 223 TYR cc_start: 0.0376 (OUTLIER) cc_final: -0.1670 (t80) REVERT: A 421 MET cc_start: 0.1219 (ttt) cc_final: 0.1014 (ttt) REVERT: A 519 MET cc_start: 0.0731 (mmm) cc_final: 0.0488 (mmm) REVERT: A 665 LYS cc_start: 0.8781 (ptpp) cc_final: 0.8523 (tppt) REVERT: A 683 LYS cc_start: 0.3932 (tttt) cc_final: 0.3544 (tttt) REVERT: A 735 LYS cc_start: 0.6707 (tptp) cc_final: 0.6233 (tptt) REVERT: A 842 LEU cc_start: 0.7399 (OUTLIER) cc_final: 0.7083 (mt) REVERT: A 930 MET cc_start: 0.5469 (mpt) cc_final: 0.2840 (ppp) REVERT: A 936 MET cc_start: 0.2980 (mmm) cc_final: 0.2250 (mtt) REVERT: B 37 SER cc_start: 0.7148 (OUTLIER) cc_final: 0.6745 (t) REVERT: B 112 LYS cc_start: -0.0376 (OUTLIER) cc_final: -0.0621 (ptpp) REVERT: B 447 ARG cc_start: 0.6178 (mmp-170) cc_final: 0.5725 (mmp80) REVERT: B 480 ARG cc_start: 0.8592 (mmp80) cc_final: 0.8245 (mmp80) REVERT: B 491 GLN cc_start: 0.8129 (tt0) cc_final: 0.7728 (tm-30) REVERT: B 923 GLU cc_start: 0.6711 (tp30) cc_final: 0.6211 (tp30) REVERT: B 930 MET cc_start: 0.1956 (ppp) cc_final: 0.0337 (ptm) REVERT: C 206 MET cc_start: 0.3981 (pmm) cc_final: 0.2788 (tpt) REVERT: C 231 MET cc_start: 0.2501 (tpt) cc_final: 0.2255 (mmm) REVERT: D 79 TYR cc_start: 0.3265 (OUTLIER) cc_final: 0.2572 (m-80) REVERT: D 257 THR cc_start: 0.3376 (OUTLIER) cc_final: 0.3168 (t) REVERT: D 361 PHE cc_start: -0.1687 (OUTLIER) cc_final: -0.3078 (m-10) REVERT: D 709 TYR cc_start: 0.7583 (t80) cc_final: 0.7128 (m-80) REVERT: D 889 LEU cc_start: -0.2102 (OUTLIER) cc_final: -0.2664 (mt) REVERT: D 936 MET cc_start: 0.0585 (ptt) cc_final: -0.0551 (ttp) REVERT: D 976 MET cc_start: -0.5567 (tmm) cc_final: -0.5843 (ttt) REVERT: D 1005 ILE cc_start: 0.2646 (OUTLIER) cc_final: 0.2185 (mp) REVERT: E 124 MET cc_start: -0.2955 (tmm) cc_final: -0.3792 (mtp) REVERT: E 215 PHE cc_start: 0.3971 (m-80) cc_final: 0.3632 (m-80) REVERT: E 447 ARG cc_start: 0.5047 (mmp-170) cc_final: 0.4410 (mmt90) REVERT: E 647 MET cc_start: 0.4418 (OUTLIER) cc_final: 0.3537 (ppp) REVERT: E 936 MET cc_start: 0.3353 (mmp) cc_final: 0.2872 (tpp) REVERT: F 219 LYS cc_start: 0.1686 (OUTLIER) cc_final: 0.1245 (pttt) outliers start: 146 outliers final: 103 residues processed: 459 average time/residue: 0.5008 time to fit residues: 365.9678 Evaluate side-chains 416 residues out of total 3592 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 114 poor density : 302 time to evaluate : 3.704 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 55 ASP Chi-restraints excluded: chain A residue 134 TYR Chi-restraints excluded: chain A residue 136 ASN Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 218 TYR Chi-restraints excluded: chain A residue 223 TYR Chi-restraints excluded: chain A residue 275 ILE Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 508 THR Chi-restraints excluded: chain A residue 550 PHE Chi-restraints excluded: chain A residue 554 ASP Chi-restraints excluded: chain A residue 579 SER Chi-restraints excluded: chain A residue 611 TYR Chi-restraints excluded: chain A residue 615 SER Chi-restraints excluded: chain A residue 645 PHE Chi-restraints excluded: chain A residue 652 PHE Chi-restraints excluded: chain A residue 740 LEU Chi-restraints excluded: chain A residue 841 LEU Chi-restraints excluded: chain A residue 842 LEU Chi-restraints excluded: chain A residue 850 LYS Chi-restraints excluded: chain B residue 32 GLU Chi-restraints excluded: chain B residue 37 SER Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain B residue 112 LYS Chi-restraints excluded: chain B residue 150 SER Chi-restraints excluded: chain B residue 168 LEU Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 208 ILE Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain B residue 263 ASN Chi-restraints excluded: chain B residue 282 TYR Chi-restraints excluded: chain B residue 346 VAL Chi-restraints excluded: chain B residue 378 TYR Chi-restraints excluded: chain B residue 395 CYS Chi-restraints excluded: chain B residue 421 MET Chi-restraints excluded: chain B residue 476 ILE Chi-restraints excluded: chain B residue 495 LEU Chi-restraints excluded: chain B residue 497 LEU Chi-restraints excluded: chain B residue 508 THR Chi-restraints excluded: chain B residue 597 GLU Chi-restraints excluded: chain B residue 611 TYR Chi-restraints excluded: chain B residue 661 ILE Chi-restraints excluded: chain B residue 670 SER Chi-restraints excluded: chain B residue 707 VAL Chi-restraints excluded: chain B residue 709 TYR Chi-restraints excluded: chain B residue 744 PHE Chi-restraints excluded: chain B residue 764 CYS Chi-restraints excluded: chain B residue 830 ASP Chi-restraints excluded: chain B residue 859 VAL Chi-restraints excluded: chain B residue 869 ILE Chi-restraints excluded: chain B residue 891 THR Chi-restraints excluded: chain B residue 925 ILE Chi-restraints excluded: chain B residue 936 MET Chi-restraints excluded: chain B residue 948 ASN Chi-restraints excluded: chain C residue 192 TYR Chi-restraints excluded: chain C residue 220 PHE Chi-restraints excluded: chain C residue 228 THR Chi-restraints excluded: chain D residue 22 LEU Chi-restraints excluded: chain D residue 26 VAL Chi-restraints excluded: chain D residue 45 PHE Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 79 TYR Chi-restraints excluded: chain D residue 114 THR Chi-restraints excluded: chain D residue 121 ILE Chi-restraints excluded: chain D residue 139 ASP Chi-restraints excluded: chain D residue 227 MET Chi-restraints excluded: chain D residue 234 LYS Chi-restraints excluded: chain D residue 239 SER Chi-restraints excluded: chain D residue 241 HIS Chi-restraints excluded: chain D residue 257 THR Chi-restraints excluded: chain D residue 361 PHE Chi-restraints excluded: chain D residue 368 ASP Chi-restraints excluded: chain D residue 388 PHE Chi-restraints excluded: chain D residue 455 TYR Chi-restraints excluded: chain D residue 550 PHE Chi-restraints excluded: chain D residue 592 LEU Chi-restraints excluded: chain D residue 776 ASP Chi-restraints excluded: chain D residue 889 LEU Chi-restraints excluded: chain D residue 912 TYR Chi-restraints excluded: chain D residue 978 HIS Chi-restraints excluded: chain D residue 979 HIS Chi-restraints excluded: chain D residue 1005 ILE Chi-restraints excluded: chain E residue 129 VAL Chi-restraints excluded: chain E residue 134 TYR Chi-restraints excluded: chain E residue 142 CYS Chi-restraints excluded: chain E residue 144 LYS Chi-restraints excluded: chain E residue 183 VAL Chi-restraints excluded: chain E residue 203 LEU Chi-restraints excluded: chain E residue 204 MET Chi-restraints excluded: chain E residue 205 LYS Chi-restraints excluded: chain E residue 222 ASP Chi-restraints excluded: chain E residue 228 LEU Chi-restraints excluded: chain E residue 257 THR Chi-restraints excluded: chain E residue 282 TYR Chi-restraints excluded: chain E residue 283 LEU Chi-restraints excluded: chain E residue 339 HIS Chi-restraints excluded: chain E residue 356 TYR Chi-restraints excluded: chain E residue 363 LEU Chi-restraints excluded: chain E residue 378 TYR Chi-restraints excluded: chain E residue 609 HIS Chi-restraints excluded: chain E residue 647 MET Chi-restraints excluded: chain E residue 661 ILE Chi-restraints excluded: chain E residue 672 SER Chi-restraints excluded: chain E residue 713 ILE Chi-restraints excluded: chain E residue 730 GLU Chi-restraints excluded: chain E residue 740 LEU Chi-restraints excluded: chain E residue 778 PHE Chi-restraints excluded: chain E residue 862 ILE Chi-restraints excluded: chain F residue 197 ASN Chi-restraints excluded: chain F residue 219 LYS Chi-restraints excluded: chain F residue 234 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 388 random chunks: chunk 228 optimal weight: 9.9990 chunk 368 optimal weight: 0.7980 chunk 224 optimal weight: 0.6980 chunk 174 optimal weight: 4.9990 chunk 256 optimal weight: 4.9990 chunk 386 optimal weight: 9.9990 chunk 355 optimal weight: 5.9990 chunk 307 optimal weight: 0.8980 chunk 31 optimal weight: 0.9980 chunk 237 optimal weight: 8.9990 chunk 188 optimal weight: 5.9990 overall best weight: 1.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 339 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 549 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 563 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 711 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 377 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 614 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 698 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 786 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 829 GLN D 196 ASN D 224 ASN ** D 598 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 867 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 115 ASN E 128 HIS ** E 377 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 491 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 610 GLN E 614 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3055 moved from start: 0.8539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 33348 Z= 0.238 Angle : 0.747 14.804 44901 Z= 0.383 Chirality : 0.045 0.272 4796 Planarity : 0.004 0.062 5697 Dihedral : 5.531 57.181 4278 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 23.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 3.06 % Allowed : 30.79 % Favored : 66.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.11 (0.13), residues: 3808 helix: -0.23 (0.10), residues: 2376 sheet: -1.38 (0.43), residues: 135 loop : -1.42 (0.16), residues: 1297 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.003 TRP D 757 HIS 0.011 0.001 HIS B 415 PHE 0.046 0.002 PHE A 722 TYR 0.029 0.002 TYR A 223 ARG 0.011 0.001 ARG D 514 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7616 Ramachandran restraints generated. 3808 Oldfield, 0 Emsley, 3808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7616 Ramachandran restraints generated. 3808 Oldfield, 0 Emsley, 3808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 428 residues out of total 3592 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 110 poor density : 318 time to evaluate : 3.530 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 223 TYR cc_start: 0.0426 (OUTLIER) cc_final: -0.1328 (t80) REVERT: A 647 MET cc_start: 0.1897 (tpt) cc_final: 0.1641 (mmm) REVERT: A 665 LYS cc_start: 0.8877 (ptpp) cc_final: 0.8569 (tppt) REVERT: A 735 LYS cc_start: 0.6839 (tptp) cc_final: 0.6525 (tptt) REVERT: A 842 LEU cc_start: 0.7275 (OUTLIER) cc_final: 0.6876 (mt) REVERT: A 930 MET cc_start: 0.5821 (mpt) cc_final: 0.3167 (ppp) REVERT: A 936 MET cc_start: 0.2642 (mmm) cc_final: 0.1898 (mtt) REVERT: B 44 PHE cc_start: 0.5579 (t80) cc_final: 0.5307 (t80) REVERT: B 98 MET cc_start: 0.0172 (tpp) cc_final: -0.0133 (tpp) REVERT: B 447 ARG cc_start: 0.6109 (mmp-170) cc_final: 0.5754 (mmp80) REVERT: B 476 ILE cc_start: 0.5956 (OUTLIER) cc_final: 0.5549 (tp) REVERT: B 491 GLN cc_start: 0.8057 (tt0) cc_final: 0.7723 (tm-30) REVERT: B 647 MET cc_start: -0.3398 (ptp) cc_final: -0.4443 (ptm) REVERT: B 819 ARG cc_start: 0.6857 (ttp-110) cc_final: 0.6634 (ptt180) REVERT: B 923 GLU cc_start: 0.6508 (tp30) cc_final: 0.6165 (tp30) REVERT: B 930 MET cc_start: 0.1567 (ppp) cc_final: 0.0213 (ptp) REVERT: C 206 MET cc_start: 0.3668 (pmm) cc_final: 0.3057 (tpt) REVERT: D 71 TYR cc_start: -0.0995 (m-80) cc_final: -0.2952 (m-80) REVERT: D 79 TYR cc_start: 0.3166 (OUTLIER) cc_final: 0.2603 (m-80) REVERT: D 361 PHE cc_start: -0.1783 (OUTLIER) cc_final: -0.3000 (m-10) REVERT: D 709 TYR cc_start: 0.7732 (t80) cc_final: 0.7141 (m-80) REVERT: D 889 LEU cc_start: -0.1559 (OUTLIER) cc_final: -0.2172 (mt) REVERT: D 936 MET cc_start: 0.0292 (ptt) cc_final: -0.0660 (ttp) REVERT: D 941 ASP cc_start: 0.6209 (p0) cc_final: 0.5845 (p0) REVERT: D 976 MET cc_start: -0.5630 (tmm) cc_final: -0.5957 (ttt) REVERT: E 124 MET cc_start: -0.3207 (tmm) cc_final: -0.3933 (mtp) REVERT: E 185 LEU cc_start: 0.3364 (OUTLIER) cc_final: 0.2999 (tt) REVERT: E 447 ARG cc_start: 0.4887 (mmp-170) cc_final: 0.4173 (mmt90) REVERT: E 647 MET cc_start: 0.4448 (OUTLIER) cc_final: 0.3697 (ppp) REVERT: E 686 GLU cc_start: 0.2249 (OUTLIER) cc_final: 0.1686 (pm20) REVERT: E 866 MET cc_start: 0.0555 (tmm) cc_final: -0.0649 (mmt) REVERT: E 936 MET cc_start: 0.3246 (mmp) cc_final: 0.3008 (mtp) REVERT: F 219 LYS cc_start: 0.1699 (OUTLIER) cc_final: 0.1207 (pttt) outliers start: 110 outliers final: 84 residues processed: 405 average time/residue: 0.4898 time to fit residues: 320.5720 Evaluate side-chains 397 residues out of total 3592 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 303 time to evaluate : 3.597 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 55 ASP Chi-restraints excluded: chain A residue 134 TYR Chi-restraints excluded: chain A residue 136 ASN Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 218 TYR Chi-restraints excluded: chain A residue 223 TYR Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 275 ILE Chi-restraints excluded: chain A residue 508 THR Chi-restraints excluded: chain A residue 579 SER Chi-restraints excluded: chain A residue 611 TYR Chi-restraints excluded: chain A residue 645 PHE Chi-restraints excluded: chain A residue 651 ASP Chi-restraints excluded: chain A residue 842 LEU Chi-restraints excluded: chain A residue 850 LYS Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain B residue 168 LEU Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 208 ILE Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain B residue 263 ASN Chi-restraints excluded: chain B residue 378 TYR Chi-restraints excluded: chain B residue 395 CYS Chi-restraints excluded: chain B residue 476 ILE Chi-restraints excluded: chain B residue 495 LEU Chi-restraints excluded: chain B residue 497 LEU Chi-restraints excluded: chain B residue 592 LEU Chi-restraints excluded: chain B residue 597 GLU Chi-restraints excluded: chain B residue 611 TYR Chi-restraints excluded: chain B residue 620 ILE Chi-restraints excluded: chain B residue 661 ILE Chi-restraints excluded: chain B residue 670 SER Chi-restraints excluded: chain B residue 707 VAL Chi-restraints excluded: chain B residue 709 TYR Chi-restraints excluded: chain B residue 764 CYS Chi-restraints excluded: chain B residue 859 VAL Chi-restraints excluded: chain B residue 869 ILE Chi-restraints excluded: chain B residue 891 THR Chi-restraints excluded: chain B residue 925 ILE Chi-restraints excluded: chain B residue 936 MET Chi-restraints excluded: chain B residue 948 ASN Chi-restraints excluded: chain C residue 192 TYR Chi-restraints excluded: chain C residue 220 PHE Chi-restraints excluded: chain C residue 228 THR Chi-restraints excluded: chain D residue 26 VAL Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 79 TYR Chi-restraints excluded: chain D residue 114 THR Chi-restraints excluded: chain D residue 121 ILE Chi-restraints excluded: chain D residue 139 ASP Chi-restraints excluded: chain D residue 192 ASN Chi-restraints excluded: chain D residue 227 MET Chi-restraints excluded: chain D residue 234 LYS Chi-restraints excluded: chain D residue 241 HIS Chi-restraints excluded: chain D residue 361 PHE Chi-restraints excluded: chain D residue 368 ASP Chi-restraints excluded: chain D residue 388 PHE Chi-restraints excluded: chain D residue 455 TYR Chi-restraints excluded: chain D residue 550 PHE Chi-restraints excluded: chain D residue 592 LEU Chi-restraints excluded: chain D residue 776 ASP Chi-restraints excluded: chain D residue 889 LEU Chi-restraints excluded: chain D residue 979 HIS Chi-restraints excluded: chain E residue 115 ASN Chi-restraints excluded: chain E residue 129 VAL Chi-restraints excluded: chain E residue 134 TYR Chi-restraints excluded: chain E residue 142 CYS Chi-restraints excluded: chain E residue 144 LYS Chi-restraints excluded: chain E residue 183 VAL Chi-restraints excluded: chain E residue 185 LEU Chi-restraints excluded: chain E residue 203 LEU Chi-restraints excluded: chain E residue 204 MET Chi-restraints excluded: chain E residue 205 LYS Chi-restraints excluded: chain E residue 222 ASP Chi-restraints excluded: chain E residue 228 LEU Chi-restraints excluded: chain E residue 257 THR Chi-restraints excluded: chain E residue 339 HIS Chi-restraints excluded: chain E residue 356 TYR Chi-restraints excluded: chain E residue 376 LYS Chi-restraints excluded: chain E residue 378 TYR Chi-restraints excluded: chain E residue 647 MET Chi-restraints excluded: chain E residue 661 ILE Chi-restraints excluded: chain E residue 672 SER Chi-restraints excluded: chain E residue 686 GLU Chi-restraints excluded: chain E residue 713 ILE Chi-restraints excluded: chain E residue 730 GLU Chi-restraints excluded: chain E residue 740 LEU Chi-restraints excluded: chain E residue 778 PHE Chi-restraints excluded: chain F residue 197 ASN Chi-restraints excluded: chain F residue 219 LYS Chi-restraints excluded: chain F residue 234 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 388 random chunks: chunk 244 optimal weight: 0.5980 chunk 327 optimal weight: 2.9990 chunk 94 optimal weight: 0.1980 chunk 283 optimal weight: 20.0000 chunk 45 optimal weight: 2.9990 chunk 85 optimal weight: 5.9990 chunk 308 optimal weight: 2.9990 chunk 129 optimal weight: 0.9990 chunk 316 optimal weight: 3.9990 chunk 39 optimal weight: 0.9980 chunk 56 optimal weight: 5.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 339 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 549 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 563 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 834 GLN ** B 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 377 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 614 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 698 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 786 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 961 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 598 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 867 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 115 ASN E 128 HIS E 133 ASN E 160 ASN ** E 377 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4733 r_free = 0.4733 target = 0.164682 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4399 r_free = 0.4399 target = 0.139640 restraints weight = 128027.903| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4445 r_free = 0.4445 target = 0.142174 restraints weight = 78035.671| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4451 r_free = 0.4451 target = 0.142939 restraints weight = 52611.977| |-----------------------------------------------------------------------------| r_work (final): 0.4357 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2966 moved from start: 0.8739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 33348 Z= 0.208 Angle : 0.720 16.871 44901 Z= 0.366 Chirality : 0.044 0.365 4796 Planarity : 0.004 0.059 5697 Dihedral : 5.339 55.230 4278 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 22.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 2.78 % Allowed : 31.35 % Favored : 65.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -0.95 (0.13), residues: 3808 helix: -0.10 (0.11), residues: 2375 sheet: -1.58 (0.41), residues: 156 loop : -1.31 (0.17), residues: 1277 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.061 0.003 TRP D 757 HIS 0.013 0.001 HIS B 415 PHE 0.048 0.002 PHE A 722 TYR 0.032 0.002 TYR A 649 ARG 0.015 0.001 ARG D 514 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7407.92 seconds wall clock time: 137 minutes 27.90 seconds (8247.90 seconds total)