Starting phenix.real_space_refine on Sat Jul 27 07:46:15 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wks_37606/07_2024/8wks_37606.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wks_37606/07_2024/8wks_37606.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.58 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wks_37606/07_2024/8wks_37606.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wks_37606/07_2024/8wks_37606.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wks_37606/07_2024/8wks_37606.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wks_37606/07_2024/8wks_37606.cif" } resolution = 3.58 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= 0.039 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 136 5.16 5 C 23835 2.51 5 N 5931 2.21 5 O 6997 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 280": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 517": "NH1" <-> "NH2" Residue "A ASP 662": "OD1" <-> "OD2" Residue "B PHE 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 195": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 204": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 525": "OD1" <-> "OD2" Residue "D PHE 639": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 180": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 188": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 195": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 205": "OE1" <-> "OE2" Residue "F TYR 418": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 742": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 743": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 750": "OD1" <-> "OD2" Residue "G TYR 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 193": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 280": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 526": "OD1" <-> "OD2" Residue "H TYR 912": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 36899 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 8190 Number of conformers: 1 Conformer: "" Number of residues, atoms: 984, 8190 Classifications: {'peptide': 984} Link IDs: {'PTRANS': 19, 'TRANS': 964} Chain: "B" Number of atoms: 1037 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1037 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 5, 'TRANS': 125} Chain breaks: 1 Chain: "C" Number of atoms: 1037 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1037 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 5, 'TRANS': 125} Chain breaks: 1 Chain: "D" Number of atoms: 8190 Number of conformers: 1 Conformer: "" Number of residues, atoms: 984, 8190 Classifications: {'peptide': 984} Link IDs: {'PTRANS': 19, 'TRANS': 964} Chain: "E" Number of atoms: 1028 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 1028 Classifications: {'peptide': 130} Link IDs: {'PTRANS': 5, 'TRANS': 124} Chain breaks: 1 Chain: "F" Number of atoms: 8190 Number of conformers: 1 Conformer: "" Number of residues, atoms: 984, 8190 Classifications: {'peptide': 984} Link IDs: {'PTRANS': 19, 'TRANS': 964} Chain: "G" Number of atoms: 1037 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1037 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 5, 'TRANS': 125} Chain breaks: 1 Chain: "H" Number of atoms: 8190 Number of conformers: 1 Conformer: "" Number of residues, atoms: 984, 8190 Classifications: {'peptide': 984} Link IDs: {'PTRANS': 19, 'TRANS': 964} Time building chain proxies: 19.90, per 1000 atoms: 0.54 Number of scatterers: 36899 At special positions: 0 Unit cell: (100, 130, 257, 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 136 16.00 O 6997 8.00 N 5931 7.00 C 23835 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: 14.52 Conformation dependent library (CDL) restraints added in 6.6 seconds 8870 Ramachandran restraints generated. 4435 Oldfield, 0 Emsley, 4435 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8486 Finding SS restraints... Secondary structure from input PDB file: 240 helices and 17 sheets defined 61.7% alpha, 4.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.88 Creating SS restraints... Processing helix chain 'A' and resid 23 through 40 removed outlier: 3.749A pdb=" N SER A 36 " --> pdb=" O GLU A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 47 through 53 removed outlier: 4.205A pdb=" N SER A 51 " --> pdb=" O GLY A 47 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LEU A 53 " --> pdb=" O GLY A 49 " (cutoff:3.500A) Processing helix chain 'A' and resid 58 through 72 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: 3.588A pdb=" N GLY A 102 " --> pdb=" O MET A 98 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ILE A 103 " --> pdb=" O ALA A 99 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N LEU A 104 " --> pdb=" O PHE A 100 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N LYS A 105 " --> pdb=" O ASP A 101 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ASP A 106 " --> pdb=" O GLY A 102 " (cutoff:3.500A) Processing helix chain 'A' and resid 115 through 122 removed outlier: 3.777A pdb=" N ASP A 119 " --> pdb=" O ASN A 115 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N LEU A 122 " --> pdb=" O HIS A 118 " (cutoff:3.500A) Processing helix chain 'A' and resid 123 through 125 No H-bonds generated for 'chain 'A' and resid 123 through 125' Processing helix chain 'A' and resid 136 through 145 Processing helix chain 'A' and resid 186 through 192 removed outlier: 3.604A pdb=" N TYR A 190 " --> pdb=" O LYS A 186 " (cutoff:3.500A) Processing helix chain 'A' and resid 192 through 197 Processing helix chain 'A' and resid 197 through 211 removed outlier: 3.530A pdb=" N ALA A 209 " --> pdb=" O LYS A 205 " (cutoff:3.500A) Processing helix chain 'A' and resid 222 through 235 removed outlier: 3.949A pdb=" N LEU A 228 " --> pdb=" O ASN A 224 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LYS A 234 " --> pdb=" O ASN A 230 " (cutoff:3.500A) Processing helix chain 'A' and resid 254 through 264 Processing helix chain 'A' and resid 281 through 295 removed outlier: 3.547A pdb=" N VAL A 289 " --> pdb=" O ARG A 285 " (cutoff:3.500A) Processing helix chain 'A' and resid 306 through 317 removed outlier: 4.021A pdb=" N ASP A 310 " --> pdb=" O ASP A 306 " (cutoff:3.500A) removed outlier: 5.897A pdb=" N ILE A 312 " --> pdb=" O VAL A 308 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N LYS A 315 " --> pdb=" O TYR A 311 " (cutoff:3.500A) Processing helix chain 'A' and resid 318 through 321 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: 4.064A pdb=" N VAL A 333 " --> pdb=" O ASP A 329 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N PHE A 334 " --> pdb=" O LEU A 330 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 329 through 334' Processing helix chain 'A' and resid 355 through 366 Processing helix chain 'A' and resid 366 through 373 removed outlier: 3.778A pdb=" N LEU A 373 " --> pdb=" O GLU A 369 " (cutoff:3.500A) Processing helix chain 'A' and resid 374 through 392 removed outlier: 4.482A pdb=" N ARG A 380 " --> pdb=" O LYS A 376 " (cutoff:3.500A) Processing helix chain 'A' and resid 411 through 416 removed outlier: 3.936A pdb=" N HIS A 415 " --> pdb=" O SER A 411 " (cutoff:3.500A) Processing helix chain 'A' and resid 417 through 425 removed outlier: 3.946A pdb=" N LYS A 423 " --> pdb=" O ASP A 419 " (cutoff:3.500A) Processing helix chain 'A' and resid 431 through 445 Processing helix chain 'A' and resid 447 through 461 Processing helix chain 'A' and resid 468 through 491 removed outlier: 3.590A pdb=" N GLN A 487 " --> pdb=" O GLN A 483 " (cutoff:3.500A) Processing helix chain 'A' and resid 508 through 520 Processing helix chain 'A' and resid 526 through 531 Processing helix chain 'A' and resid 532 through 539 Processing helix chain 'A' and resid 540 through 546 removed outlier: 4.516A pdb=" N PHE A 544 " --> pdb=" O ILE A 541 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N SER A 546 " --> pdb=" O GLU A 543 " (cutoff:3.500A) Processing helix chain 'A' and resid 552 through 571 Processing helix chain 'A' and resid 579 through 597 removed outlier: 3.555A pdb=" N VAL A 583 " --> pdb=" O SER A 579 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N VAL A 584 " --> pdb=" O SER A 580 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N LEU A 585 " --> pdb=" O ASP A 581 " (cutoff:3.500A) Processing helix chain 'A' and resid 600 through 604 removed outlier: 3.861A pdb=" N VAL A 603 " --> pdb=" O LEU A 600 " (cutoff:3.500A) Processing helix chain 'A' and resid 605 through 628 Processing helix chain 'A' and resid 648 through 659 removed outlier: 3.553A pdb=" N ASN A 654 " --> pdb=" O TYR A 650 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N PHE A 659 " --> pdb=" O ILE A 655 " (cutoff:3.500A) Processing helix chain 'A' and resid 660 through 671 removed outlier: 3.740A pdb=" N ASN A 666 " --> pdb=" O ASP A 662 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LEU A 667 " --> pdb=" O ASP A 663 " (cutoff:3.500A) Processing helix chain 'A' and resid 680 through 700 Processing helix chain 'A' and resid 709 through 723 removed outlier: 4.350A pdb=" N SER A 714 " --> pdb=" O THR A 710 " (cutoff:3.500A) removed outlier: 4.609A pdb=" N GLU A 715 " --> pdb=" O GLN A 711 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N PHE A 722 " --> pdb=" O ALA A 718 " (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 743 Processing helix chain 'A' and resid 750 through 765 removed outlier: 3.571A pdb=" N TYR A 755 " --> pdb=" O ILE A 751 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N VAL A 756 " --> pdb=" O GLY A 752 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N LEU A 761 " --> pdb=" O TRP A 757 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N CYS A 764 " --> pdb=" O ARG A 760 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ASN A 765 " --> pdb=" O LEU A 761 " (cutoff:3.500A) Processing helix chain 'A' and resid 768 through 786 removed outlier: 3.560A pdb=" N ASP A 776 " --> pdb=" O ILE A 772 " (cutoff:3.500A) Processing helix chain 'A' and resid 787 through 789 No H-bonds generated for 'chain 'A' and resid 787 through 789' Processing helix chain 'A' and resid 800 through 812 removed outlier: 3.711A pdb=" N TYR A 804 " --> pdb=" O TYR A 800 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N PHE A 811 " --> pdb=" O LEU A 807 " (cutoff:3.500A) Processing helix chain 'A' and resid 817 through 826 removed outlier: 3.748A pdb=" N THR A 824 " --> pdb=" O LEU A 820 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N LEU A 825 " --> pdb=" O SER A 821 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N CYS A 826 " --> pdb=" O GLU A 822 " (cutoff:3.500A) Processing helix chain 'A' and resid 831 through 840 removed outlier: 4.013A pdb=" N ILE A 835 " --> pdb=" O LYS A 831 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LYS A 840 " --> pdb=" O ASP A 836 " (cutoff:3.500A) Processing helix chain 'A' and resid 841 through 845 Processing helix chain 'A' and resid 846 through 857 removed outlier: 3.735A pdb=" N HIS A 852 " --> pdb=" O ASN A 848 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N LEU A 853 " --> pdb=" O ALA A 849 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N LEU A 854 " --> pdb=" O LYS A 850 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N PHE A 856 " --> pdb=" O HIS A 852 " (cutoff:3.500A) Processing helix chain 'A' and resid 861 through 871 removed outlier: 4.101A pdb=" N ARG A 870 " --> pdb=" O MET A 866 " (cutoff:3.500A) Processing helix chain 'A' and resid 878 through 899 removed outlier: 3.562A pdb=" N GLU A 882 " --> pdb=" O THR A 878 " (cutoff:3.500A) Processing helix chain 'A' and resid 912 through 922 removed outlier: 3.557A pdb=" N PHE A 916 " --> pdb=" O TYR A 912 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ILE A 918 " --> pdb=" O SER A 914 " (cutoff:3.500A) Processing helix chain 'A' and resid 928 through 933 Processing helix chain 'A' and resid 937 through 945 Processing helix chain 'A' and resid 950 through 955 removed outlier: 6.098A pdb=" N ILE A 955 " --> pdb=" O LYS A 952 " (cutoff:3.500A) Processing helix chain 'A' and resid 956 through 962 removed outlier: 4.135A pdb=" N LYS A 960 " --> pdb=" O PRO A 956 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ASN A 961 " --> pdb=" O SER A 957 " (cutoff:3.500A) Processing helix chain 'A' and resid 963 through 971 Processing helix chain 'A' and resid 975 through 991 removed outlier: 3.759A pdb=" N HIS A 979 " --> pdb=" O HIS A 975 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N LYS A 989 " --> pdb=" O LYS A 985 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ASN A 990 " --> pdb=" O GLU A 986 " (cutoff:3.500A) Processing helix chain 'A' and resid 993 through 1002 removed outlier: 3.649A pdb=" N LEU A 997 " --> pdb=" O ASP A 993 " (cutoff:3.500A) Processing helix chain 'B' and resid 181 through 185 Processing helix chain 'C' and resid 69 through 75 removed outlier: 4.413A pdb=" N MET C 75 " --> pdb=" O GLU C 71 " (cutoff:3.500A) Processing helix chain 'D' and resid 23 through 40 removed outlier: 3.502A pdb=" N GLU D 28 " --> pdb=" O ASN D 24 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N CYS D 29 " --> pdb=" O ASN D 25 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N GLU D 32 " --> pdb=" O GLU D 28 " (cutoff:3.500A) Processing helix chain 'D' and resid 48 through 54 removed outlier: 3.794A pdb=" N THR D 52 " --> pdb=" O ALA D 48 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N LEU D 53 " --> pdb=" O GLY D 49 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N SER D 54 " --> pdb=" O VAL D 50 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 48 through 54' Processing helix chain 'D' and resid 58 through 72 Processing helix chain 'D' and resid 80 through 95 removed outlier: 3.648A pdb=" N LEU D 85 " --> pdb=" O SER D 81 " (cutoff:3.500A) Proline residue: D 88 - end of helix Processing helix chain 'D' and resid 95 through 109 removed outlier: 4.089A pdb=" N ALA D 99 " --> pdb=" O LYS D 95 " (cutoff:3.500A) Processing helix chain 'D' and resid 115 through 122 removed outlier: 3.805A pdb=" N ASP D 119 " --> pdb=" O ASN D 115 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N LEU D 122 " --> pdb=" O HIS D 118 " (cutoff:3.500A) Processing helix chain 'D' and resid 136 through 146 removed outlier: 3.641A pdb=" N ALA D 141 " --> pdb=" O LEU D 137 " (cutoff:3.500A) Processing helix chain 'D' and resid 154 through 160 Processing helix chain 'D' and resid 173 through 177 removed outlier: 4.101A pdb=" N LYS D 176 " --> pdb=" O ASP D 173 " (cutoff:3.500A) Processing helix chain 'D' and resid 186 through 192 removed outlier: 3.661A pdb=" N TYR D 190 " --> pdb=" O LYS D 186 " (cutoff:3.500A) Processing helix chain 'D' and resid 192 through 197 Processing helix chain 'D' and resid 197 through 211 removed outlier: 3.745A pdb=" N ILE D 208 " --> pdb=" O MET D 204 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N THR D 210 " --> pdb=" O THR D 206 " (cutoff:3.500A) Processing helix chain 'D' and resid 222 through 235 removed outlier: 3.588A pdb=" N LEU D 235 " --> pdb=" O TRP D 231 " (cutoff:3.500A) Processing helix chain 'D' and resid 254 through 265 Processing helix chain 'D' and resid 271 through 275 Processing helix chain 'D' and resid 281 through 296 Processing helix chain 'D' and resid 298 through 302 Processing helix chain 'D' and resid 305 through 317 removed outlier: 4.314A pdb=" N ASP D 310 " --> pdb=" O ASP D 306 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N TYR D 311 " --> pdb=" O GLU D 307 " (cutoff:3.500A) removed outlier: 3.840A 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 327 through 332 removed outlier: 4.011A pdb=" N LYS D 331 " --> pdb=" O ILE D 328 " (cutoff:3.500A) Processing helix chain 'D' and resid 355 through 366 removed outlier: 4.219A pdb=" N GLU D 365 " --> pdb=" O PHE D 361 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N SER D 366 " --> pdb=" O GLU D 362 " (cutoff:3.500A) Processing helix chain 'D' and resid 366 through 372 removed outlier: 3.785A pdb=" N ARG D 370 " --> pdb=" O SER D 366 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N SER D 371 " --> pdb=" O CYS D 367 " (cutoff:3.500A) Processing helix chain 'D' and resid 374 through 391 Processing helix chain 'D' and resid 417 through 426 removed outlier: 3.695A pdb=" N LYS D 423 " --> pdb=" O ASP D 419 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N GLU D 426 " --> pdb=" O LYS D 422 " (cutoff:3.500A) Processing helix chain 'D' and resid 431 through 446 Processing helix chain 'D' and resid 447 through 461 removed outlier: 3.660A pdb=" N LEU D 460 " --> pdb=" O SER D 456 " (cutoff:3.500A) Processing helix chain 'D' and resid 467 through 494 Processing helix chain 'D' and resid 495 through 501 removed outlier: 3.917A pdb=" N THR D 499 " --> pdb=" O LEU D 495 " (cutoff:3.500A) Processing helix chain 'D' and resid 508 through 519 removed outlier: 3.512A pdb=" N GLU D 516 " --> pdb=" O LEU D 512 " (cutoff:3.500A) Processing helix chain 'D' and resid 532 through 539 removed outlier: 3.531A pdb=" N GLN D 536 " --> pdb=" O PRO D 532 " (cutoff:3.500A) Processing helix chain 'D' and resid 540 through 546 removed outlier: 4.258A pdb=" N PHE D 544 " --> pdb=" O ILE D 541 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N SER D 546 " --> pdb=" O GLU D 543 " (cutoff:3.500A) Processing helix chain 'D' and resid 552 through 572 Processing helix chain 'D' and resid 579 through 597 Processing helix chain 'D' and resid 600 through 604 removed outlier: 3.540A pdb=" N VAL D 603 " --> pdb=" O LEU D 600 " (cutoff:3.500A) Processing helix chain 'D' and resid 605 through 628 Processing helix chain 'D' and resid 648 through 658 Processing helix chain 'D' and resid 660 through 671 Processing helix chain 'D' and resid 681 through 701 removed outlier: 4.125A pdb=" N GLU D 686 " --> pdb=" O GLU D 682 " (cutoff:3.500A) removed outlier: 4.753A pdb=" N TYR D 687 " --> pdb=" O LYS D 683 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N GLU D 694 " --> pdb=" O GLY D 690 " (cutoff:3.500A) Processing helix chain 'D' and resid 705 through 722 removed outlier: 3.529A pdb=" N GLN D 711 " --> pdb=" O VAL D 707 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N SER D 714 " --> pdb=" O THR D 710 " (cutoff:3.500A) removed outlier: 5.079A pdb=" N GLU D 715 " --> pdb=" O GLN D 711 " (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: 3.763A pdb=" N TYR D 755 " --> pdb=" O ILE D 751 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N VAL D 756 " --> pdb=" O GLY D 752 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N ASN D 765 " --> pdb=" O LEU D 761 " (cutoff:3.500A) Processing helix chain 'D' and resid 768 through 785 removed outlier: 3.521A pdb=" N ILE D 772 " --> pdb=" O PRO D 768 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ILE D 774 " --> pdb=" O SER D 770 " (cutoff:3.500A) Processing helix chain 'D' and resid 786 through 788 No H-bonds generated for 'chain 'D' and resid 786 through 788' Processing helix chain 'D' and resid 800 through 812 removed outlier: 3.927A pdb=" N TYR D 804 " --> pdb=" O TYR D 800 " (cutoff:3.500A) Processing helix chain 'D' and resid 817 through 823 removed outlier: 3.538A pdb=" N ILE D 823 " --> pdb=" O ARG D 819 " (cutoff:3.500A) Processing helix chain 'D' and resid 831 through 840 removed outlier: 3.815A pdb=" N PHE D 839 " --> pdb=" O ILE D 835 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N LYS D 840 " --> pdb=" O ASP D 836 " (cutoff:3.500A) Processing helix chain 'D' and resid 841 through 845 Processing helix chain 'D' and resid 846 through 855 Processing helix chain 'D' and resid 862 through 872 removed outlier: 4.142A pdb=" N MET D 866 " --> pdb=" O ILE D 862 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ASN D 867 " --> pdb=" O ASN D 863 " (cutoff:3.500A) Processing helix chain 'D' and resid 878 through 902 removed outlier: 3.503A pdb=" N THR D 891 " --> pdb=" O GLU D 887 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ARG D 892 " --> pdb=" O TYR D 888 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N LYS D 893 " --> pdb=" O LEU D 889 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N VAL D 894 " --> pdb=" O GLU D 890 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ASN D 895 " --> pdb=" O THR D 891 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N VAL D 898 " --> pdb=" O VAL D 894 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N GLU D 901 " --> pdb=" O ILE D 897 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N LYS D 902 " --> pdb=" O VAL D 898 " (cutoff:3.500A) Processing helix chain 'D' and resid 911 through 922 removed outlier: 3.648A pdb=" N LEU D 922 " --> pdb=" O ILE D 918 " (cutoff:3.500A) Processing helix chain 'D' and resid 928 through 933 removed outlier: 3.677A pdb=" N PHE D 933 " --> pdb=" O LYS D 929 " (cutoff:3.500A) Processing helix chain 'D' and resid 937 through 945 Processing helix chain 'D' and resid 950 through 954 Processing helix chain 'D' and resid 955 through 962 Processing helix chain 'D' and resid 964 through 970 Processing helix chain 'D' and resid 976 through 991 removed outlier: 3.854A pdb=" N VAL D 980 " --> pdb=" O MET D 976 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N GLU D 982 " --> pdb=" O HIS D 978 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N VAL D 983 " --> pdb=" O HIS D 979 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N VAL D 988 " --> pdb=" O LEU D 984 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N LYS D 989 " --> pdb=" O LYS D 985 " (cutoff:3.500A) Processing helix chain 'D' and resid 993 through 1003 removed outlier: 3.613A pdb=" N LEU D 997 " --> pdb=" O ASP D 993 " (cutoff:3.500A) Processing helix chain 'E' and resid 44 through 48 Processing helix chain 'E' and resid 70 through 74 Processing helix chain 'F' and resid 23 through 40 removed outlier: 3.649A pdb=" N GLU F 28 " --> pdb=" O ASN F 24 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N CYS F 29 " --> pdb=" O ASN F 25 " (cutoff:3.500A) Processing helix chain 'F' and resid 47 through 54 removed outlier: 3.968A pdb=" N SER F 51 " --> pdb=" O GLY F 47 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N SER F 54 " --> pdb=" O VAL F 50 " (cutoff:3.500A) Processing helix chain 'F' and resid 58 through 71 removed outlier: 3.568A pdb=" N ASP F 64 " --> pdb=" O TRP F 60 " (cutoff:3.500A) Processing helix chain 'F' and resid 80 through 95 removed outlier: 3.526A pdb=" N LEU F 85 " --> pdb=" O SER F 81 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ILE F 87 " --> pdb=" O GLU F 83 " (cutoff:3.500A) Proline residue: F 88 - end of helix Processing helix chain 'F' and resid 96 through 109 removed outlier: 3.650A pdb=" N ILE F 103 " --> pdb=" O ALA F 99 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N GLN F 109 " --> pdb=" O LYS F 105 " (cutoff:3.500A) Processing helix chain 'F' and resid 115 through 122 removed outlier: 4.057A pdb=" N ASP F 119 " --> pdb=" O ASN F 115 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N LYS F 120 " --> pdb=" O PRO F 116 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N LEU F 122 " --> pdb=" O HIS F 118 " (cutoff:3.500A) Processing helix chain 'F' and resid 136 through 146 Processing helix chain 'F' and resid 154 through 160 removed outlier: 3.891A pdb=" N VAL F 158 " --> pdb=" O ALA F 154 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N ALA F 159 " --> pdb=" O GLU F 155 " (cutoff:3.500A) Processing helix chain 'F' and resid 179 through 183 Processing helix chain 'F' and resid 186 through 192 Processing helix chain 'F' and resid 192 through 197 Processing helix chain 'F' and resid 197 through 211 removed outlier: 3.591A pdb=" N MET F 204 " --> pdb=" O ILE F 200 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N ALA F 209 " --> pdb=" O LYS F 205 " (cutoff:3.500A) Processing helix chain 'F' and resid 223 through 233 Processing helix chain 'F' and resid 254 through 265 Processing helix chain 'F' and resid 271 through 275 Processing helix chain 'F' and resid 281 through 296 removed outlier: 4.209A pdb=" N ARG F 285 " --> pdb=" O ASP F 281 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N LEU F 293 " --> pdb=" O VAL F 289 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ILE F 294 " --> pdb=" O MET F 290 " (cutoff:3.500A) Processing helix chain 'F' and resid 297 through 302 removed outlier: 3.976A pdb=" N PHE F 301 " --> pdb=" O GLN F 297 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N ILE F 302 " --> pdb=" O GLU F 298 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 297 through 302' Processing helix chain 'F' and resid 304 through 317 removed outlier: 4.093A pdb=" N ILE F 309 " --> pdb=" O ASP F 305 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N ASP F 310 " --> pdb=" O ASP F 306 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N TYR F 311 " --> pdb=" O GLU F 307 " (cutoff:3.500A) Processing helix chain 'F' and resid 318 through 322 removed outlier: 3.653A pdb=" N ALA F 321 " --> pdb=" O PRO F 318 " (cutoff:3.500A) Processing helix chain 'F' and resid 329 through 334 removed outlier: 4.123A pdb=" N VAL F 333 " --> pdb=" O ASP F 329 " (cutoff:3.500A) Processing helix chain 'F' and resid 355 through 366 removed outlier: 3.540A pdb=" N GLU F 365 " --> pdb=" O PHE F 361 " (cutoff:3.500A) Processing helix chain 'F' and resid 366 through 373 removed outlier: 3.801A pdb=" N LEU F 373 " --> pdb=" O GLU F 369 " (cutoff:3.500A) Processing helix chain 'F' and resid 374 through 391 Processing helix chain 'F' and resid 412 through 416 removed outlier: 3.596A pdb=" N HIS F 415 " --> pdb=" O LEU F 412 " (cutoff:3.500A) Processing helix chain 'F' and resid 417 through 427 removed outlier: 3.603A pdb=" N MET F 421 " --> pdb=" O LYS F 417 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LYS F 422 " --> pdb=" O TYR F 418 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N LYS F 423 " --> pdb=" O ASP F 419 " (cutoff:3.500A) Processing helix chain 'F' and resid 431 through 446 Processing helix chain 'F' and resid 448 through 462 removed outlier: 3.917A pdb=" N ASP F 453 " --> pdb=" O GLU F 449 " (cutoff:3.500A) Processing helix chain 'F' and resid 468 through 493 removed outlier: 3.578A pdb=" N THR F 490 " --> pdb=" O THR F 486 " (cutoff:3.500A) Processing helix chain 'F' and resid 495 through 501 Processing helix chain 'F' and resid 508 through 519 Processing helix chain 'F' and resid 523 through 525 No H-bonds generated for 'chain 'F' and resid 523 through 525' Processing helix chain 'F' and resid 526 through 531 Processing helix chain 'F' and resid 532 through 539 Processing helix chain 'F' and resid 542 through 547 removed outlier: 3.779A pdb=" N SER F 546 " --> pdb=" O LEU F 542 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N ASP F 547 " --> pdb=" O GLU F 543 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 542 through 547' Processing helix chain 'F' and resid 552 through 572 removed outlier: 3.633A pdb=" N SER F 570 " --> pdb=" O ARG F 566 " (cutoff:3.500A) Processing helix chain 'F' and resid 579 through 597 Processing helix chain 'F' and resid 600 through 604 removed outlier: 3.777A pdb=" N VAL F 603 " --> pdb=" O LEU F 600 " (cutoff:3.500A) Processing helix chain 'F' and resid 605 through 629 removed outlier: 3.862A pdb=" N TYR F 611 " --> pdb=" O GLU F 607 " (cutoff:3.500A) Processing helix chain 'F' and resid 648 through 657 Processing helix chain 'F' and resid 660 through 671 removed outlier: 3.745A pdb=" N ASN F 666 " --> pdb=" O ASP F 662 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N LEU F 667 " --> pdb=" O ASP F 663 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N GLU F 668 " --> pdb=" O ILE F 664 " (cutoff:3.500A) Processing helix chain 'F' and resid 672 through 676 removed outlier: 3.729A pdb=" N LYS F 675 " --> pdb=" O SER F 672 " (cutoff:3.500A) Processing helix chain 'F' and resid 680 through 701 removed outlier: 3.769A pdb=" N GLN F 698 " --> pdb=" O GLU F 694 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N PHE F 699 " --> pdb=" O ILE F 695 " (cutoff:3.500A) Processing helix chain 'F' and resid 705 through 722 removed outlier: 4.286A pdb=" N SER F 714 " --> pdb=" O THR F 710 " (cutoff:3.500A) removed outlier: 4.978A pdb=" N GLU F 715 " --> pdb=" O GLN F 711 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ALA F 718 " --> pdb=" O SER F 714 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N PHE F 722 " --> pdb=" O ALA F 718 " (cutoff:3.500A) Processing helix chain 'F' and resid 729 through 743 removed outlier: 3.596A pdb=" N LYS F 738 " --> pdb=" O GLY F 734 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N ALA F 739 " --> pdb=" O LYS F 735 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N LEU F 740 " --> pdb=" O ILE F 736 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N LEU F 741 " --> pdb=" O VAL F 737 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N TYR F 743 " --> pdb=" O ALA F 739 " (cutoff:3.500A) Processing helix chain 'F' and resid 751 through 762 removed outlier: 4.184A pdb=" N VAL F 756 " --> pdb=" O GLY F 752 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N TRP F 757 " --> pdb=" O LYS F 753 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N LEU F 761 " --> pdb=" O TRP F 757 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N THR F 762 " --> pdb=" O LEU F 758 " (cutoff:3.500A) Processing helix chain 'F' and resid 768 through 786 removed outlier: 3.541A pdb=" N ILE F 772 " --> pdb=" O PRO F 768 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ILE F 775 " --> pdb=" O ILE F 771 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ASP F 776 " --> pdb=" O ILE F 772 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N PHE F 778 " --> pdb=" O ILE F 774 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N LEU F 779 " --> pdb=" O ILE F 775 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N VAL F 780 " --> pdb=" O ASP F 776 " (cutoff:3.500A) removed outlier: 4.577A pdb=" N LEU F 781 " --> pdb=" O ASP F 777 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N GLN F 782 " --> pdb=" O PHE F 778 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ALA F 783 " --> pdb=" O LEU F 779 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N GLU F 784 " --> pdb=" O VAL F 780 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N HIS F 786 " --> pdb=" O GLN F 782 " (cutoff:3.500A) Processing helix chain 'F' and resid 800 through 812 removed outlier: 3.998A pdb=" N TYR F 804 " --> pdb=" O TYR F 800 " (cutoff:3.500A) Processing helix chain 'F' and resid 817 through 827 removed outlier: 3.781A pdb=" N GLU F 822 " --> pdb=" O LYS F 818 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ILE F 823 " --> pdb=" O ARG F 819 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N CYS F 826 " --> pdb=" O GLU F 822 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N LEU F 827 " --> pdb=" O ILE F 823 " (cutoff:3.500A) Processing helix chain 'F' and resid 832 through 840 removed outlier: 4.220A pdb=" N ASP F 836 " --> pdb=" O GLN F 832 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N PHE F 837 " --> pdb=" O LYS F 833 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N LYS F 840 " --> pdb=" O ASP F 836 " (cutoff:3.500A) Processing helix chain 'F' and resid 846 through 853 Processing helix chain 'F' and resid 861 through 872 removed outlier: 3.574A pdb=" N ILE F 869 " --> pdb=" O LEU F 865 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ARG F 870 " --> pdb=" O MET F 866 " (cutoff:3.500A) Processing helix chain 'F' and resid 878 through 902 removed outlier: 3.605A pdb=" N GLU F 899 " --> pdb=" O ASN F 895 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N LYS F 900 " --> pdb=" O TYR F 896 " (cutoff:3.500A) Processing helix chain 'F' and resid 911 through 922 removed outlier: 3.690A pdb=" N PHE F 916 " --> pdb=" O TYR F 912 " (cutoff:3.500A) Processing helix chain 'F' and resid 928 through 933 removed outlier: 3.935A pdb=" N GLU F 932 " --> pdb=" O SER F 928 " (cutoff:3.500A) Processing helix chain 'F' and resid 937 through 945 Processing helix chain 'F' and resid 957 through 962 removed outlier: 4.014A pdb=" N ASN F 961 " --> pdb=" O SER F 957 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N TYR F 962 " --> pdb=" O TRP F 958 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 957 through 962' Processing helix chain 'F' and resid 963 through 973 Processing helix chain 'F' and resid 974 through 976 No H-bonds generated for 'chain 'F' and resid 974 through 976' Processing helix chain 'F' and resid 977 through 990 removed outlier: 3.808A pdb=" N GLU F 986 " --> pdb=" O GLU F 982 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N LYS F 989 " --> pdb=" O LYS F 985 " (cutoff:3.500A) Processing helix chain 'F' and resid 993 through 1003 removed outlier: 3.827A pdb=" N LEU F 997 " --> pdb=" O ASP F 993 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LEU F1000 " --> pdb=" O TYR F 996 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N TYR F1003 " --> pdb=" O ILE F 999 " (cutoff:3.500A) Processing helix chain 'G' and resid 69 through 74 removed outlier: 3.815A pdb=" N LEU G 73 " --> pdb=" O ASP G 69 " (cutoff:3.500A) Processing helix chain 'H' and resid 25 through 38 removed outlier: 3.535A pdb=" N CYS H 29 " --> pdb=" O ASN H 25 " (cutoff:3.500A) Processing helix chain 'H' and resid 48 through 54 removed outlier: 3.792A pdb=" N THR H 52 " --> pdb=" O ALA H 48 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N LEU H 53 " --> pdb=" O GLY H 49 " (cutoff:3.500A) Processing helix chain 'H' and resid 58 through 71 Processing helix chain 'H' and resid 80 through 108 Proline residue: H 88 - end of helix removed outlier: 6.439A pdb=" N GLU H 97 " --> pdb=" O ASN H 93 " (cutoff:3.500A) removed outlier: 8.636A pdb=" N MET H 98 " --> pdb=" O VAL H 94 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N ALA H 99 " --> pdb=" O LYS H 95 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ILE H 103 " --> pdb=" O ALA H 99 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N LEU H 104 " --> pdb=" O PHE H 100 " (cutoff:3.500A) Processing helix chain 'H' and resid 115 through 124 removed outlier: 3.903A pdb=" N ASP H 119 " --> pdb=" O ASN H 115 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N LEU H 122 " --> pdb=" O HIS H 118 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N MET H 124 " --> pdb=" O LYS H 120 " (cutoff:3.500A) Processing helix chain 'H' and resid 136 through 146 Processing helix chain 'H' and resid 154 through 160 Processing helix chain 'H' and resid 186 through 192 removed outlier: 3.701A pdb=" N TYR H 190 " --> pdb=" O LYS H 186 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N LEU H 191 " --> pdb=" O GLU H 187 " (cutoff:3.500A) Processing helix chain 'H' and resid 192 through 197 Processing helix chain 'H' and resid 197 through 211 removed outlier: 3.659A pdb=" N LYS H 205 " --> pdb=" O SER H 201 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N THR H 210 " --> pdb=" O THR H 206 " (cutoff:3.500A) Processing helix chain 'H' and resid 222 through 236 Processing helix chain 'H' and resid 254 through 265 Processing helix chain 'H' and resid 270 through 275 removed outlier: 3.550A pdb=" N LEU H 274 " --> pdb=" O ASP H 270 " (cutoff:3.500A) Processing helix chain 'H' and resid 284 through 296 removed outlier: 3.553A pdb=" N VAL H 289 " --> pdb=" O ARG H 285 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N LEU H 292 " --> pdb=" O ALA H 288 " (cutoff:3.500A) Processing helix chain 'H' and resid 297 through 302 removed outlier: 3.681A pdb=" N ILE H 302 " --> pdb=" O GLU H 298 " (cutoff:3.500A) Processing helix chain 'H' and resid 305 through 317 removed outlier: 4.327A pdb=" N ASP H 310 " --> pdb=" O ASP H 306 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N TYR H 311 " --> pdb=" O GLU H 307 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N LYS H 315 " --> pdb=" O TYR H 311 " (cutoff:3.500A) Processing helix chain 'H' and resid 318 through 321 removed outlier: 3.588A pdb=" N ALA H 321 " --> pdb=" O PRO H 318 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 318 through 321' Processing helix chain 'H' and resid 326 through 332 removed outlier: 4.151A pdb=" N LYS H 331 " --> pdb=" O ILE H 328 " (cutoff:3.500A) Processing helix chain 'H' and resid 356 through 366 Processing helix chain 'H' and resid 366 through 373 removed outlier: 3.892A pdb=" N ARG H 370 " --> pdb=" O SER H 366 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N SER H 371 " --> pdb=" O CYS H 367 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LYS H 372 " --> pdb=" O ASP H 368 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LEU H 373 " --> pdb=" O GLU H 369 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 366 through 373' Processing helix chain 'H' and resid 374 through 392 removed outlier: 4.334A pdb=" N ARG H 380 " --> pdb=" O LYS H 376 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLU H 389 " --> pdb=" O PHE H 385 " (cutoff:3.500A) Processing helix chain 'H' and resid 396 through 400 removed outlier: 3.715A pdb=" N ASP H 399 " --> pdb=" O MET H 396 " (cutoff:3.500A) Processing helix chain 'H' and resid 417 through 426 removed outlier: 3.546A pdb=" N MET H 421 " --> pdb=" O LYS H 417 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LYS H 422 " --> pdb=" O TYR H 418 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N LYS H 423 " --> pdb=" O ASP H 419 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N GLU H 426 " --> pdb=" O LYS H 422 " (cutoff:3.500A) Processing helix chain 'H' and resid 431 through 445 Processing helix chain 'H' and resid 447 through 461 removed outlier: 4.022A pdb=" N ASP H 453 " --> pdb=" O GLU H 449 " (cutoff:3.500A) Processing helix chain 'H' and resid 467 through 494 removed outlier: 4.060A pdb=" N LEU H 473 " --> pdb=" O CYS H 469 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N SER H 474 " --> pdb=" O VAL H 470 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLN H 487 " --> pdb=" O GLN H 483 " (cutoff:3.500A) Processing helix chain 'H' and resid 495 through 501 removed outlier: 3.727A pdb=" N THR H 499 " --> pdb=" O LEU H 495 " (cutoff:3.500A) Processing helix chain 'H' and resid 508 through 519 removed outlier: 3.842A pdb=" N LEU H 512 " --> pdb=" O THR H 508 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ALA H 513 " --> pdb=" O ASP H 509 " (cutoff:3.500A) Processing helix chain 'H' and resid 526 through 531 Processing helix chain 'H' and resid 532 through 539 Processing helix chain 'H' and resid 542 through 547 removed outlier: 3.951A pdb=" N SER H 546 " --> pdb=" O LEU H 542 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N ASP H 547 " --> pdb=" O GLU H 543 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 542 through 547' Processing helix chain 'H' and resid 550 through 572 removed outlier: 4.109A pdb=" N ASP H 554 " --> pdb=" O PHE H 550 " (cutoff:3.500A) Processing helix chain 'H' and resid 579 through 597 removed outlier: 3.698A pdb=" N VAL H 583 " --> pdb=" O SER H 579 " (cutoff:3.500A) Processing helix chain 'H' and resid 598 through 604 removed outlier: 6.619A pdb=" N TRP H 601 " --> pdb=" O ASN H 598 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N SER H 602 " --> pdb=" O CYS H 599 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N VAL H 603 " --> pdb=" O LEU H 600 " (cutoff:3.500A) Processing helix chain 'H' and resid 605 through 628 removed outlier: 3.502A pdb=" N MET H 616 " --> pdb=" O ILE H 612 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N LEU H 618 " --> pdb=" O ASN H 614 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N LEU H 619 " --> pdb=" O SER H 615 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ARG H 627 " --> pdb=" O ALA H 623 " (cutoff:3.500A) Processing helix chain 'H' and resid 648 through 659 Processing helix chain 'H' and resid 660 through 671 removed outlier: 3.900A pdb=" N LYS H 665 " --> pdb=" O ILE H 661 " (cutoff:3.500A) Processing helix chain 'H' and resid 682 through 701 removed outlier: 3.659A pdb=" N GLU H 686 " --> pdb=" O GLU H 682 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ALA H 701 " --> pdb=" O LYS H 697 " (cutoff:3.500A) Processing helix chain 'H' and resid 705 through 722 removed outlier: 3.535A pdb=" N TYR H 709 " --> pdb=" O ASN H 705 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N THR H 710 " --> pdb=" O VAL H 706 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N GLN H 711 " --> pdb=" O VAL H 707 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N SER H 714 " --> pdb=" O THR H 710 " (cutoff:3.500A) removed outlier: 4.829A pdb=" N GLU H 715 " --> pdb=" O GLN H 711 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ALA H 718 " --> pdb=" O SER H 714 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N TYR H 721 " --> pdb=" O LYS H 717 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N PHE H 722 " --> pdb=" O ALA H 718 " (cutoff:3.500A) Processing helix chain 'H' and resid 723 through 725 No H-bonds generated for 'chain 'H' and resid 723 through 725' Processing helix chain 'H' and resid 729 through 741 removed outlier: 3.959A pdb=" N VAL H 737 " --> pdb=" O LEU H 733 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N LEU H 741 " --> pdb=" O VAL H 737 " (cutoff:3.500A) Processing helix chain 'H' and resid 750 through 761 removed outlier: 3.533A pdb=" N ARG H 754 " --> pdb=" O ASP H 750 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N TRP H 757 " --> pdb=" O LYS H 753 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LEU H 761 " --> pdb=" O TRP H 757 " (cutoff:3.500A) Processing helix chain 'H' and resid 768 through 785 removed outlier: 3.650A pdb=" N ILE H 772 " --> pdb=" O PRO H 768 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N SER H 773 " --> pdb=" O LYS H 769 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N PHE H 778 " --> pdb=" O ILE H 774 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N LEU H 779 " --> pdb=" O ILE H 775 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N VAL H 780 " --> pdb=" O ASP H 776 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N LEU H 781 " --> pdb=" O ASP H 777 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N GLN H 782 " --> pdb=" O PHE H 778 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ALA H 783 " --> pdb=" O LEU H 779 " (cutoff:3.500A) Processing helix chain 'H' and resid 786 through 788 No H-bonds generated for 'chain 'H' and resid 786 through 788' Processing helix chain 'H' and resid 801 through 812 removed outlier: 4.015A pdb=" N GLY H 805 " --> pdb=" O SER H 801 " (cutoff:3.500A) Processing helix chain 'H' and resid 817 through 824 removed outlier: 3.889A pdb=" N THR H 824 " --> pdb=" O LEU H 820 " (cutoff:3.500A) Processing helix chain 'H' and resid 832 through 840 removed outlier: 4.021A pdb=" N ASP H 836 " --> pdb=" O GLN H 832 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N PHE H 837 " --> pdb=" O LYS H 833 " (cutoff:3.500A) Processing helix chain 'H' and resid 841 through 845 Processing helix chain 'H' and resid 846 through 856 removed outlier: 3.513A pdb=" N SER H 851 " --> pdb=" O THR H 847 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N HIS H 852 " --> pdb=" O ASN H 848 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N PHE H 856 " --> pdb=" O HIS H 852 " (cutoff:3.500A) Processing helix chain 'H' and resid 862 through 872 removed outlier: 3.705A pdb=" N MET H 866 " --> pdb=" O ILE H 862 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N ARG H 870 " --> pdb=" O MET H 866 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ILE H 871 " --> pdb=" O ASN H 867 " (cutoff:3.500A) Processing helix chain 'H' and resid 878 through 903 removed outlier: 4.057A pdb=" N LEU H 884 " --> pdb=" O GLU H 880 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ILE H 885 " --> pdb=" O HIS H 881 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ILE H 886 " --> pdb=" O GLU H 882 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N GLU H 887 " --> pdb=" O GLU H 883 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N TYR H 888 " --> pdb=" O LEU H 884 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LYS H 893 " --> pdb=" O LEU H 889 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LYS H 900 " --> pdb=" O TYR H 896 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N GLU H 901 " --> pdb=" O ILE H 897 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N LYS H 902 " --> pdb=" O VAL H 898 " (cutoff:3.500A) Processing helix chain 'H' and resid 912 through 922 removed outlier: 3.812A pdb=" N GLY H 917 " --> pdb=" O MET H 913 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ILE H 918 " --> pdb=" O SER H 914 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N TRP H 919 " --> pdb=" O THR H 915 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N TYR H 920 " --> pdb=" O PHE H 916 " (cutoff:3.500A) Processing helix chain 'H' and resid 929 through 933 Processing helix chain 'H' and resid 937 through 945 Processing helix chain 'H' and resid 955 through 962 removed outlier: 3.616A pdb=" N TYR H 962 " --> pdb=" O LEU H 959 " (cutoff:3.500A) Processing helix chain 'H' and resid 963 through 971 Processing helix chain 'H' and resid 976 through 990 removed outlier: 3.583A pdb=" N GLU H 982 " --> pdb=" O HIS H 978 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N LYS H 989 " --> pdb=" O LYS H 985 " (cutoff:3.500A) Processing helix chain 'H' and resid 994 through 1003 Processing sheet with id=AA1, first strand: chain 'A' and resid 150 through 152 removed outlier: 8.043A pdb=" N ILE A 130 " --> pdb=" O LEU A 42 " (cutoff:3.500A) removed outlier: 5.941A pdb=" N PHE A 44 " --> pdb=" O ILE A 130 " (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 'B' and resid 67 through 68 removed outlier: 6.860A pdb=" N PHE B 13 " --> pdb=" O VAL B 22 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N THR B 24 " --> pdb=" O VAL B 11 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N VAL B 11 " --> pdb=" O THR B 24 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N ASP B 10 " --> pdb=" O ILE B 178 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ILE B 178 " --> pdb=" O ASP B 10 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 60 through 63 removed outlier: 4.318A pdb=" N THR B 29 " --> pdb=" O THR B 62 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 198 through 200 removed outlier: 3.509A pdb=" N GLU B 221 " --> pdb=" O SER B 199 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 176 through 177 removed outlier: 6.511A pdb=" N THR C 62 " --> pdb=" O GLN C 28 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N ALA C 30 " --> pdb=" O ASN C 60 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N ASN C 60 " --> pdb=" O ALA C 30 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N PHE C 32 " --> pdb=" O GLU C 58 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N GLU C 58 " --> pdb=" O PHE C 32 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N ILE C 59 " --> pdb=" O ALA C 222 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N ALA C 222 " --> pdb=" O ILE C 59 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N LEU C 61 " --> pdb=" O PHE C 220 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 224 through 225 Processing sheet with id=AA8, first strand: chain 'D' and resid 150 through 152 removed outlier: 5.928A pdb=" N SER D 150 " --> pdb=" O LEU D 167 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N LYS D 169 " --> pdb=" O SER D 150 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N ILE D 152 " --> pdb=" O LYS D 169 " (cutoff:3.500A) removed outlier: 6.967A pdb=" N VAL D 129 " --> pdb=" O LEU D 168 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N LEU D 42 " --> pdb=" O HIS D 128 " (cutoff:3.500A) removed outlier: 8.244A pdb=" N ILE D 130 " --> pdb=" O LEU D 42 " (cutoff:3.500A) removed outlier: 6.073A pdb=" N PHE D 44 " --> pdb=" O ILE D 130 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N PHE D 245 " --> pdb=" O ILE D 269 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 338 through 340 Processing sheet with id=AB1, first strand: chain 'E' and resid 21 through 25 removed outlier: 6.715A pdb=" N PHE E 13 " --> pdb=" O VAL E 22 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N THR E 24 " --> pdb=" O VAL E 11 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N VAL E 11 " --> pdb=" O THR E 24 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ASP E 10 " --> pdb=" O ILE E 178 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ILE E 178 " --> pdb=" O ASP E 10 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 198 through 199 removed outlier: 3.640A pdb=" N SER E 199 " --> pdb=" O GLU E 221 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N GLU E 221 " --> pdb=" O SER E 199 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N LEU E 61 " --> pdb=" O PHE E 220 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N ILE E 59 " --> pdb=" O ALA E 222 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N ASN E 60 " --> pdb=" O ALA E 30 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N ALA E 30 " --> pdb=" O ASN E 60 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N THR E 62 " --> pdb=" O GLN E 28 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N TYR H 574 " --> pdb=" O ALA E 30 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 150 through 152 removed outlier: 5.791A pdb=" N SER F 150 " --> pdb=" O LEU F 167 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N LYS F 169 " --> pdb=" O SER F 150 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N ILE F 152 " --> pdb=" O LYS F 169 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N VAL F 129 " --> pdb=" O LEU F 168 " (cutoff:3.500A) removed outlier: 7.050A pdb=" N LEU F 42 " --> pdb=" O HIS F 128 " (cutoff:3.500A) removed outlier: 8.391A pdb=" N ILE F 130 " --> pdb=" O LEU F 42 " (cutoff:3.500A) removed outlier: 6.028A pdb=" N PHE F 44 " --> pdb=" O ILE F 130 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N VAL F 43 " --> pdb=" O VAL F 214 " (cutoff:3.500A) removed outlier: 7.798A pdb=" N ILE F 216 " --> pdb=" O VAL F 43 " (cutoff:3.500A) removed outlier: 5.841A pdb=" N PHE F 45 " --> pdb=" O ILE F 216 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'F' and resid 338 through 340 Processing sheet with id=AB5, first strand: chain 'G' and resid 14 through 15 removed outlier: 3.861A pdb=" N LYS G 14 " --> pdb=" O GLU G 174 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N GLU G 174 " --> pdb=" O LYS G 14 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'G' and resid 27 through 30 removed outlier: 6.421A pdb=" N THR G 62 " --> pdb=" O GLN G 28 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'H' and resid 150 through 152 removed outlier: 6.037A pdb=" N PHE H 44 " --> pdb=" O ILE H 130 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'H' and resid 338 through 340 1583 hydrogen bonds defined for protein. 4530 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: 13.49 Time building geometry restraints manager: 15.91 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: 11554 1.34 - 1.46: 6510 1.46 - 1.58: 19442 1.58 - 1.70: 1 1.70 - 1.82: 232 Bond restraints: 37739 Sorted by residual: bond pdb=" N ILE A 515 " pdb=" CA ILE A 515 " ideal model delta sigma weight residual 1.461 1.496 -0.035 1.19e-02 7.06e+03 8.68e+00 bond pdb=" N VAL H 584 " pdb=" CA VAL H 584 " ideal model delta sigma weight residual 1.461 1.495 -0.034 1.19e-02 7.06e+03 8.26e+00 bond pdb=" N ASN H 192 " pdb=" CA ASN H 192 " ideal model delta sigma weight residual 1.458 1.488 -0.030 1.12e-02 7.97e+03 7.14e+00 bond pdb=" N ILE H 582 " pdb=" CA ILE H 582 " ideal model delta sigma weight residual 1.460 1.492 -0.032 1.21e-02 6.83e+03 6.96e+00 bond pdb=" N ARG A 517 " pdb=" CA ARG A 517 " ideal model delta sigma weight residual 1.459 1.489 -0.030 1.16e-02 7.43e+03 6.91e+00 ... (remaining 37734 not shown) Histogram of bond angle deviations from ideal: 98.48 - 105.60: 406 105.60 - 112.73: 19035 112.73 - 119.86: 12933 119.86 - 126.99: 18217 126.99 - 134.12: 273 Bond angle restraints: 50864 Sorted by residual: angle pdb=" CB GLN B 28 " pdb=" CG GLN B 28 " pdb=" CD GLN B 28 " ideal model delta sigma weight residual 112.60 119.87 -7.27 1.70e+00 3.46e-01 1.83e+01 angle pdb=" CB MET D 396 " pdb=" CG MET D 396 " pdb=" SD MET D 396 " ideal model delta sigma weight residual 112.70 124.93 -12.23 3.00e+00 1.11e-01 1.66e+01 angle pdb=" CA PRO C 49 " pdb=" N PRO C 49 " pdb=" CD PRO C 49 " ideal model delta sigma weight residual 112.00 106.35 5.65 1.40e+00 5.10e-01 1.63e+01 angle pdb=" CB MET F 204 " pdb=" CG MET F 204 " pdb=" SD MET F 204 " ideal model delta sigma weight residual 112.70 123.99 -11.29 3.00e+00 1.11e-01 1.42e+01 angle pdb=" N SER D 54 " pdb=" CA SER D 54 " pdb=" C SER D 54 " ideal model delta sigma weight residual 113.21 108.90 4.31 1.15e+00 7.56e-01 1.41e+01 ... (remaining 50859 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.96: 19414 17.96 - 35.93: 2415 35.93 - 53.89: 459 53.89 - 71.85: 202 71.85 - 89.82: 28 Dihedral angle restraints: 22518 sinusoidal: 9309 harmonic: 13209 Sorted by residual: dihedral pdb=" CA ALA E 179 " pdb=" C ALA E 179 " pdb=" N TYR E 180 " pdb=" CA TYR E 180 " ideal model delta harmonic sigma weight residual 180.00 155.24 24.76 0 5.00e+00 4.00e-02 2.45e+01 dihedral pdb=" CA GLN B 194 " pdb=" C GLN B 194 " pdb=" N PHE B 195 " pdb=" CA PHE B 195 " ideal model delta harmonic sigma weight residual 180.00 157.27 22.73 0 5.00e+00 4.00e-02 2.07e+01 dihedral pdb=" CA MET A 704 " pdb=" C MET A 704 " pdb=" N ASN A 705 " pdb=" CA ASN A 705 " ideal model delta harmonic sigma weight residual 180.00 159.85 20.15 0 5.00e+00 4.00e-02 1.62e+01 ... (remaining 22515 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 4032 0.040 - 0.080: 1070 0.080 - 0.120: 275 0.120 - 0.159: 31 0.159 - 0.199: 3 Chirality restraints: 5411 Sorted by residual: chirality pdb=" CA ILE H 582 " pdb=" N ILE H 582 " pdb=" C ILE H 582 " pdb=" CB ILE H 582 " both_signs ideal model delta sigma weight residual False 2.43 2.63 -0.20 2.00e-01 2.50e+01 9.93e-01 chirality pdb=" CA LEU H 585 " pdb=" N LEU H 585 " pdb=" C LEU H 585 " pdb=" CB LEU H 585 " both_signs ideal model delta sigma weight residual False 2.51 2.68 -0.17 2.00e-01 2.50e+01 7.16e-01 chirality pdb=" CA VAL H 583 " pdb=" N VAL H 583 " pdb=" C VAL H 583 " pdb=" CB VAL H 583 " both_signs ideal model delta sigma weight residual False 2.44 2.60 -0.16 2.00e-01 2.50e+01 6.61e-01 ... (remaining 5408 not shown) Planarity restraints: 6518 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR A 56 " -0.043 5.00e-02 4.00e+02 6.42e-02 6.59e+00 pdb=" N PRO A 57 " 0.111 5.00e-02 4.00e+02 pdb=" CA PRO A 57 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO A 57 " -0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASN H 125 " 0.009 2.00e-02 2.50e+03 1.74e-02 3.02e+00 pdb=" C ASN H 125 " -0.030 2.00e-02 2.50e+03 pdb=" O ASN H 125 " 0.011 2.00e-02 2.50e+03 pdb=" N PRO H 126 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE G 52 " -0.008 2.00e-02 2.50e+03 1.67e-02 2.78e+00 pdb=" C ILE G 52 " 0.029 2.00e-02 2.50e+03 pdb=" O ILE G 52 " -0.011 2.00e-02 2.50e+03 pdb=" N LEU G 53 " -0.010 2.00e-02 2.50e+03 ... (remaining 6515 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 3144 2.74 - 3.28: 40879 3.28 - 3.82: 63541 3.82 - 4.36: 77064 4.36 - 4.90: 124274 Nonbonded interactions: 308902 Sorted by model distance: nonbonded pdb=" O SER D 817 " pdb=" OG SER D 821 " model vdw 2.201 2.440 nonbonded pdb=" OH TYR A 800 " pdb=" O ASP B 225 " model vdw 2.207 2.440 nonbonded pdb=" O GLU D 181 " pdb=" OH TYR D 197 " model vdw 2.209 2.440 nonbonded pdb=" O VAL C 11 " pdb=" OG1 THR C 24 " model vdw 2.211 2.440 nonbonded pdb=" O GLU A 362 " pdb=" OG SER A 366 " model vdw 2.211 2.440 ... (remaining 308897 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' selection = chain 'D' selection = chain 'F' selection = chain 'H' } ncs_group { reference = (chain 'B' and (resid 9 through 76 or resid 173 through 234)) selection = (chain 'C' and (resid 9 through 76 or resid 173 through 234)) selection = chain 'E' selection = (chain 'G' and (resid 9 through 76 or resid 173 through 234)) } 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: 6.950 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: 1.310 Check model and map are aligned: 0.270 Set scattering table: 0.330 Process input model: 96.430 Find NCS groups from input model: 1.550 Set up NCS constraints: 0.160 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 109.870 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7945 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 0.115 37739 Z= 0.163 Angle : 0.563 12.226 50864 Z= 0.300 Chirality : 0.039 0.199 5411 Planarity : 0.003 0.064 6518 Dihedral : 16.804 89.818 14032 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 11.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer: Outliers : 0.37 % Allowed : 22.37 % Favored : 77.26 % 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: -0.31 (0.12), residues: 4435 helix: 0.67 (0.11), residues: 2126 sheet: -1.65 (0.34), residues: 230 loop : -0.92 (0.13), residues: 2079 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 60 HIS 0.006 0.001 HIS F 658 PHE 0.018 0.001 PHE F 742 TYR 0.022 0.001 TYR A 356 ARG 0.007 0.000 ARG H 629 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8870 Ramachandran restraints generated. 4435 Oldfield, 0 Emsley, 4435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8870 Ramachandran restraints generated. 4435 Oldfield, 0 Emsley, 4435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 322 residues out of total 4055 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 307 time to evaluate : 5.221 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 974 LYS cc_start: 0.7959 (tptp) cc_final: 0.7652 (mmmt) REVERT: C 53 LEU cc_start: 0.6968 (mm) cc_final: 0.6406 (tp) REVERT: C 175 TYR cc_start: 0.6170 (p90) cc_final: 0.5958 (p90) REVERT: C 231 MET cc_start: 0.6440 (mtt) cc_final: 0.6173 (mtt) REVERT: D 976 MET cc_start: 0.5785 (pmm) cc_final: 0.5238 (mpp) REVERT: E 75 MET cc_start: 0.0340 (pmm) cc_final: -0.1619 (tpp) REVERT: F 519 MET cc_start: 0.7189 (mmm) cc_final: 0.6987 (tpt) REVERT: F 722 PHE cc_start: 0.8723 (m-80) cc_final: 0.8365 (m-80) REVERT: F 763 LYS cc_start: 0.5134 (tptt) cc_final: 0.4518 (mttp) REVERT: H 498 LEU cc_start: 0.7232 (OUTLIER) cc_final: 0.6977 (pp) REVERT: H 519 MET cc_start: 0.6937 (tmm) cc_final: 0.6553 (tmm) REVERT: H 526 ASP cc_start: 0.8601 (p0) cc_final: 0.8369 (p0) REVERT: H 569 MET cc_start: 0.8933 (tmm) cc_final: 0.8637 (tpp) REVERT: H 702 ASN cc_start: 0.8243 (t0) cc_final: 0.8042 (p0) REVERT: H 758 LEU cc_start: 0.8674 (mt) cc_final: 0.8312 (pp) REVERT: H 913 MET cc_start: 0.7125 (tmm) cc_final: 0.6663 (tmm) outliers start: 15 outliers final: 3 residues processed: 317 average time/residue: 0.4930 time to fit residues: 257.6780 Evaluate side-chains 226 residues out of total 4055 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 222 time to evaluate : 4.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 728 LEU Chi-restraints excluded: chain H residue 227 MET Chi-restraints excluded: chain H residue 498 LEU Chi-restraints excluded: chain H residue 584 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 374 optimal weight: 0.0270 chunk 336 optimal weight: 3.9990 chunk 186 optimal weight: 0.0970 chunk 114 optimal weight: 10.0000 chunk 227 optimal weight: 5.9990 chunk 179 optimal weight: 7.9990 chunk 348 optimal weight: 3.9990 chunk 134 optimal weight: 0.2980 chunk 211 optimal weight: 6.9990 chunk 259 optimal weight: 8.9990 chunk 403 optimal weight: 8.9990 overall best weight: 1.6840 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 666 ASN A 786 HIS ** B 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 563 ASN ** D 961 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 711 GLN ** H 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 323 GLN ** H 614 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 927 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8009 moved from start: 0.1609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 37739 Z= 0.202 Angle : 0.553 11.141 50864 Z= 0.293 Chirality : 0.040 0.165 5411 Planarity : 0.003 0.064 6518 Dihedral : 4.020 39.083 4899 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 14.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 2.54 % Allowed : 20.81 % Favored : 76.65 % 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: -0.30 (0.13), residues: 4435 helix: 0.73 (0.11), residues: 2338 sheet: -2.11 (0.34), residues: 206 loop : -1.10 (0.14), residues: 1891 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 231 HIS 0.008 0.001 HIS F 658 PHE 0.016 0.001 PHE D 943 TYR 0.025 0.001 TYR A 755 ARG 0.009 0.000 ARG H 892 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8870 Ramachandran restraints generated. 4435 Oldfield, 0 Emsley, 4435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8870 Ramachandran restraints generated. 4435 Oldfield, 0 Emsley, 4435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 337 residues out of total 4055 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 234 time to evaluate : 3.941 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 713 ILE cc_start: 0.9145 (OUTLIER) cc_final: 0.8878 (mt) REVERT: A 913 MET cc_start: 0.7926 (OUTLIER) cc_final: 0.7418 (mmm) REVERT: A 974 LYS cc_start: 0.7985 (tptp) cc_final: 0.7671 (mmmt) REVERT: A 987 ARG cc_start: 0.7945 (OUTLIER) cc_final: 0.7389 (tpm170) REVERT: C 231 MET cc_start: 0.6382 (mtt) cc_final: 0.6135 (mtt) REVERT: D 683 LYS cc_start: 0.9110 (OUTLIER) cc_final: 0.8852 (ttpp) REVERT: D 936 MET cc_start: 0.5248 (tpp) cc_final: 0.4980 (tpp) REVERT: D 976 MET cc_start: 0.6023 (pmm) cc_final: 0.5212 (mpp) REVERT: E 68 PHE cc_start: 0.4475 (OUTLIER) cc_final: 0.3902 (t80) REVERT: E 231 MET cc_start: 0.0506 (mmt) cc_final: -0.1447 (mmp) REVERT: F 228 LEU cc_start: 0.9377 (OUTLIER) cc_final: 0.9127 (tt) REVERT: F 368 ASP cc_start: 0.8881 (OUTLIER) cc_final: 0.8525 (p0) REVERT: F 763 LYS cc_start: 0.5228 (tptt) cc_final: 0.4577 (mttp) REVERT: F 979 HIS cc_start: 0.7138 (OUTLIER) cc_final: 0.5600 (m-70) REVERT: G 64 LYS cc_start: 0.7957 (mmtm) cc_final: 0.7724 (tppt) REVERT: H 227 MET cc_start: 0.8677 (tmm) cc_final: 0.8450 (tmm) REVERT: H 445 LEU cc_start: 0.9227 (OUTLIER) cc_final: 0.8912 (mm) REVERT: H 450 GLU cc_start: 0.7545 (OUTLIER) cc_final: 0.7236 (mp0) REVERT: H 519 MET cc_start: 0.6938 (tmm) cc_final: 0.6183 (tmm) REVERT: H 526 ASP cc_start: 0.8530 (p0) cc_final: 0.8328 (p0) REVERT: H 913 MET cc_start: 0.6990 (tmm) cc_final: 0.6601 (tmm) outliers start: 103 outliers final: 46 residues processed: 327 average time/residue: 0.4452 time to fit residues: 247.9553 Evaluate side-chains 262 residues out of total 4055 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 206 time to evaluate : 4.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 TYR Chi-restraints excluded: chain A residue 434 ASP Chi-restraints excluded: chain A residue 493 ASN Chi-restraints excluded: chain A residue 499 THR Chi-restraints excluded: chain A residue 556 VAL Chi-restraints excluded: chain A residue 603 VAL Chi-restraints excluded: chain A residue 676 ILE Chi-restraints excluded: chain A residue 713 ILE Chi-restraints excluded: chain A residue 761 LEU Chi-restraints excluded: chain A residue 913 MET Chi-restraints excluded: chain A residue 987 ARG Chi-restraints excluded: chain B residue 199 SER Chi-restraints excluded: chain D residue 66 TYR Chi-restraints excluded: chain D residue 151 VAL Chi-restraints excluded: chain D residue 200 ILE Chi-restraints excluded: chain D residue 305 ASP Chi-restraints excluded: chain D residue 673 ILE Chi-restraints excluded: chain D residue 683 LYS Chi-restraints excluded: chain D residue 707 VAL Chi-restraints excluded: chain D residue 756 VAL Chi-restraints excluded: chain E residue 52 ILE Chi-restraints excluded: chain E residue 68 PHE Chi-restraints excluded: chain E residue 197 ASN Chi-restraints excluded: chain E residue 226 THR Chi-restraints excluded: chain F residue 157 ASP Chi-restraints excluded: chain F residue 228 LEU Chi-restraints excluded: chain F residue 301 PHE Chi-restraints excluded: chain F residue 368 ASP Chi-restraints excluded: chain F residue 403 LEU Chi-restraints excluded: chain F residue 554 ASP Chi-restraints excluded: chain F residue 658 HIS Chi-restraints excluded: chain F residue 807 LEU Chi-restraints excluded: chain F residue 823 ILE Chi-restraints excluded: chain F residue 915 THR Chi-restraints excluded: chain F residue 928 SER Chi-restraints excluded: chain F residue 930 MET Chi-restraints excluded: chain F residue 955 ILE Chi-restraints excluded: chain F residue 979 HIS Chi-restraints excluded: chain G residue 29 THR Chi-restraints excluded: chain G residue 221 GLU Chi-restraints excluded: chain G residue 233 VAL Chi-restraints excluded: chain H residue 23 ASP Chi-restraints excluded: chain H residue 30 ILE Chi-restraints excluded: chain H residue 200 ILE Chi-restraints excluded: chain H residue 255 ASN Chi-restraints excluded: chain H residue 399 ASP Chi-restraints excluded: chain H residue 419 ASP Chi-restraints excluded: chain H residue 445 LEU Chi-restraints excluded: chain H residue 450 GLU Chi-restraints excluded: chain H residue 554 ASP Chi-restraints excluded: chain H residue 636 PHE Chi-restraints excluded: chain H residue 651 ASP Chi-restraints excluded: chain H residue 662 ASP Chi-restraints excluded: chain H residue 673 ILE Chi-restraints excluded: chain H residue 764 CYS Chi-restraints excluded: chain H residue 883 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 224 optimal weight: 20.0000 chunk 125 optimal weight: 6.9990 chunk 335 optimal weight: 20.0000 chunk 274 optimal weight: 0.9990 chunk 111 optimal weight: 9.9990 chunk 403 optimal weight: 8.9990 chunk 436 optimal weight: 5.9990 chunk 359 optimal weight: 3.9990 chunk 400 optimal weight: 6.9990 chunk 137 optimal weight: 6.9990 chunk 324 optimal weight: 4.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 236 GLN ** A 477 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 786 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 765 ASN ** D 797 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 829 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 834 GLN ** D 961 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 349 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 658 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 711 GLN F 829 GLN F 832 GLN F 881 HIS F 990 ASN H 299 ASN ** H 536 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 591 ASN ** H 614 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 810 HIS H 867 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8188 moved from start: 0.2987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.081 37739 Z= 0.431 Angle : 0.697 12.677 50864 Z= 0.373 Chirality : 0.044 0.175 5411 Planarity : 0.005 0.062 6518 Dihedral : 4.572 26.324 4891 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 23.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.98 % Favored : 94.02 % Rotamer: Outliers : 5.01 % Allowed : 20.76 % Favored : 74.23 % 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: -0.63 (0.12), residues: 4435 helix: 0.40 (0.10), residues: 2344 sheet: -2.27 (0.34), residues: 215 loop : -1.18 (0.14), residues: 1876 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 59 HIS 0.013 0.002 HIS D 978 PHE 0.026 0.002 PHE D 174 TYR 0.035 0.002 TYR A1003 ARG 0.005 0.001 ARG D 566 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8870 Ramachandran restraints generated. 4435 Oldfield, 0 Emsley, 4435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8870 Ramachandran restraints generated. 4435 Oldfield, 0 Emsley, 4435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 411 residues out of total 4055 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 203 poor density : 208 time to evaluate : 4.321 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 442 LEU cc_start: 0.8533 (OUTLIER) cc_final: 0.8190 (tp) REVERT: A 631 ILE cc_start: 0.8687 (OUTLIER) cc_final: 0.8352 (mp) REVERT: A 713 ILE cc_start: 0.9184 (OUTLIER) cc_final: 0.8854 (mt) REVERT: A 913 MET cc_start: 0.7940 (OUTLIER) cc_final: 0.7495 (mmm) REVERT: A 987 ARG cc_start: 0.8211 (OUTLIER) cc_final: 0.7809 (tpm170) REVERT: B 39 GLU cc_start: 0.6484 (OUTLIER) cc_final: 0.4942 (mp0) REVERT: B 190 ASP cc_start: 0.4230 (OUTLIER) cc_final: 0.3986 (m-30) REVERT: D 281 ASP cc_start: 0.7993 (OUTLIER) cc_final: 0.7764 (p0) REVERT: D 531 MET cc_start: 0.9049 (tmm) cc_final: 0.8647 (tmm) REVERT: D 784 GLU cc_start: 0.8821 (mt-10) cc_final: 0.8384 (mt-10) REVERT: E 228 THR cc_start: 0.5524 (m) cc_final: 0.5284 (m) REVERT: F 61 ARG cc_start: 0.8497 (OUTLIER) cc_final: 0.8245 (mtm110) REVERT: F 368 ASP cc_start: 0.8901 (OUTLIER) cc_final: 0.8570 (p0) REVERT: F 396 MET cc_start: 0.7907 (ttt) cc_final: 0.7668 (ttt) REVERT: F 569 MET cc_start: 0.7213 (ptp) cc_final: 0.6564 (mtm) REVERT: F 763 LYS cc_start: 0.5458 (tptt) cc_final: 0.4622 (mttp) REVERT: F 797 ASN cc_start: 0.7697 (OUTLIER) cc_final: 0.7140 (p0) REVERT: F 979 HIS cc_start: 0.6715 (OUTLIER) cc_final: 0.5800 (m-70) REVERT: H 432 ILE cc_start: 0.8933 (OUTLIER) cc_final: 0.8718 (mt) REVERT: H 450 GLU cc_start: 0.7314 (OUTLIER) cc_final: 0.6895 (mp0) REVERT: H 498 LEU cc_start: 0.7499 (OUTLIER) cc_final: 0.7267 (pp) REVERT: H 519 MET cc_start: 0.7239 (tmm) cc_final: 0.6599 (tmm) outliers start: 203 outliers final: 100 residues processed: 387 average time/residue: 0.4816 time to fit residues: 321.2881 Evaluate side-chains 305 residues out of total 4055 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 115 poor density : 190 time to evaluate : 4.670 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 134 TYR Chi-restraints excluded: chain A residue 200 ILE Chi-restraints excluded: chain A residue 234 LYS Chi-restraints excluded: chain A residue 236 GLN Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 328 ILE Chi-restraints excluded: chain A residue 434 ASP Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 459 ILE Chi-restraints excluded: chain A residue 493 ASN Chi-restraints excluded: chain A residue 499 THR Chi-restraints excluded: chain A residue 565 VAL Chi-restraints excluded: chain A residue 588 LEU Chi-restraints excluded: chain A residue 598 ASN Chi-restraints excluded: chain A residue 603 VAL Chi-restraints excluded: chain A residue 631 ILE Chi-restraints excluded: chain A residue 676 ILE Chi-restraints excluded: chain A residue 713 ILE Chi-restraints excluded: chain A residue 761 LEU Chi-restraints excluded: chain A residue 851 SER Chi-restraints excluded: chain A residue 873 LEU Chi-restraints excluded: chain A residue 913 MET Chi-restraints excluded: chain A residue 978 HIS Chi-restraints excluded: chain A residue 987 ARG Chi-restraints excluded: chain A residue 990 ASN Chi-restraints excluded: chain A residue 1004 PHE Chi-restraints excluded: chain B residue 39 GLU Chi-restraints excluded: chain B residue 52 ILE Chi-restraints excluded: chain B residue 190 ASP Chi-restraints excluded: chain D residue 66 TYR Chi-restraints excluded: chain D residue 142 CYS Chi-restraints excluded: chain D residue 143 TRP Chi-restraints excluded: chain D residue 151 VAL Chi-restraints excluded: chain D residue 200 ILE Chi-restraints excluded: chain D residue 262 GLU Chi-restraints excluded: chain D residue 281 ASP Chi-restraints excluded: chain D residue 305 ASP Chi-restraints excluded: chain D residue 328 ILE Chi-restraints excluded: chain D residue 454 LEU Chi-restraints excluded: chain D residue 508 THR Chi-restraints excluded: chain D residue 515 ILE Chi-restraints excluded: chain D residue 662 ASP Chi-restraints excluded: chain D residue 673 ILE Chi-restraints excluded: chain D residue 707 VAL Chi-restraints excluded: chain D residue 756 VAL Chi-restraints excluded: chain D residue 776 ASP Chi-restraints excluded: chain D residue 859 VAL Chi-restraints excluded: chain D residue 937 ASP Chi-restraints excluded: chain D residue 969 LYS Chi-restraints excluded: chain E residue 52 ILE Chi-restraints excluded: chain E residue 63 VAL Chi-restraints excluded: chain E residue 68 PHE Chi-restraints excluded: chain E residue 70 LEU Chi-restraints excluded: chain E residue 187 VAL Chi-restraints excluded: chain E residue 197 ASN Chi-restraints excluded: chain E residue 226 THR Chi-restraints excluded: chain F residue 61 ARG Chi-restraints excluded: chain F residue 124 MET Chi-restraints excluded: chain F residue 157 ASP Chi-restraints excluded: chain F residue 294 ILE Chi-restraints excluded: chain F residue 301 PHE Chi-restraints excluded: chain F residue 368 ASP Chi-restraints excluded: chain F residue 399 ASP Chi-restraints excluded: chain F residue 403 LEU Chi-restraints excluded: chain F residue 467 ASN Chi-restraints excluded: chain F residue 584 VAL Chi-restraints excluded: chain F residue 619 LEU Chi-restraints excluded: chain F residue 658 HIS Chi-restraints excluded: chain F residue 722 PHE Chi-restraints excluded: chain F residue 728 LEU Chi-restraints excluded: chain F residue 761 LEU Chi-restraints excluded: chain F residue 775 ILE Chi-restraints excluded: chain F residue 797 ASN Chi-restraints excluded: chain F residue 807 LEU Chi-restraints excluded: chain F residue 814 ASN Chi-restraints excluded: chain F residue 823 ILE Chi-restraints excluded: chain F residue 866 MET Chi-restraints excluded: chain F residue 915 THR Chi-restraints excluded: chain F residue 929 LYS Chi-restraints excluded: chain F residue 930 MET Chi-restraints excluded: chain F residue 955 ILE Chi-restraints excluded: chain F residue 979 HIS Chi-restraints excluded: chain F residue 1004 PHE Chi-restraints excluded: chain G residue 29 THR Chi-restraints excluded: chain G residue 63 VAL Chi-restraints excluded: chain G residue 221 GLU Chi-restraints excluded: chain G residue 231 MET Chi-restraints excluded: chain G residue 233 VAL Chi-restraints excluded: chain H residue 23 ASP Chi-restraints excluded: chain H residue 30 ILE Chi-restraints excluded: chain H residue 135 ASP Chi-restraints excluded: chain H residue 200 ILE Chi-restraints excluded: chain H residue 255 ASN Chi-restraints excluded: chain H residue 305 ASP Chi-restraints excluded: chain H residue 399 ASP Chi-restraints excluded: chain H residue 432 ILE Chi-restraints excluded: chain H residue 450 GLU Chi-restraints excluded: chain H residue 464 ASP Chi-restraints excluded: chain H residue 498 LEU Chi-restraints excluded: chain H residue 524 ILE Chi-restraints excluded: chain H residue 547 ASP Chi-restraints excluded: chain H residue 554 ASP Chi-restraints excluded: chain H residue 558 LEU Chi-restraints excluded: chain H residue 636 PHE Chi-restraints excluded: chain H residue 662 ASP Chi-restraints excluded: chain H residue 673 ILE Chi-restraints excluded: chain H residue 691 ILE Chi-restraints excluded: chain H residue 726 VAL Chi-restraints excluded: chain H residue 764 CYS Chi-restraints excluded: chain H residue 810 HIS Chi-restraints excluded: chain H residue 883 GLU Chi-restraints excluded: chain H residue 986 GLU Chi-restraints excluded: chain H residue 1004 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 399 optimal weight: 1.9990 chunk 303 optimal weight: 0.9980 chunk 209 optimal weight: 7.9990 chunk 44 optimal weight: 1.9990 chunk 192 optimal weight: 0.9980 chunk 271 optimal weight: 0.9980 chunk 405 optimal weight: 1.9990 chunk 429 optimal weight: 0.0980 chunk 211 optimal weight: 1.9990 chunk 384 optimal weight: 0.6980 chunk 115 optimal weight: 2.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 961 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 349 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 563 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 210 ASN ** H 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 299 ASN H 536 GLN H 591 ASN ** H 614 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 810 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8091 moved from start: 0.2917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.050 37739 Z= 0.152 Angle : 0.531 13.482 50864 Z= 0.274 Chirality : 0.039 0.160 5411 Planarity : 0.003 0.049 6518 Dihedral : 4.179 24.553 4891 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 15.16 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.26 % Favored : 95.72 % Rotamer: Outliers : 3.11 % Allowed : 22.22 % Favored : 74.67 % 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: -0.24 (0.13), residues: 4435 helix: 0.76 (0.11), residues: 2336 sheet: -2.04 (0.34), residues: 228 loop : -1.03 (0.15), residues: 1871 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP E 72 HIS 0.008 0.001 HIS F 658 PHE 0.016 0.001 PHE E 67 TYR 0.024 0.001 TYR A 755 ARG 0.009 0.000 ARG H 760 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8870 Ramachandran restraints generated. 4435 Oldfield, 0 Emsley, 4435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8870 Ramachandran restraints generated. 4435 Oldfield, 0 Emsley, 4435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 339 residues out of total 4055 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 126 poor density : 213 time to evaluate : 4.317 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: A 204 MET cc_start: 0.8996 (tmm) cc_final: 0.8222 (tmm) REVERT: A 442 LEU cc_start: 0.8366 (OUTLIER) cc_final: 0.8033 (tp) REVERT: A 613 ARG cc_start: 0.8167 (OUTLIER) cc_final: 0.7853 (ttm170) REVERT: A 713 ILE cc_start: 0.9022 (OUTLIER) cc_final: 0.8697 (mt) REVERT: A 974 LYS cc_start: 0.8213 (tptp) cc_final: 0.7833 (mmmt) REVERT: A 987 ARG cc_start: 0.8120 (OUTLIER) cc_final: 0.7608 (tpm170) REVERT: B 177 THR cc_start: 0.5342 (OUTLIER) cc_final: 0.4881 (p) REVERT: B 205 GLU cc_start: 0.7592 (pp20) cc_final: 0.7290 (pp20) REVERT: C 206 MET cc_start: 0.7133 (ppp) cc_final: 0.6914 (ptm) REVERT: D 531 MET cc_start: 0.8571 (OUTLIER) cc_final: 0.8217 (ttt) REVERT: D 784 GLU cc_start: 0.8791 (mt-10) cc_final: 0.8320 (mt-10) REVERT: E 68 PHE cc_start: 0.4193 (OUTLIER) cc_final: 0.3655 (t80) REVERT: E 228 THR cc_start: 0.5297 (m) cc_final: 0.5015 (m) REVERT: F 368 ASP cc_start: 0.8879 (OUTLIER) cc_final: 0.8620 (p0) REVERT: F 763 LYS cc_start: 0.5166 (tptt) cc_final: 0.4315 (mtmm) REVERT: F 797 ASN cc_start: 0.7303 (OUTLIER) cc_final: 0.6639 (p0) REVERT: F 979 HIS cc_start: 0.6962 (OUTLIER) cc_final: 0.5914 (m-70) REVERT: H 193 TYR cc_start: 0.8316 (t80) cc_final: 0.8099 (t80) REVERT: H 432 ILE cc_start: 0.8845 (OUTLIER) cc_final: 0.8632 (mt) REVERT: H 450 GLU cc_start: 0.7289 (OUTLIER) cc_final: 0.6885 (mp0) REVERT: H 498 LEU cc_start: 0.7305 (OUTLIER) cc_final: 0.7076 (pp) REVERT: H 519 MET cc_start: 0.7167 (tmm) cc_final: 0.6488 (tmm) outliers start: 126 outliers final: 63 residues processed: 323 average time/residue: 0.4319 time to fit residues: 239.7824 Evaluate side-chains 274 residues out of total 4055 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 198 time to evaluate : 4.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 TYR Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain A residue 339 HIS Chi-restraints excluded: chain A residue 434 ASP Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 499 THR Chi-restraints excluded: chain A residue 508 THR Chi-restraints excluded: chain A residue 603 VAL Chi-restraints excluded: chain A residue 613 ARG Chi-restraints excluded: chain A residue 619 LEU Chi-restraints excluded: chain A residue 706 VAL Chi-restraints excluded: chain A residue 713 ILE Chi-restraints excluded: chain A residue 761 LEU Chi-restraints excluded: chain A residue 821 SER Chi-restraints excluded: chain A residue 978 HIS Chi-restraints excluded: chain A residue 987 ARG Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain D residue 46 VAL Chi-restraints excluded: chain D residue 142 CYS Chi-restraints excluded: chain D residue 200 ILE Chi-restraints excluded: chain D residue 328 ILE Chi-restraints excluded: chain D residue 463 ILE Chi-restraints excluded: chain D residue 531 MET Chi-restraints excluded: chain D residue 673 ILE Chi-restraints excluded: chain D residue 707 VAL Chi-restraints excluded: chain D residue 776 ASP Chi-restraints excluded: chain D residue 937 ASP Chi-restraints excluded: chain D residue 1001 MET Chi-restraints excluded: chain E residue 21 LEU Chi-restraints excluded: chain E residue 52 ILE Chi-restraints excluded: chain E residue 68 PHE Chi-restraints excluded: chain E residue 178 ILE Chi-restraints excluded: chain E residue 197 ASN Chi-restraints excluded: chain F residue 134 TYR Chi-restraints excluded: chain F residue 157 ASP Chi-restraints excluded: chain F residue 294 ILE Chi-restraints excluded: chain F residue 301 PHE Chi-restraints excluded: chain F residue 368 ASP Chi-restraints excluded: chain F residue 372 LYS Chi-restraints excluded: chain F residue 403 LEU Chi-restraints excluded: chain F residue 467 ASN Chi-restraints excluded: chain F residue 619 LEU Chi-restraints excluded: chain F residue 658 HIS Chi-restraints excluded: chain F residue 722 PHE Chi-restraints excluded: chain F residue 728 LEU Chi-restraints excluded: chain F residue 797 ASN Chi-restraints excluded: chain F residue 807 LEU Chi-restraints excluded: chain F residue 823 ILE Chi-restraints excluded: chain F residue 928 SER Chi-restraints excluded: chain F residue 929 LYS Chi-restraints excluded: chain F residue 955 ILE Chi-restraints excluded: chain F residue 979 HIS Chi-restraints excluded: chain F residue 1004 PHE Chi-restraints excluded: chain G residue 29 THR Chi-restraints excluded: chain G residue 221 GLU Chi-restraints excluded: chain G residue 231 MET Chi-restraints excluded: chain H residue 23 ASP Chi-restraints excluded: chain H residue 135 ASP Chi-restraints excluded: chain H residue 200 ILE Chi-restraints excluded: chain H residue 255 ASN Chi-restraints excluded: chain H residue 305 ASP Chi-restraints excluded: chain H residue 399 ASP Chi-restraints excluded: chain H residue 432 ILE Chi-restraints excluded: chain H residue 450 GLU Chi-restraints excluded: chain H residue 498 LEU Chi-restraints excluded: chain H residue 547 ASP Chi-restraints excluded: chain H residue 636 PHE Chi-restraints excluded: chain H residue 651 ASP Chi-restraints excluded: chain H residue 673 ILE Chi-restraints excluded: chain H residue 684 ILE Chi-restraints excluded: chain H residue 693 GLU Chi-restraints excluded: chain H residue 726 VAL Chi-restraints excluded: chain H residue 810 HIS Chi-restraints excluded: chain H residue 883 GLU Chi-restraints excluded: chain H residue 930 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 357 optimal weight: 0.2980 chunk 243 optimal weight: 0.8980 chunk 6 optimal weight: 0.1980 chunk 319 optimal weight: 7.9990 chunk 177 optimal weight: 0.6980 chunk 366 optimal weight: 1.9990 chunk 296 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 219 optimal weight: 0.6980 chunk 385 optimal weight: 3.9990 chunk 108 optimal weight: 1.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- 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 263 ASN A 711 GLN ** D 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 230 ASN ** D 961 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 349 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 382 ASN F 415 HIS ** F 563 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 195 GLN ** H 614 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 810 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8069 moved from start: 0.2992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 37739 Z= 0.137 Angle : 0.502 14.894 50864 Z= 0.259 Chirality : 0.039 0.223 5411 Planarity : 0.003 0.048 6518 Dihedral : 3.967 24.634 4891 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 14.14 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.53 % Favored : 95.45 % Rotamer: Outliers : 2.76 % Allowed : 22.24 % Favored : 74.99 % 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: -0.12 (0.13), residues: 4435 helix: 0.88 (0.11), residues: 2345 sheet: -2.11 (0.33), residues: 241 loop : -0.99 (0.15), residues: 1849 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP E 72 HIS 0.007 0.001 HIS F 658 PHE 0.030 0.001 PHE B 220 TYR 0.022 0.001 TYR A 755 ARG 0.005 0.000 ARG H 760 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8870 Ramachandran restraints generated. 4435 Oldfield, 0 Emsley, 4435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8870 Ramachandran restraints generated. 4435 Oldfield, 0 Emsley, 4435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 320 residues out of total 4055 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 112 poor density : 208 time to evaluate : 4.428 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 204 MET cc_start: 0.8989 (tmm) cc_final: 0.8238 (tmm) REVERT: A 613 ARG cc_start: 0.8149 (OUTLIER) cc_final: 0.7929 (ttm170) REVERT: A 713 ILE cc_start: 0.9005 (OUTLIER) cc_final: 0.8679 (mt) REVERT: A 974 LYS cc_start: 0.8109 (tptp) cc_final: 0.7739 (mmmt) REVERT: B 177 THR cc_start: 0.5349 (OUTLIER) cc_final: 0.5036 (p) REVERT: B 205 GLU cc_start: 0.7592 (pp20) cc_final: 0.7192 (pp20) REVERT: C 206 MET cc_start: 0.6969 (ppp) cc_final: 0.6759 (ptm) REVERT: D 135 ASP cc_start: 0.8189 (OUTLIER) cc_final: 0.7531 (m-30) REVERT: D 784 GLU cc_start: 0.8801 (mt-10) cc_final: 0.8362 (mt-10) REVERT: E 68 PHE cc_start: 0.4262 (OUTLIER) cc_final: 0.3757 (t80) REVERT: E 228 THR cc_start: 0.5305 (m) cc_final: 0.5057 (m) REVERT: E 231 MET cc_start: 0.0994 (mmp) cc_final: 0.0192 (mmp) REVERT: F 763 LYS cc_start: 0.5154 (tptt) cc_final: 0.4356 (mtmm) REVERT: F 797 ASN cc_start: 0.7253 (OUTLIER) cc_final: 0.6604 (p0) REVERT: F 979 HIS cc_start: 0.7098 (OUTLIER) cc_final: 0.6076 (m-70) REVERT: H 193 TYR cc_start: 0.8208 (t80) cc_final: 0.7994 (t80) REVERT: H 450 GLU cc_start: 0.7316 (OUTLIER) cc_final: 0.6914 (pm20) REVERT: H 498 LEU cc_start: 0.7239 (OUTLIER) cc_final: 0.7019 (pp) REVERT: H 519 MET cc_start: 0.7095 (tmm) cc_final: 0.6378 (tmm) REVERT: H 913 MET cc_start: 0.7238 (tmm) cc_final: 0.7030 (tmm) outliers start: 112 outliers final: 70 residues processed: 308 average time/residue: 0.4681 time to fit residues: 250.5134 Evaluate side-chains 281 residues out of total 4055 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 202 time to evaluate : 4.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 ASP Chi-restraints excluded: chain A residue 134 TYR Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 339 HIS Chi-restraints excluded: chain A residue 499 THR Chi-restraints excluded: chain A residue 508 THR Chi-restraints excluded: chain A residue 603 VAL Chi-restraints excluded: chain A residue 613 ARG Chi-restraints excluded: chain A residue 619 LEU Chi-restraints excluded: chain A residue 713 ILE Chi-restraints excluded: chain A residue 761 LEU Chi-restraints excluded: chain A residue 978 HIS Chi-restraints excluded: chain B residue 45 ILE Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 209 GLU Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain D residue 46 VAL Chi-restraints excluded: chain D residue 66 TYR Chi-restraints excluded: chain D residue 135 ASP Chi-restraints excluded: chain D residue 142 CYS Chi-restraints excluded: chain D residue 200 ILE Chi-restraints excluded: chain D residue 322 LEU Chi-restraints excluded: chain D residue 554 ASP Chi-restraints excluded: chain D residue 673 ILE Chi-restraints excluded: chain D residue 707 VAL Chi-restraints excluded: chain D residue 776 ASP Chi-restraints excluded: chain D residue 859 VAL Chi-restraints excluded: chain D residue 937 ASP Chi-restraints excluded: chain E residue 52 ILE Chi-restraints excluded: chain E residue 68 PHE Chi-restraints excluded: chain E residue 178 ILE Chi-restraints excluded: chain E residue 197 ASN Chi-restraints excluded: chain F residue 157 ASP Chi-restraints excluded: chain F residue 294 ILE Chi-restraints excluded: chain F residue 301 PHE Chi-restraints excluded: chain F residue 372 LYS Chi-restraints excluded: chain F residue 403 LEU Chi-restraints excluded: chain F residue 467 ASN Chi-restraints excluded: chain F residue 476 ILE Chi-restraints excluded: chain F residue 619 LEU Chi-restraints excluded: chain F residue 658 HIS Chi-restraints excluded: chain F residue 661 ILE Chi-restraints excluded: chain F residue 722 PHE Chi-restraints excluded: chain F residue 728 LEU Chi-restraints excluded: chain F residue 797 ASN Chi-restraints excluded: chain F residue 823 ILE Chi-restraints excluded: chain F residue 866 MET Chi-restraints excluded: chain F residue 929 LYS Chi-restraints excluded: chain F residue 955 ILE Chi-restraints excluded: chain F residue 979 HIS Chi-restraints excluded: chain F residue 1004 PHE Chi-restraints excluded: chain G residue 29 THR Chi-restraints excluded: chain G residue 221 GLU Chi-restraints excluded: chain G residue 231 MET Chi-restraints excluded: chain H residue 23 ASP Chi-restraints excluded: chain H residue 46 VAL Chi-restraints excluded: chain H residue 135 ASP Chi-restraints excluded: chain H residue 194 ASP Chi-restraints excluded: chain H residue 200 ILE Chi-restraints excluded: chain H residue 227 MET Chi-restraints excluded: chain H residue 255 ASN Chi-restraints excluded: chain H residue 305 ASP Chi-restraints excluded: chain H residue 399 ASP Chi-restraints excluded: chain H residue 419 ASP Chi-restraints excluded: chain H residue 445 LEU Chi-restraints excluded: chain H residue 450 GLU Chi-restraints excluded: chain H residue 498 LEU Chi-restraints excluded: chain H residue 509 ASP Chi-restraints excluded: chain H residue 636 PHE Chi-restraints excluded: chain H residue 651 ASP Chi-restraints excluded: chain H residue 684 ILE Chi-restraints excluded: chain H residue 702 ASN Chi-restraints excluded: chain H residue 726 VAL Chi-restraints excluded: chain H residue 810 HIS Chi-restraints excluded: chain H residue 824 THR Chi-restraints excluded: chain H residue 880 GLU Chi-restraints excluded: chain H residue 883 GLU Chi-restraints excluded: chain H residue 930 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 144 optimal weight: 3.9990 chunk 386 optimal weight: 9.9990 chunk 84 optimal weight: 4.9990 chunk 251 optimal weight: 9.9990 chunk 105 optimal weight: 6.9990 chunk 429 optimal weight: 5.9990 chunk 356 optimal weight: 0.0770 chunk 198 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 142 optimal weight: 0.8980 chunk 225 optimal weight: 0.0020 overall best weight: 0.9950 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 961 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 202 ASN ** F 349 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 563 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 614 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 810 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8074 moved from start: 0.3087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 37739 Z= 0.147 Angle : 0.500 14.648 50864 Z= 0.255 Chirality : 0.038 0.156 5411 Planarity : 0.003 0.047 6518 Dihedral : 3.898 24.250 4891 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 14.29 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.67 % Favored : 95.31 % Rotamer: Outliers : 2.93 % Allowed : 22.19 % Favored : 74.87 % 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: -0.06 (0.13), residues: 4435 helix: 0.95 (0.11), residues: 2346 sheet: -2.11 (0.33), residues: 234 loop : -0.98 (0.15), residues: 1855 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP E 72 HIS 0.007 0.001 HIS F 658 PHE 0.027 0.001 PHE B 220 TYR 0.023 0.001 TYR A 755 ARG 0.010 0.000 ARG E 15 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8870 Ramachandran restraints generated. 4435 Oldfield, 0 Emsley, 4435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8870 Ramachandran restraints generated. 4435 Oldfield, 0 Emsley, 4435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 330 residues out of total 4055 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 119 poor density : 211 time to evaluate : 4.295 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 204 MET cc_start: 0.8987 (tmm) cc_final: 0.8233 (tmm) REVERT: A 613 ARG cc_start: 0.8091 (OUTLIER) cc_final: 0.7884 (ttm170) REVERT: A 713 ILE cc_start: 0.9016 (OUTLIER) cc_final: 0.8668 (mt) REVERT: A 821 SER cc_start: 0.8821 (OUTLIER) cc_final: 0.8595 (p) REVERT: A 913 MET cc_start: 0.7907 (OUTLIER) cc_final: 0.7348 (mmm) REVERT: A 974 LYS cc_start: 0.8196 (tptp) cc_final: 0.7801 (mmmt) REVERT: B 177 THR cc_start: 0.5426 (OUTLIER) cc_final: 0.5144 (p) REVERT: B 205 GLU cc_start: 0.7583 (pp20) cc_final: 0.7158 (pp20) REVERT: C 206 MET cc_start: 0.6902 (ppp) cc_final: 0.6646 (ptm) REVERT: D 135 ASP cc_start: 0.8073 (OUTLIER) cc_final: 0.7330 (m-30) REVERT: D 683 LYS cc_start: 0.9177 (OUTLIER) cc_final: 0.8843 (ttpp) REVERT: D 784 GLU cc_start: 0.8810 (mt-10) cc_final: 0.8392 (mt-10) REVERT: E 68 PHE cc_start: 0.4272 (OUTLIER) cc_final: 0.3727 (t80) REVERT: E 228 THR cc_start: 0.5496 (m) cc_final: 0.5275 (m) REVERT: F 763 LYS cc_start: 0.5309 (tptt) cc_final: 0.4506 (mtmm) REVERT: F 797 ASN cc_start: 0.7198 (OUTLIER) cc_final: 0.6558 (p0) REVERT: F 936 MET cc_start: 0.4065 (mtt) cc_final: 0.2750 (mtt) REVERT: F 979 HIS cc_start: 0.7058 (OUTLIER) cc_final: 0.6055 (m-70) REVERT: H 193 TYR cc_start: 0.8183 (t80) cc_final: 0.7968 (t80) REVERT: H 450 GLU cc_start: 0.7299 (OUTLIER) cc_final: 0.6917 (pm20) REVERT: H 498 LEU cc_start: 0.7247 (OUTLIER) cc_final: 0.7027 (pp) REVERT: H 519 MET cc_start: 0.7086 (tmm) cc_final: 0.6360 (tmm) REVERT: H 951 TYR cc_start: 0.5782 (OUTLIER) cc_final: 0.5567 (m-80) outliers start: 119 outliers final: 76 residues processed: 313 average time/residue: 0.4325 time to fit residues: 231.3428 Evaluate side-chains 287 residues out of total 4055 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 198 time to evaluate : 4.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 ASP Chi-restraints excluded: chain A residue 134 TYR Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 339 HIS Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 508 THR Chi-restraints excluded: chain A residue 603 VAL Chi-restraints excluded: chain A residue 613 ARG Chi-restraints excluded: chain A residue 706 VAL Chi-restraints excluded: chain A residue 713 ILE Chi-restraints excluded: chain A residue 761 LEU Chi-restraints excluded: chain A residue 821 SER Chi-restraints excluded: chain A residue 913 MET Chi-restraints excluded: chain A residue 978 HIS Chi-restraints excluded: chain B residue 175 TYR Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 209 GLU Chi-restraints excluded: chain B residue 219 LYS Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain D residue 33 ILE Chi-restraints excluded: chain D residue 46 VAL Chi-restraints excluded: chain D residue 66 TYR Chi-restraints excluded: chain D residue 135 ASP Chi-restraints excluded: chain D residue 142 CYS Chi-restraints excluded: chain D residue 200 ILE Chi-restraints excluded: chain D residue 275 ILE Chi-restraints excluded: chain D residue 322 LEU Chi-restraints excluded: chain D residue 463 ILE Chi-restraints excluded: chain D residue 554 ASP Chi-restraints excluded: chain D residue 662 ASP Chi-restraints excluded: chain D residue 671 CYS Chi-restraints excluded: chain D residue 673 ILE Chi-restraints excluded: chain D residue 683 LYS Chi-restraints excluded: chain D residue 707 VAL Chi-restraints excluded: chain D residue 776 ASP Chi-restraints excluded: chain D residue 859 VAL Chi-restraints excluded: chain D residue 937 ASP Chi-restraints excluded: chain E residue 52 ILE Chi-restraints excluded: chain E residue 68 PHE Chi-restraints excluded: chain E residue 178 ILE Chi-restraints excluded: chain E residue 197 ASN Chi-restraints excluded: chain F residue 134 TYR Chi-restraints excluded: chain F residue 157 ASP Chi-restraints excluded: chain F residue 294 ILE Chi-restraints excluded: chain F residue 299 ASN Chi-restraints excluded: chain F residue 301 PHE Chi-restraints excluded: chain F residue 372 LYS Chi-restraints excluded: chain F residue 403 LEU Chi-restraints excluded: chain F residue 467 ASN Chi-restraints excluded: chain F residue 476 ILE Chi-restraints excluded: chain F residue 554 ASP Chi-restraints excluded: chain F residue 619 LEU Chi-restraints excluded: chain F residue 658 HIS Chi-restraints excluded: chain F residue 661 ILE Chi-restraints excluded: chain F residue 722 PHE Chi-restraints excluded: chain F residue 728 LEU Chi-restraints excluded: chain F residue 797 ASN Chi-restraints excluded: chain F residue 807 LEU Chi-restraints excluded: chain F residue 823 ILE Chi-restraints excluded: chain F residue 866 MET Chi-restraints excluded: chain F residue 929 LYS Chi-restraints excluded: chain F residue 955 ILE Chi-restraints excluded: chain F residue 979 HIS Chi-restraints excluded: chain F residue 1004 PHE Chi-restraints excluded: chain G residue 29 THR Chi-restraints excluded: chain G residue 45 ILE Chi-restraints excluded: chain G residue 221 GLU Chi-restraints excluded: chain G residue 231 MET Chi-restraints excluded: chain H residue 23 ASP Chi-restraints excluded: chain H residue 200 ILE Chi-restraints excluded: chain H residue 227 MET Chi-restraints excluded: chain H residue 255 ASN Chi-restraints excluded: chain H residue 305 ASP Chi-restraints excluded: chain H residue 399 ASP Chi-restraints excluded: chain H residue 419 ASP Chi-restraints excluded: chain H residue 450 GLU Chi-restraints excluded: chain H residue 498 LEU Chi-restraints excluded: chain H residue 509 ASP Chi-restraints excluded: chain H residue 636 PHE Chi-restraints excluded: chain H residue 651 ASP Chi-restraints excluded: chain H residue 673 ILE Chi-restraints excluded: chain H residue 684 ILE Chi-restraints excluded: chain H residue 702 ASN Chi-restraints excluded: chain H residue 726 VAL Chi-restraints excluded: chain H residue 880 GLU Chi-restraints excluded: chain H residue 883 GLU Chi-restraints excluded: chain H residue 930 MET Chi-restraints excluded: chain H residue 951 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 414 optimal weight: 4.9990 chunk 48 optimal weight: 6.9990 chunk 244 optimal weight: 5.9990 chunk 313 optimal weight: 5.9990 chunk 243 optimal weight: 3.9990 chunk 361 optimal weight: 0.0970 chunk 239 optimal weight: 4.9990 chunk 427 optimal weight: 7.9990 chunk 267 optimal weight: 4.9990 chunk 260 optimal weight: 10.0000 chunk 197 optimal weight: 1.9990 overall best weight: 3.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 786 HIS ** D 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 829 GLN ** D 939 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 961 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 349 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 457 ASN ** F 563 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 614 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8168 moved from start: 0.3559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 37739 Z= 0.302 Angle : 0.589 15.063 50864 Z= 0.308 Chirality : 0.041 0.166 5411 Planarity : 0.004 0.050 6518 Dihedral : 4.203 24.923 4891 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 19.58 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.70 % Favored : 94.27 % Rotamer: Outliers : 3.50 % Allowed : 22.34 % Favored : 74.16 % 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: 4435 helix: 0.82 (0.11), residues: 2366 sheet: -2.06 (0.33), residues: 237 loop : -1.04 (0.15), residues: 1832 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP D 143 HIS 0.021 0.001 HIS H 810 PHE 0.023 0.002 PHE B 220 TYR 0.026 0.002 TYR A1003 ARG 0.004 0.001 ARG F 627 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8870 Ramachandran restraints generated. 4435 Oldfield, 0 Emsley, 4435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8870 Ramachandran restraints generated. 4435 Oldfield, 0 Emsley, 4435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 340 residues out of total 4055 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 142 poor density : 198 time to evaluate : 4.430 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: A 204 MET cc_start: 0.9011 (tmm) cc_final: 0.8260 (tmm) REVERT: A 713 ILE cc_start: 0.9157 (OUTLIER) cc_final: 0.8818 (mt) REVERT: A 913 MET cc_start: 0.7925 (OUTLIER) cc_final: 0.7405 (mmm) REVERT: A 1001 MET cc_start: 0.8875 (tpp) cc_final: 0.8588 (tmm) REVERT: B 39 GLU cc_start: 0.5981 (OUTLIER) cc_final: 0.4927 (mp0) REVERT: B 177 THR cc_start: 0.6080 (OUTLIER) cc_final: 0.5762 (p) REVERT: B 205 GLU cc_start: 0.7652 (pp20) cc_final: 0.7209 (pp20) REVERT: D 281 ASP cc_start: 0.7723 (OUTLIER) cc_final: 0.7459 (p0) REVERT: D 547 ASP cc_start: 0.8048 (p0) cc_final: 0.7831 (p0) REVERT: D 683 LYS cc_start: 0.9218 (OUTLIER) cc_final: 0.8880 (ttpp) REVERT: D 936 MET cc_start: 0.5717 (mmt) cc_final: 0.5504 (tpp) REVERT: E 228 THR cc_start: 0.5186 (m) cc_final: 0.4943 (m) REVERT: F 763 LYS cc_start: 0.5416 (tptt) cc_final: 0.4473 (ptpp) REVERT: F 797 ASN cc_start: 0.7155 (OUTLIER) cc_final: 0.6526 (p0) REVERT: F 936 MET cc_start: 0.4184 (mtt) cc_final: 0.2926 (mtt) REVERT: F 979 HIS cc_start: 0.7016 (OUTLIER) cc_final: 0.6287 (m-70) REVERT: G 176 ARG cc_start: 0.6393 (mpt180) cc_final: 0.5902 (mmt-90) REVERT: H 193 TYR cc_start: 0.8400 (t80) cc_final: 0.8165 (t80) REVERT: H 450 GLU cc_start: 0.7387 (OUTLIER) cc_final: 0.6973 (pm20) REVERT: H 498 LEU cc_start: 0.7091 (OUTLIER) cc_final: 0.6885 (pp) REVERT: H 519 MET cc_start: 0.7347 (tmm) cc_final: 0.6648 (tmm) REVERT: H 951 TYR cc_start: 0.5941 (OUTLIER) cc_final: 0.5415 (m-80) outliers start: 142 outliers final: 101 residues processed: 318 average time/residue: 0.4457 time to fit residues: 244.3355 Evaluate side-chains 307 residues out of total 4055 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 112 poor density : 195 time to evaluate : 5.193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 ASP Chi-restraints excluded: chain A residue 134 TYR Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain A residue 255 ASN Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 328 ILE Chi-restraints excluded: chain A residue 343 ASN Chi-restraints excluded: chain A residue 434 ASP Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 508 THR Chi-restraints excluded: chain A residue 603 VAL Chi-restraints excluded: chain A residue 706 VAL Chi-restraints excluded: chain A residue 713 ILE Chi-restraints excluded: chain A residue 761 LEU Chi-restraints excluded: chain A residue 821 SER Chi-restraints excluded: chain A residue 913 MET Chi-restraints excluded: chain A residue 978 HIS Chi-restraints excluded: chain A residue 1004 PHE Chi-restraints excluded: chain B residue 39 GLU Chi-restraints excluded: chain B residue 45 ILE Chi-restraints excluded: chain B residue 175 TYR Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 209 GLU Chi-restraints excluded: chain B residue 219 LYS Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 192 TYR Chi-restraints excluded: chain D residue 33 ILE Chi-restraints excluded: chain D residue 66 TYR Chi-restraints excluded: chain D residue 135 ASP Chi-restraints excluded: chain D residue 138 ILE Chi-restraints excluded: chain D residue 142 CYS Chi-restraints excluded: chain D residue 200 ILE Chi-restraints excluded: chain D residue 275 ILE Chi-restraints excluded: chain D residue 281 ASP Chi-restraints excluded: chain D residue 322 LEU Chi-restraints excluded: chain D residue 437 LYS Chi-restraints excluded: chain D residue 463 ILE Chi-restraints excluded: chain D residue 662 ASP Chi-restraints excluded: chain D residue 671 CYS Chi-restraints excluded: chain D residue 673 ILE Chi-restraints excluded: chain D residue 683 LYS Chi-restraints excluded: chain D residue 707 VAL Chi-restraints excluded: chain D residue 776 ASP Chi-restraints excluded: chain D residue 859 VAL Chi-restraints excluded: chain D residue 937 ASP Chi-restraints excluded: chain E residue 11 VAL Chi-restraints excluded: chain E residue 52 ILE Chi-restraints excluded: chain E residue 68 PHE Chi-restraints excluded: chain E residue 175 TYR Chi-restraints excluded: chain E residue 178 ILE Chi-restraints excluded: chain E residue 187 VAL Chi-restraints excluded: chain E residue 197 ASN Chi-restraints excluded: chain E residue 226 THR Chi-restraints excluded: chain F residue 124 MET Chi-restraints excluded: chain F residue 134 TYR Chi-restraints excluded: chain F residue 157 ASP Chi-restraints excluded: chain F residue 228 LEU Chi-restraints excluded: chain F residue 294 ILE Chi-restraints excluded: chain F residue 299 ASN Chi-restraints excluded: chain F residue 301 PHE Chi-restraints excluded: chain F residue 372 LYS Chi-restraints excluded: chain F residue 399 ASP Chi-restraints excluded: chain F residue 403 LEU Chi-restraints excluded: chain F residue 467 ASN Chi-restraints excluded: chain F residue 476 ILE Chi-restraints excluded: chain F residue 619 LEU Chi-restraints excluded: chain F residue 658 HIS Chi-restraints excluded: chain F residue 659 PHE Chi-restraints excluded: chain F residue 661 ILE Chi-restraints excluded: chain F residue 722 PHE Chi-restraints excluded: chain F residue 728 LEU Chi-restraints excluded: chain F residue 797 ASN Chi-restraints excluded: chain F residue 807 LEU Chi-restraints excluded: chain F residue 814 ASN Chi-restraints excluded: chain F residue 823 ILE Chi-restraints excluded: chain F residue 866 MET Chi-restraints excluded: chain F residue 955 ILE Chi-restraints excluded: chain F residue 979 HIS Chi-restraints excluded: chain F residue 1004 PHE Chi-restraints excluded: chain G residue 45 ILE Chi-restraints excluded: chain G residue 63 VAL Chi-restraints excluded: chain G residue 221 GLU Chi-restraints excluded: chain G residue 231 MET Chi-restraints excluded: chain H residue 23 ASP Chi-restraints excluded: chain H residue 134 TYR Chi-restraints excluded: chain H residue 135 ASP Chi-restraints excluded: chain H residue 142 CYS Chi-restraints excluded: chain H residue 200 ILE Chi-restraints excluded: chain H residue 227 MET Chi-restraints excluded: chain H residue 255 ASN Chi-restraints excluded: chain H residue 305 ASP Chi-restraints excluded: chain H residue 399 ASP Chi-restraints excluded: chain H residue 419 ASP Chi-restraints excluded: chain H residue 450 GLU Chi-restraints excluded: chain H residue 498 LEU Chi-restraints excluded: chain H residue 499 THR Chi-restraints excluded: chain H residue 509 ASP Chi-restraints excluded: chain H residue 547 ASP Chi-restraints excluded: chain H residue 554 ASP Chi-restraints excluded: chain H residue 558 LEU Chi-restraints excluded: chain H residue 636 PHE Chi-restraints excluded: chain H residue 662 ASP Chi-restraints excluded: chain H residue 673 ILE Chi-restraints excluded: chain H residue 684 ILE Chi-restraints excluded: chain H residue 702 ASN Chi-restraints excluded: chain H residue 726 VAL Chi-restraints excluded: chain H residue 788 ASP Chi-restraints excluded: chain H residue 880 GLU Chi-restraints excluded: chain H residue 883 GLU Chi-restraints excluded: chain H residue 930 MET Chi-restraints excluded: chain H residue 951 TYR Chi-restraints excluded: chain H residue 997 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 264 optimal weight: 0.8980 chunk 170 optimal weight: 0.9990 chunk 255 optimal weight: 6.9990 chunk 128 optimal weight: 5.9990 chunk 84 optimal weight: 3.9990 chunk 82 optimal weight: 0.8980 chunk 272 optimal weight: 9.9990 chunk 291 optimal weight: 1.9990 chunk 211 optimal weight: 0.9980 chunk 39 optimal weight: 0.9990 chunk 336 optimal weight: 1.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- 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** ** D 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 765 ASN ** D 832 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 939 GLN ** D 961 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 349 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 563 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 614 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8105 moved from start: 0.3525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 37739 Z= 0.152 Angle : 0.530 15.317 50864 Z= 0.267 Chirality : 0.039 0.159 5411 Planarity : 0.003 0.048 6518 Dihedral : 4.037 24.020 4891 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 15.40 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.74 % Favored : 95.24 % Rotamer: Outliers : 2.84 % Allowed : 23.01 % Favored : 74.16 % 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 (0.13), residues: 4435 helix: 0.94 (0.11), residues: 2366 sheet: -2.05 (0.33), residues: 234 loop : -1.01 (0.15), residues: 1835 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 60 HIS 0.007 0.001 HIS F 658 PHE 0.026 0.001 PHE B 220 TYR 0.032 0.001 TYR A 755 ARG 0.004 0.000 ARG H 760 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8870 Ramachandran restraints generated. 4435 Oldfield, 0 Emsley, 4435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8870 Ramachandran restraints generated. 4435 Oldfield, 0 Emsley, 4435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 324 residues out of total 4055 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 115 poor density : 209 time to evaluate : 4.584 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: A 204 MET cc_start: 0.8964 (tmm) cc_final: 0.8215 (tmm) REVERT: A 713 ILE cc_start: 0.9050 (OUTLIER) cc_final: 0.8718 (mt) REVERT: A 1001 MET cc_start: 0.8816 (tpp) cc_final: 0.8527 (tmm) REVERT: B 177 THR cc_start: 0.5853 (OUTLIER) cc_final: 0.5562 (p) REVERT: B 205 GLU cc_start: 0.7622 (pp20) cc_final: 0.7171 (pp20) REVERT: D 281 ASP cc_start: 0.7496 (OUTLIER) cc_final: 0.7178 (p0) REVERT: E 68 PHE cc_start: 0.4651 (OUTLIER) cc_final: 0.4038 (t80) REVERT: E 228 THR cc_start: 0.5160 (m) cc_final: 0.4911 (m) REVERT: E 231 MET cc_start: 0.0974 (mmp) cc_final: 0.0098 (mmp) REVERT: F 763 LYS cc_start: 0.5333 (tptt) cc_final: 0.4453 (mtmm) REVERT: F 797 ASN cc_start: 0.7101 (OUTLIER) cc_final: 0.6450 (p0) REVERT: F 936 MET cc_start: 0.4088 (mtt) cc_final: 0.2802 (mtt) REVERT: F 979 HIS cc_start: 0.6915 (OUTLIER) cc_final: 0.6202 (m-70) REVERT: H 193 TYR cc_start: 0.8312 (t80) cc_final: 0.8061 (t80) REVERT: H 450 GLU cc_start: 0.7343 (OUTLIER) cc_final: 0.6939 (pm20) REVERT: H 498 LEU cc_start: 0.7285 (OUTLIER) cc_final: 0.7070 (pp) REVERT: H 519 MET cc_start: 0.7263 (tmm) cc_final: 0.6587 (tmm) REVERT: H 951 TYR cc_start: 0.5797 (OUTLIER) cc_final: 0.5547 (m-80) outliers start: 115 outliers final: 91 residues processed: 309 average time/residue: 0.4321 time to fit residues: 231.2645 Evaluate side-chains 297 residues out of total 4055 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 197 time to evaluate : 4.493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 ASP Chi-restraints excluded: chain A residue 134 TYR Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain A residue 200 ILE Chi-restraints excluded: chain A residue 255 ASN Chi-restraints excluded: chain A residue 343 ASN Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 508 THR Chi-restraints excluded: chain A residue 603 VAL Chi-restraints excluded: chain A residue 706 VAL Chi-restraints excluded: chain A residue 713 ILE Chi-restraints excluded: chain A residue 761 LEU Chi-restraints excluded: chain A residue 821 SER Chi-restraints excluded: chain A residue 978 HIS Chi-restraints excluded: chain B residue 45 ILE Chi-restraints excluded: chain B residue 175 TYR Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 209 GLU Chi-restraints excluded: chain B residue 219 LYS Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain D residue 33 ILE Chi-restraints excluded: chain D residue 66 TYR Chi-restraints excluded: chain D residue 135 ASP Chi-restraints excluded: chain D residue 142 CYS Chi-restraints excluded: chain D residue 200 ILE Chi-restraints excluded: chain D residue 275 ILE Chi-restraints excluded: chain D residue 281 ASP Chi-restraints excluded: chain D residue 322 LEU Chi-restraints excluded: chain D residue 463 ILE Chi-restraints excluded: chain D residue 520 THR Chi-restraints excluded: chain D residue 662 ASP Chi-restraints excluded: chain D residue 671 CYS Chi-restraints excluded: chain D residue 673 ILE Chi-restraints excluded: chain D residue 707 VAL Chi-restraints excluded: chain D residue 776 ASP Chi-restraints excluded: chain D residue 859 VAL Chi-restraints excluded: chain D residue 937 ASP Chi-restraints excluded: chain D residue 988 VAL Chi-restraints excluded: chain E residue 11 VAL Chi-restraints excluded: chain E residue 52 ILE Chi-restraints excluded: chain E residue 68 PHE Chi-restraints excluded: chain E residue 175 TYR Chi-restraints excluded: chain E residue 178 ILE Chi-restraints excluded: chain E residue 197 ASN Chi-restraints excluded: chain F residue 134 TYR Chi-restraints excluded: chain F residue 157 ASP Chi-restraints excluded: chain F residue 287 SER Chi-restraints excluded: chain F residue 294 ILE Chi-restraints excluded: chain F residue 301 PHE Chi-restraints excluded: chain F residue 370 ARG Chi-restraints excluded: chain F residue 372 LYS Chi-restraints excluded: chain F residue 403 LEU Chi-restraints excluded: chain F residue 467 ASN Chi-restraints excluded: chain F residue 476 ILE Chi-restraints excluded: chain F residue 619 LEU Chi-restraints excluded: chain F residue 658 HIS Chi-restraints excluded: chain F residue 659 PHE Chi-restraints excluded: chain F residue 722 PHE Chi-restraints excluded: chain F residue 728 LEU Chi-restraints excluded: chain F residue 797 ASN Chi-restraints excluded: chain F residue 807 LEU Chi-restraints excluded: chain F residue 823 ILE Chi-restraints excluded: chain F residue 866 MET Chi-restraints excluded: chain F residue 955 ILE Chi-restraints excluded: chain F residue 979 HIS Chi-restraints excluded: chain F residue 1004 PHE Chi-restraints excluded: chain G residue 12 TYR Chi-restraints excluded: chain G residue 29 THR Chi-restraints excluded: chain G residue 45 ILE Chi-restraints excluded: chain G residue 63 VAL Chi-restraints excluded: chain G residue 221 GLU Chi-restraints excluded: chain G residue 231 MET Chi-restraints excluded: chain H residue 23 ASP Chi-restraints excluded: chain H residue 134 TYR Chi-restraints excluded: chain H residue 135 ASP Chi-restraints excluded: chain H residue 142 CYS Chi-restraints excluded: chain H residue 200 ILE Chi-restraints excluded: chain H residue 227 MET Chi-restraints excluded: chain H residue 255 ASN Chi-restraints excluded: chain H residue 305 ASP Chi-restraints excluded: chain H residue 399 ASP Chi-restraints excluded: chain H residue 419 ASP Chi-restraints excluded: chain H residue 450 GLU Chi-restraints excluded: chain H residue 498 LEU Chi-restraints excluded: chain H residue 554 ASP Chi-restraints excluded: chain H residue 636 PHE Chi-restraints excluded: chain H residue 651 ASP Chi-restraints excluded: chain H residue 662 ASP Chi-restraints excluded: chain H residue 673 ILE Chi-restraints excluded: chain H residue 684 ILE Chi-restraints excluded: chain H residue 702 ASN Chi-restraints excluded: chain H residue 726 VAL Chi-restraints excluded: chain H residue 788 ASP Chi-restraints excluded: chain H residue 824 THR Chi-restraints excluded: chain H residue 880 GLU Chi-restraints excluded: chain H residue 883 GLU Chi-restraints excluded: chain H residue 928 SER Chi-restraints excluded: chain H residue 930 MET Chi-restraints excluded: chain H residue 951 TYR Chi-restraints excluded: chain H residue 1004 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 389 optimal weight: 4.9990 chunk 409 optimal weight: 5.9990 chunk 374 optimal weight: 0.0060 chunk 398 optimal weight: 0.9990 chunk 240 optimal weight: 10.0000 chunk 173 optimal weight: 0.6980 chunk 313 optimal weight: 0.9980 chunk 122 optimal weight: 0.9980 chunk 360 optimal weight: 5.9990 chunk 377 optimal weight: 0.5980 chunk 397 optimal weight: 0.6980 overall best weight: 0.5996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 992 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 765 ASN ** D 832 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 961 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 349 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 563 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 681 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 475 GLN ** H 614 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8076 moved from start: 0.3539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.053 37739 Z= 0.139 Angle : 0.527 15.684 50864 Z= 0.262 Chirality : 0.038 0.156 5411 Planarity : 0.003 0.047 6518 Dihedral : 3.882 23.457 4891 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 14.09 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.76 % Favored : 95.22 % Rotamer: Outliers : 2.61 % Allowed : 23.18 % Favored : 74.20 % 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: 0.05 (0.13), residues: 4435 helix: 1.03 (0.11), residues: 2361 sheet: -2.04 (0.32), residues: 248 loop : -0.93 (0.15), residues: 1826 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 60 HIS 0.010 0.001 HIS A 975 PHE 0.024 0.001 PHE B 220 TYR 0.032 0.001 TYR A 755 ARG 0.004 0.000 ARG F 627 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8870 Ramachandran restraints generated. 4435 Oldfield, 0 Emsley, 4435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8870 Ramachandran restraints generated. 4435 Oldfield, 0 Emsley, 4435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 322 residues out of total 4055 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 216 time to evaluate : 4.485 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: A 204 MET cc_start: 0.8945 (tmm) cc_final: 0.8270 (tmm) REVERT: A 279 GLU cc_start: 0.8756 (pm20) cc_final: 0.8292 (mm-30) REVERT: A 713 ILE cc_start: 0.9016 (OUTLIER) cc_final: 0.8655 (mt) REVERT: B 177 THR cc_start: 0.5683 (OUTLIER) cc_final: 0.5387 (p) REVERT: B 205 GLU cc_start: 0.7600 (pp20) cc_final: 0.7196 (pp20) REVERT: B 209 GLU cc_start: 0.8457 (OUTLIER) cc_final: 0.8230 (mm-30) REVERT: C 206 MET cc_start: 0.6484 (ppp) cc_final: 0.6248 (ptm) REVERT: D 281 ASP cc_start: 0.7217 (OUTLIER) cc_final: 0.6891 (p0) REVERT: D 936 MET cc_start: 0.5283 (mmt) cc_final: 0.5048 (tpp) REVERT: D 976 MET cc_start: 0.6676 (pmm) cc_final: 0.6441 (pmm) REVERT: E 228 THR cc_start: 0.5127 (m) cc_final: 0.4868 (m) REVERT: E 231 MET cc_start: 0.0859 (mmp) cc_final: 0.0131 (mmp) REVERT: F 396 MET cc_start: 0.6962 (ttt) cc_final: 0.6410 (tmm) REVERT: F 763 LYS cc_start: 0.5278 (tptt) cc_final: 0.4456 (mtmm) REVERT: F 797 ASN cc_start: 0.7079 (OUTLIER) cc_final: 0.6342 (p0) REVERT: F 936 MET cc_start: 0.4025 (mtt) cc_final: 0.2736 (mtt) REVERT: F 979 HIS cc_start: 0.6860 (OUTLIER) cc_final: 0.6021 (m-70) REVERT: H 193 TYR cc_start: 0.8224 (t80) cc_final: 0.7978 (t80) REVERT: H 450 GLU cc_start: 0.7457 (OUTLIER) cc_final: 0.7075 (pm20) REVERT: H 498 LEU cc_start: 0.7176 (OUTLIER) cc_final: 0.6944 (pp) REVERT: H 519 MET cc_start: 0.7164 (tmm) cc_final: 0.6473 (tmm) outliers start: 106 outliers final: 79 residues processed: 307 average time/residue: 0.4363 time to fit residues: 230.7367 Evaluate side-chains 293 residues out of total 4055 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 206 time to evaluate : 4.652 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 ASP Chi-restraints excluded: chain A residue 134 TYR Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain A residue 200 ILE Chi-restraints excluded: chain A residue 255 ASN Chi-restraints excluded: chain A residue 343 ASN Chi-restraints excluded: chain A residue 508 THR Chi-restraints excluded: chain A residue 603 VAL Chi-restraints excluded: chain A residue 706 VAL Chi-restraints excluded: chain A residue 713 ILE Chi-restraints excluded: chain A residue 761 LEU Chi-restraints excluded: chain A residue 978 HIS Chi-restraints excluded: chain B residue 45 ILE Chi-restraints excluded: chain B residue 175 TYR Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 209 GLU Chi-restraints excluded: chain B residue 219 LYS Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain D residue 33 ILE Chi-restraints excluded: chain D residue 66 TYR Chi-restraints excluded: chain D residue 135 ASP Chi-restraints excluded: chain D residue 142 CYS Chi-restraints excluded: chain D residue 200 ILE Chi-restraints excluded: chain D residue 275 ILE Chi-restraints excluded: chain D residue 281 ASP Chi-restraints excluded: chain D residue 322 LEU Chi-restraints excluded: chain D residue 463 ILE Chi-restraints excluded: chain D residue 520 THR Chi-restraints excluded: chain D residue 524 ILE Chi-restraints excluded: chain D residue 662 ASP Chi-restraints excluded: chain D residue 671 CYS Chi-restraints excluded: chain D residue 673 ILE Chi-restraints excluded: chain D residue 776 ASP Chi-restraints excluded: chain D residue 859 VAL Chi-restraints excluded: chain D residue 937 ASP Chi-restraints excluded: chain D residue 988 VAL Chi-restraints excluded: chain E residue 11 VAL Chi-restraints excluded: chain E residue 52 ILE Chi-restraints excluded: chain E residue 68 PHE Chi-restraints excluded: chain E residue 178 ILE Chi-restraints excluded: chain E residue 197 ASN Chi-restraints excluded: chain F residue 294 ILE Chi-restraints excluded: chain F residue 301 PHE Chi-restraints excluded: chain F residue 370 ARG Chi-restraints excluded: chain F residue 372 LYS Chi-restraints excluded: chain F residue 476 ILE Chi-restraints excluded: chain F residue 619 LEU Chi-restraints excluded: chain F residue 658 HIS Chi-restraints excluded: chain F residue 659 PHE Chi-restraints excluded: chain F residue 661 ILE Chi-restraints excluded: chain F residue 722 PHE Chi-restraints excluded: chain F residue 728 LEU Chi-restraints excluded: chain F residue 797 ASN Chi-restraints excluded: chain F residue 807 LEU Chi-restraints excluded: chain F residue 823 ILE Chi-restraints excluded: chain F residue 866 MET Chi-restraints excluded: chain F residue 955 ILE Chi-restraints excluded: chain F residue 979 HIS Chi-restraints excluded: chain F residue 1004 PHE Chi-restraints excluded: chain G residue 12 TYR Chi-restraints excluded: chain G residue 29 THR Chi-restraints excluded: chain G residue 45 ILE Chi-restraints excluded: chain G residue 221 GLU Chi-restraints excluded: chain G residue 231 MET Chi-restraints excluded: chain H residue 23 ASP Chi-restraints excluded: chain H residue 134 TYR Chi-restraints excluded: chain H residue 142 CYS Chi-restraints excluded: chain H residue 200 ILE Chi-restraints excluded: chain H residue 227 MET Chi-restraints excluded: chain H residue 255 ASN Chi-restraints excluded: chain H residue 280 TYR Chi-restraints excluded: chain H residue 399 ASP Chi-restraints excluded: chain H residue 419 ASP Chi-restraints excluded: chain H residue 450 GLU Chi-restraints excluded: chain H residue 464 ASP Chi-restraints excluded: chain H residue 498 LEU Chi-restraints excluded: chain H residue 636 PHE Chi-restraints excluded: chain H residue 651 ASP Chi-restraints excluded: chain H residue 662 ASP Chi-restraints excluded: chain H residue 673 ILE Chi-restraints excluded: chain H residue 684 ILE Chi-restraints excluded: chain H residue 702 ASN Chi-restraints excluded: chain H residue 726 VAL Chi-restraints excluded: chain H residue 880 GLU Chi-restraints excluded: chain H residue 883 GLU Chi-restraints excluded: chain H residue 930 MET Chi-restraints excluded: chain H residue 1004 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 261 optimal weight: 8.9990 chunk 421 optimal weight: 2.9990 chunk 257 optimal weight: 6.9990 chunk 200 optimal weight: 10.0000 chunk 293 optimal weight: 1.9990 chunk 442 optimal weight: 5.9990 chunk 407 optimal weight: 1.9990 chunk 352 optimal weight: 0.9980 chunk 36 optimal weight: 3.9990 chunk 272 optimal weight: 0.9990 chunk 215 optimal weight: 5.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 705 ASN ** D 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 536 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 832 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 910 ASN ** D 961 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 349 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 563 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 195 GLN ** H 614 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8119 moved from start: 0.3697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 37739 Z= 0.198 Angle : 0.552 15.716 50864 Z= 0.276 Chirality : 0.039 0.227 5411 Planarity : 0.003 0.046 6518 Dihedral : 3.964 23.679 4891 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 16.18 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.21 % Favored : 94.77 % Rotamer: Outliers : 2.44 % Allowed : 23.38 % Favored : 74.18 % 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: 0.04 (0.13), residues: 4435 helix: 1.04 (0.11), residues: 2368 sheet: -2.01 (0.32), residues: 243 loop : -0.99 (0.15), residues: 1824 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 60 HIS 0.009 0.001 HIS A 975 PHE 0.020 0.001 PHE B 220 TYR 0.031 0.001 TYR A 755 ARG 0.004 0.000 ARG F 627 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8870 Ramachandran restraints generated. 4435 Oldfield, 0 Emsley, 4435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8870 Ramachandran restraints generated. 4435 Oldfield, 0 Emsley, 4435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 4055 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 203 time to evaluate : 4.338 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 204 MET cc_start: 0.8973 (tmm) cc_final: 0.8238 (tmm) REVERT: A 713 ILE cc_start: 0.9082 (OUTLIER) cc_final: 0.8730 (mt) REVERT: B 177 THR cc_start: 0.6146 (OUTLIER) cc_final: 0.5895 (p) REVERT: B 205 GLU cc_start: 0.7607 (pp20) cc_final: 0.7206 (pp20) REVERT: C 206 MET cc_start: 0.6635 (ppp) cc_final: 0.6231 (ptm) REVERT: C 231 MET cc_start: 0.7762 (ttt) cc_final: 0.7505 (ttp) REVERT: D 281 ASP cc_start: 0.7424 (OUTLIER) cc_final: 0.7098 (p0) REVERT: E 228 THR cc_start: 0.5129 (m) cc_final: 0.4881 (m) REVERT: F 763 LYS cc_start: 0.5300 (tptt) cc_final: 0.4494 (ptpp) REVERT: F 797 ASN cc_start: 0.7053 (OUTLIER) cc_final: 0.6440 (p0) REVERT: F 936 MET cc_start: 0.3978 (mtt) cc_final: 0.2858 (mtt) REVERT: F 979 HIS cc_start: 0.6927 (OUTLIER) cc_final: 0.6237 (m-70) REVERT: G 176 ARG cc_start: 0.6450 (mpt180) cc_final: 0.6111 (mmt180) REVERT: H 193 TYR cc_start: 0.8327 (t80) cc_final: 0.8090 (t80) REVERT: H 450 GLU cc_start: 0.7356 (OUTLIER) cc_final: 0.6945 (pm20) REVERT: H 498 LEU cc_start: 0.7201 (OUTLIER) cc_final: 0.6989 (pp) REVERT: H 519 MET cc_start: 0.7222 (tmm) cc_final: 0.6518 (tmm) outliers start: 99 outliers final: 83 residues processed: 287 average time/residue: 0.4411 time to fit residues: 217.3127 Evaluate side-chains 290 residues out of total 4055 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 200 time to evaluate : 4.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 ASP Chi-restraints excluded: chain A residue 134 TYR Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain A residue 200 ILE Chi-restraints excluded: chain A residue 255 ASN Chi-restraints excluded: chain A residue 603 VAL Chi-restraints excluded: chain A residue 706 VAL Chi-restraints excluded: chain A residue 713 ILE Chi-restraints excluded: chain A residue 761 LEU Chi-restraints excluded: chain A residue 978 HIS Chi-restraints excluded: chain B residue 45 ILE Chi-restraints excluded: chain B residue 175 TYR Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 209 GLU Chi-restraints excluded: chain B residue 219 LYS Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain D residue 33 ILE Chi-restraints excluded: chain D residue 66 TYR Chi-restraints excluded: chain D residue 135 ASP Chi-restraints excluded: chain D residue 142 CYS Chi-restraints excluded: chain D residue 200 ILE Chi-restraints excluded: chain D residue 275 ILE Chi-restraints excluded: chain D residue 281 ASP Chi-restraints excluded: chain D residue 322 LEU Chi-restraints excluded: chain D residue 463 ILE Chi-restraints excluded: chain D residue 508 THR Chi-restraints excluded: chain D residue 520 THR Chi-restraints excluded: chain D residue 524 ILE Chi-restraints excluded: chain D residue 662 ASP Chi-restraints excluded: chain D residue 671 CYS Chi-restraints excluded: chain D residue 673 ILE Chi-restraints excluded: chain D residue 776 ASP Chi-restraints excluded: chain D residue 859 VAL Chi-restraints excluded: chain D residue 937 ASP Chi-restraints excluded: chain D residue 988 VAL Chi-restraints excluded: chain E residue 11 VAL Chi-restraints excluded: chain E residue 52 ILE Chi-restraints excluded: chain E residue 68 PHE Chi-restraints excluded: chain E residue 178 ILE Chi-restraints excluded: chain E residue 197 ASN Chi-restraints excluded: chain E residue 226 THR Chi-restraints excluded: chain F residue 134 TYR Chi-restraints excluded: chain F residue 294 ILE Chi-restraints excluded: chain F residue 299 ASN Chi-restraints excluded: chain F residue 301 PHE Chi-restraints excluded: chain F residue 370 ARG Chi-restraints excluded: chain F residue 372 LYS Chi-restraints excluded: chain F residue 476 ILE Chi-restraints excluded: chain F residue 619 LEU Chi-restraints excluded: chain F residue 658 HIS Chi-restraints excluded: chain F residue 659 PHE Chi-restraints excluded: chain F residue 661 ILE Chi-restraints excluded: chain F residue 722 PHE Chi-restraints excluded: chain F residue 728 LEU Chi-restraints excluded: chain F residue 797 ASN Chi-restraints excluded: chain F residue 807 LEU Chi-restraints excluded: chain F residue 823 ILE Chi-restraints excluded: chain F residue 866 MET Chi-restraints excluded: chain F residue 955 ILE Chi-restraints excluded: chain F residue 979 HIS Chi-restraints excluded: chain F residue 1004 PHE Chi-restraints excluded: chain G residue 12 TYR Chi-restraints excluded: chain G residue 45 ILE Chi-restraints excluded: chain G residue 63 VAL Chi-restraints excluded: chain G residue 221 GLU Chi-restraints excluded: chain G residue 231 MET Chi-restraints excluded: chain H residue 23 ASP Chi-restraints excluded: chain H residue 134 TYR Chi-restraints excluded: chain H residue 135 ASP Chi-restraints excluded: chain H residue 142 CYS Chi-restraints excluded: chain H residue 200 ILE Chi-restraints excluded: chain H residue 227 MET Chi-restraints excluded: chain H residue 255 ASN Chi-restraints excluded: chain H residue 305 ASP Chi-restraints excluded: chain H residue 399 ASP Chi-restraints excluded: chain H residue 419 ASP Chi-restraints excluded: chain H residue 450 GLU Chi-restraints excluded: chain H residue 464 ASP Chi-restraints excluded: chain H residue 498 LEU Chi-restraints excluded: chain H residue 509 ASP Chi-restraints excluded: chain H residue 636 PHE Chi-restraints excluded: chain H residue 651 ASP Chi-restraints excluded: chain H residue 662 ASP Chi-restraints excluded: chain H residue 673 ILE Chi-restraints excluded: chain H residue 684 ILE Chi-restraints excluded: chain H residue 702 ASN Chi-restraints excluded: chain H residue 726 VAL Chi-restraints excluded: chain H residue 880 GLU Chi-restraints excluded: chain H residue 883 GLU Chi-restraints excluded: chain H residue 1004 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 279 optimal weight: 0.0570 chunk 375 optimal weight: 5.9990 chunk 107 optimal weight: 4.9990 chunk 324 optimal weight: 4.9990 chunk 52 optimal weight: 0.0870 chunk 97 optimal weight: 7.9990 chunk 352 optimal weight: 0.5980 chunk 147 optimal weight: 1.9990 chunk 362 optimal weight: 0.7980 chunk 44 optimal weight: 0.0970 chunk 64 optimal weight: 1.9990 overall best weight: 0.3274 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 992 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 765 ASN ** D 832 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 910 ASN D 939 GLN ** D 961 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 349 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 563 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 681 GLN H 263 ASN H 461 ASN ** H 614 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.067058 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.052825 restraints weight = 210889.764| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.054274 restraints weight = 112764.269| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.055195 restraints weight = 73506.239| |-----------------------------------------------------------------------------| r_work (final): 0.3535 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8070 moved from start: 0.3690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 37739 Z= 0.129 Angle : 0.541 15.691 50864 Z= 0.266 Chirality : 0.039 0.153 5411 Planarity : 0.003 0.046 6518 Dihedral : 3.858 22.828 4891 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 13.35 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.64 % Favored : 95.33 % Rotamer: Outliers : 2.12 % Allowed : 23.75 % Favored : 74.13 % 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: 0.07 (0.13), residues: 4435 helix: 1.05 (0.11), residues: 2353 sheet: -2.15 (0.33), residues: 224 loop : -0.93 (0.15), residues: 1858 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 60 HIS 0.010 0.001 HIS A 975 PHE 0.027 0.001 PHE B 220 TYR 0.031 0.001 TYR A 755 ARG 0.004 0.000 ARG H 760 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6786.35 seconds wall clock time: 124 minutes 20.68 seconds (7460.68 seconds total)