Starting phenix.real_space_refine on Tue Aug 26 14:06:48 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8z18_39718/08_2025/8z18_39718.cif Found real_map, /net/cci-nas-00/data/ceres_data/8z18_39718/08_2025/8z18_39718.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.94 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8z18_39718/08_2025/8z18_39718.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8z18_39718/08_2025/8z18_39718.map" model { file = "/net/cci-nas-00/data/ceres_data/8z18_39718/08_2025/8z18_39718.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8z18_39718/08_2025/8z18_39718.cif" } resolution = 3.94 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= 0.001 sd= 0.012 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 138 5.16 5 C 24242 2.51 5 N 6038 2.21 5 O 7135 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 24 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 37553 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 8188 Number of conformers: 1 Conformer: "" Number of residues, atoms: 983, 8188 Classifications: {'peptide': 983} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 963} Chain: "B" Number of atoms: 8310 Number of conformers: 1 Conformer: "" Number of residues, atoms: 997, 8310 Classifications: {'peptide': 997} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 977} Chain: "C" Number of atoms: 8188 Number of conformers: 1 Conformer: "" Number of residues, atoms: 983, 8188 Classifications: {'peptide': 983} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 963} Chain: "D" Number of atoms: 8310 Number of conformers: 1 Conformer: "" Number of residues, atoms: 997, 8310 Classifications: {'peptide': 997} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 977} Chain: "E" Number of atoms: 1149 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 1149 Classifications: {'peptide': 145} Link IDs: {'PTRANS': 5, 'TRANS': 139} Chain breaks: 1 Chain: "F" Number of atoms: 1149 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 1149 Classifications: {'peptide': 145} Link IDs: {'PTRANS': 5, 'TRANS': 139} Chain breaks: 1 Chain: "G" Number of atoms: 1110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 1110 Classifications: {'peptide': 139} Link IDs: {'PTRANS': 5, 'TRANS': 133} Chain breaks: 2 Chain: "H" Number of atoms: 1149 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 1149 Classifications: {'peptide': 145} Link IDs: {'PTRANS': 5, 'TRANS': 139} Chain breaks: 1 Time building chain proxies: 9.02, per 1000 atoms: 0.24 Number of scatterers: 37553 At special positions: 0 Unit cell: (100.656, 133.276, 257.232, 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 138 16.00 O 7135 8.00 N 6038 7.00 C 24242 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.20 Conformation dependent library (CDL) restraints added in 1.6 seconds Enol-peptide restraints added in 1.2 microseconds 9016 Ramachandran restraints generated. 4508 Oldfield, 0 Emsley, 4508 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8638 Finding SS restraints... Secondary structure from input PDB file: 243 helices and 19 sheets defined 64.8% alpha, 7.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.56 Creating SS restraints... Processing helix chain 'A' and resid 23 through 40 Processing helix chain 'A' and resid 47 through 54 removed outlier: 3.727A pdb=" N SER A 51 " --> pdb=" O GLY A 47 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N LEU A 53 " --> pdb=" O GLY A 49 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N SER A 54 " --> pdb=" O VAL A 50 " (cutoff:3.500A) Processing helix chain 'A' and resid 58 through 72 removed outlier: 3.744A pdb=" N LEU A 62 " --> pdb=" O GLN A 58 " (cutoff:3.500A) Processing helix chain 'A' and resid 80 through 95 Proline residue: A 88 - end of helix Processing helix chain 'A' and resid 95 through 109 removed outlier: 4.172A pdb=" N ALA A 99 " --> pdb=" O LYS A 95 " (cutoff:3.500A) Processing helix chain 'A' and resid 115 through 123 removed outlier: 3.657A pdb=" N ASP A 119 " --> pdb=" O ASN A 115 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N LEU A 122 " --> pdb=" O HIS A 118 " (cutoff:3.500A) Processing helix chain 'A' and resid 136 through 146 Processing helix chain 'A' and resid 154 through 160 removed outlier: 3.833A pdb=" N VAL A 158 " --> pdb=" O ALA A 154 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N ALA A 159 " --> pdb=" O GLU A 155 " (cutoff:3.500A) Processing helix chain 'A' and resid 179 through 183 Processing helix chain 'A' and resid 186 through 192 Processing helix chain 'A' and resid 192 through 197 Processing helix chain 'A' and resid 197 through 211 removed outlier: 3.549A pdb=" N SER A 201 " --> pdb=" O TYR A 197 " (cutoff:3.500A) Processing helix chain 'A' and resid 222 through 236 Processing helix chain 'A' and resid 254 through 265 Processing helix chain 'A' and resid 271 through 275 Processing helix chain 'A' and resid 281 through 299 removed outlier: 3.506A pdb=" N ARG A 285 " --> pdb=" O ASP A 281 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N GLN A 297 " --> pdb=" O LEU A 293 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N GLU A 298 " --> pdb=" O ILE A 294 " (cutoff:3.500A) Processing helix chain 'A' and resid 304 through 322 Proline residue: A 318 - end of helix removed outlier: 4.277A pdb=" N ALA A 321 " --> pdb=" O SER A 317 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N LEU A 322 " --> pdb=" O PRO A 318 " (cutoff:3.500A) Processing helix chain 'A' and resid 326 through 334 removed outlier: 3.903A pdb=" N LYS A 331 " --> pdb=" O LYS A 327 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N HIS A 332 " --> pdb=" O ILE A 328 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N VAL A 333 " --> pdb=" O ASP A 329 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N PHE A 334 " --> pdb=" O LEU A 330 " (cutoff:3.500A) Processing helix chain 'A' and resid 355 through 366 Processing helix chain 'A' and resid 366 through 373 removed outlier: 3.800A pdb=" N LEU A 373 " --> pdb=" O GLU A 369 " (cutoff:3.500A) Processing helix chain 'A' and resid 374 through 391 Processing helix chain 'A' and resid 411 through 416 Processing helix chain 'A' and resid 417 through 427 Processing helix chain 'A' and resid 431 through 445 Processing helix chain 'A' and resid 447 through 464 removed outlier: 4.519A pdb=" N ASP A 464 " --> pdb=" O LEU A 460 " (cutoff:3.500A) Processing helix chain 'A' and resid 467 through 494 Processing helix chain 'A' and resid 495 through 501 Processing helix chain 'A' and resid 508 through 519 removed outlier: 3.904A pdb=" N MET A 519 " --> pdb=" O ILE A 515 " (cutoff:3.500A) Processing helix chain 'A' and resid 523 through 531 removed outlier: 4.270A pdb=" N PHE A 528 " --> pdb=" O ILE A 524 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N ASN A 529 " --> pdb=" O ASP A 525 " (cutoff:3.500A) Processing helix chain 'A' and resid 532 through 539 Processing helix chain 'A' and resid 542 through 547 Processing helix chain 'A' and resid 551 through 572 Processing helix chain 'A' and resid 579 through 598 Processing helix chain 'A' and resid 600 through 604 Processing helix chain 'A' and resid 605 through 628 Processing helix chain 'A' and resid 634 through 639 removed outlier: 3.831A pdb=" N PHE A 638 " --> pdb=" O LEU A 634 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N PHE A 639 " --> pdb=" O GLY A 635 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 634 through 639' Processing helix chain 'A' and resid 648 through 659 Processing helix chain 'A' and resid 660 through 671 Processing helix chain 'A' and resid 672 through 676 Processing helix chain 'A' and resid 680 through 701 removed outlier: 3.765A pdb=" N ALA A 701 " --> pdb=" O LYS A 697 " (cutoff:3.500A) Processing helix chain 'A' and resid 705 through 723 removed outlier: 4.230A pdb=" N SER A 714 " --> pdb=" O THR A 710 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N GLU A 715 " --> pdb=" O GLN A 711 " (cutoff:3.500A) Processing helix chain 'A' and resid 729 through 743 Processing helix chain 'A' and resid 750 through 765 removed outlier: 4.236A pdb=" N CYS A 764 " --> pdb=" O ARG A 760 " (cutoff:3.500A) Processing helix chain 'A' and resid 768 through 788 removed outlier: 4.308A pdb=" N ASP A 788 " --> pdb=" O GLU A 784 " (cutoff:3.500A) Processing helix chain 'A' and resid 800 through 812 removed outlier: 3.620A pdb=" N TYR A 804 " --> pdb=" O TYR A 800 " (cutoff:3.500A) Processing helix chain 'A' and resid 817 through 827 Processing helix chain 'A' and resid 831 through 841 removed outlier: 3.512A pdb=" N LYS A 840 " --> pdb=" O ASP A 836 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N LEU A 841 " --> pdb=" O PHE A 837 " (cutoff:3.500A) Processing helix chain 'A' and resid 842 through 845 Processing helix chain 'A' and resid 846 through 857 Processing helix chain 'A' and resid 861 through 872 Processing helix chain 'A' and resid 878 through 902 removed outlier: 3.764A pdb=" N GLU A 901 " --> pdb=" O ILE A 897 " (cutoff:3.500A) Processing helix chain 'A' and resid 908 through 922 removed outlier: 3.714A pdb=" N TYR A 912 " --> pdb=" O SER A 908 " (cutoff:3.500A) Processing helix chain 'A' and resid 928 through 934 removed outlier: 3.663A pdb=" N GLU A 932 " --> pdb=" O SER A 928 " (cutoff:3.500A) Processing helix chain 'A' and resid 940 through 945 Processing helix chain 'A' and resid 950 through 954 Processing helix chain 'A' and resid 955 through 956 No H-bonds generated for 'chain 'A' and resid 955 through 956' Processing helix chain 'A' and resid 957 through 962 removed outlier: 4.097A pdb=" N ASN A 961 " --> pdb=" O SER A 957 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N TYR A 962 " --> pdb=" O TRP A 958 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 957 through 962' Processing helix chain 'A' and resid 963 through 973 Processing helix chain 'A' and resid 973 through 991 removed outlier: 4.520A pdb=" N HIS A 978 " --> pdb=" O LYS A 974 " (cutoff:3.500A) removed outlier: 5.993A pdb=" N HIS A 979 " --> pdb=" O HIS A 975 " (cutoff:3.500A) Processing helix chain 'A' and resid 993 through 1003 Processing helix chain 'B' and resid 10 through 19 Processing helix chain 'B' and resid 23 through 39 Processing helix chain 'B' and resid 47 through 54 removed outlier: 3.526A pdb=" N SER B 51 " --> pdb=" O GLY B 47 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N SER B 54 " --> pdb=" O VAL B 50 " (cutoff:3.500A) Processing helix chain 'B' and resid 58 through 72 removed outlier: 3.783A pdb=" N LEU B 62 " --> pdb=" O GLN B 58 " (cutoff:3.500A) Processing helix chain 'B' and resid 80 through 95 Proline residue: B 88 - end of helix Processing helix chain 'B' and resid 96 through 109 removed outlier: 3.966A pdb=" N PHE B 100 " --> pdb=" O GLY B 96 " (cutoff:3.500A) Processing helix chain 'B' and resid 115 through 121 removed outlier: 3.513A pdb=" N ASP B 119 " --> pdb=" O ASN B 115 " (cutoff:3.500A) Processing helix chain 'B' and resid 122 through 125 Processing helix chain 'B' and resid 136 through 146 removed outlier: 3.612A pdb=" N TRP B 143 " --> pdb=" O ASP B 139 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ARG B 145 " --> pdb=" O ALA B 141 " (cutoff:3.500A) Processing helix chain 'B' and resid 155 through 159 Processing helix chain 'B' and resid 179 through 183 Processing helix chain 'B' and resid 186 through 192 Processing helix chain 'B' and resid 192 through 197 Processing helix chain 'B' and resid 197 through 211 removed outlier: 3.581A pdb=" N THR B 206 " --> pdb=" O ASN B 202 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N THR B 210 " --> pdb=" O THR B 206 " (cutoff:3.500A) Processing helix chain 'B' and resid 222 through 234 Processing helix chain 'B' and resid 254 through 265 Processing helix chain 'B' and resid 271 through 275 Processing helix chain 'B' and resid 281 through 298 removed outlier: 3.517A pdb=" N GLU B 298 " --> pdb=" O ILE B 294 " (cutoff:3.500A) Processing helix chain 'B' and resid 304 through 306 No H-bonds generated for 'chain 'B' and resid 304 through 306' Processing helix chain 'B' and resid 307 through 317 Processing helix chain 'B' and resid 318 through 322 removed outlier: 3.905A pdb=" N ALA B 321 " --> pdb=" O PRO B 318 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N LEU B 322 " --> pdb=" O LEU B 319 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 318 through 322' Processing helix chain 'B' and resid 329 through 334 removed outlier: 3.810A pdb=" N VAL B 333 " --> pdb=" O ASP B 329 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N PHE B 334 " --> pdb=" O LEU B 330 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 329 through 334' Processing helix chain 'B' and resid 357 through 366 Processing helix chain 'B' and resid 366 through 372 Processing helix chain 'B' and resid 374 through 392 Processing helix chain 'B' and resid 418 through 427 Processing helix chain 'B' and resid 431 through 445 Processing helix chain 'B' and resid 447 through 466 Processing helix chain 'B' and resid 467 through 501 removed outlier: 5.421A pdb=" N LEU B 497 " --> pdb=" O ASN B 493 " (cutoff:3.500A) removed outlier: 5.186A pdb=" N LEU B 498 " --> pdb=" O GLY B 494 " (cutoff:3.500A) Processing helix chain 'B' and resid 508 through 519 Processing helix chain 'B' and resid 523 through 527 Processing helix chain 'B' and resid 532 through 539 Processing helix chain 'B' and resid 540 through 546 Processing helix chain 'B' and resid 553 through 572 Processing helix chain 'B' and resid 579 through 598 Processing helix chain 'B' and resid 600 through 604 removed outlier: 4.075A pdb=" N VAL B 603 " --> pdb=" O LEU B 600 " (cutoff:3.500A) Processing helix chain 'B' and resid 605 through 629 Processing helix chain 'B' and resid 632 through 639 Processing helix chain 'B' and resid 648 through 659 Processing helix chain 'B' and resid 660 through 671 Processing helix chain 'B' and resid 680 through 701 Processing helix chain 'B' and resid 705 through 723 removed outlier: 4.600A pdb=" N SER B 714 " --> pdb=" O THR B 710 " (cutoff:3.500A) removed outlier: 4.883A pdb=" N GLU B 715 " --> pdb=" O GLN B 711 " (cutoff:3.500A) Processing helix chain 'B' and resid 729 through 742 Processing helix chain 'B' and resid 750 through 765 Processing helix chain 'B' and resid 768 through 786 Processing helix chain 'B' and resid 800 through 812 Processing helix chain 'B' and resid 817 through 827 Processing helix chain 'B' and resid 828 through 830 No H-bonds generated for 'chain 'B' and resid 828 through 830' Processing helix chain 'B' and resid 831 through 841 Processing helix chain 'B' and resid 842 through 845 Processing helix chain 'B' and resid 846 through 857 Processing helix chain 'B' and resid 861 through 872 Processing helix chain 'B' and resid 878 through 902 removed outlier: 4.040A pdb=" N GLU B 901 " --> pdb=" O ILE B 897 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N LYS B 902 " --> pdb=" O VAL B 898 " (cutoff:3.500A) Processing helix chain 'B' and resid 908 through 922 removed outlier: 3.834A pdb=" N TYR B 912 " --> pdb=" O SER B 908 " (cutoff:3.500A) Processing helix chain 'B' and resid 928 through 933 Processing helix chain 'B' and resid 937 through 945 Processing helix chain 'B' and resid 955 through 961 Processing helix chain 'B' and resid 963 through 973 Processing helix chain 'B' and resid 973 through 991 removed outlier: 3.956A pdb=" N HIS B 979 " --> pdb=" O HIS B 975 " (cutoff:3.500A) Processing helix chain 'B' and resid 993 through 1004 removed outlier: 3.695A pdb=" N TYR B1003 " --> pdb=" O ILE B 999 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N PHE B1004 " --> pdb=" O LEU B1000 " (cutoff:3.500A) Processing helix chain 'C' and resid 24 through 39 Processing helix chain 'C' and resid 47 through 54 removed outlier: 4.196A pdb=" N SER C 51 " --> pdb=" O GLY C 47 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N SER C 54 " --> pdb=" O VAL C 50 " (cutoff:3.500A) Processing helix chain 'C' and resid 58 through 72 removed outlier: 3.549A pdb=" N LEU C 62 " --> pdb=" O GLN C 58 " (cutoff:3.500A) Processing helix chain 'C' and resid 80 through 95 Proline residue: C 88 - end of helix Processing helix chain 'C' and resid 96 through 109 removed outlier: 3.536A pdb=" N PHE C 100 " --> pdb=" O GLY C 96 " (cutoff:3.500A) Processing helix chain 'C' and resid 115 through 124 removed outlier: 4.271A pdb=" N ASP C 119 " --> pdb=" O ASN C 115 " (cutoff:3.500A) Processing helix chain 'C' and resid 136 through 146 Processing helix chain 'C' and resid 154 through 160 removed outlier: 4.252A pdb=" N ALA C 159 " --> pdb=" O GLU C 155 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ASN C 160 " --> pdb=" O GLU C 156 " (cutoff:3.500A) Processing helix chain 'C' and resid 186 through 192 removed outlier: 3.722A pdb=" N TYR C 190 " --> pdb=" O LYS C 186 " (cutoff:3.500A) Processing helix chain 'C' and resid 192 through 197 Processing helix chain 'C' and resid 197 through 211 Processing helix chain 'C' and resid 222 through 236 removed outlier: 3.621A pdb=" N LEU C 235 " --> pdb=" O TRP C 231 " (cutoff:3.500A) Processing helix chain 'C' and resid 254 through 265 Processing helix chain 'C' and resid 271 through 275 Processing helix chain 'C' and resid 281 through 299 removed outlier: 3.528A pdb=" N SER C 296 " --> pdb=" O LEU C 292 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N GLU C 298 " --> pdb=" O ILE C 294 " (cutoff:3.500A) Processing helix chain 'C' and resid 305 through 317 removed outlier: 4.116A pdb=" N ILE C 309 " --> pdb=" O ASP C 305 " (cutoff:3.500A) Processing helix chain 'C' and resid 318 through 321 Processing helix chain 'C' and resid 329 through 334 removed outlier: 4.112A pdb=" N VAL C 333 " --> pdb=" O ASP C 329 " (cutoff:3.500A) Processing helix chain 'C' and resid 355 through 366 Processing helix chain 'C' and resid 366 through 372 Processing helix chain 'C' and resid 374 through 392 Processing helix chain 'C' and resid 411 through 416 Processing helix chain 'C' and resid 417 through 427 Processing helix chain 'C' and resid 431 through 445 Processing helix chain 'C' and resid 447 through 461 Processing helix chain 'C' and resid 467 through 493 Processing helix chain 'C' and resid 494 through 501 removed outlier: 4.339A pdb=" N LEU C 498 " --> pdb=" O GLY C 494 " (cutoff:3.500A) Processing helix chain 'C' and resid 508 through 519 Processing helix chain 'C' and resid 525 through 531 removed outlier: 4.037A pdb=" N ASN C 529 " --> pdb=" O ASP C 525 " (cutoff:3.500A) Processing helix chain 'C' and resid 532 through 539 Processing helix chain 'C' and resid 542 through 547 removed outlier: 3.560A pdb=" N SER C 546 " --> pdb=" O LEU C 542 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N ASP C 547 " --> pdb=" O GLU C 543 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 542 through 547' Processing helix chain 'C' and resid 551 through 572 Processing helix chain 'C' and resid 579 through 598 Processing helix chain 'C' and resid 600 through 604 removed outlier: 3.603A pdb=" N VAL C 603 " --> pdb=" O LEU C 600 " (cutoff:3.500A) Processing helix chain 'C' and resid 605 through 628 removed outlier: 3.678A pdb=" N THR C 628 " --> pdb=" O GLU C 624 " (cutoff:3.500A) Processing helix chain 'C' and resid 634 through 639 removed outlier: 3.521A pdb=" N PHE C 638 " --> pdb=" O LEU C 634 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N PHE C 639 " --> pdb=" O GLY C 635 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 634 through 639' Processing helix chain 'C' and resid 648 through 659 Processing helix chain 'C' and resid 660 through 671 Processing helix chain 'C' and resid 672 through 676 removed outlier: 3.583A pdb=" N LYS C 675 " --> pdb=" O SER C 672 " (cutoff:3.500A) Processing helix chain 'C' and resid 680 through 701 removed outlier: 4.113A pdb=" N ALA C 701 " --> pdb=" O LYS C 697 " (cutoff:3.500A) Processing helix chain 'C' and resid 705 through 722 removed outlier: 3.808A pdb=" N THR C 710 " --> pdb=" O VAL C 706 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N GLN C 711 " --> pdb=" O VAL C 707 " (cutoff:3.500A) removed outlier: 4.872A pdb=" N SER C 714 " --> pdb=" O THR C 710 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N GLU C 715 " --> pdb=" O GLN C 711 " (cutoff:3.500A) Processing helix chain 'C' and resid 729 through 743 Processing helix chain 'C' and resid 750 through 764 removed outlier: 4.494A pdb=" N CYS C 764 " --> pdb=" O ARG C 760 " (cutoff:3.500A) Processing helix chain 'C' and resid 768 through 786 Processing helix chain 'C' and resid 800 through 812 Processing helix chain 'C' and resid 817 through 827 Processing helix chain 'C' and resid 831 through 841 removed outlier: 3.525A pdb=" N LYS C 840 " --> pdb=" O ASP C 836 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N LEU C 841 " --> pdb=" O PHE C 837 " (cutoff:3.500A) Processing helix chain 'C' and resid 842 through 845 Processing helix chain 'C' and resid 846 through 857 Processing helix chain 'C' and resid 861 through 872 Processing helix chain 'C' and resid 878 through 902 removed outlier: 3.698A pdb=" N GLU C 901 " --> pdb=" O ILE C 897 " (cutoff:3.500A) Processing helix chain 'C' and resid 908 through 922 Processing helix chain 'C' and resid 928 through 934 removed outlier: 3.780A pdb=" N GLU C 932 " --> pdb=" O SER C 928 " (cutoff:3.500A) Processing helix chain 'C' and resid 939 through 945 Processing helix chain 'C' and resid 955 through 961 Processing helix chain 'C' and resid 963 through 973 Processing helix chain 'C' and resid 973 through 991 removed outlier: 4.649A pdb=" N HIS C 978 " --> pdb=" O LYS C 974 " (cutoff:3.500A) removed outlier: 5.572A pdb=" N HIS C 979 " --> pdb=" O HIS C 975 " (cutoff:3.500A) Processing helix chain 'C' and resid 993 through 1003 removed outlier: 3.658A pdb=" N LEU C 997 " --> pdb=" O ASP C 993 " (cutoff:3.500A) Processing helix chain 'D' and resid 10 through 19 Processing helix chain 'D' and resid 23 through 39 Processing helix chain 'D' and resid 47 through 54 removed outlier: 3.955A pdb=" N SER D 51 " --> pdb=" O GLY D 47 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N SER D 54 " --> pdb=" O VAL D 50 " (cutoff:3.500A) Processing helix chain 'D' and resid 58 through 72 removed outlier: 3.929A pdb=" N LEU D 62 " --> pdb=" O GLN D 58 " (cutoff:3.500A) Processing helix chain 'D' and resid 80 through 96 Proline residue: D 88 - end of helix Processing helix chain 'D' and resid 96 through 109 removed outlier: 3.595A pdb=" N PHE D 100 " --> pdb=" O GLY D 96 " (cutoff:3.500A) Processing helix chain 'D' and resid 115 through 123 Processing helix chain 'D' and resid 136 through 146 removed outlier: 3.622A pdb=" N ARG D 145 " --> pdb=" O ALA D 141 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N GLY D 146 " --> pdb=" O CYS D 142 " (cutoff:3.500A) Processing helix chain 'D' and resid 154 through 160 removed outlier: 3.793A pdb=" N ALA D 159 " --> pdb=" O GLU D 155 " (cutoff:3.500A) Processing helix chain 'D' and resid 179 through 183 Processing helix chain 'D' and resid 186 through 192 Processing helix chain 'D' and resid 192 through 197 Processing helix chain 'D' and resid 197 through 211 Processing helix chain 'D' and resid 222 through 235 Processing helix chain 'D' and resid 254 through 264 Processing helix chain 'D' and resid 271 through 275 Processing helix chain 'D' and resid 281 through 296 Processing helix chain 'D' and resid 307 through 317 Processing helix chain 'D' and resid 318 through 321 removed outlier: 3.689A pdb=" N ALA D 321 " --> pdb=" O PRO D 318 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 318 through 321' Processing helix chain 'D' and resid 326 through 335 removed outlier: 3.792A pdb=" N LYS D 331 " --> pdb=" O ILE D 328 " (cutoff:3.500A) Processing helix chain 'D' and resid 357 through 366 Processing helix chain 'D' and resid 366 through 372 Processing helix chain 'D' and resid 374 through 392 Processing helix chain 'D' and resid 396 through 400 Processing helix chain 'D' and resid 418 through 427 Processing helix chain 'D' and resid 431 through 445 Processing helix chain 'D' and resid 447 through 466 Processing helix chain 'D' and resid 467 through 495 Processing helix chain 'D' and resid 495 through 501 Processing helix chain 'D' and resid 508 through 519 Processing helix chain 'D' and resid 523 through 527 Processing helix chain 'D' and resid 532 through 539 Processing helix chain 'D' and resid 540 through 546 removed outlier: 3.791A pdb=" N PHE D 544 " --> pdb=" O ILE D 541 " (cutoff:3.500A) Processing helix chain 'D' and resid 553 through 572 Processing helix chain 'D' and resid 579 through 597 Processing helix chain 'D' and resid 600 through 604 removed outlier: 3.722A pdb=" N VAL D 603 " --> pdb=" O LEU D 600 " (cutoff:3.500A) Processing helix chain 'D' and resid 605 through 629 removed outlier: 3.625A pdb=" N ARG D 627 " --> pdb=" O ALA D 623 " (cutoff:3.500A) Processing helix chain 'D' and resid 632 through 639 Processing helix chain 'D' and resid 648 through 659 Processing helix chain 'D' and resid 660 through 671 Processing helix chain 'D' and resid 672 through 676 Processing helix chain 'D' and resid 680 through 701 Processing helix chain 'D' and resid 705 through 723 removed outlier: 3.689A pdb=" N GLN D 711 " --> pdb=" O VAL D 707 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N SER D 714 " --> pdb=" O THR D 710 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N GLU D 715 " --> pdb=" O GLN D 711 " (cutoff:3.500A) Processing helix chain 'D' and resid 729 through 744 removed outlier: 3.661A pdb=" N PHE D 744 " --> pdb=" O LEU D 740 " (cutoff:3.500A) Processing helix chain 'D' and resid 750 through 765 Processing helix chain 'D' and resid 768 through 786 Processing helix chain 'D' and resid 800 through 812 removed outlier: 3.811A pdb=" N TYR D 804 " --> pdb=" O TYR D 800 " (cutoff:3.500A) Processing helix chain 'D' and resid 817 through 827 Processing helix chain 'D' and resid 828 through 830 No H-bonds generated for 'chain 'D' and resid 828 through 830' Processing helix chain 'D' and resid 831 through 841 Processing helix chain 'D' and resid 846 through 857 Processing helix chain 'D' and resid 861 through 872 removed outlier: 3.882A pdb=" N ILE D 871 " --> pdb=" O ASN D 867 " (cutoff:3.500A) Processing helix chain 'D' and resid 878 through 902 removed outlier: 3.854A pdb=" N GLU D 901 " --> pdb=" O ILE D 897 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N LYS D 902 " --> pdb=" O VAL D 898 " (cutoff:3.500A) Processing helix chain 'D' and resid 908 through 922 removed outlier: 3.698A pdb=" N TYR D 912 " --> pdb=" O SER D 908 " (cutoff:3.500A) Processing helix chain 'D' and resid 928 through 933 Processing helix chain 'D' and resid 937 through 945 Processing helix chain 'D' and resid 955 through 961 Processing helix chain 'D' and resid 963 through 973 Processing helix chain 'D' and resid 973 through 991 removed outlier: 4.066A pdb=" N HIS D 979 " --> pdb=" O HIS D 975 " (cutoff:3.500A) Processing helix chain 'D' and resid 993 through 1003 removed outlier: 3.730A pdb=" N TYR D1003 " --> pdb=" O ILE D 999 " (cutoff:3.500A) Processing helix chain 'E' and resid 69 through 76 removed outlier: 3.542A pdb=" N THR E 76 " --> pdb=" O TRP E 72 " (cutoff:3.500A) Processing helix chain 'F' and resid 69 through 76 Processing helix chain 'G' and resid 36 through 40 Processing helix chain 'G' and resid 69 through 76 removed outlier: 3.551A pdb=" N THR G 76 " --> pdb=" O TRP G 72 " (cutoff:3.500A) Processing helix chain 'H' and resid 69 through 76 Processing sheet with id=AA1, first strand: chain 'A' and resid 42 through 46 removed outlier: 6.551A pdb=" N ILE A 213 " --> pdb=" O PHE A 244 " (cutoff:3.500A) removed outlier: 7.799A pdb=" N ILE A 246 " --> pdb=" O ILE A 213 " (cutoff:3.500A) removed outlier: 7.024A pdb=" N PHE A 215 " --> pdb=" O ILE A 246 " (cutoff:3.500A) removed outlier: 8.093A pdb=" N ARG A 267 " --> pdb=" O HIS A 241 " (cutoff:3.500A) removed outlier: 7.804A pdb=" N ILE A 269 " --> pdb=" O PRO A 243 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N PHE A 245 " --> pdb=" O ILE A 269 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 150 through 152 removed outlier: 6.362A pdb=" N SER A 150 " --> pdb=" O LEU A 167 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 345 through 346 Processing sheet with id=AA4, first strand: chain 'A' and resid 574 through 575 removed outlier: 6.347A pdb=" N PHE F 23 " --> pdb=" O PHE F 68 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N PHE F 68 " --> pdb=" O PHE F 23 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N ALA F 25 " --> pdb=" O ALA F 66 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N ALA F 66 " --> pdb=" O ALA F 25 " (cutoff:3.500A) removed outlier: 5.214A pdb=" N ALA F 27 " --> pdb=" O LYS F 64 " (cutoff:3.500A) removed outlier: 5.529A pdb=" N LYS F 64 " --> pdb=" O ALA F 27 " (cutoff:3.500A) removed outlier: 5.130A pdb=" N ILE F 59 " --> pdb=" O ALA F 222 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LEU F 61 " --> pdb=" O PHE F 220 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N VAL F 63 " --> pdb=" O ILE F 218 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N ILE F 218 " --> pdb=" O VAL F 63 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N TYR F 171 " --> pdb=" O VAL F 198 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N VAL F 11 " --> pdb=" O THR F 24 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N THR F 24 " --> pdb=" O VAL F 11 " (cutoff:3.500A) removed outlier: 6.953A pdb=" N PHE F 13 " --> pdb=" O VAL F 22 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 646 through 647 removed outlier: 3.588A pdb=" N MET A 647 " --> pdb=" O ARG A 677 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'B' and resid 128 through 129 removed outlier: 3.760A pdb=" N HIS B 128 " --> pdb=" O LEU B 42 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N ILE B 213 " --> pdb=" O PHE B 244 " (cutoff:3.500A) removed outlier: 8.085A pdb=" N ILE B 246 " --> pdb=" O ILE B 213 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N PHE B 215 " --> pdb=" O ILE B 246 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N PHE B 245 " --> pdb=" O ILE B 269 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 150 through 152 Processing sheet with id=AA8, first strand: chain 'B' and resid 338 through 340 Processing sheet with id=AA9, first strand: chain 'B' and resid 573 through 575 removed outlier: 7.073A pdb=" N THR E 62 " --> pdb=" O GLN E 28 " (cutoff:3.500A) removed outlier: 4.947A pdb=" N ALA E 30 " --> pdb=" O ASN E 60 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N ASN E 60 " --> pdb=" O ALA E 30 " (cutoff:3.500A) removed outlier: 4.929A pdb=" N PHE E 32 " --> pdb=" O GLU E 58 " (cutoff:3.500A) removed outlier: 7.240A pdb=" N GLU E 58 " --> pdb=" O PHE E 32 " (cutoff:3.500A) removed outlier: 5.003A pdb=" N GLN E 34 " --> pdb=" O GLU E 56 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N GLU E 56 " --> pdb=" O GLN E 34 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ILE E 218 " --> pdb=" O VAL E 63 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 573 through 575 removed outlier: 6.702A pdb=" N PHE E 13 " --> pdb=" O VAL E 22 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N THR E 24 " --> pdb=" O VAL E 11 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N VAL E 11 " --> pdb=" O THR E 24 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N TYR E 192 " --> pdb=" O ILE E 235 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 794 through 795 Processing sheet with id=AB3, first strand: chain 'C' and resid 166 through 169 removed outlier: 4.451A pdb=" N HIS C 128 " --> pdb=" O LEU C 42 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N PHE C 44 " --> pdb=" O HIS C 128 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N ILE C 213 " --> pdb=" O PHE C 244 " (cutoff:3.500A) removed outlier: 7.053A pdb=" N ILE C 246 " --> pdb=" O ILE C 213 " (cutoff:3.500A) removed outlier: 5.784A pdb=" N PHE C 215 " --> pdb=" O ILE C 246 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 345 through 346 Processing sheet with id=AB5, first strand: chain 'C' and resid 574 through 575 removed outlier: 4.205A pdb=" N GLU H 26 " --> pdb=" O ASN H 65 " (cutoff:3.500A) removed outlier: 5.229A pdb=" N ASN H 65 " --> pdb=" O GLU H 26 " (cutoff:3.500A) removed outlier: 5.985A pdb=" N GLN H 28 " --> pdb=" O VAL H 63 " (cutoff:3.500A) removed outlier: 7.135A pdb=" N VAL H 63 " --> pdb=" O GLN H 28 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N ALA H 30 " --> pdb=" O LEU H 61 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N LEU H 61 " --> pdb=" O ALA H 30 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N PHE H 32 " --> pdb=" O ILE H 59 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N ILE H 59 " --> pdb=" O PHE H 32 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N GLN H 34 " --> pdb=" O LYS H 57 " (cutoff:3.500A) removed outlier: 6.953A pdb=" N LYS H 57 " --> pdb=" O GLN H 34 " (cutoff:3.500A) removed outlier: 5.530A pdb=" N ILE H 59 " --> pdb=" O ALA H 222 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ALA H 222 " --> pdb=" O ILE H 59 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N GLU H 221 " --> pdb=" O SER H 199 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N SER H 199 " --> pdb=" O GLU H 221 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N TYR H 171 " --> pdb=" O VAL H 198 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N VAL H 11 " --> pdb=" O THR H 24 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N THR H 24 " --> pdb=" O VAL H 11 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N PHE H 13 " --> pdb=" O VAL H 22 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 150 through 152 removed outlier: 5.965A pdb=" N SER D 150 " --> pdb=" O LEU D 167 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N LYS D 169 " --> pdb=" O SER D 150 " (cutoff:3.500A) removed outlier: 6.159A pdb=" N ILE D 152 " --> pdb=" O LYS D 169 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N VAL D 129 " --> pdb=" O LEU D 168 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 338 through 340 Processing sheet with id=AB8, first strand: chain 'F' and resid 176 through 178 Processing sheet with id=AB9, first strand: chain 'G' and resid 233 through 235 removed outlier: 3.617A pdb=" N GLU G 221 " --> pdb=" O SER G 199 " (cutoff:3.500A) removed outlier: 5.094A pdb=" N ILE G 59 " --> pdb=" O ALA G 222 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N GLU G 56 " --> pdb=" O GLN G 34 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N GLN G 34 " --> pdb=" O GLU G 56 " (cutoff:3.500A) removed outlier: 7.053A pdb=" N GLU G 58 " --> pdb=" O PHE G 32 " (cutoff:3.500A) removed outlier: 4.819A pdb=" N PHE G 32 " --> pdb=" O GLU G 58 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N ASN G 60 " --> pdb=" O ALA G 30 " (cutoff:3.500A) removed outlier: 4.726A pdb=" N ALA G 30 " --> pdb=" O ASN G 60 " (cutoff:3.500A) removed outlier: 7.013A pdb=" N THR G 62 " --> pdb=" O GLN G 28 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N ALA G 66 " --> pdb=" O THR G 24 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N THR G 24 " --> pdb=" O ALA G 66 " (cutoff:3.500A) removed outlier: 5.031A pdb=" N PHE G 68 " --> pdb=" O VAL G 22 " (cutoff:3.500A) removed outlier: 7.915A pdb=" N VAL G 22 " --> pdb=" O PHE G 68 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N PHE G 13 " --> pdb=" O VAL G 22 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N THR G 24 " --> pdb=" O VAL G 11 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N VAL G 11 " --> pdb=" O THR G 24 " (cutoff:3.500A) removed outlier: 7.336A pdb=" N TYR G 171 " --> pdb=" O ASN G 197 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N ASN G 197 " --> pdb=" O TYR G 171 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'H' and resid 176 through 178 1998 hydrogen bonds defined for protein. 5793 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 9.08 Time building geometry restraints manager: 4.25 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.30: 6358 1.30 - 1.43: 10456 1.43 - 1.56: 21345 1.56 - 1.69: 9 1.69 - 1.82: 236 Bond restraints: 38404 Sorted by residual: bond pdb=" C PHE E 13 " pdb=" O PHE E 13 " ideal model delta sigma weight residual 1.235 1.165 0.071 1.23e-02 6.61e+03 3.30e+01 bond pdb=" C HIS A 339 " pdb=" O HIS A 339 " ideal model delta sigma weight residual 1.235 1.172 0.063 1.20e-02 6.94e+03 2.74e+01 bond pdb=" C ASN D 861 " pdb=" O ASN D 861 " ideal model delta sigma weight residual 1.235 1.196 0.039 1.08e-02 8.57e+03 1.31e+01 bond pdb=" C ASN E 60 " pdb=" O ASN E 60 " ideal model delta sigma weight residual 1.234 1.193 0.042 1.22e-02 6.72e+03 1.16e+01 bond pdb=" C ASN C 278 " pdb=" O ASN C 278 " ideal model delta sigma weight residual 1.234 1.188 0.047 1.38e-02 5.25e+03 1.15e+01 ... (remaining 38399 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.84: 50938 2.84 - 5.67: 729 5.67 - 8.51: 86 8.51 - 11.34: 6 11.34 - 14.18: 1 Bond angle restraints: 51760 Sorted by residual: angle pdb=" N MET B 21 " pdb=" CA MET B 21 " pdb=" C MET B 21 " ideal model delta sigma weight residual 113.88 99.70 14.18 1.23e+00 6.61e-01 1.33e+02 angle pdb=" N PHE G 204 " pdb=" CA PHE G 204 " pdb=" C PHE G 204 " ideal model delta sigma weight residual 110.97 102.47 8.50 1.09e+00 8.42e-01 6.08e+01 angle pdb=" N ASN D1002 " pdb=" CA ASN D1002 " pdb=" C ASN D1002 " ideal model delta sigma weight residual 111.28 119.74 -8.46 1.09e+00 8.42e-01 6.03e+01 angle pdb=" N ASN B 136 " pdb=" CA ASN B 136 " pdb=" C ASN B 136 " ideal model delta sigma weight residual 113.17 105.25 7.92 1.26e+00 6.30e-01 3.96e+01 angle pdb=" N LYS C 304 " pdb=" CA LYS C 304 " pdb=" C LYS C 304 " ideal model delta sigma weight residual 110.53 118.49 -7.96 1.32e+00 5.74e-01 3.64e+01 ... (remaining 51755 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 19726 17.95 - 35.90: 2531 35.90 - 53.86: 536 53.86 - 71.81: 91 71.81 - 89.76: 46 Dihedral angle restraints: 22930 sinusoidal: 9489 harmonic: 13441 Sorted by residual: dihedral pdb=" CA TYR B 166 " pdb=" C TYR B 166 " pdb=" N LEU B 167 " pdb=" CA LEU B 167 " ideal model delta harmonic sigma weight residual 180.00 158.96 21.04 0 5.00e+00 4.00e-02 1.77e+01 dihedral pdb=" CA GLY A 355 " pdb=" C GLY A 355 " pdb=" N TYR A 356 " pdb=" CA TYR A 356 " ideal model delta harmonic sigma weight residual -180.00 -160.61 -19.39 0 5.00e+00 4.00e-02 1.50e+01 dihedral pdb=" CA THR A 906 " pdb=" C THR A 906 " pdb=" N PHE A 907 " pdb=" CA PHE A 907 " ideal model delta harmonic sigma weight residual 180.00 161.15 18.85 0 5.00e+00 4.00e-02 1.42e+01 ... (remaining 22927 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 4605 0.059 - 0.119: 791 0.119 - 0.178: 96 0.178 - 0.238: 17 0.238 - 0.297: 1 Chirality restraints: 5510 Sorted by residual: chirality pdb=" CG LEU B 274 " pdb=" CB LEU B 274 " pdb=" CD1 LEU B 274 " pdb=" CD2 LEU B 274 " both_signs ideal model delta sigma weight residual False -2.59 -2.29 -0.30 2.00e-01 2.50e+01 2.21e+00 chirality pdb=" CG LEU A 460 " pdb=" CB LEU A 460 " pdb=" CD1 LEU A 460 " pdb=" CD2 LEU A 460 " both_signs ideal model delta sigma weight residual False -2.59 -2.36 -0.23 2.00e-01 2.50e+01 1.35e+00 chirality pdb=" CG LEU A 820 " pdb=" CB LEU A 820 " pdb=" CD1 LEU A 820 " pdb=" CD2 LEU A 820 " both_signs ideal model delta sigma weight residual False -2.59 -2.36 -0.23 2.00e-01 2.50e+01 1.32e+00 ... (remaining 5507 not shown) Planarity restraints: 6633 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE D 916 " -0.023 2.00e-02 2.50e+03 2.50e-02 1.10e+01 pdb=" CG PHE D 916 " 0.058 2.00e-02 2.50e+03 pdb=" CD1 PHE D 916 " -0.018 2.00e-02 2.50e+03 pdb=" CD2 PHE D 916 " -0.011 2.00e-02 2.50e+03 pdb=" CE1 PHE D 916 " 0.004 2.00e-02 2.50e+03 pdb=" CE2 PHE D 916 " -0.003 2.00e-02 2.50e+03 pdb=" CZ PHE D 916 " -0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 757 " -0.027 2.00e-02 2.50e+03 1.98e-02 9.76e+00 pdb=" CG TRP A 757 " 0.053 2.00e-02 2.50e+03 pdb=" CD1 TRP A 757 " -0.018 2.00e-02 2.50e+03 pdb=" CD2 TRP A 757 " 0.004 2.00e-02 2.50e+03 pdb=" NE1 TRP A 757 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP A 757 " -0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP A 757 " -0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 757 " -0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 757 " -0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP A 757 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 589 " 0.025 2.00e-02 2.50e+03 2.16e-02 9.30e+00 pdb=" CG TYR A 589 " -0.052 2.00e-02 2.50e+03 pdb=" CD1 TYR A 589 " 0.015 2.00e-02 2.50e+03 pdb=" CD2 TYR A 589 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR A 589 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 TYR A 589 " 0.011 2.00e-02 2.50e+03 pdb=" CZ TYR A 589 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR A 589 " 0.001 2.00e-02 2.50e+03 ... (remaining 6630 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 3147 2.74 - 3.28: 43696 3.28 - 3.82: 68296 3.82 - 4.36: 81092 4.36 - 4.90: 130748 Nonbonded interactions: 326979 Sorted by model distance: nonbonded pdb=" O TYR C 414 " pdb=" NH2 ARG C 657 " model vdw 2.196 3.120 nonbonded pdb=" N GLY D 935 " pdb=" OD1 ASP D 941 " model vdw 2.196 3.120 nonbonded pdb=" OG1 THR B 828 " pdb=" OD2 ASP B 830 " model vdw 2.207 3.040 nonbonded pdb=" O HIS B 852 " pdb=" OG SER B 855 " model vdw 2.219 3.040 nonbonded pdb=" O LEU D 634 " pdb=" OG SER D 637 " model vdw 2.224 3.040 ... (remaining 326974 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and resid 23 through 1005) selection = chain 'C' selection = (chain 'D' and resid 23 through 1005) } ncs_group { reference = (chain 'E' and (resid 3 through 41 or resid 48 through 238)) selection = (chain 'F' and (resid 3 through 41 or resid 48 through 238)) selection = chain 'G' selection = (chain 'H' and (resid 3 through 41 or resid 48 through 238)) } 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: 6.060 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.590 Check model and map are aligned: 0.110 Set scattering table: 0.110 Process input model: 36.430 Find NCS groups from input model: 0.830 Set up NCS constraints: 0.090 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:1.550 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6259 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 : 0.005 0.082 38404 Z= 0.268 Angle : 0.856 14.180 51760 Z= 0.497 Chirality : 0.046 0.297 5510 Planarity : 0.005 0.059 6633 Dihedral : 16.521 89.762 14292 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 0.75 % Allowed : 20.65 % Favored : 78.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.73 (0.12), residues: 4508 helix: 0.31 (0.10), residues: 2571 sheet: -1.19 (0.30), residues: 251 loop : -1.53 (0.14), residues: 1686 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 86 TYR 0.052 0.002 TYR A 589 PHE 0.058 0.002 PHE D 916 TRP 0.053 0.002 TRP A 757 HIS 0.012 0.001 HIS A 786 Details of bonding type rmsd covalent geometry : bond 0.00474 (38404) covalent geometry : angle 0.85561 (51760) hydrogen bonds : bond 0.16251 ( 1996) hydrogen bonds : angle 7.02019 ( 5793) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9016 Ramachandran restraints generated. 4508 Oldfield, 0 Emsley, 4508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9016 Ramachandran restraints generated. 4508 Oldfield, 0 Emsley, 4508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 829 residues out of total 4131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 798 time to evaluate : 1.643 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 193 TYR cc_start: 0.6936 (t80) cc_final: 0.6484 (t80) REVERT: A 334 PHE cc_start: 0.6371 (m-80) cc_final: 0.6136 (m-80) REVERT: A 360 PHE cc_start: 0.9061 (t80) cc_final: 0.8765 (t80) REVERT: A 368 ASP cc_start: 0.9375 (t70) cc_final: 0.9101 (p0) REVERT: A 381 PHE cc_start: 0.8961 (t80) cc_final: 0.8660 (t80) REVERT: A 481 ILE cc_start: 0.3516 (tt) cc_final: 0.3162 (mt) REVERT: A 487 GLN cc_start: 0.7164 (mt0) cc_final: 0.5921 (pt0) REVERT: A 597 GLU cc_start: 0.7728 (mm-30) cc_final: 0.6488 (mt-10) REVERT: A 638 PHE cc_start: 0.5767 (m-80) cc_final: 0.4430 (m-80) REVERT: A 647 MET cc_start: -0.0026 (mmt) cc_final: -0.0338 (mmt) REVERT: A 949 PHE cc_start: 0.6978 (t80) cc_final: 0.6693 (t80) REVERT: B 45 PHE cc_start: 0.5992 (t80) cc_final: 0.5741 (t80) REVERT: B 70 LEU cc_start: 0.7336 (mt) cc_final: 0.7106 (mt) REVERT: B 87 ILE cc_start: 0.9255 (mm) cc_final: 0.8935 (mp) REVERT: B 357 MET cc_start: 0.8600 (tpp) cc_final: 0.7916 (tpp) REVERT: B 361 PHE cc_start: 0.8558 (m-80) cc_final: 0.7853 (m-80) REVERT: B 370 ARG cc_start: 0.5499 (ttt180) cc_final: 0.4479 (ttp80) REVERT: B 396 MET cc_start: 0.4219 (tpp) cc_final: 0.2287 (tpp) REVERT: B 453 ASP cc_start: 0.8215 (m-30) cc_final: 0.8011 (p0) REVERT: B 507 PHE cc_start: 0.6956 (m-10) cc_final: 0.6585 (m-10) REVERT: B 569 MET cc_start: 0.6191 (tmm) cc_final: 0.5089 (mmt) REVERT: B 624 GLU cc_start: 0.8387 (tp30) cc_final: 0.8142 (mm-30) REVERT: B 918 ILE cc_start: 0.7489 (mt) cc_final: 0.7240 (mt) REVERT: B 933 PHE cc_start: 0.7950 (m-80) cc_final: 0.7476 (m-80) REVERT: C 126 PRO cc_start: 0.6977 (Cg_endo) cc_final: 0.6683 (Cg_exo) REVERT: C 200 ILE cc_start: 0.7725 (mm) cc_final: 0.7350 (mm) REVERT: C 700 SER cc_start: 0.7518 (m) cc_final: 0.7228 (t) REVERT: D 62 LEU cc_start: 0.6929 (mp) cc_final: 0.6679 (mp) REVERT: D 301 PHE cc_start: 0.6264 (m-80) cc_final: 0.5957 (m-10) REVERT: D 325 ILE cc_start: 0.8526 (pt) cc_final: 0.8315 (pt) REVERT: D 394 ILE cc_start: 0.8484 (mm) cc_final: 0.8282 (mm) REVERT: D 721 TYR cc_start: 0.7075 (t80) cc_final: 0.6658 (t80) REVERT: D 744 PHE cc_start: 0.7534 (t80) cc_final: 0.7069 (t80) REVERT: D 749 LEU cc_start: 0.8528 (tp) cc_final: 0.7585 (tp) REVERT: D 782 GLN cc_start: 0.7669 (mm-40) cc_final: 0.6862 (mp10) REVERT: D 802 ARG cc_start: 0.7419 (ptt90) cc_final: 0.7033 (tmt-80) REVERT: D 835 ILE cc_start: 0.6628 (mt) cc_final: 0.6313 (mt) REVERT: E 73 LEU cc_start: 0.7880 (tp) cc_final: 0.7648 (pp) REVERT: F 64 LYS cc_start: 0.8382 (tmtt) cc_final: 0.8062 (tptp) REVERT: F 75 MET cc_start: 0.8501 (ppp) cc_final: 0.8253 (ppp) REVERT: F 171 TYR cc_start: 0.8554 (m-80) cc_final: 0.8224 (m-80) REVERT: F 191 ILE cc_start: 0.7727 (tp) cc_final: 0.7291 (tp) REVERT: F 223 LEU cc_start: 0.9080 (mt) cc_final: 0.8617 (tp) REVERT: H 195 PHE cc_start: 0.8078 (m-80) cc_final: 0.7836 (m-80) outliers start: 31 outliers final: 13 residues processed: 817 average time/residue: 0.2669 time to fit residues: 348.7608 Evaluate side-chains 630 residues out of total 4131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 617 time to evaluate : 1.571 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 304 LYS Chi-restraints excluded: chain A residue 519 MET Chi-restraints excluded: chain A residue 588 LEU Chi-restraints excluded: chain A residue 620 ILE Chi-restraints excluded: chain A residue 763 LYS Chi-restraints excluded: chain A residue 987 ARG Chi-restraints excluded: chain B residue 143 TRP Chi-restraints excluded: chain B residue 558 LEU Chi-restraints excluded: chain C residue 83 GLU Chi-restraints excluded: chain C residue 325 ILE Chi-restraints excluded: chain C residue 845 LEU Chi-restraints excluded: chain E residue 231 MET Chi-restraints excluded: chain H residue 62 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 449 random chunks: chunk 432 optimal weight: 0.8980 chunk 197 optimal weight: 10.0000 chunk 388 optimal weight: 10.0000 chunk 215 optimal weight: 0.9990 chunk 20 optimal weight: 3.9990 chunk 132 optimal weight: 9.9990 chunk 261 optimal weight: 0.4980 chunk 248 optimal weight: 0.0030 chunk 207 optimal weight: 0.9990 chunk 401 optimal weight: 20.0000 chunk 424 optimal weight: 5.9990 overall best weight: 0.6794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 39 ASN ** A 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 202 ASN ** A 323 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 457 ASN A 536 GLN A 563 ASN A 591 ASN ** A 765 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 910 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 990 ASN B 58 GLN B 196 ASN B 377 GLN B 386 ASN B 503 HIS ** B 563 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 503 HIS C 548 ASN ** D 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 297 GLN D 299 ASN D 339 HIS D 386 ASN ** D 598 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 654 ASN D 705 ASN D 797 ASN D 973 ASN D 975 HIS D 990 ASN E 181 ASN E 212 ASN F 210 ASN H 65 ASN H 181 ASN H 197 ASN H 210 ASN Total number of N/Q/H flips: 31 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4585 r_free = 0.4585 target = 0.166295 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4162 r_free = 0.4162 target = 0.136873 restraints weight = 102444.269| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.4144 r_free = 0.4144 target = 0.137260 restraints weight = 72345.633| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4152 r_free = 0.4152 target = 0.137719 restraints weight = 58806.274| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.4154 r_free = 0.4154 target = 0.137900 restraints weight = 53392.226| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4178 r_free = 0.4178 target = 0.139408 restraints weight = 45347.451| |-----------------------------------------------------------------------------| r_work (final): 0.4172 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6348 moved from start: 0.2085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 38404 Z= 0.165 Angle : 0.697 12.280 51760 Z= 0.359 Chirality : 0.044 0.270 5510 Planarity : 0.005 0.112 6633 Dihedral : 5.340 75.672 5014 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 12.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 3.07 % Allowed : 20.38 % Favored : 76.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.37 (0.12), residues: 4508 helix: 0.56 (0.10), residues: 2635 sheet: -1.09 (0.31), residues: 237 loop : -1.36 (0.15), residues: 1636 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG D 517 TYR 0.037 0.002 TYR B 313 PHE 0.048 0.002 PHE D 916 TRP 0.039 0.003 TRP A 757 HIS 0.010 0.001 HIS D 786 Details of bonding type rmsd covalent geometry : bond 0.00374 (38404) covalent geometry : angle 0.69658 (51760) hydrogen bonds : bond 0.04916 ( 1996) hydrogen bonds : angle 5.58938 ( 5793) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9016 Ramachandran restraints generated. 4508 Oldfield, 0 Emsley, 4508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9016 Ramachandran restraints generated. 4508 Oldfield, 0 Emsley, 4508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 813 residues out of total 4131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 127 poor density : 686 time to evaluate : 1.565 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 98 MET cc_start: 0.8430 (pmm) cc_final: 0.7847 (pmm) REVERT: A 193 TYR cc_start: 0.6700 (t80) cc_final: 0.6423 (t80) REVERT: A 204 MET cc_start: 0.7402 (tmm) cc_final: 0.6987 (tmm) REVERT: A 228 LEU cc_start: 0.7544 (mt) cc_final: 0.7164 (mt) REVERT: A 230 ASN cc_start: 0.7875 (t0) cc_final: 0.7649 (t0) REVERT: A 334 PHE cc_start: 0.5794 (m-80) cc_final: 0.5147 (m-80) REVERT: A 368 ASP cc_start: 0.8933 (t70) cc_final: 0.8607 (p0) REVERT: A 597 GLU cc_start: 0.7986 (mm-30) cc_final: 0.6618 (mt-10) REVERT: A 720 LEU cc_start: 0.8355 (OUTLIER) cc_final: 0.7880 (mm) REVERT: A 995 ARG cc_start: 0.8983 (mmm160) cc_final: 0.8598 (mmm160) REVERT: B 35 GLU cc_start: 0.5714 (tp30) cc_final: 0.5189 (mt-10) REVERT: B 70 LEU cc_start: 0.7362 (mt) cc_final: 0.7023 (mt) REVERT: B 360 PHE cc_start: 0.8672 (t80) cc_final: 0.8330 (t80) REVERT: B 624 GLU cc_start: 0.7813 (tp30) cc_final: 0.7529 (mm-30) REVERT: B 741 LEU cc_start: 0.9154 (OUTLIER) cc_final: 0.8598 (mt) REVERT: B 845 LEU cc_start: 0.7100 (pp) cc_final: 0.6866 (pp) REVERT: B 913 MET cc_start: 0.7761 (ptp) cc_final: 0.7416 (ptp) REVERT: B 976 MET cc_start: 0.4137 (OUTLIER) cc_final: 0.3207 (ppp) REVERT: C 91 PHE cc_start: 0.8095 (t80) cc_final: 0.7889 (t80) REVERT: C 200 ILE cc_start: 0.7743 (mm) cc_final: 0.7360 (mm) REVERT: C 700 SER cc_start: 0.7516 (m) cc_final: 0.7040 (t) REVERT: C 1000 LEU cc_start: 0.8974 (OUTLIER) cc_final: 0.8681 (mt) REVERT: D 21 MET cc_start: 0.8251 (mmm) cc_final: 0.7972 (mmm) REVERT: D 65 LYS cc_start: 0.8269 (mmmt) cc_final: 0.7014 (mmmt) REVERT: D 101 ASP cc_start: 0.5807 (OUTLIER) cc_final: 0.5524 (t70) REVERT: D 218 TYR cc_start: 0.6884 (OUTLIER) cc_final: 0.5543 (t80) REVERT: D 455 TYR cc_start: 0.6418 (OUTLIER) cc_final: 0.6127 (m-80) REVERT: D 782 GLN cc_start: 0.7377 (mm-40) cc_final: 0.6729 (mp10) REVERT: D 835 ILE cc_start: 0.6048 (mt) cc_final: 0.5414 (mt) REVERT: D 976 MET cc_start: 0.4940 (ptp) cc_final: 0.4731 (ptp) REVERT: E 73 LEU cc_start: 0.8057 (tp) cc_final: 0.7758 (pp) REVERT: F 13 PHE cc_start: 0.6240 (t80) cc_final: 0.5379 (t80) REVERT: F 220 PHE cc_start: 0.7298 (OUTLIER) cc_final: 0.6840 (m-80) REVERT: F 223 LEU cc_start: 0.8176 (mt) cc_final: 0.7886 (tp) REVERT: G 51 TYR cc_start: 0.5383 (t80) cc_final: 0.5114 (t80) outliers start: 127 outliers final: 56 residues processed: 761 average time/residue: 0.2526 time to fit residues: 314.1229 Evaluate side-chains 642 residues out of total 4131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 578 time to evaluate : 1.537 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 TRP Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 131 THR Chi-restraints excluded: chain A residue 280 TYR Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 495 LEU Chi-restraints excluded: chain A residue 588 LEU Chi-restraints excluded: chain A residue 620 ILE Chi-restraints excluded: chain A residue 720 LEU Chi-restraints excluded: chain A residue 763 LYS Chi-restraints excluded: chain A residue 987 ARG Chi-restraints excluded: chain A residue 1003 TYR Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 143 TRP Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain B residue 498 LEU Chi-restraints excluded: chain B residue 515 ILE Chi-restraints excluded: chain B residue 558 LEU Chi-restraints excluded: chain B residue 573 SER Chi-restraints excluded: chain B residue 741 LEU Chi-restraints excluded: chain B residue 828 THR Chi-restraints excluded: chain B residue 976 MET Chi-restraints excluded: chain B residue 1005 ILE Chi-restraints excluded: chain C residue 79 TYR Chi-restraints excluded: chain C residue 82 ASP Chi-restraints excluded: chain C residue 106 ASP Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 134 TYR Chi-restraints excluded: chain C residue 218 TYR Chi-restraints excluded: chain C residue 225 ILE Chi-restraints excluded: chain C residue 236 GLN Chi-restraints excluded: chain C residue 346 VAL Chi-restraints excluded: chain C residue 411 SER Chi-restraints excluded: chain C residue 495 LEU Chi-restraints excluded: chain C residue 744 PHE Chi-restraints excluded: chain C residue 978 HIS Chi-restraints excluded: chain C residue 1000 LEU Chi-restraints excluded: chain D residue 101 ASP Chi-restraints excluded: chain D residue 134 TYR Chi-restraints excluded: chain D residue 213 ILE Chi-restraints excluded: chain D residue 218 TYR Chi-restraints excluded: chain D residue 342 VAL Chi-restraints excluded: chain D residue 357 MET Chi-restraints excluded: chain D residue 445 LEU Chi-restraints excluded: chain D residue 455 TYR Chi-restraints excluded: chain D residue 595 LEU Chi-restraints excluded: chain D residue 609 HIS Chi-restraints excluded: chain D residue 618 LEU Chi-restraints excluded: chain D residue 810 HIS Chi-restraints excluded: chain D residue 830 ASP Chi-restraints excluded: chain D residue 994 LYS Chi-restraints excluded: chain E residue 8 THR Chi-restraints excluded: chain E residue 11 VAL Chi-restraints excluded: chain E residue 31 SER Chi-restraints excluded: chain E residue 37 SER Chi-restraints excluded: chain F residue 173 VAL Chi-restraints excluded: chain F residue 187 VAL Chi-restraints excluded: chain F residue 192 TYR Chi-restraints excluded: chain F residue 220 PHE Chi-restraints excluded: chain F residue 234 VAL Chi-restraints excluded: chain H residue 62 THR Chi-restraints excluded: chain H residue 67 PHE Chi-restraints excluded: chain H residue 187 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 449 random chunks: chunk 293 optimal weight: 6.9990 chunk 109 optimal weight: 0.5980 chunk 134 optimal weight: 20.0000 chunk 147 optimal weight: 0.1980 chunk 432 optimal weight: 0.7980 chunk 7 optimal weight: 0.9990 chunk 338 optimal weight: 2.9990 chunk 80 optimal weight: 20.0000 chunk 167 optimal weight: 5.9990 chunk 239 optimal weight: 0.9990 chunk 422 optimal weight: 9.9990 overall best weight: 0.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 236 GLN ** A 323 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 475 GLN ** A 563 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 765 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 910 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 973 ASN B 125 ASN B 297 GLN B 491 GLN B 503 HIS ** B 536 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 797 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 278 ASN C 503 HIS C 881 HIS C 978 HIS ** D 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 93 ASN ** D 598 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 765 ASN D 905 GLN ** F 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4575 r_free = 0.4575 target = 0.165302 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4154 r_free = 0.4154 target = 0.136207 restraints weight = 102072.939| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4126 r_free = 0.4126 target = 0.135834 restraints weight = 76100.421| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4147 r_free = 0.4147 target = 0.137251 restraints weight = 55421.747| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4152 r_free = 0.4152 target = 0.137599 restraints weight = 48227.915| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4156 r_free = 0.4156 target = 0.137838 restraints weight = 43815.962| |-----------------------------------------------------------------------------| r_work (final): 0.4152 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6380 moved from start: 0.2768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 38404 Z= 0.150 Angle : 0.664 12.793 51760 Z= 0.340 Chirality : 0.043 0.212 5510 Planarity : 0.004 0.083 6633 Dihedral : 5.110 56.831 4997 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 13.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 2.86 % Allowed : 21.40 % Favored : 75.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.29 (0.12), residues: 4508 helix: 0.60 (0.10), residues: 2632 sheet: -0.91 (0.30), residues: 256 loop : -1.32 (0.15), residues: 1620 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 593 TYR 0.035 0.002 TYR B 324 PHE 0.056 0.002 PHE D 916 TRP 0.051 0.003 TRP A 757 HIS 0.006 0.001 HIS C 349 Details of bonding type rmsd covalent geometry : bond 0.00338 (38404) covalent geometry : angle 0.66447 (51760) hydrogen bonds : bond 0.04499 ( 1996) hydrogen bonds : angle 5.31873 ( 5793) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9016 Ramachandran restraints generated. 4508 Oldfield, 0 Emsley, 4508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9016 Ramachandran restraints generated. 4508 Oldfield, 0 Emsley, 4508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 744 residues out of total 4131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 118 poor density : 626 time to evaluate : 1.544 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 98 MET cc_start: 0.8456 (pmm) cc_final: 0.7944 (pmm) REVERT: A 108 PHE cc_start: 0.7844 (m-80) cc_final: 0.7574 (m-80) REVERT: A 193 TYR cc_start: 0.6690 (t80) cc_final: 0.6411 (t80) REVERT: A 204 MET cc_start: 0.7386 (tmm) cc_final: 0.6789 (tmm) REVERT: A 230 ASN cc_start: 0.7859 (t0) cc_final: 0.7490 (t0) REVERT: A 334 PHE cc_start: 0.5640 (m-80) cc_final: 0.4874 (m-80) REVERT: A 368 ASP cc_start: 0.8957 (t70) cc_final: 0.8630 (p0) REVERT: A 487 GLN cc_start: 0.6301 (mt0) cc_final: 0.5304 (pt0) REVERT: A 491 GLN cc_start: 0.8290 (tp-100) cc_final: 0.8012 (tp-100) REVERT: A 495 LEU cc_start: 0.8404 (mp) cc_final: 0.8051 (tp) REVERT: A 517 ARG cc_start: 0.5923 (ttp80) cc_final: 0.5615 (ptm160) REVERT: A 597 GLU cc_start: 0.7998 (mm-30) cc_final: 0.6665 (mt-10) REVERT: A 720 LEU cc_start: 0.8496 (OUTLIER) cc_final: 0.8196 (mm) REVERT: A 778 PHE cc_start: 0.8234 (t80) cc_final: 0.7550 (t80) REVERT: A 995 ARG cc_start: 0.8967 (mmm160) cc_final: 0.8613 (mmm160) REVERT: B 35 GLU cc_start: 0.5701 (tp30) cc_final: 0.5195 (mt-10) REVERT: B 70 LEU cc_start: 0.7420 (mt) cc_final: 0.7109 (mt) REVERT: B 124 MET cc_start: 0.6921 (mmp) cc_final: 0.6468 (mmp) REVERT: B 256 GLU cc_start: 0.7734 (mt-10) cc_final: 0.7175 (mt-10) REVERT: B 445 LEU cc_start: 0.8507 (OUTLIER) cc_final: 0.8023 (tp) REVERT: B 569 MET cc_start: 0.6691 (tmm) cc_final: 0.5785 (mmt) REVERT: B 593 ARG cc_start: 0.7547 (ttt90) cc_final: 0.7318 (ttt90) REVERT: B 711 GLN cc_start: 0.8230 (tp40) cc_final: 0.7528 (tp40) REVERT: B 741 LEU cc_start: 0.9183 (OUTLIER) cc_final: 0.8898 (mm) REVERT: B 845 LEU cc_start: 0.7094 (pp) cc_final: 0.6784 (pp) REVERT: B 919 TRP cc_start: 0.6311 (m-10) cc_final: 0.5744 (m-90) REVERT: B 933 PHE cc_start: 0.7423 (m-80) cc_final: 0.7125 (m-80) REVERT: C 173 ASP cc_start: 0.7446 (p0) cc_final: 0.7146 (p0) REVERT: C 182 ASN cc_start: 0.8183 (t0) cc_final: 0.7716 (t0) REVERT: C 200 ILE cc_start: 0.7836 (mm) cc_final: 0.7381 (mm) REVERT: C 700 SER cc_start: 0.7645 (m) cc_final: 0.7284 (t) REVERT: C 733 LEU cc_start: 0.9124 (tp) cc_final: 0.8870 (tt) REVERT: C 827 LEU cc_start: 0.8176 (OUTLIER) cc_final: 0.7695 (tp) REVERT: D 65 LYS cc_start: 0.8022 (mmmt) cc_final: 0.7744 (mmmt) REVERT: D 101 ASP cc_start: 0.5817 (OUTLIER) cc_final: 0.5272 (t0) REVERT: D 204 MET cc_start: 0.7746 (tmm) cc_final: 0.7080 (tmm) REVERT: D 218 TYR cc_start: 0.7045 (OUTLIER) cc_final: 0.5604 (t80) REVERT: D 495 LEU cc_start: 0.8308 (tp) cc_final: 0.8032 (pp) REVERT: D 721 TYR cc_start: 0.6455 (t80) cc_final: 0.6192 (t80) REVERT: D 835 ILE cc_start: 0.5859 (mt) cc_final: 0.5579 (mt) REVERT: D 976 MET cc_start: 0.4927 (ptp) cc_final: 0.4716 (ptp) REVERT: E 29 THR cc_start: 0.8479 (p) cc_final: 0.8228 (p) REVERT: E 73 LEU cc_start: 0.8140 (tp) cc_final: 0.7903 (pp) REVERT: E 206 MET cc_start: 0.4705 (ptt) cc_final: 0.4342 (ptt) REVERT: F 75 MET cc_start: 0.8076 (ppp) cc_final: 0.7655 (ppp) REVERT: F 183 ASP cc_start: 0.4982 (p0) cc_final: 0.3892 (m-30) REVERT: F 220 PHE cc_start: 0.7233 (OUTLIER) cc_final: 0.6661 (m-80) REVERT: F 223 LEU cc_start: 0.8146 (mt) cc_final: 0.7837 (tp) REVERT: G 51 TYR cc_start: 0.5388 (t80) cc_final: 0.5124 (t80) outliers start: 118 outliers final: 60 residues processed: 696 average time/residue: 0.2456 time to fit residues: 279.8418 Evaluate side-chains 620 residues out of total 4131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 553 time to evaluate : 1.501 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 TRP Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 130 ILE Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 481 ILE Chi-restraints excluded: chain A residue 515 ILE Chi-restraints excluded: chain A residue 588 LEU Chi-restraints excluded: chain A residue 649 TYR Chi-restraints excluded: chain A residue 671 CYS Chi-restraints excluded: chain A residue 720 LEU Chi-restraints excluded: chain A residue 987 ARG Chi-restraints excluded: chain A residue 1003 TYR Chi-restraints excluded: chain B residue 143 TRP Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain B residue 251 SER Chi-restraints excluded: chain B residue 445 LEU Chi-restraints excluded: chain B residue 524 ILE Chi-restraints excluded: chain B residue 528 PHE Chi-restraints excluded: chain B residue 558 LEU Chi-restraints excluded: chain B residue 573 SER Chi-restraints excluded: chain B residue 741 LEU Chi-restraints excluded: chain C residue 45 PHE Chi-restraints excluded: chain C residue 82 ASP Chi-restraints excluded: chain C residue 134 TYR Chi-restraints excluded: chain C residue 218 TYR Chi-restraints excluded: chain C residue 225 ILE Chi-restraints excluded: chain C residue 325 ILE Chi-restraints excluded: chain C residue 346 VAL Chi-restraints excluded: chain C residue 347 VAL Chi-restraints excluded: chain C residue 411 SER Chi-restraints excluded: chain C residue 495 LEU Chi-restraints excluded: chain C residue 600 LEU Chi-restraints excluded: chain C residue 744 PHE Chi-restraints excluded: chain C residue 827 LEU Chi-restraints excluded: chain C residue 844 LEU Chi-restraints excluded: chain C residue 978 HIS Chi-restraints excluded: chain D residue 69 GLU Chi-restraints excluded: chain D residue 101 ASP Chi-restraints excluded: chain D residue 122 LEU Chi-restraints excluded: chain D residue 134 TYR Chi-restraints excluded: chain D residue 213 ILE Chi-restraints excluded: chain D residue 218 TYR Chi-restraints excluded: chain D residue 342 VAL Chi-restraints excluded: chain D residue 347 VAL Chi-restraints excluded: chain D residue 396 MET Chi-restraints excluded: chain D residue 543 GLU Chi-restraints excluded: chain D residue 556 VAL Chi-restraints excluded: chain D residue 595 LEU Chi-restraints excluded: chain D residue 618 LEU Chi-restraints excluded: chain D residue 810 HIS Chi-restraints excluded: chain D residue 830 ASP Chi-restraints excluded: chain D residue 885 ILE Chi-restraints excluded: chain D residue 916 PHE Chi-restraints excluded: chain D residue 966 LEU Chi-restraints excluded: chain D residue 994 LYS Chi-restraints excluded: chain D residue 995 ARG Chi-restraints excluded: chain E residue 8 THR Chi-restraints excluded: chain E residue 11 VAL Chi-restraints excluded: chain E residue 37 SER Chi-restraints excluded: chain F residue 192 TYR Chi-restraints excluded: chain F residue 220 PHE Chi-restraints excluded: chain F residue 234 VAL Chi-restraints excluded: chain H residue 62 THR Chi-restraints excluded: chain H residue 67 PHE Chi-restraints excluded: chain H residue 187 VAL Chi-restraints excluded: chain H residue 234 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 449 random chunks: chunk 381 optimal weight: 0.9990 chunk 205 optimal weight: 3.9990 chunk 253 optimal weight: 0.3980 chunk 20 optimal weight: 0.8980 chunk 225 optimal weight: 0.1980 chunk 113 optimal weight: 5.9990 chunk 23 optimal weight: 5.9990 chunk 315 optimal weight: 3.9990 chunk 160 optimal weight: 3.9990 chunk 166 optimal weight: 9.9990 chunk 446 optimal weight: 4.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 39 ASN ** A 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 125 ASN ** A 323 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 351 ASN A 457 ASN ** A 563 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 765 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 910 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 171 HIS B 192 ASN B 349 HIS B 536 GLN C 67 HIS ** C 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 351 ASN C 978 HIS ** D 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 598 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 797 ASN H 65 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4543 r_free = 0.4543 target = 0.163030 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4103 r_free = 0.4103 target = 0.133044 restraints weight = 103071.412| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.4067 r_free = 0.4067 target = 0.132326 restraints weight = 82109.909| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4076 r_free = 0.4076 target = 0.132866 restraints weight = 61334.348| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4086 r_free = 0.4086 target = 0.133541 restraints weight = 52855.505| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4096 r_free = 0.4096 target = 0.134187 restraints weight = 46510.524| |-----------------------------------------------------------------------------| r_work (final): 0.4090 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6507 moved from start: 0.3284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 38404 Z= 0.169 Angle : 0.667 12.999 51760 Z= 0.340 Chirality : 0.042 0.205 5510 Planarity : 0.004 0.069 6633 Dihedral : 5.093 63.333 4991 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 14.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 3.32 % Allowed : 22.83 % Favored : 73.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.28 (0.12), residues: 4508 helix: 0.60 (0.10), residues: 2636 sheet: -0.98 (0.29), residues: 265 loop : -1.27 (0.15), residues: 1607 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 247 TYR 0.043 0.002 TYR B 313 PHE 0.056 0.002 PHE D 916 TRP 0.056 0.003 TRP A 757 HIS 0.016 0.001 HIS C 978 Details of bonding type rmsd covalent geometry : bond 0.00385 (38404) covalent geometry : angle 0.66657 (51760) hydrogen bonds : bond 0.04320 ( 1996) hydrogen bonds : angle 5.25729 ( 5793) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9016 Ramachandran restraints generated. 4508 Oldfield, 0 Emsley, 4508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9016 Ramachandran restraints generated. 4508 Oldfield, 0 Emsley, 4508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 744 residues out of total 4131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 137 poor density : 607 time to evaluate : 1.583 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 98 MET cc_start: 0.8521 (pmm) cc_final: 0.8085 (pmm) REVERT: A 118 HIS cc_start: 0.5923 (m-70) cc_final: 0.5684 (m-70) REVERT: A 204 MET cc_start: 0.7532 (tmm) cc_final: 0.6788 (tmm) REVERT: A 241 HIS cc_start: 0.4784 (OUTLIER) cc_final: 0.4568 (m90) REVERT: A 334 PHE cc_start: 0.5641 (m-80) cc_final: 0.4920 (m-80) REVERT: A 368 ASP cc_start: 0.8943 (t70) cc_final: 0.8604 (p0) REVERT: A 389 GLU cc_start: 0.8268 (OUTLIER) cc_final: 0.8059 (tm-30) REVERT: A 481 ILE cc_start: 0.3860 (OUTLIER) cc_final: 0.3612 (mt) REVERT: A 487 GLN cc_start: 0.6334 (mt0) cc_final: 0.5413 (pt0) REVERT: A 491 GLN cc_start: 0.8192 (tp-100) cc_final: 0.7974 (tp-100) REVERT: A 495 LEU cc_start: 0.8435 (mp) cc_final: 0.8088 (tp) REVERT: A 517 ARG cc_start: 0.5955 (ttp80) cc_final: 0.5465 (ptm160) REVERT: A 535 PHE cc_start: 0.7640 (m-80) cc_final: 0.7266 (m-80) REVERT: A 597 GLU cc_start: 0.8050 (mm-30) cc_final: 0.6694 (mt-10) REVERT: A 647 MET cc_start: 0.0469 (mmt) cc_final: 0.0022 (mmt) REVERT: A 930 MET cc_start: 0.3339 (ttt) cc_final: 0.3055 (mtp) REVERT: A 995 ARG cc_start: 0.8938 (mmm160) cc_final: 0.8641 (mmm160) REVERT: B 35 GLU cc_start: 0.5617 (tp30) cc_final: 0.5229 (mt-10) REVERT: B 70 LEU cc_start: 0.7540 (mt) cc_final: 0.7231 (mt) REVERT: B 124 MET cc_start: 0.7097 (mmp) cc_final: 0.6714 (mmp) REVERT: B 218 TYR cc_start: 0.5011 (m-80) cc_final: 0.4418 (m-80) REVERT: B 396 MET cc_start: 0.2916 (mmm) cc_final: 0.1917 (mmm) REVERT: B 445 LEU cc_start: 0.8540 (OUTLIER) cc_final: 0.8082 (tp) REVERT: B 482 TYR cc_start: 0.7304 (t80) cc_final: 0.6819 (t80) REVERT: B 569 MET cc_start: 0.6948 (tmm) cc_final: 0.6162 (mmt) REVERT: B 741 LEU cc_start: 0.9111 (OUTLIER) cc_final: 0.8777 (mm) REVERT: B 845 LEU cc_start: 0.7008 (pp) cc_final: 0.6788 (pp) REVERT: B 919 TRP cc_start: 0.6506 (m-10) cc_final: 0.6078 (m-90) REVERT: B 933 PHE cc_start: 0.7670 (m-80) cc_final: 0.7443 (m-80) REVERT: C 173 ASP cc_start: 0.7614 (p0) cc_final: 0.7381 (p0) REVERT: C 182 ASN cc_start: 0.8222 (t0) cc_final: 0.7838 (t0) REVERT: C 200 ILE cc_start: 0.7929 (mm) cc_final: 0.7437 (mm) REVERT: C 700 SER cc_start: 0.7530 (m) cc_final: 0.7208 (p) REVERT: C 936 MET cc_start: 0.5918 (OUTLIER) cc_final: 0.5088 (tpt) REVERT: D 21 MET cc_start: 0.8179 (mmm) cc_final: 0.7955 (mmm) REVERT: D 101 ASP cc_start: 0.6067 (OUTLIER) cc_final: 0.5681 (t0) REVERT: D 106 ASP cc_start: 0.8539 (p0) cc_final: 0.8339 (p0) REVERT: D 218 TYR cc_start: 0.7125 (OUTLIER) cc_final: 0.5671 (t80) REVERT: D 455 TYR cc_start: 0.6598 (OUTLIER) cc_final: 0.5971 (m-10) REVERT: D 721 TYR cc_start: 0.6532 (t80) cc_final: 0.6181 (t80) REVERT: D 835 ILE cc_start: 0.6024 (mt) cc_final: 0.5774 (mt) REVERT: D 844 LEU cc_start: 0.5732 (mp) cc_final: 0.4592 (tp) REVERT: D 976 MET cc_start: 0.5035 (ptp) cc_final: 0.4824 (ptp) REVERT: E 29 THR cc_start: 0.8289 (p) cc_final: 0.8064 (p) REVERT: E 73 LEU cc_start: 0.8213 (tp) cc_final: 0.8002 (pp) REVERT: E 206 MET cc_start: 0.4756 (OUTLIER) cc_final: 0.4454 (ptt) REVERT: F 214 LEU cc_start: 0.5783 (OUTLIER) cc_final: 0.5582 (pp) REVERT: F 223 LEU cc_start: 0.8059 (mt) cc_final: 0.7755 (tp) REVERT: G 51 TYR cc_start: 0.5599 (t80) cc_final: 0.5375 (t80) REVERT: H 64 LYS cc_start: 0.8113 (pttp) cc_final: 0.7739 (pttp) REVERT: H 65 ASN cc_start: 0.7117 (m110) cc_final: 0.6891 (p0) outliers start: 137 outliers final: 91 residues processed: 694 average time/residue: 0.2466 time to fit residues: 280.6815 Evaluate side-chains 661 residues out of total 4131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 559 time to evaluate : 1.565 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 TRP Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 130 ILE Chi-restraints excluded: chain A residue 131 THR Chi-restraints excluded: chain A residue 234 LYS Chi-restraints excluded: chain A residue 241 HIS Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 389 GLU Chi-restraints excluded: chain A residue 415 HIS Chi-restraints excluded: chain A residue 454 LEU Chi-restraints excluded: chain A residue 481 ILE Chi-restraints excluded: chain A residue 485 ILE Chi-restraints excluded: chain A residue 515 ILE Chi-restraints excluded: chain A residue 519 MET Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 588 LEU Chi-restraints excluded: chain A residue 649 TYR Chi-restraints excluded: chain A residue 671 CYS Chi-restraints excluded: chain A residue 919 TRP Chi-restraints excluded: chain A residue 987 ARG Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 97 GLU Chi-restraints excluded: chain B residue 134 TYR Chi-restraints excluded: chain B residue 143 TRP Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain B residue 227 MET Chi-restraints excluded: chain B residue 251 SER Chi-restraints excluded: chain B residue 278 ASN Chi-restraints excluded: chain B residue 310 ASP Chi-restraints excluded: chain B residue 445 LEU Chi-restraints excluded: chain B residue 459 ILE Chi-restraints excluded: chain B residue 515 ILE Chi-restraints excluded: chain B residue 524 ILE Chi-restraints excluded: chain B residue 528 PHE Chi-restraints excluded: chain B residue 558 LEU Chi-restraints excluded: chain B residue 573 SER Chi-restraints excluded: chain B residue 649 TYR Chi-restraints excluded: chain B residue 741 LEU Chi-restraints excluded: chain B residue 749 LEU Chi-restraints excluded: chain B residue 862 ILE Chi-restraints excluded: chain B residue 1005 ILE Chi-restraints excluded: chain C residue 45 PHE Chi-restraints excluded: chain C residue 82 ASP Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 134 TYR Chi-restraints excluded: chain C residue 155 GLU Chi-restraints excluded: chain C residue 218 TYR Chi-restraints excluded: chain C residue 225 ILE Chi-restraints excluded: chain C residue 236 GLN Chi-restraints excluded: chain C residue 325 ILE Chi-restraints excluded: chain C residue 347 VAL Chi-restraints excluded: chain C residue 411 SER Chi-restraints excluded: chain C residue 463 ILE Chi-restraints excluded: chain C residue 474 SER Chi-restraints excluded: chain C residue 495 LEU Chi-restraints excluded: chain C residue 600 LEU Chi-restraints excluded: chain C residue 664 ILE Chi-restraints excluded: chain C residue 744 PHE Chi-restraints excluded: chain C residue 827 LEU Chi-restraints excluded: chain C residue 844 LEU Chi-restraints excluded: chain C residue 936 MET Chi-restraints excluded: chain D residue 69 GLU Chi-restraints excluded: chain D residue 101 ASP Chi-restraints excluded: chain D residue 122 LEU Chi-restraints excluded: chain D residue 134 TYR Chi-restraints excluded: chain D residue 213 ILE Chi-restraints excluded: chain D residue 218 TYR Chi-restraints excluded: chain D residue 232 VAL Chi-restraints excluded: chain D residue 280 TYR Chi-restraints excluded: chain D residue 342 VAL Chi-restraints excluded: chain D residue 347 VAL Chi-restraints excluded: chain D residue 363 LEU Chi-restraints excluded: chain D residue 396 MET Chi-restraints excluded: chain D residue 445 LEU Chi-restraints excluded: chain D residue 455 TYR Chi-restraints excluded: chain D residue 482 TYR Chi-restraints excluded: chain D residue 543 GLU Chi-restraints excluded: chain D residue 556 VAL Chi-restraints excluded: chain D residue 595 LEU Chi-restraints excluded: chain D residue 618 LEU Chi-restraints excluded: chain D residue 810 HIS Chi-restraints excluded: chain D residue 830 ASP Chi-restraints excluded: chain D residue 885 ILE Chi-restraints excluded: chain D residue 916 PHE Chi-restraints excluded: chain D residue 966 LEU Chi-restraints excluded: chain D residue 986 GLU Chi-restraints excluded: chain D residue 995 ARG Chi-restraints excluded: chain E residue 8 THR Chi-restraints excluded: chain E residue 11 VAL Chi-restraints excluded: chain E residue 31 SER Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain E residue 173 VAL Chi-restraints excluded: chain E residue 206 MET Chi-restraints excluded: chain F residue 192 TYR Chi-restraints excluded: chain F residue 214 LEU Chi-restraints excluded: chain F residue 234 VAL Chi-restraints excluded: chain H residue 62 THR Chi-restraints excluded: chain H residue 67 PHE Chi-restraints excluded: chain H residue 187 VAL Chi-restraints excluded: chain H residue 234 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 449 random chunks: chunk 220 optimal weight: 0.8980 chunk 236 optimal weight: 0.9980 chunk 276 optimal weight: 1.9990 chunk 105 optimal weight: 8.9990 chunk 24 optimal weight: 4.9990 chunk 245 optimal weight: 2.9990 chunk 154 optimal weight: 0.0970 chunk 200 optimal weight: 8.9990 chunk 433 optimal weight: 0.0970 chunk 4 optimal weight: 3.9990 chunk 441 optimal weight: 3.9990 overall best weight: 0.8178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 202 ASN ** A 765 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 910 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 39 ASN B 536 GLN ** C 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 224 ASN C 351 ASN ** D 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 598 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 797 ASN E 47 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4548 r_free = 0.4548 target = 0.163456 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4110 r_free = 0.4110 target = 0.133548 restraints weight = 103904.720| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4097 r_free = 0.4097 target = 0.133975 restraints weight = 76786.779| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4103 r_free = 0.4103 target = 0.134371 restraints weight = 61214.879| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4110 r_free = 0.4110 target = 0.134829 restraints weight = 52589.783| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4124 r_free = 0.4124 target = 0.135744 restraints weight = 46115.395| |-----------------------------------------------------------------------------| r_work (final): 0.4115 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6457 moved from start: 0.3647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 38404 Z= 0.144 Angle : 0.658 14.085 51760 Z= 0.333 Chirality : 0.042 0.292 5510 Planarity : 0.004 0.063 6633 Dihedral : 5.046 65.804 4991 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 14.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 3.51 % Allowed : 23.43 % Favored : 73.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.19 (0.12), residues: 4508 helix: 0.68 (0.10), residues: 2640 sheet: -1.04 (0.29), residues: 268 loop : -1.24 (0.15), residues: 1600 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG C 587 TYR 0.034 0.002 TYR B 313 PHE 0.055 0.002 PHE D 916 TRP 0.055 0.002 TRP A 757 HIS 0.007 0.001 HIS C 349 Details of bonding type rmsd covalent geometry : bond 0.00324 (38404) covalent geometry : angle 0.65826 (51760) hydrogen bonds : bond 0.04138 ( 1996) hydrogen bonds : angle 5.14749 ( 5793) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9016 Ramachandran restraints generated. 4508 Oldfield, 0 Emsley, 4508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9016 Ramachandran restraints generated. 4508 Oldfield, 0 Emsley, 4508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 749 residues out of total 4131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 145 poor density : 604 time to evaluate : 1.639 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 98 MET cc_start: 0.8660 (pmm) cc_final: 0.8251 (pmm) REVERT: A 204 MET cc_start: 0.7451 (tmm) cc_final: 0.6694 (tmm) REVERT: A 230 ASN cc_start: 0.7939 (t0) cc_final: 0.7718 (t0) REVERT: A 334 PHE cc_start: 0.5428 (m-80) cc_final: 0.5120 (m-80) REVERT: A 368 ASP cc_start: 0.8837 (t70) cc_final: 0.8521 (p0) REVERT: A 487 GLN cc_start: 0.6243 (mt0) cc_final: 0.5390 (pt0) REVERT: A 495 LEU cc_start: 0.8421 (mp) cc_final: 0.8094 (tp) REVERT: A 517 ARG cc_start: 0.6164 (ttp80) cc_final: 0.5672 (ptm160) REVERT: A 535 PHE cc_start: 0.7577 (m-80) cc_final: 0.7232 (m-80) REVERT: A 597 GLU cc_start: 0.7983 (mm-30) cc_final: 0.6723 (mt-10) REVERT: A 910 ASN cc_start: 0.8691 (m110) cc_final: 0.8115 (m110) REVERT: A 930 MET cc_start: 0.3531 (ttt) cc_final: 0.3208 (mtp) REVERT: A 954 PHE cc_start: 0.8278 (t80) cc_final: 0.7809 (t80) REVERT: A 995 ARG cc_start: 0.8905 (mmm160) cc_final: 0.8648 (mmm160) REVERT: B 35 GLU cc_start: 0.5900 (tp30) cc_final: 0.5494 (mt-10) REVERT: B 70 LEU cc_start: 0.7593 (mt) cc_final: 0.7290 (mt) REVERT: B 124 MET cc_start: 0.7132 (mmp) cc_final: 0.6802 (mmp) REVERT: B 218 TYR cc_start: 0.5040 (m-80) cc_final: 0.4555 (m-80) REVERT: B 227 MET cc_start: 0.5639 (OUTLIER) cc_final: 0.5303 (ttp) REVERT: B 283 LEU cc_start: 0.8334 (OUTLIER) cc_final: 0.7829 (tt) REVERT: B 391 ASN cc_start: 0.5314 (OUTLIER) cc_final: 0.4882 (m-40) REVERT: B 396 MET cc_start: 0.2665 (mmm) cc_final: 0.1881 (mmm) REVERT: B 445 LEU cc_start: 0.8635 (OUTLIER) cc_final: 0.7928 (tp) REVERT: B 482 TYR cc_start: 0.7363 (t80) cc_final: 0.6833 (t80) REVERT: B 569 MET cc_start: 0.6784 (tmm) cc_final: 0.6183 (mmt) REVERT: B 593 ARG cc_start: 0.7400 (ttt90) cc_final: 0.6939 (ttt90) REVERT: B 711 GLN cc_start: 0.8052 (tp40) cc_final: 0.6879 (tp40) REVERT: B 741 LEU cc_start: 0.9046 (OUTLIER) cc_final: 0.8569 (mm) REVERT: B 757 TRP cc_start: 0.7774 (m100) cc_final: 0.7528 (m100) REVERT: B 919 TRP cc_start: 0.6708 (m-10) cc_final: 0.6181 (m-90) REVERT: B 960 LYS cc_start: 0.8380 (pttt) cc_final: 0.8021 (ptpt) REVERT: B 963 ASN cc_start: 0.7437 (m110) cc_final: 0.7226 (t0) REVERT: C 98 MET cc_start: 0.7648 (tpp) cc_final: 0.7317 (mmm) REVERT: C 182 ASN cc_start: 0.8163 (t0) cc_final: 0.7756 (t0) REVERT: C 200 ILE cc_start: 0.7839 (mm) cc_final: 0.7427 (mm) REVERT: C 346 VAL cc_start: 0.6049 (p) cc_final: 0.5817 (p) REVERT: C 700 SER cc_start: 0.7539 (m) cc_final: 0.7283 (p) REVERT: C 827 LEU cc_start: 0.8019 (OUTLIER) cc_final: 0.7499 (tp) REVERT: C 890 GLU cc_start: 0.7994 (tp30) cc_final: 0.7601 (tp30) REVERT: C 1000 LEU cc_start: 0.8901 (mm) cc_final: 0.8665 (mm) REVERT: D 101 ASP cc_start: 0.6070 (OUTLIER) cc_final: 0.5607 (t0) REVERT: D 106 ASP cc_start: 0.8531 (p0) cc_final: 0.8245 (p0) REVERT: D 204 MET cc_start: 0.7156 (tmm) cc_final: 0.6625 (tmm) REVERT: D 218 TYR cc_start: 0.7098 (OUTLIER) cc_final: 0.5588 (t80) REVERT: D 455 TYR cc_start: 0.6547 (OUTLIER) cc_final: 0.5976 (m-10) REVERT: D 721 TYR cc_start: 0.6536 (t80) cc_final: 0.6246 (t80) REVERT: D 753 LYS cc_start: 0.8095 (mmtp) cc_final: 0.7613 (mmmt) REVERT: D 844 LEU cc_start: 0.5858 (mp) cc_final: 0.4899 (tp) REVERT: D 936 MET cc_start: 0.8380 (mmp) cc_final: 0.8089 (mmm) REVERT: D 976 MET cc_start: 0.4990 (ptp) cc_final: 0.4784 (ptp) REVERT: E 37 SER cc_start: 0.5622 (OUTLIER) cc_final: 0.5032 (p) REVERT: E 73 LEU cc_start: 0.8262 (tp) cc_final: 0.8000 (pp) REVERT: E 206 MET cc_start: 0.4902 (ptt) cc_final: 0.4682 (ptt) REVERT: F 75 MET cc_start: 0.7947 (ppp) cc_final: 0.7490 (ppp) REVERT: F 183 ASP cc_start: 0.5114 (p0) cc_final: 0.4091 (m-30) REVERT: F 206 MET cc_start: 0.4172 (mmm) cc_final: 0.3745 (mmm) REVERT: F 214 LEU cc_start: 0.5922 (OUTLIER) cc_final: 0.5721 (pp) REVERT: F 223 LEU cc_start: 0.7964 (mt) cc_final: 0.7219 (mt) REVERT: G 51 TYR cc_start: 0.5625 (t80) cc_final: 0.5274 (t80) REVERT: H 64 LYS cc_start: 0.8130 (pttp) cc_final: 0.7777 (pttp) outliers start: 145 outliers final: 87 residues processed: 696 average time/residue: 0.2486 time to fit residues: 283.9326 Evaluate side-chains 653 residues out of total 4131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 555 time to evaluate : 1.618 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 PHE Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 130 ILE Chi-restraints excluded: chain A residue 131 THR Chi-restraints excluded: chain A residue 234 LYS Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 360 PHE Chi-restraints excluded: chain A residue 454 LEU Chi-restraints excluded: chain A residue 485 ILE Chi-restraints excluded: chain A residue 515 ILE Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 588 LEU Chi-restraints excluded: chain A residue 671 CYS Chi-restraints excluded: chain A residue 919 TRP Chi-restraints excluded: chain A residue 987 ARG Chi-restraints excluded: chain B residue 97 GLU Chi-restraints excluded: chain B residue 134 TYR Chi-restraints excluded: chain B residue 143 TRP Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain B residue 227 MET Chi-restraints excluded: chain B residue 251 SER Chi-restraints excluded: chain B residue 274 LEU Chi-restraints excluded: chain B residue 283 LEU Chi-restraints excluded: chain B residue 348 ARG Chi-restraints excluded: chain B residue 391 ASN Chi-restraints excluded: chain B residue 445 LEU Chi-restraints excluded: chain B residue 459 ILE Chi-restraints excluded: chain B residue 518 GLU Chi-restraints excluded: chain B residue 519 MET Chi-restraints excluded: chain B residue 524 ILE Chi-restraints excluded: chain B residue 528 PHE Chi-restraints excluded: chain B residue 558 LEU Chi-restraints excluded: chain B residue 741 LEU Chi-restraints excluded: chain B residue 749 LEU Chi-restraints excluded: chain B residue 845 LEU Chi-restraints excluded: chain B residue 862 ILE Chi-restraints excluded: chain B residue 1005 ILE Chi-restraints excluded: chain C residue 45 PHE Chi-restraints excluded: chain C residue 82 ASP Chi-restraints excluded: chain C residue 104 LEU Chi-restraints excluded: chain C residue 115 ASN Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 134 TYR Chi-restraints excluded: chain C residue 194 ASP Chi-restraints excluded: chain C residue 218 TYR Chi-restraints excluded: chain C residue 225 ILE Chi-restraints excluded: chain C residue 236 GLN Chi-restraints excluded: chain C residue 325 ILE Chi-restraints excluded: chain C residue 333 VAL Chi-restraints excluded: chain C residue 347 VAL Chi-restraints excluded: chain C residue 411 SER Chi-restraints excluded: chain C residue 495 LEU Chi-restraints excluded: chain C residue 600 LEU Chi-restraints excluded: chain C residue 744 PHE Chi-restraints excluded: chain C residue 827 LEU Chi-restraints excluded: chain C residue 844 LEU Chi-restraints excluded: chain C residue 978 HIS Chi-restraints excluded: chain D residue 69 GLU Chi-restraints excluded: chain D residue 101 ASP Chi-restraints excluded: chain D residue 107 PHE Chi-restraints excluded: chain D residue 134 TYR Chi-restraints excluded: chain D residue 213 ILE Chi-restraints excluded: chain D residue 218 TYR Chi-restraints excluded: chain D residue 232 VAL Chi-restraints excluded: chain D residue 293 LEU Chi-restraints excluded: chain D residue 342 VAL Chi-restraints excluded: chain D residue 347 VAL Chi-restraints excluded: chain D residue 396 MET Chi-restraints excluded: chain D residue 421 MET Chi-restraints excluded: chain D residue 445 LEU Chi-restraints excluded: chain D residue 455 TYR Chi-restraints excluded: chain D residue 556 VAL Chi-restraints excluded: chain D residue 595 LEU Chi-restraints excluded: chain D residue 618 LEU Chi-restraints excluded: chain D residue 661 ILE Chi-restraints excluded: chain D residue 810 HIS Chi-restraints excluded: chain D residue 830 ASP Chi-restraints excluded: chain D residue 885 ILE Chi-restraints excluded: chain D residue 916 PHE Chi-restraints excluded: chain D residue 966 LEU Chi-restraints excluded: chain D residue 967 LEU Chi-restraints excluded: chain D residue 986 GLU Chi-restraints excluded: chain D residue 995 ARG Chi-restraints excluded: chain E residue 8 THR Chi-restraints excluded: chain E residue 37 SER Chi-restraints excluded: chain E residue 51 TYR Chi-restraints excluded: chain E residue 173 VAL Chi-restraints excluded: chain E residue 175 TYR Chi-restraints excluded: chain F residue 187 VAL Chi-restraints excluded: chain F residue 192 TYR Chi-restraints excluded: chain F residue 214 LEU Chi-restraints excluded: chain F residue 234 VAL Chi-restraints excluded: chain G residue 50 LEU Chi-restraints excluded: chain H residue 62 THR Chi-restraints excluded: chain H residue 67 PHE Chi-restraints excluded: chain H residue 187 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 449 random chunks: chunk 164 optimal weight: 3.9990 chunk 369 optimal weight: 3.9990 chunk 158 optimal weight: 1.9990 chunk 8 optimal weight: 0.8980 chunk 240 optimal weight: 0.9980 chunk 192 optimal weight: 0.1980 chunk 413 optimal weight: 4.9990 chunk 270 optimal weight: 0.9990 chunk 253 optimal weight: 0.9990 chunk 355 optimal weight: 0.9990 chunk 29 optimal weight: 3.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 118 HIS A 241 HIS ** A 323 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 563 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 765 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 910 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 477 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 536 GLN B 978 HIS C 115 ASN ** C 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 171 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 236 GLN D 549 GLN F 212 ASN G 28 GLN H 65 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4545 r_free = 0.4545 target = 0.162958 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4101 r_free = 0.4101 target = 0.132661 restraints weight = 103530.618| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.4077 r_free = 0.4077 target = 0.132618 restraints weight = 78130.872| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4085 r_free = 0.4085 target = 0.133148 restraints weight = 57234.768| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4093 r_free = 0.4093 target = 0.133605 restraints weight = 49919.989| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4096 r_free = 0.4096 target = 0.133815 restraints weight = 45940.401| |-----------------------------------------------------------------------------| r_work (final): 0.4084 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6512 moved from start: 0.3958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 38404 Z= 0.142 Angle : 0.660 14.168 51760 Z= 0.334 Chirality : 0.042 0.210 5510 Planarity : 0.004 0.067 6633 Dihedral : 5.006 67.044 4991 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 14.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 3.53 % Allowed : 23.87 % Favored : 72.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.15 (0.12), residues: 4508 helix: 0.73 (0.10), residues: 2625 sheet: -1.09 (0.29), residues: 280 loop : -1.22 (0.15), residues: 1603 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 145 TYR 0.037 0.002 TYR B 313 PHE 0.054 0.002 PHE D 916 TRP 0.052 0.002 TRP A 231 HIS 0.007 0.001 HIS B 978 Details of bonding type rmsd covalent geometry : bond 0.00323 (38404) covalent geometry : angle 0.65981 (51760) hydrogen bonds : bond 0.04071 ( 1996) hydrogen bonds : angle 5.05886 ( 5793) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9016 Ramachandran restraints generated. 4508 Oldfield, 0 Emsley, 4508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9016 Ramachandran restraints generated. 4508 Oldfield, 0 Emsley, 4508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 736 residues out of total 4131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 146 poor density : 590 time to evaluate : 1.578 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 98 MET cc_start: 0.8671 (pmm) cc_final: 0.8377 (pmm) REVERT: A 204 MET cc_start: 0.7477 (tmm) cc_final: 0.6750 (tmm) REVERT: A 334 PHE cc_start: 0.5635 (m-80) cc_final: 0.5212 (m-80) REVERT: A 368 ASP cc_start: 0.8871 (t70) cc_final: 0.8524 (p0) REVERT: A 487 GLN cc_start: 0.6153 (mt0) cc_final: 0.5316 (pt0) REVERT: A 495 LEU cc_start: 0.8450 (mp) cc_final: 0.8123 (tp) REVERT: A 517 ARG cc_start: 0.6080 (ttp80) cc_final: 0.5352 (ptm160) REVERT: A 535 PHE cc_start: 0.7606 (m-80) cc_final: 0.7296 (m-80) REVERT: A 597 GLU cc_start: 0.7946 (mm-30) cc_final: 0.6673 (mt-10) REVERT: A 647 MET cc_start: 0.0989 (mmt) cc_final: 0.0508 (mmt) REVERT: A 778 PHE cc_start: 0.8162 (t80) cc_final: 0.7586 (t80) REVERT: A 930 MET cc_start: 0.3657 (ttt) cc_final: 0.3257 (mtp) REVERT: A 942 PHE cc_start: 0.8363 (t80) cc_final: 0.8054 (t80) REVERT: A 954 PHE cc_start: 0.8301 (t80) cc_final: 0.7806 (t80) REVERT: A 995 ARG cc_start: 0.8947 (mmm160) cc_final: 0.8709 (mmm160) REVERT: B 35 GLU cc_start: 0.5800 (tp30) cc_final: 0.5446 (mt-10) REVERT: B 70 LEU cc_start: 0.7522 (mt) cc_final: 0.7239 (mt) REVERT: B 124 MET cc_start: 0.7182 (mmp) cc_final: 0.6842 (mmp) REVERT: B 218 TYR cc_start: 0.5041 (m-80) cc_final: 0.4572 (m-80) REVERT: B 227 MET cc_start: 0.5696 (OUTLIER) cc_final: 0.5330 (ttp) REVERT: B 283 LEU cc_start: 0.8335 (OUTLIER) cc_final: 0.7857 (tt) REVERT: B 391 ASN cc_start: 0.5384 (OUTLIER) cc_final: 0.4936 (m-40) REVERT: B 445 LEU cc_start: 0.8630 (OUTLIER) cc_final: 0.8007 (tp) REVERT: B 482 TYR cc_start: 0.7296 (t80) cc_final: 0.6819 (t80) REVERT: B 536 GLN cc_start: 0.8863 (OUTLIER) cc_final: 0.8333 (tp40) REVERT: B 741 LEU cc_start: 0.8823 (OUTLIER) cc_final: 0.8448 (mm) REVERT: B 757 TRP cc_start: 0.7830 (m100) cc_final: 0.7629 (m100) REVERT: B 919 TRP cc_start: 0.6845 (m-10) cc_final: 0.6228 (m-90) REVERT: B 929 LYS cc_start: 0.9307 (mmmt) cc_final: 0.8896 (tppt) REVERT: B 954 PHE cc_start: 0.8463 (t80) cc_final: 0.8191 (t80) REVERT: B 960 LYS cc_start: 0.8478 (pttt) cc_final: 0.8185 (mttp) REVERT: B 963 ASN cc_start: 0.7395 (m110) cc_final: 0.7120 (t0) REVERT: C 182 ASN cc_start: 0.8085 (t0) cc_final: 0.7708 (t0) REVERT: C 200 ILE cc_start: 0.7961 (mm) cc_final: 0.7545 (mm) REVERT: C 700 SER cc_start: 0.7474 (m) cc_final: 0.7255 (p) REVERT: C 827 LEU cc_start: 0.8054 (OUTLIER) cc_final: 0.7556 (tp) REVERT: C 890 GLU cc_start: 0.8147 (tp30) cc_final: 0.7737 (tp30) REVERT: D 101 ASP cc_start: 0.6123 (OUTLIER) cc_final: 0.5899 (t70) REVERT: D 106 ASP cc_start: 0.8474 (p0) cc_final: 0.8170 (p0) REVERT: D 204 MET cc_start: 0.7099 (tmm) cc_final: 0.6684 (tmt) REVERT: D 218 TYR cc_start: 0.7133 (OUTLIER) cc_final: 0.5568 (t80) REVERT: D 455 TYR cc_start: 0.6569 (OUTLIER) cc_final: 0.5690 (m-10) REVERT: D 567 SER cc_start: 0.8969 (OUTLIER) cc_final: 0.8621 (m) REVERT: D 664 ILE cc_start: 0.8281 (mm) cc_final: 0.7857 (mm) REVERT: D 753 LYS cc_start: 0.8121 (mmtp) cc_final: 0.7603 (mmmt) REVERT: D 844 LEU cc_start: 0.6064 (mp) cc_final: 0.5184 (tp) REVERT: E 37 SER cc_start: 0.5664 (OUTLIER) cc_final: 0.5105 (p) REVERT: E 73 LEU cc_start: 0.8383 (tp) cc_final: 0.8112 (pp) REVERT: E 206 MET cc_start: 0.4727 (OUTLIER) cc_final: 0.4477 (ptt) REVERT: F 183 ASP cc_start: 0.5169 (p0) cc_final: 0.4243 (m-30) REVERT: F 195 PHE cc_start: 0.7964 (m-10) cc_final: 0.7690 (m-80) REVERT: F 214 LEU cc_start: 0.6043 (OUTLIER) cc_final: 0.5809 (pp) REVERT: F 220 PHE cc_start: 0.7421 (m-80) cc_final: 0.7138 (m-80) REVERT: F 223 LEU cc_start: 0.8113 (mt) cc_final: 0.7350 (mt) REVERT: G 51 TYR cc_start: 0.5769 (t80) cc_final: 0.5420 (t80) outliers start: 146 outliers final: 94 residues processed: 681 average time/residue: 0.2496 time to fit residues: 277.4684 Evaluate side-chains 652 residues out of total 4131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 544 time to evaluate : 1.422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 PHE Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 130 ILE Chi-restraints excluded: chain A residue 131 THR Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 360 PHE Chi-restraints excluded: chain A residue 454 LEU Chi-restraints excluded: chain A residue 485 ILE Chi-restraints excluded: chain A residue 515 ILE Chi-restraints excluded: chain A residue 519 MET Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 588 LEU Chi-restraints excluded: chain A residue 649 TYR Chi-restraints excluded: chain A residue 671 CYS Chi-restraints excluded: chain A residue 919 TRP Chi-restraints excluded: chain A residue 987 ARG Chi-restraints excluded: chain B residue 97 GLU Chi-restraints excluded: chain B residue 132 THR Chi-restraints excluded: chain B residue 134 TYR Chi-restraints excluded: chain B residue 143 TRP Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain B residue 227 MET Chi-restraints excluded: chain B residue 251 SER Chi-restraints excluded: chain B residue 283 LEU Chi-restraints excluded: chain B residue 310 ASP Chi-restraints excluded: chain B residue 391 ASN Chi-restraints excluded: chain B residue 445 LEU Chi-restraints excluded: chain B residue 459 ILE Chi-restraints excluded: chain B residue 518 GLU Chi-restraints excluded: chain B residue 524 ILE Chi-restraints excluded: chain B residue 528 PHE Chi-restraints excluded: chain B residue 536 GLN Chi-restraints excluded: chain B residue 558 LEU Chi-restraints excluded: chain B residue 573 SER Chi-restraints excluded: chain B residue 649 TYR Chi-restraints excluded: chain B residue 741 LEU Chi-restraints excluded: chain B residue 749 LEU Chi-restraints excluded: chain B residue 845 LEU Chi-restraints excluded: chain B residue 862 ILE Chi-restraints excluded: chain B residue 1005 ILE Chi-restraints excluded: chain C residue 45 PHE Chi-restraints excluded: chain C residue 82 ASP Chi-restraints excluded: chain C residue 104 LEU Chi-restraints excluded: chain C residue 115 ASN Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 134 TYR Chi-restraints excluded: chain C residue 218 TYR Chi-restraints excluded: chain C residue 225 ILE Chi-restraints excluded: chain C residue 236 GLN Chi-restraints excluded: chain C residue 325 ILE Chi-restraints excluded: chain C residue 346 VAL Chi-restraints excluded: chain C residue 347 VAL Chi-restraints excluded: chain C residue 373 LEU Chi-restraints excluded: chain C residue 411 SER Chi-restraints excluded: chain C residue 474 SER Chi-restraints excluded: chain C residue 495 LEU Chi-restraints excluded: chain C residue 600 LEU Chi-restraints excluded: chain C residue 664 ILE Chi-restraints excluded: chain C residue 728 LEU Chi-restraints excluded: chain C residue 744 PHE Chi-restraints excluded: chain C residue 827 LEU Chi-restraints excluded: chain C residue 844 LEU Chi-restraints excluded: chain C residue 978 HIS Chi-restraints excluded: chain D residue 101 ASP Chi-restraints excluded: chain D residue 107 PHE Chi-restraints excluded: chain D residue 134 TYR Chi-restraints excluded: chain D residue 213 ILE Chi-restraints excluded: chain D residue 216 ILE Chi-restraints excluded: chain D residue 218 TYR Chi-restraints excluded: chain D residue 232 VAL Chi-restraints excluded: chain D residue 280 TYR Chi-restraints excluded: chain D residue 293 LEU Chi-restraints excluded: chain D residue 342 VAL Chi-restraints excluded: chain D residue 347 VAL Chi-restraints excluded: chain D residue 396 MET Chi-restraints excluded: chain D residue 421 MET Chi-restraints excluded: chain D residue 445 LEU Chi-restraints excluded: chain D residue 455 TYR Chi-restraints excluded: chain D residue 482 TYR Chi-restraints excluded: chain D residue 556 VAL Chi-restraints excluded: chain D residue 567 SER Chi-restraints excluded: chain D residue 595 LEU Chi-restraints excluded: chain D residue 618 LEU Chi-restraints excluded: chain D residue 661 ILE Chi-restraints excluded: chain D residue 810 HIS Chi-restraints excluded: chain D residue 830 ASP Chi-restraints excluded: chain D residue 885 ILE Chi-restraints excluded: chain D residue 966 LEU Chi-restraints excluded: chain D residue 967 LEU Chi-restraints excluded: chain D residue 986 GLU Chi-restraints excluded: chain D residue 995 ARG Chi-restraints excluded: chain E residue 8 THR Chi-restraints excluded: chain E residue 29 THR Chi-restraints excluded: chain E residue 37 SER Chi-restraints excluded: chain E residue 50 LEU Chi-restraints excluded: chain E residue 51 TYR Chi-restraints excluded: chain E residue 173 VAL Chi-restraints excluded: chain E residue 206 MET Chi-restraints excluded: chain E residue 214 LEU Chi-restraints excluded: chain E residue 218 ILE Chi-restraints excluded: chain F residue 187 VAL Chi-restraints excluded: chain F residue 214 LEU Chi-restraints excluded: chain F residue 234 VAL Chi-restraints excluded: chain G residue 50 LEU Chi-restraints excluded: chain H residue 62 THR Chi-restraints excluded: chain H residue 67 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 449 random chunks: chunk 186 optimal weight: 10.0000 chunk 301 optimal weight: 0.0040 chunk 190 optimal weight: 10.0000 chunk 163 optimal weight: 3.9990 chunk 30 optimal weight: 0.8980 chunk 348 optimal weight: 0.7980 chunk 193 optimal weight: 10.0000 chunk 266 optimal weight: 0.8980 chunk 264 optimal weight: 1.9990 chunk 306 optimal weight: 0.9990 chunk 345 optimal weight: 4.9990 overall best weight: 0.7194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 118 HIS ** A 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 323 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 563 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 610 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 765 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 477 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 536 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 654 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 89 GLN ** C 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 171 HIS D 224 ASN ** D 598 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4548 r_free = 0.4548 target = 0.163088 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4109 r_free = 0.4109 target = 0.133033 restraints weight = 103414.238| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.4078 r_free = 0.4078 target = 0.132759 restraints weight = 78723.118| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4090 r_free = 0.4090 target = 0.133452 restraints weight = 59205.909| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4098 r_free = 0.4098 target = 0.133902 restraints weight = 52425.982| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4103 r_free = 0.4103 target = 0.134217 restraints weight = 44901.368| |-----------------------------------------------------------------------------| r_work (final): 0.4094 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6504 moved from start: 0.4210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 38404 Z= 0.142 Angle : 0.682 13.404 51760 Z= 0.342 Chirality : 0.042 0.175 5510 Planarity : 0.004 0.079 6633 Dihedral : 5.015 67.911 4991 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 14.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 3.12 % Allowed : 24.72 % Favored : 72.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.14 (0.12), residues: 4508 helix: 0.74 (0.10), residues: 2624 sheet: -1.19 (0.29), residues: 287 loop : -1.19 (0.15), residues: 1597 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG A 359 TYR 0.037 0.002 TYR B 313 PHE 0.066 0.002 PHE D 916 TRP 0.057 0.003 TRP D 919 HIS 0.010 0.001 HIS B 852 Details of bonding type rmsd covalent geometry : bond 0.00321 (38404) covalent geometry : angle 0.68160 (51760) hydrogen bonds : bond 0.04013 ( 1996) hydrogen bonds : angle 5.03187 ( 5793) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9016 Ramachandran restraints generated. 4508 Oldfield, 0 Emsley, 4508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9016 Ramachandran restraints generated. 4508 Oldfield, 0 Emsley, 4508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 704 residues out of total 4131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 129 poor density : 575 time to evaluate : 1.524 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 98 MET cc_start: 0.8737 (pmm) cc_final: 0.8423 (pmm) REVERT: A 204 MET cc_start: 0.7527 (tmm) cc_final: 0.6729 (tmm) REVERT: A 334 PHE cc_start: 0.5602 (m-80) cc_final: 0.5133 (m-80) REVERT: A 368 ASP cc_start: 0.8833 (t70) cc_final: 0.8483 (p0) REVERT: A 487 GLN cc_start: 0.6144 (mt0) cc_final: 0.5640 (pt0) REVERT: A 495 LEU cc_start: 0.8408 (mp) cc_final: 0.8127 (tp) REVERT: A 517 ARG cc_start: 0.6149 (ttp80) cc_final: 0.5539 (ptm160) REVERT: A 535 PHE cc_start: 0.7584 (m-80) cc_final: 0.7321 (m-80) REVERT: A 597 GLU cc_start: 0.7891 (mm-30) cc_final: 0.6632 (mt-10) REVERT: A 647 MET cc_start: 0.0980 (mmt) cc_final: 0.0478 (mmt) REVERT: A 778 PHE cc_start: 0.8181 (t80) cc_final: 0.7629 (t80) REVERT: A 930 MET cc_start: 0.3724 (ttt) cc_final: 0.3249 (mtp) REVERT: A 954 PHE cc_start: 0.8312 (t80) cc_final: 0.7871 (t80) REVERT: B 35 GLU cc_start: 0.5872 (tp30) cc_final: 0.5489 (mt-10) REVERT: B 70 LEU cc_start: 0.7511 (mt) cc_final: 0.7227 (mt) REVERT: B 124 MET cc_start: 0.7279 (mmp) cc_final: 0.6953 (mmp) REVERT: B 218 TYR cc_start: 0.5154 (m-80) cc_final: 0.4714 (m-80) REVERT: B 283 LEU cc_start: 0.8350 (OUTLIER) cc_final: 0.7869 (tt) REVERT: B 391 ASN cc_start: 0.5490 (OUTLIER) cc_final: 0.5070 (m-40) REVERT: B 445 LEU cc_start: 0.8665 (OUTLIER) cc_final: 0.8024 (tp) REVERT: B 482 TYR cc_start: 0.7398 (t80) cc_final: 0.6923 (t80) REVERT: B 536 GLN cc_start: 0.8692 (pp30) cc_final: 0.8379 (tt0) REVERT: B 740 LEU cc_start: 0.9431 (mt) cc_final: 0.9190 (tt) REVERT: B 929 LYS cc_start: 0.9315 (mmmt) cc_final: 0.8874 (tppt) REVERT: B 960 LYS cc_start: 0.8394 (pttt) cc_final: 0.8059 (ptpt) REVERT: B 963 ASN cc_start: 0.7397 (m110) cc_final: 0.7136 (t0) REVERT: C 61 ARG cc_start: 0.8244 (mtt180) cc_final: 0.7973 (ptt-90) REVERT: C 155 GLU cc_start: 0.5024 (OUTLIER) cc_final: 0.4467 (mm-30) REVERT: C 182 ASN cc_start: 0.8039 (t0) cc_final: 0.7773 (t0) REVERT: C 200 ILE cc_start: 0.7912 (mm) cc_final: 0.7491 (mm) REVERT: C 890 GLU cc_start: 0.8115 (tp30) cc_final: 0.7740 (tp30) REVERT: D 65 LYS cc_start: 0.7854 (mmmt) cc_final: 0.6923 (tptp) REVERT: D 68 GLU cc_start: 0.7621 (tp30) cc_final: 0.7259 (tm-30) REVERT: D 106 ASP cc_start: 0.8408 (p0) cc_final: 0.8111 (p0) REVERT: D 204 MET cc_start: 0.7139 (tmm) cc_final: 0.6179 (tmm) REVERT: D 218 TYR cc_start: 0.7100 (OUTLIER) cc_final: 0.5553 (t80) REVERT: D 455 TYR cc_start: 0.6573 (OUTLIER) cc_final: 0.5830 (m-10) REVERT: D 567 SER cc_start: 0.8934 (OUTLIER) cc_final: 0.8620 (m) REVERT: D 721 TYR cc_start: 0.6951 (t80) cc_final: 0.6542 (t80) REVERT: D 753 LYS cc_start: 0.8127 (mmtp) cc_final: 0.7462 (mmmt) REVERT: D 844 LEU cc_start: 0.6072 (mp) cc_final: 0.5205 (tp) REVERT: D 936 MET cc_start: 0.8274 (mmp) cc_final: 0.7907 (mmm) REVERT: E 37 SER cc_start: 0.5694 (OUTLIER) cc_final: 0.5134 (p) REVERT: E 73 LEU cc_start: 0.8379 (tp) cc_final: 0.8120 (pp) REVERT: E 206 MET cc_start: 0.4577 (OUTLIER) cc_final: 0.4362 (ptt) REVERT: F 183 ASP cc_start: 0.5181 (p0) cc_final: 0.4303 (m-30) REVERT: F 195 PHE cc_start: 0.7915 (m-10) cc_final: 0.7633 (m-80) REVERT: F 223 LEU cc_start: 0.8106 (mt) cc_final: 0.7359 (mt) outliers start: 129 outliers final: 97 residues processed: 653 average time/residue: 0.2469 time to fit residues: 264.4839 Evaluate side-chains 642 residues out of total 4131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 536 time to evaluate : 1.545 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 PHE Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 130 ILE Chi-restraints excluded: chain A residue 131 THR Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 360 PHE Chi-restraints excluded: chain A residue 395 CYS Chi-restraints excluded: chain A residue 454 LEU Chi-restraints excluded: chain A residue 485 ILE Chi-restraints excluded: chain A residue 515 ILE Chi-restraints excluded: chain A residue 519 MET Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 588 LEU Chi-restraints excluded: chain A residue 649 TYR Chi-restraints excluded: chain A residue 671 CYS Chi-restraints excluded: chain A residue 842 LEU Chi-restraints excluded: chain A residue 919 TRP Chi-restraints excluded: chain A residue 987 ARG Chi-restraints excluded: chain B residue 97 GLU Chi-restraints excluded: chain B residue 132 THR Chi-restraints excluded: chain B residue 134 TYR Chi-restraints excluded: chain B residue 143 TRP Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain B residue 227 MET Chi-restraints excluded: chain B residue 251 SER Chi-restraints excluded: chain B residue 283 LEU Chi-restraints excluded: chain B residue 310 ASP Chi-restraints excluded: chain B residue 391 ASN Chi-restraints excluded: chain B residue 445 LEU Chi-restraints excluded: chain B residue 459 ILE Chi-restraints excluded: chain B residue 518 GLU Chi-restraints excluded: chain B residue 524 ILE Chi-restraints excluded: chain B residue 528 PHE Chi-restraints excluded: chain B residue 558 LEU Chi-restraints excluded: chain B residue 583 VAL Chi-restraints excluded: chain B residue 654 ASN Chi-restraints excluded: chain B residue 845 LEU Chi-restraints excluded: chain B residue 862 ILE Chi-restraints excluded: chain B residue 1005 ILE Chi-restraints excluded: chain C residue 45 PHE Chi-restraints excluded: chain C residue 82 ASP Chi-restraints excluded: chain C residue 89 GLN Chi-restraints excluded: chain C residue 104 LEU Chi-restraints excluded: chain C residue 115 ASN Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 134 TYR Chi-restraints excluded: chain C residue 155 GLU Chi-restraints excluded: chain C residue 218 TYR Chi-restraints excluded: chain C residue 225 ILE Chi-restraints excluded: chain C residue 236 GLN Chi-restraints excluded: chain C residue 325 ILE Chi-restraints excluded: chain C residue 346 VAL Chi-restraints excluded: chain C residue 347 VAL Chi-restraints excluded: chain C residue 411 SER Chi-restraints excluded: chain C residue 474 SER Chi-restraints excluded: chain C residue 495 LEU Chi-restraints excluded: chain C residue 600 LEU Chi-restraints excluded: chain C residue 664 ILE Chi-restraints excluded: chain C residue 728 LEU Chi-restraints excluded: chain C residue 744 PHE Chi-restraints excluded: chain C residue 827 LEU Chi-restraints excluded: chain C residue 844 LEU Chi-restraints excluded: chain C residue 978 HIS Chi-restraints excluded: chain D residue 107 PHE Chi-restraints excluded: chain D residue 134 TYR Chi-restraints excluded: chain D residue 213 ILE Chi-restraints excluded: chain D residue 216 ILE Chi-restraints excluded: chain D residue 218 TYR Chi-restraints excluded: chain D residue 232 VAL Chi-restraints excluded: chain D residue 293 LEU Chi-restraints excluded: chain D residue 342 VAL Chi-restraints excluded: chain D residue 347 VAL Chi-restraints excluded: chain D residue 396 MET Chi-restraints excluded: chain D residue 421 MET Chi-restraints excluded: chain D residue 445 LEU Chi-restraints excluded: chain D residue 455 TYR Chi-restraints excluded: chain D residue 482 TYR Chi-restraints excluded: chain D residue 556 VAL Chi-restraints excluded: chain D residue 567 SER Chi-restraints excluded: chain D residue 595 LEU Chi-restraints excluded: chain D residue 618 LEU Chi-restraints excluded: chain D residue 661 ILE Chi-restraints excluded: chain D residue 810 HIS Chi-restraints excluded: chain D residue 885 ILE Chi-restraints excluded: chain D residue 916 PHE Chi-restraints excluded: chain D residue 966 LEU Chi-restraints excluded: chain D residue 967 LEU Chi-restraints excluded: chain D residue 995 ARG Chi-restraints excluded: chain E residue 8 THR Chi-restraints excluded: chain E residue 11 VAL Chi-restraints excluded: chain E residue 37 SER Chi-restraints excluded: chain E residue 50 LEU Chi-restraints excluded: chain E residue 51 TYR Chi-restraints excluded: chain E residue 173 VAL Chi-restraints excluded: chain E residue 175 TYR Chi-restraints excluded: chain E residue 206 MET Chi-restraints excluded: chain E residue 214 LEU Chi-restraints excluded: chain F residue 173 VAL Chi-restraints excluded: chain F residue 187 VAL Chi-restraints excluded: chain F residue 234 VAL Chi-restraints excluded: chain G residue 50 LEU Chi-restraints excluded: chain H residue 62 THR Chi-restraints excluded: chain H residue 67 PHE Chi-restraints excluded: chain H residue 187 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 449 random chunks: chunk 400 optimal weight: 6.9990 chunk 341 optimal weight: 0.9990 chunk 41 optimal weight: 0.9980 chunk 396 optimal weight: 9.9990 chunk 333 optimal weight: 0.6980 chunk 393 optimal weight: 0.9980 chunk 303 optimal weight: 2.9990 chunk 258 optimal weight: 4.9990 chunk 428 optimal weight: 4.9990 chunk 192 optimal weight: 0.6980 chunk 43 optimal weight: 3.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 118 HIS ** A 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 278 ASN ** A 323 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 536 GLN ** A 563 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 610 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 765 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 477 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 536 GLN ** B 654 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 978 HIS C 89 GLN C 115 ASN ** C 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 881 HIS ** D 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 47 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4542 r_free = 0.4542 target = 0.163059 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4107 r_free = 0.4107 target = 0.133482 restraints weight = 103042.174| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.4090 r_free = 0.4090 target = 0.133755 restraints weight = 76459.482| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.4104 r_free = 0.4104 target = 0.134691 restraints weight = 58907.611| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.4105 r_free = 0.4105 target = 0.134692 restraints weight = 54856.749| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4107 r_free = 0.4107 target = 0.134825 restraints weight = 47120.375| |-----------------------------------------------------------------------------| r_work (final): 0.4097 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6504 moved from start: 0.4455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 38404 Z= 0.146 Angle : 0.690 12.665 51760 Z= 0.346 Chirality : 0.042 0.235 5510 Planarity : 0.004 0.073 6633 Dihedral : 5.029 69.158 4991 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 14.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 3.27 % Allowed : 24.79 % Favored : 71.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.15 (0.12), residues: 4508 helix: 0.74 (0.10), residues: 2633 sheet: -1.18 (0.29), residues: 287 loop : -1.24 (0.15), residues: 1588 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 760 TYR 0.054 0.002 TYR B 313 PHE 0.066 0.002 PHE D 916 TRP 0.051 0.003 TRP A 231 HIS 0.008 0.001 HIS B 852 Details of bonding type rmsd covalent geometry : bond 0.00331 (38404) covalent geometry : angle 0.68954 (51760) hydrogen bonds : bond 0.03983 ( 1996) hydrogen bonds : angle 5.02449 ( 5793) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9016 Ramachandran restraints generated. 4508 Oldfield, 0 Emsley, 4508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9016 Ramachandran restraints generated. 4508 Oldfield, 0 Emsley, 4508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 703 residues out of total 4131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 135 poor density : 568 time to evaluate : 1.617 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 98 MET cc_start: 0.8784 (pmm) cc_final: 0.8524 (pmm) REVERT: A 204 MET cc_start: 0.7602 (tmm) cc_final: 0.7128 (tmm) REVERT: A 334 PHE cc_start: 0.5517 (m-80) cc_final: 0.5104 (m-80) REVERT: A 368 ASP cc_start: 0.8743 (t70) cc_final: 0.8372 (p0) REVERT: A 487 GLN cc_start: 0.6249 (mt0) cc_final: 0.5738 (pt0) REVERT: A 495 LEU cc_start: 0.8376 (mp) cc_final: 0.8125 (tp) REVERT: A 535 PHE cc_start: 0.7528 (m-80) cc_final: 0.7281 (m-80) REVERT: A 597 GLU cc_start: 0.7879 (mm-30) cc_final: 0.6680 (mt-10) REVERT: A 647 MET cc_start: 0.1089 (mmt) cc_final: 0.0567 (mmt) REVERT: A 930 MET cc_start: 0.3741 (ttt) cc_final: 0.3384 (mtp) REVERT: A 954 PHE cc_start: 0.8270 (t80) cc_final: 0.7861 (t80) REVERT: B 35 GLU cc_start: 0.5804 (tp30) cc_final: 0.5486 (mt-10) REVERT: B 70 LEU cc_start: 0.7483 (mt) cc_final: 0.7198 (mt) REVERT: B 97 GLU cc_start: 0.6069 (OUTLIER) cc_final: 0.5806 (tp30) REVERT: B 124 MET cc_start: 0.7295 (mmp) cc_final: 0.6892 (mmp) REVERT: B 218 TYR cc_start: 0.5049 (m-80) cc_final: 0.4633 (m-80) REVERT: B 283 LEU cc_start: 0.8417 (OUTLIER) cc_final: 0.7933 (tt) REVERT: B 361 PHE cc_start: 0.8892 (OUTLIER) cc_final: 0.8044 (m-10) REVERT: B 391 ASN cc_start: 0.5399 (OUTLIER) cc_final: 0.5008 (m-40) REVERT: B 445 LEU cc_start: 0.8647 (OUTLIER) cc_final: 0.7990 (tp) REVERT: B 482 TYR cc_start: 0.7444 (t80) cc_final: 0.6996 (t80) REVERT: B 929 LYS cc_start: 0.9330 (mmmt) cc_final: 0.9007 (tppt) REVERT: B 960 LYS cc_start: 0.8378 (pttt) cc_final: 0.8054 (ptpt) REVERT: B 963 ASN cc_start: 0.7444 (m110) cc_final: 0.7219 (t0) REVERT: C 61 ARG cc_start: 0.8214 (mtt180) cc_final: 0.7905 (ptt-90) REVERT: C 91 PHE cc_start: 0.7908 (t80) cc_final: 0.7663 (t80) REVERT: C 182 ASN cc_start: 0.7927 (t0) cc_final: 0.7637 (t0) REVERT: C 200 ILE cc_start: 0.7969 (mm) cc_final: 0.7538 (mm) REVERT: C 396 MET cc_start: 0.5703 (tpt) cc_final: 0.5034 (tpp) REVERT: C 688 LEU cc_start: 0.7873 (mt) cc_final: 0.7659 (mt) REVERT: C 890 GLU cc_start: 0.8107 (tp30) cc_final: 0.7714 (tp30) REVERT: C 967 LEU cc_start: 0.9014 (mt) cc_final: 0.8732 (tt) REVERT: D 65 LYS cc_start: 0.7799 (mmmt) cc_final: 0.6901 (tptp) REVERT: D 68 GLU cc_start: 0.7551 (tp30) cc_final: 0.7176 (tm-30) REVERT: D 106 ASP cc_start: 0.8347 (p0) cc_final: 0.8034 (p0) REVERT: D 204 MET cc_start: 0.7221 (OUTLIER) cc_final: 0.6572 (tmm) REVERT: D 218 TYR cc_start: 0.7086 (OUTLIER) cc_final: 0.5591 (t80) REVERT: D 455 TYR cc_start: 0.6632 (OUTLIER) cc_final: 0.5840 (m-10) REVERT: D 567 SER cc_start: 0.8955 (OUTLIER) cc_final: 0.8605 (m) REVERT: D 721 TYR cc_start: 0.6992 (t80) cc_final: 0.6386 (t80) REVERT: D 728 LEU cc_start: 0.5835 (mt) cc_final: 0.5537 (tp) REVERT: D 753 LYS cc_start: 0.8048 (mmtp) cc_final: 0.7408 (mmmt) REVERT: D 835 ILE cc_start: 0.6574 (mt) cc_final: 0.6255 (mt) REVERT: D 844 LEU cc_start: 0.6036 (mp) cc_final: 0.5205 (tp) REVERT: D 936 MET cc_start: 0.8243 (mmp) cc_final: 0.7947 (mmm) REVERT: E 37 SER cc_start: 0.5706 (OUTLIER) cc_final: 0.5131 (p) REVERT: E 73 LEU cc_start: 0.8407 (tp) cc_final: 0.8159 (pp) REVERT: F 195 PHE cc_start: 0.7878 (m-10) cc_final: 0.7607 (m-80) REVERT: F 223 LEU cc_start: 0.7955 (mt) cc_final: 0.7209 (mt) outliers start: 135 outliers final: 103 residues processed: 642 average time/residue: 0.2559 time to fit residues: 269.7656 Evaluate side-chains 646 residues out of total 4131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 533 time to evaluate : 1.571 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 PHE Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 130 ILE Chi-restraints excluded: chain A residue 131 THR Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 360 PHE Chi-restraints excluded: chain A residue 395 CYS Chi-restraints excluded: chain A residue 454 LEU Chi-restraints excluded: chain A residue 485 ILE Chi-restraints excluded: chain A residue 515 ILE Chi-restraints excluded: chain A residue 519 MET Chi-restraints excluded: chain A residue 588 LEU Chi-restraints excluded: chain A residue 649 TYR Chi-restraints excluded: chain A residue 671 CYS Chi-restraints excluded: chain A residue 919 TRP Chi-restraints excluded: chain A residue 987 ARG Chi-restraints excluded: chain B residue 97 GLU Chi-restraints excluded: chain B residue 132 THR Chi-restraints excluded: chain B residue 134 TYR Chi-restraints excluded: chain B residue 143 TRP Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain B residue 251 SER Chi-restraints excluded: chain B residue 283 LEU Chi-restraints excluded: chain B residue 310 ASP Chi-restraints excluded: chain B residue 348 ARG Chi-restraints excluded: chain B residue 361 PHE Chi-restraints excluded: chain B residue 391 ASN Chi-restraints excluded: chain B residue 445 LEU Chi-restraints excluded: chain B residue 459 ILE Chi-restraints excluded: chain B residue 518 GLU Chi-restraints excluded: chain B residue 519 MET Chi-restraints excluded: chain B residue 524 ILE Chi-restraints excluded: chain B residue 528 PHE Chi-restraints excluded: chain B residue 558 LEU Chi-restraints excluded: chain B residue 573 SER Chi-restraints excluded: chain B residue 583 VAL Chi-restraints excluded: chain B residue 649 TYR Chi-restraints excluded: chain B residue 654 ASN Chi-restraints excluded: chain B residue 807 LEU Chi-restraints excluded: chain B residue 845 LEU Chi-restraints excluded: chain B residue 862 ILE Chi-restraints excluded: chain B residue 1005 ILE Chi-restraints excluded: chain C residue 45 PHE Chi-restraints excluded: chain C residue 82 ASP Chi-restraints excluded: chain C residue 104 LEU Chi-restraints excluded: chain C residue 115 ASN Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 134 TYR Chi-restraints excluded: chain C residue 218 TYR Chi-restraints excluded: chain C residue 225 ILE Chi-restraints excluded: chain C residue 236 GLN Chi-restraints excluded: chain C residue 260 TYR Chi-restraints excluded: chain C residue 325 ILE Chi-restraints excluded: chain C residue 346 VAL Chi-restraints excluded: chain C residue 347 VAL Chi-restraints excluded: chain C residue 411 SER Chi-restraints excluded: chain C residue 474 SER Chi-restraints excluded: chain C residue 495 LEU Chi-restraints excluded: chain C residue 600 LEU Chi-restraints excluded: chain C residue 664 ILE Chi-restraints excluded: chain C residue 744 PHE Chi-restraints excluded: chain C residue 827 LEU Chi-restraints excluded: chain C residue 844 LEU Chi-restraints excluded: chain C residue 978 HIS Chi-restraints excluded: chain D residue 101 ASP Chi-restraints excluded: chain D residue 107 PHE Chi-restraints excluded: chain D residue 134 TYR Chi-restraints excluded: chain D residue 204 MET Chi-restraints excluded: chain D residue 213 ILE Chi-restraints excluded: chain D residue 214 VAL Chi-restraints excluded: chain D residue 216 ILE Chi-restraints excluded: chain D residue 218 TYR Chi-restraints excluded: chain D residue 232 VAL Chi-restraints excluded: chain D residue 280 TYR Chi-restraints excluded: chain D residue 293 LEU Chi-restraints excluded: chain D residue 342 VAL Chi-restraints excluded: chain D residue 347 VAL Chi-restraints excluded: chain D residue 360 PHE Chi-restraints excluded: chain D residue 396 MET Chi-restraints excluded: chain D residue 421 MET Chi-restraints excluded: chain D residue 445 LEU Chi-restraints excluded: chain D residue 455 TYR Chi-restraints excluded: chain D residue 482 TYR Chi-restraints excluded: chain D residue 556 VAL Chi-restraints excluded: chain D residue 567 SER Chi-restraints excluded: chain D residue 595 LEU Chi-restraints excluded: chain D residue 618 LEU Chi-restraints excluded: chain D residue 661 ILE Chi-restraints excluded: chain D residue 810 HIS Chi-restraints excluded: chain D residue 885 ILE Chi-restraints excluded: chain D residue 916 PHE Chi-restraints excluded: chain D residue 966 LEU Chi-restraints excluded: chain D residue 967 LEU Chi-restraints excluded: chain D residue 995 ARG Chi-restraints excluded: chain E residue 8 THR Chi-restraints excluded: chain E residue 37 SER Chi-restraints excluded: chain E residue 50 LEU Chi-restraints excluded: chain E residue 51 TYR Chi-restraints excluded: chain E residue 173 VAL Chi-restraints excluded: chain E residue 175 TYR Chi-restraints excluded: chain E residue 214 LEU Chi-restraints excluded: chain E residue 218 ILE Chi-restraints excluded: chain F residue 70 LEU Chi-restraints excluded: chain F residue 173 VAL Chi-restraints excluded: chain F residue 187 VAL Chi-restraints excluded: chain F residue 234 VAL Chi-restraints excluded: chain G residue 50 LEU Chi-restraints excluded: chain H residue 62 THR Chi-restraints excluded: chain H residue 67 PHE Chi-restraints excluded: chain H residue 187 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 449 random chunks: chunk 160 optimal weight: 7.9990 chunk 71 optimal weight: 3.9990 chunk 129 optimal weight: 0.0570 chunk 267 optimal weight: 2.9990 chunk 175 optimal weight: 0.6980 chunk 259 optimal weight: 0.7980 chunk 39 optimal weight: 1.9990 chunk 377 optimal weight: 0.9990 chunk 357 optimal weight: 3.9990 chunk 272 optimal weight: 2.9990 chunk 205 optimal weight: 0.8980 overall best weight: 0.6900 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 118 HIS ** A 323 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 563 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 610 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 765 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 852 HIS A 973 ASN ** B 477 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 536 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 654 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 978 HIS ** C 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 115 ASN ** C 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 598 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 765 ASN D 867 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4545 r_free = 0.4545 target = 0.162862 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4115 r_free = 0.4115 target = 0.133492 restraints weight = 103858.506| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4100 r_free = 0.4100 target = 0.133657 restraints weight = 75630.010| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4114 r_free = 0.4114 target = 0.134642 restraints weight = 54052.351| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4119 r_free = 0.4119 target = 0.135007 restraints weight = 48169.828| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4122 r_free = 0.4122 target = 0.135203 restraints weight = 44190.314| |-----------------------------------------------------------------------------| r_work (final): 0.4112 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6483 moved from start: 0.4647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 38404 Z= 0.140 Angle : 0.697 13.760 51760 Z= 0.349 Chirality : 0.043 0.238 5510 Planarity : 0.004 0.075 6633 Dihedral : 5.021 70.378 4991 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 14.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 2.83 % Allowed : 25.30 % Favored : 71.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.15 (0.12), residues: 4508 helix: 0.74 (0.10), residues: 2630 sheet: -1.25 (0.29), residues: 287 loop : -1.22 (0.15), residues: 1591 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG C 175 TYR 0.031 0.002 TYR A 743 PHE 0.065 0.002 PHE D 916 TRP 0.050 0.003 TRP A 231 HIS 0.014 0.001 HIS A 852 Details of bonding type rmsd covalent geometry : bond 0.00317 (38404) covalent geometry : angle 0.69710 (51760) hydrogen bonds : bond 0.03958 ( 1996) hydrogen bonds : angle 4.99224 ( 5793) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9016 Ramachandran restraints generated. 4508 Oldfield, 0 Emsley, 4508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9016 Ramachandran restraints generated. 4508 Oldfield, 0 Emsley, 4508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 685 residues out of total 4131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 568 time to evaluate : 1.536 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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: 0.7531 (tmm) cc_final: 0.7066 (tmm) REVERT: A 334 PHE cc_start: 0.5485 (m-80) cc_final: 0.5028 (m-80) REVERT: A 368 ASP cc_start: 0.8799 (t70) cc_final: 0.8418 (p0) REVERT: A 487 GLN cc_start: 0.6148 (mt0) cc_final: 0.5712 (pt0) REVERT: A 535 PHE cc_start: 0.7560 (m-80) cc_final: 0.7318 (m-80) REVERT: A 597 GLU cc_start: 0.7832 (mm-30) cc_final: 0.6644 (mt-10) REVERT: A 647 MET cc_start: 0.1159 (mmt) cc_final: 0.0609 (mmt) REVERT: A 873 LEU cc_start: 0.8066 (tp) cc_final: 0.7807 (tt) REVERT: A 930 MET cc_start: 0.3718 (ttt) cc_final: 0.3408 (ttt) REVERT: A 954 PHE cc_start: 0.8266 (t80) cc_final: 0.7805 (t80) REVERT: A 995 ARG cc_start: 0.8935 (mmm160) cc_final: 0.8570 (mmm160) REVERT: B 35 GLU cc_start: 0.5712 (tp30) cc_final: 0.5451 (mt-10) REVERT: B 70 LEU cc_start: 0.7511 (mt) cc_final: 0.7234 (mt) REVERT: B 124 MET cc_start: 0.7245 (mmp) cc_final: 0.6943 (mmp) REVERT: B 218 TYR cc_start: 0.5017 (m-80) cc_final: 0.4669 (m-80) REVERT: B 283 LEU cc_start: 0.8423 (OUTLIER) cc_final: 0.7928 (tt) REVERT: B 361 PHE cc_start: 0.8816 (OUTLIER) cc_final: 0.8173 (m-10) REVERT: B 391 ASN cc_start: 0.5331 (OUTLIER) cc_final: 0.4952 (m-40) REVERT: B 445 LEU cc_start: 0.8677 (OUTLIER) cc_final: 0.8035 (tp) REVERT: B 482 TYR cc_start: 0.7401 (t80) cc_final: 0.6975 (t80) REVERT: B 960 LYS cc_start: 0.8369 (pttt) cc_final: 0.8056 (ptpt) REVERT: B 963 ASN cc_start: 0.7456 (m110) cc_final: 0.7229 (t0) REVERT: B 976 MET cc_start: 0.3353 (ptt) cc_final: 0.2539 (ppp) REVERT: C 61 ARG cc_start: 0.8162 (mtt180) cc_final: 0.7876 (ptt-90) REVERT: C 200 ILE cc_start: 0.7905 (mm) cc_final: 0.7502 (mm) REVERT: C 396 MET cc_start: 0.5721 (tpt) cc_final: 0.5044 (tpp) REVERT: C 890 GLU cc_start: 0.8094 (tp30) cc_final: 0.7706 (tp30) REVERT: C 967 LEU cc_start: 0.8987 (mt) cc_final: 0.8704 (tt) REVERT: C 1003 TYR cc_start: 0.7188 (OUTLIER) cc_final: 0.6893 (m-80) REVERT: D 35 GLU cc_start: 0.8045 (pp20) cc_final: 0.7656 (tp30) REVERT: D 65 LYS cc_start: 0.7887 (mmmt) cc_final: 0.6987 (tptp) REVERT: D 68 GLU cc_start: 0.7499 (tp30) cc_final: 0.7091 (tm-30) REVERT: D 106 ASP cc_start: 0.8310 (p0) cc_final: 0.7988 (p0) REVERT: D 218 TYR cc_start: 0.7135 (OUTLIER) cc_final: 0.5686 (t80) REVERT: D 455 TYR cc_start: 0.6661 (OUTLIER) cc_final: 0.6053 (m-10) REVERT: D 567 SER cc_start: 0.9000 (OUTLIER) cc_final: 0.8615 (m) REVERT: D 721 TYR cc_start: 0.7011 (t80) cc_final: 0.6441 (t80) REVERT: D 753 LYS cc_start: 0.8086 (mmtp) cc_final: 0.7412 (mmmt) REVERT: D 835 ILE cc_start: 0.6549 (mt) cc_final: 0.6228 (mt) REVERT: D 844 LEU cc_start: 0.6061 (mp) cc_final: 0.5252 (tp) REVERT: D 936 MET cc_start: 0.8193 (mmp) cc_final: 0.7938 (mmm) REVERT: E 37 SER cc_start: 0.5697 (OUTLIER) cc_final: 0.5112 (p) REVERT: E 73 LEU cc_start: 0.8441 (tp) cc_final: 0.8188 (pp) REVERT: E 206 MET cc_start: 0.3521 (ptt) cc_final: 0.3248 (ptt) REVERT: F 195 PHE cc_start: 0.7946 (m-10) cc_final: 0.7625 (m-80) REVERT: F 223 LEU cc_start: 0.7904 (mt) cc_final: 0.7165 (mt) outliers start: 117 outliers final: 94 residues processed: 632 average time/residue: 0.2454 time to fit residues: 254.7129 Evaluate side-chains 636 residues out of total 4131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 533 time to evaluate : 1.840 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 PHE Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 130 ILE Chi-restraints excluded: chain A residue 131 THR Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 360 PHE Chi-restraints excluded: chain A residue 454 LEU Chi-restraints excluded: chain A residue 485 ILE Chi-restraints excluded: chain A residue 515 ILE Chi-restraints excluded: chain A residue 519 MET Chi-restraints excluded: chain A residue 541 ILE Chi-restraints excluded: chain A residue 588 LEU Chi-restraints excluded: chain A residue 649 TYR Chi-restraints excluded: chain A residue 671 CYS Chi-restraints excluded: chain A residue 919 TRP Chi-restraints excluded: chain A residue 987 ARG Chi-restraints excluded: chain B residue 132 THR Chi-restraints excluded: chain B residue 134 TYR Chi-restraints excluded: chain B residue 143 TRP Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain B residue 251 SER Chi-restraints excluded: chain B residue 283 LEU Chi-restraints excluded: chain B residue 310 ASP Chi-restraints excluded: chain B residue 361 PHE Chi-restraints excluded: chain B residue 391 ASN Chi-restraints excluded: chain B residue 445 LEU Chi-restraints excluded: chain B residue 459 ILE Chi-restraints excluded: chain B residue 518 GLU Chi-restraints excluded: chain B residue 519 MET Chi-restraints excluded: chain B residue 524 ILE Chi-restraints excluded: chain B residue 528 PHE Chi-restraints excluded: chain B residue 558 LEU Chi-restraints excluded: chain B residue 583 VAL Chi-restraints excluded: chain B residue 649 TYR Chi-restraints excluded: chain B residue 654 ASN Chi-restraints excluded: chain B residue 676 ILE Chi-restraints excluded: chain B residue 845 LEU Chi-restraints excluded: chain B residue 862 ILE Chi-restraints excluded: chain B residue 1005 ILE Chi-restraints excluded: chain C residue 45 PHE Chi-restraints excluded: chain C residue 82 ASP Chi-restraints excluded: chain C residue 104 LEU Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 134 TYR Chi-restraints excluded: chain C residue 213 ILE Chi-restraints excluded: chain C residue 218 TYR Chi-restraints excluded: chain C residue 225 ILE Chi-restraints excluded: chain C residue 236 GLN Chi-restraints excluded: chain C residue 260 TYR Chi-restraints excluded: chain C residue 325 ILE Chi-restraints excluded: chain C residue 346 VAL Chi-restraints excluded: chain C residue 347 VAL Chi-restraints excluded: chain C residue 474 SER Chi-restraints excluded: chain C residue 495 LEU Chi-restraints excluded: chain C residue 600 LEU Chi-restraints excluded: chain C residue 664 ILE Chi-restraints excluded: chain C residue 744 PHE Chi-restraints excluded: chain C residue 827 LEU Chi-restraints excluded: chain C residue 862 ILE Chi-restraints excluded: chain C residue 978 HIS Chi-restraints excluded: chain C residue 1003 TYR Chi-restraints excluded: chain D residue 101 ASP Chi-restraints excluded: chain D residue 107 PHE Chi-restraints excluded: chain D residue 134 TYR Chi-restraints excluded: chain D residue 213 ILE Chi-restraints excluded: chain D residue 214 VAL Chi-restraints excluded: chain D residue 216 ILE Chi-restraints excluded: chain D residue 218 TYR Chi-restraints excluded: chain D residue 232 VAL Chi-restraints excluded: chain D residue 280 TYR Chi-restraints excluded: chain D residue 342 VAL Chi-restraints excluded: chain D residue 347 VAL Chi-restraints excluded: chain D residue 360 PHE Chi-restraints excluded: chain D residue 396 MET Chi-restraints excluded: chain D residue 421 MET Chi-restraints excluded: chain D residue 445 LEU Chi-restraints excluded: chain D residue 455 TYR Chi-restraints excluded: chain D residue 556 VAL Chi-restraints excluded: chain D residue 567 SER Chi-restraints excluded: chain D residue 595 LEU Chi-restraints excluded: chain D residue 618 LEU Chi-restraints excluded: chain D residue 661 ILE Chi-restraints excluded: chain D residue 810 HIS Chi-restraints excluded: chain D residue 885 ILE Chi-restraints excluded: chain D residue 916 PHE Chi-restraints excluded: chain D residue 966 LEU Chi-restraints excluded: chain D residue 967 LEU Chi-restraints excluded: chain D residue 995 ARG Chi-restraints excluded: chain E residue 8 THR Chi-restraints excluded: chain E residue 37 SER Chi-restraints excluded: chain E residue 50 LEU Chi-restraints excluded: chain E residue 51 TYR Chi-restraints excluded: chain E residue 173 VAL Chi-restraints excluded: chain E residue 214 LEU Chi-restraints excluded: chain E residue 218 ILE Chi-restraints excluded: chain F residue 187 VAL Chi-restraints excluded: chain F residue 234 VAL Chi-restraints excluded: chain G residue 173 VAL Chi-restraints excluded: chain H residue 62 THR Chi-restraints excluded: chain H residue 67 PHE Chi-restraints excluded: chain H residue 187 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 449 random chunks: chunk 426 optimal weight: 4.9990 chunk 439 optimal weight: 10.0000 chunk 123 optimal weight: 0.7980 chunk 256 optimal weight: 0.6980 chunk 85 optimal weight: 0.0470 chunk 222 optimal weight: 6.9990 chunk 339 optimal weight: 0.9990 chunk 418 optimal weight: 9.9990 chunk 157 optimal weight: 0.2980 chunk 330 optimal weight: 0.0980 chunk 83 optimal weight: 10.0000 overall best weight: 0.3878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 118 HIS ** A 323 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 563 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 765 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 332 HIS ** B 477 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 536 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 654 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 224 ASN C 491 GLN ** D 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 598 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 197 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4559 r_free = 0.4559 target = 0.163793 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4126 r_free = 0.4126 target = 0.134640 restraints weight = 101147.772| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4100 r_free = 0.4100 target = 0.133862 restraints weight = 74559.708| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4112 r_free = 0.4112 target = 0.134737 restraints weight = 54204.793| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4118 r_free = 0.4118 target = 0.135161 restraints weight = 48928.043| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4124 r_free = 0.4124 target = 0.135543 restraints weight = 44155.330| |-----------------------------------------------------------------------------| r_work (final): 0.4115 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6483 moved from start: 0.4838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 38404 Z= 0.133 Angle : 0.716 19.038 51760 Z= 0.356 Chirality : 0.043 0.283 5510 Planarity : 0.004 0.076 6633 Dihedral : 5.031 72.212 4991 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 14.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 2.54 % Allowed : 25.76 % Favored : 71.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.11 (0.12), residues: 4508 helix: 0.78 (0.10), residues: 2628 sheet: -1.26 (0.29), residues: 282 loop : -1.21 (0.15), residues: 1598 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 175 TYR 0.055 0.002 TYR G 51 PHE 0.064 0.002 PHE D 916 TRP 0.060 0.003 TRP A 231 HIS 0.008 0.001 HIS B 978 Details of bonding type rmsd covalent geometry : bond 0.00295 (38404) covalent geometry : angle 0.71555 (51760) hydrogen bonds : bond 0.03900 ( 1996) hydrogen bonds : angle 4.94933 ( 5793) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9016 Ramachandran restraints generated. 4508 Oldfield, 0 Emsley, 4508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9016 Ramachandran restraints generated. 4508 Oldfield, 0 Emsley, 4508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 680 residues out of total 4131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 575 time to evaluate : 1.549 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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: 0.7555 (tmm) cc_final: 0.7074 (tmm) REVERT: A 334 PHE cc_start: 0.5515 (m-80) cc_final: 0.5005 (m-80) REVERT: A 368 ASP cc_start: 0.8868 (t70) cc_final: 0.8463 (p0) REVERT: A 487 GLN cc_start: 0.6160 (mt0) cc_final: 0.5668 (pt0) REVERT: A 597 GLU cc_start: 0.7803 (mm-30) cc_final: 0.6621 (mt-10) REVERT: A 647 MET cc_start: 0.1104 (mmt) cc_final: 0.0594 (mmt) REVERT: A 873 LEU cc_start: 0.8071 (tp) cc_final: 0.7826 (tt) REVERT: A 930 MET cc_start: 0.3816 (ttt) cc_final: 0.3519 (ttt) REVERT: A 954 PHE cc_start: 0.8320 (t80) cc_final: 0.7849 (t80) REVERT: A 995 ARG cc_start: 0.8894 (mmm160) cc_final: 0.8547 (mmm160) REVERT: B 35 GLU cc_start: 0.5758 (tp30) cc_final: 0.5470 (mt-10) REVERT: B 70 LEU cc_start: 0.7430 (mt) cc_final: 0.7177 (mt) REVERT: B 124 MET cc_start: 0.7235 (mmp) cc_final: 0.6968 (mmp) REVERT: B 218 TYR cc_start: 0.5003 (m-80) cc_final: 0.4720 (m-80) REVERT: B 227 MET cc_start: 0.4919 (mtm) cc_final: 0.4665 (ttp) REVERT: B 283 LEU cc_start: 0.8380 (OUTLIER) cc_final: 0.7904 (tt) REVERT: B 391 ASN cc_start: 0.5404 (OUTLIER) cc_final: 0.5123 (m-40) REVERT: B 421 MET cc_start: 0.6236 (ttm) cc_final: 0.5855 (ttm) REVERT: B 445 LEU cc_start: 0.8654 (OUTLIER) cc_final: 0.8233 (tp) REVERT: B 482 TYR cc_start: 0.7370 (t80) cc_final: 0.6890 (t80) REVERT: B 536 GLN cc_start: 0.8914 (pp30) cc_final: 0.8193 (tp40) REVERT: B 593 ARG cc_start: 0.7139 (ttt90) cc_final: 0.6670 (ttt90) REVERT: B 929 LYS cc_start: 0.9356 (mmmt) cc_final: 0.9050 (tppt) REVERT: B 960 LYS cc_start: 0.8387 (pttt) cc_final: 0.8088 (ptpt) REVERT: B 963 ASN cc_start: 0.7515 (m110) cc_final: 0.7188 (t0) REVERT: B 976 MET cc_start: 0.3588 (ptt) cc_final: 0.2571 (ppp) REVERT: C 61 ARG cc_start: 0.8157 (mtt180) cc_final: 0.7873 (ptt-90) REVERT: C 200 ILE cc_start: 0.7763 (mm) cc_final: 0.7388 (mm) REVERT: C 396 MET cc_start: 0.5523 (tpt) cc_final: 0.4996 (tpp) REVERT: C 757 TRP cc_start: 0.7052 (m-10) cc_final: 0.6426 (m-10) REVERT: C 890 GLU cc_start: 0.8174 (tp30) cc_final: 0.7781 (tp30) REVERT: C 967 LEU cc_start: 0.8992 (mt) cc_final: 0.8736 (tt) REVERT: C 1003 TYR cc_start: 0.7201 (OUTLIER) cc_final: 0.6950 (m-80) REVERT: D 39 ASN cc_start: 0.7585 (p0) cc_final: 0.7084 (t0) REVERT: D 65 LYS cc_start: 0.7847 (mmmt) cc_final: 0.6796 (tptp) REVERT: D 68 GLU cc_start: 0.7526 (tp30) cc_final: 0.7080 (tm-30) REVERT: D 69 GLU cc_start: 0.7745 (mp0) cc_final: 0.7028 (mp0) REVERT: D 106 ASP cc_start: 0.8367 (p0) cc_final: 0.8062 (p0) REVERT: D 218 TYR cc_start: 0.7051 (OUTLIER) cc_final: 0.5599 (t80) REVERT: D 261 TYR cc_start: 0.7321 (m-80) cc_final: 0.7104 (m-80) REVERT: D 567 SER cc_start: 0.8911 (OUTLIER) cc_final: 0.8629 (m) REVERT: D 595 LEU cc_start: 0.7137 (OUTLIER) cc_final: 0.6732 (tp) REVERT: D 835 ILE cc_start: 0.6593 (mt) cc_final: 0.6280 (mt) REVERT: D 844 LEU cc_start: 0.6099 (mp) cc_final: 0.5303 (tp) REVERT: D 936 MET cc_start: 0.8243 (mmp) cc_final: 0.8006 (mmm) REVERT: E 37 SER cc_start: 0.5787 (OUTLIER) cc_final: 0.5242 (p) REVERT: E 73 LEU cc_start: 0.8525 (tp) cc_final: 0.8217 (pp) REVERT: E 206 MET cc_start: 0.3098 (ptt) cc_final: 0.2817 (ptt) REVERT: F 183 ASP cc_start: 0.5238 (p0) cc_final: 0.4378 (m-30) REVERT: F 195 PHE cc_start: 0.8084 (m-10) cc_final: 0.7743 (m-80) REVERT: F 223 LEU cc_start: 0.8006 (mt) cc_final: 0.7271 (mt) REVERT: H 34 GLN cc_start: 0.8152 (pm20) cc_final: 0.7743 (pm20) outliers start: 105 outliers final: 82 residues processed: 633 average time/residue: 0.2434 time to fit residues: 254.4467 Evaluate side-chains 632 residues out of total 4131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 542 time to evaluate : 1.583 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 PHE Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 130 ILE Chi-restraints excluded: chain A residue 131 THR Chi-restraints excluded: chain A residue 134 TYR Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 360 PHE Chi-restraints excluded: chain A residue 395 CYS Chi-restraints excluded: chain A residue 485 ILE Chi-restraints excluded: chain A residue 515 ILE Chi-restraints excluded: chain A residue 519 MET Chi-restraints excluded: chain A residue 541 ILE Chi-restraints excluded: chain A residue 588 LEU Chi-restraints excluded: chain A residue 671 CYS Chi-restraints excluded: chain A residue 919 TRP Chi-restraints excluded: chain A residue 987 ARG Chi-restraints excluded: chain B residue 132 THR Chi-restraints excluded: chain B residue 134 TYR Chi-restraints excluded: chain B residue 143 TRP Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain B residue 251 SER Chi-restraints excluded: chain B residue 283 LEU Chi-restraints excluded: chain B residue 310 ASP Chi-restraints excluded: chain B residue 391 ASN Chi-restraints excluded: chain B residue 445 LEU Chi-restraints excluded: chain B residue 459 ILE Chi-restraints excluded: chain B residue 518 GLU Chi-restraints excluded: chain B residue 528 PHE Chi-restraints excluded: chain B residue 558 LEU Chi-restraints excluded: chain B residue 583 VAL Chi-restraints excluded: chain B residue 654 ASN Chi-restraints excluded: chain B residue 845 LEU Chi-restraints excluded: chain B residue 862 ILE Chi-restraints excluded: chain B residue 1005 ILE Chi-restraints excluded: chain C residue 45 PHE Chi-restraints excluded: chain C residue 82 ASP Chi-restraints excluded: chain C residue 104 LEU Chi-restraints excluded: chain C residue 118 HIS Chi-restraints excluded: chain C residue 134 TYR Chi-restraints excluded: chain C residue 218 TYR Chi-restraints excluded: chain C residue 224 ASN Chi-restraints excluded: chain C residue 225 ILE Chi-restraints excluded: chain C residue 236 GLN Chi-restraints excluded: chain C residue 260 TYR Chi-restraints excluded: chain C residue 325 ILE Chi-restraints excluded: chain C residue 346 VAL Chi-restraints excluded: chain C residue 347 VAL Chi-restraints excluded: chain C residue 600 LEU Chi-restraints excluded: chain C residue 664 ILE Chi-restraints excluded: chain C residue 744 PHE Chi-restraints excluded: chain C residue 827 LEU Chi-restraints excluded: chain C residue 862 ILE Chi-restraints excluded: chain C residue 978 HIS Chi-restraints excluded: chain C residue 1003 TYR Chi-restraints excluded: chain D residue 101 ASP Chi-restraints excluded: chain D residue 107 PHE Chi-restraints excluded: chain D residue 134 TYR Chi-restraints excluded: chain D residue 213 ILE Chi-restraints excluded: chain D residue 214 VAL Chi-restraints excluded: chain D residue 216 ILE Chi-restraints excluded: chain D residue 218 TYR Chi-restraints excluded: chain D residue 280 TYR Chi-restraints excluded: chain D residue 342 VAL Chi-restraints excluded: chain D residue 347 VAL Chi-restraints excluded: chain D residue 396 MET Chi-restraints excluded: chain D residue 421 MET Chi-restraints excluded: chain D residue 445 LEU Chi-restraints excluded: chain D residue 556 VAL Chi-restraints excluded: chain D residue 567 SER Chi-restraints excluded: chain D residue 595 LEU Chi-restraints excluded: chain D residue 661 ILE Chi-restraints excluded: chain D residue 810 HIS Chi-restraints excluded: chain D residue 885 ILE Chi-restraints excluded: chain D residue 916 PHE Chi-restraints excluded: chain D residue 966 LEU Chi-restraints excluded: chain D residue 995 ARG Chi-restraints excluded: chain E residue 8 THR Chi-restraints excluded: chain E residue 37 SER Chi-restraints excluded: chain E residue 50 LEU Chi-restraints excluded: chain E residue 51 TYR Chi-restraints excluded: chain E residue 173 VAL Chi-restraints excluded: chain E residue 175 TYR Chi-restraints excluded: chain E residue 214 LEU Chi-restraints excluded: chain E residue 218 ILE Chi-restraints excluded: chain F residue 187 VAL Chi-restraints excluded: chain F residue 234 VAL Chi-restraints excluded: chain H residue 62 THR Chi-restraints excluded: chain H residue 67 PHE Chi-restraints excluded: chain H residue 187 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 449 random chunks: chunk 417 optimal weight: 1.9990 chunk 275 optimal weight: 4.9990 chunk 205 optimal weight: 0.9990 chunk 309 optimal weight: 0.9980 chunk 404 optimal weight: 6.9990 chunk 73 optimal weight: 7.9990 chunk 390 optimal weight: 2.9990 chunk 64 optimal weight: 5.9990 chunk 357 optimal weight: 0.9980 chunk 61 optimal weight: 2.9990 chunk 262 optimal weight: 0.8980 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 118 HIS ** A 323 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 491 GLN ** A 563 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 610 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 765 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 224 ASN ** B 477 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 536 GLN ** B 654 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 978 HIS ** C 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 224 ASN C 477 ASN ** D 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 598 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4530 r_free = 0.4530 target = 0.162088 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4088 r_free = 0.4088 target = 0.132174 restraints weight = 103665.765| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.4053 r_free = 0.4053 target = 0.131526 restraints weight = 82442.009| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4066 r_free = 0.4066 target = 0.132348 restraints weight = 62177.739| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4074 r_free = 0.4074 target = 0.132869 restraints weight = 53474.008| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4079 r_free = 0.4079 target = 0.133145 restraints weight = 47131.655| |-----------------------------------------------------------------------------| r_work (final): 0.4067 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6570 moved from start: 0.5026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 38404 Z= 0.163 Angle : 0.729 16.269 51760 Z= 0.366 Chirality : 0.044 0.280 5510 Planarity : 0.004 0.074 6633 Dihedral : 5.096 73.778 4991 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 15.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 2.52 % Allowed : 26.36 % Favored : 71.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.18 (0.12), residues: 4508 helix: 0.74 (0.10), residues: 2639 sheet: -1.31 (0.28), residues: 299 loop : -1.28 (0.15), residues: 1570 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 175 TYR 0.035 0.002 TYR B 313 PHE 0.063 0.002 PHE D 916 TRP 0.058 0.003 TRP A 231 HIS 0.008 0.001 HIS A 503 Details of bonding type rmsd covalent geometry : bond 0.00375 (38404) covalent geometry : angle 0.72943 (51760) hydrogen bonds : bond 0.04016 ( 1996) hydrogen bonds : angle 5.00102 ( 5793) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7741.10 seconds wall clock time: 135 minutes 37.92 seconds (8137.92 seconds total)