Starting phenix.real_space_refine on Sat Sep 28 02:53:22 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7q4w_13819/09_2024/7q4w_13819_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7q4w_13819/09_2024/7q4w_13819.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.78 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7q4w_13819/09_2024/7q4w_13819.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7q4w_13819/09_2024/7q4w_13819.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7q4w_13819/09_2024/7q4w_13819_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7q4w_13819/09_2024/7q4w_13819_neut.cif" } resolution = 3.78 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.020 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: 7 Type Number sf(0) Gaussians Fe 64 7.16 5 Zn 2 6.06 5 P 2 5.49 5 S 210 5.16 5 C 11256 2.51 5 N 3040 2.21 5 O 3476 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 32 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 18050 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 4442 Number of conformers: 1 Conformer: "" Number of residues, atoms: 583, 4442 Classifications: {'peptide': 583} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 24, 'TRANS': 556} Chain: "B" Number of atoms: 3513 Number of conformers: 1 Conformer: "" Number of residues, atoms: 470, 3513 Classifications: {'peptide': 470} Link IDs: {'PCIS': 2, 'PTRANS': 22, 'TRANS': 445} Chain: "C" Number of atoms: 974 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 974 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 5, 'TRANS': 123} Chain: "E" Number of atoms: 4442 Number of conformers: 1 Conformer: "" Number of residues, atoms: 583, 4442 Classifications: {'peptide': 583} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 24, 'TRANS': 556} Chain: "F" Number of atoms: 3513 Number of conformers: 1 Conformer: "" Number of residues, atoms: 470, 3513 Classifications: {'peptide': 470} Link IDs: {'PCIS': 2, 'PTRANS': 22, 'TRANS': 445} Chain: "G" Number of atoms: 974 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 974 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 5, 'TRANS': 123} Chain: "A" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 36 Unusual residues: {'FES': 1, 'SF4': 4} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "B" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 56 Unusual residues: {' ZN': 1, 'FMN': 1, 'SF4': 3} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "C" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Unusual residues: {'FES': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 36 Unusual residues: {'FES': 1, 'SF4': 4} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "F" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 56 Unusual residues: {' ZN': 1, 'FMN': 1, 'SF4': 3} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "G" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Unusual residues: {'FES': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2683 SG CYS A 356 79.040 90.185 93.283 1.00 55.53 S ATOM 3823 SG CYS A 506 77.735 90.226 97.939 1.00 64.09 S ATOM 3802 SG CYS A 502 73.922 90.559 92.187 1.00 56.24 S ATOM 1444 SG CYS A 191 73.999 92.678 81.096 1.00 58.82 S ATOM 1485 SG CYS A 197 70.594 87.726 82.732 1.00 46.23 S ATOM 1204 SG CYS A 158 67.282 93.300 82.072 1.00 53.68 S ATOM 1466 SG CYS A 194 70.774 90.566 85.880 1.00 57.00 S ATOM 1152 SG CYS A 151 61.454 81.748 80.542 1.00 45.67 S ATOM 1515 SG CYS A 201 66.034 80.332 80.970 1.00 42.42 S ATOM 1178 SG CYS A 154 64.476 86.208 79.277 1.00 46.25 S ATOM 1130 SG CYS A 148 63.768 81.841 75.123 1.00 49.38 S ATOM 838 SG CYS A 109 65.558 71.895 81.176 1.00 48.08 S ATOM 770 SG CYS A 100 67.521 67.832 77.363 1.00 50.11 S ATOM 790 SG CYS A 103 70.505 71.498 77.247 1.00 52.29 S ATOM 770 SG CYS A 100 67.521 67.832 77.363 1.00 50.11 S ATOM 388 SG CYS A 50 48.406 76.625 85.093 1.00 61.80 S ATOM 483 SG CYS A 64 49.269 80.222 84.605 1.00 64.13 S ATOM 278 SG CYS A 36 53.538 80.774 82.738 1.00 53.01 S ATOM 363 SG CYS A 47 52.218 77.522 82.373 1.00 48.25 S ATOM 6897 SG CYS B 457 48.632 86.075 70.216 1.00 62.38 S ATOM 6936 SG CYS B 463 47.935 81.601 67.007 1.00 56.06 S ATOM 7240 SG CYS B 503 44.577 85.172 70.074 1.00 64.70 S ATOM 6916 SG CYS B 460 48.459 79.616 72.158 1.00 51.09 S ATOM 7833 SG CYS B 581 56.724 69.157 32.886 1.00 96.97 S ATOM 7871 SG CYS B 587 53.156 72.787 28.796 1.00 94.54 S ATOM 7683 SG CYS B 561 59.571 72.030 28.339 1.00100.77 S ATOM 7856 SG CYS B 584 56.849 75.770 32.873 1.00100.46 S ATOM 7617 SG CYS B 551 49.740 69.848 18.940 1.00 97.09 S ATOM 7636 SG CYS B 554 52.193 75.709 17.222 1.00107.48 S ATOM 7654 SG CYS B 557 54.219 72.509 22.697 1.00104.75 S ATOM 7899 SG CYS B 591 48.034 74.479 21.571 1.00103.75 S ATOM 6757 SG CYS B 440 42.441 69.935 45.479 1.00 89.10 S ATOM 7483 SG CYS B 533 43.684 69.354 41.950 1.00 88.06 S ATOM 7512 SG CYS B 538 46.244 69.774 44.748 1.00 89.45 S ATOM 8603 SG CYS C 83 41.668 91.737 48.133 1.00 97.37 S ATOM 8633 SG CYS C 88 40.266 90.083 45.292 1.00 95.83 S ATOM 8603 SG CYS C 83 41.668 91.737 48.133 1.00 97.37 S ATOM 8903 SG CYS C 124 40.591 90.906 52.054 1.00101.39 S ATOM 8925 SG CYS C 128 37.542 91.672 49.523 1.00101.71 S ATOM 11612 SG CYS E 356 57.539 38.415 93.280 1.00 56.31 S ATOM 12731 SG CYS E 502 63.824 38.360 91.937 1.00 59.65 S ATOM 12752 SG CYS E 506 59.645 37.905 97.332 1.00 62.85 S ATOM 10373 SG CYS E 191 63.317 35.965 81.111 1.00 58.14 S ATOM 10414 SG CYS E 197 66.681 40.885 82.717 1.00 42.71 S ATOM 10133 SG CYS E 158 70.056 35.357 82.069 1.00 53.12 S ATOM 10395 SG CYS E 194 66.500 38.029 85.864 1.00 54.95 S ATOM 10107 SG CYS E 154 72.923 42.305 79.323 1.00 46.62 S ATOM 10081 SG CYS E 151 75.809 46.879 80.398 1.00 44.48 S ATOM 10081 SG CYS E 151 75.809 46.879 80.398 1.00 44.48 S ATOM 10444 SG CYS E 201 71.314 48.145 80.951 1.00 42.88 S ATOM 10059 SG CYS E 148 73.505 47.136 75.737 1.00 43.49 S ATOM 9767 SG CYS E 109 71.644 56.708 81.174 1.00 51.46 S ATOM 9699 SG CYS E 100 69.893 60.756 77.391 1.00 51.64 S ATOM 9719 SG CYS E 103 66.799 57.272 77.345 1.00 54.06 S ATOM 9719 SG CYS E 103 66.799 57.272 77.345 1.00 54.06 S ATOM 9699 SG CYS E 100 69.893 60.756 77.391 1.00 51.64 S ATOM 9317 SG CYS E 50 88.769 51.938 84.969 1.00 60.84 S ATOM 9412 SG CYS E 64 88.309 48.294 84.576 1.00 61.26 S ATOM 9207 SG CYS E 36 83.846 48.023 82.540 1.00 49.64 S ATOM 9292 SG CYS E 47 84.943 51.153 82.129 1.00 47.40 S ATOM 15686 SG CYS F 440 94.911 58.469 45.547 1.00 89.41 S ATOM 16412 SG CYS F 533 93.827 59.304 41.991 1.00 87.24 S ATOM 16441 SG CYS F 538 91.185 58.897 44.728 1.00 89.17 S ATOM 15826 SG CYS F 457 88.368 42.042 70.196 1.00 65.19 S ATOM 15865 SG CYS F 463 89.855 47.154 67.353 1.00 56.65 S ATOM 16169 SG CYS F 503 92.265 45.829 69.665 1.00 61.81 S ATOM 16169 SG CYS F 503 92.265 45.829 69.665 1.00 61.81 S ATOM 15845 SG CYS F 460 89.106 48.686 72.453 1.00 52.66 S ATOM 16800 SG CYS F 587 84.133 55.696 28.595 1.00 95.36 S ATOM 16612 SG CYS F 561 77.752 56.485 28.341 1.00 99.39 S ATOM 16762 SG CYS F 581 80.533 60.007 31.186 1.00 97.30 S ATOM 16785 SG CYS F 584 80.550 53.032 32.871 1.00101.57 S ATOM 16546 SG CYS F 551 87.521 58.656 18.842 1.00 95.75 S ATOM 16565 SG CYS F 554 84.861 52.554 17.502 1.00104.67 S ATOM 16583 SG CYS F 557 82.970 56.060 22.563 1.00102.59 S ATOM 16828 SG CYS F 591 89.213 54.093 21.456 1.00101.45 S ATOM 17532 SG CYS G 83 94.538 35.891 46.980 1.00 99.48 S ATOM 17562 SG CYS G 88 96.098 39.506 47.359 1.00101.65 S ATOM 17832 SG CYS G 124 97.571 37.144 51.621 1.00104.15 S ATOM 17854 SG CYS G 128 99.407 36.839 48.344 1.00100.22 S Time building chain proxies: 10.20, per 1000 atoms: 0.57 Number of scatterers: 18050 At special positions: 0 Unit cell: (138.43, 129.71, 130.8, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 2 29.99 Fe 64 26.01 S 210 16.00 P 2 15.00 O 3476 8.00 N 3040 7.00 C 11256 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: 4.28 Conformation dependent library (CDL) restraints added in 2.3 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" FES A 605 " pdb="FE2 FES A 605 " - pdb=" SG CYS A 47 " pdb="FE1 FES A 605 " - pdb=" SG CYS A 50 " pdb="FE1 FES A 605 " - pdb=" SG CYS A 64 " pdb="FE2 FES A 605 " - pdb=" SG CYS A 36 " pdb=" FES C 201 " pdb="FE1 FES C 201 " - pdb=" SG CYS C 83 " pdb="FE1 FES C 201 " - pdb=" SG CYS C 88 " pdb="FE2 FES C 201 " - pdb=" SG CYS C 128 " pdb="FE2 FES C 201 " - pdb=" SG CYS C 124 " pdb=" FES E 605 " pdb="FE2 FES E 605 " - pdb=" SG CYS E 47 " pdb="FE1 FES E 605 " - pdb=" SG CYS E 50 " pdb="FE1 FES E 605 " - pdb=" SG CYS E 64 " pdb="FE2 FES E 605 " - pdb=" SG CYS E 36 " pdb=" FES G 201 " pdb="FE2 FES G 201 " - pdb=" SG CYS G 128 " pdb="FE1 FES G 201 " - pdb=" SG CYS G 88 " pdb="FE1 FES G 201 " - pdb=" SG CYS G 83 " pdb="FE2 FES G 201 " - pdb=" SG CYS G 124 " pdb=" SF4 A 601 " pdb="FE3 SF4 A 601 " - pdb=" SG CYS A 506 " pdb="FE1 SF4 A 601 " - pdb=" SG CYS A 356 " pdb="FE4 SF4 A 601 " - pdb=" SG CYS A 502 " pdb="FE2 SF4 A 601 " - pdb=" SD MET A 500 " pdb=" SF4 A 602 " pdb="FE4 SF4 A 602 " - pdb=" SG CYS A 194 " pdb="FE2 SF4 A 602 " - pdb=" SG CYS A 197 " pdb="FE3 SF4 A 602 " - pdb=" SG CYS A 158 " pdb="FE1 SF4 A 602 " - pdb=" SG CYS A 191 " pdb=" SF4 A 603 " pdb="FE1 SF4 A 603 " - pdb=" SG CYS A 151 " pdb="FE2 SF4 A 603 " - pdb=" SG CYS A 201 " pdb="FE4 SF4 A 603 " - pdb=" SG CYS A 148 " pdb="FE3 SF4 A 603 " - pdb=" SG CYS A 154 " pdb=" SF4 A 604 " pdb="FE4 SF4 A 604 " - pdb=" NE2 HIS A 96 " pdb="FE1 SF4 A 604 " - pdb=" SG CYS A 109 " pdb="FE2 SF4 A 604 " - pdb=" SG CYS A 100 " pdb="FE3 SF4 A 604 " - pdb=" SG CYS A 103 " pdb=" SF4 B 602 " pdb="FE2 SF4 B 602 " - pdb=" SG CYS B 463 " pdb="FE1 SF4 B 602 " - pdb=" SG CYS B 457 " pdb="FE4 SF4 B 602 " - pdb=" SG CYS B 460 " pdb="FE3 SF4 B 602 " - pdb=" SG CYS B 503 " pdb=" SF4 B 603 " pdb="FE4 SF4 B 603 " - pdb=" SG CYS B 584 " pdb="FE2 SF4 B 603 " - pdb=" SG CYS B 587 " pdb="FE3 SF4 B 603 " - pdb=" SG CYS B 561 " pdb="FE1 SF4 B 603 " - pdb=" SG CYS B 581 " pdb=" SF4 B 604 " pdb="FE2 SF4 B 604 " - pdb=" SG CYS B 554 " pdb="FE1 SF4 B 604 " - pdb=" SG CYS B 551 " pdb="FE3 SF4 B 604 " - pdb=" SG CYS B 557 " pdb="FE4 SF4 B 604 " - pdb=" SG CYS B 591 " pdb=" SF4 E 601 " pdb="FE2 SF4 E 601 " - pdb=" SG CYS E 356 " pdb="FE3 SF4 E 601 " - pdb=" SG CYS E 502 " pdb="FE4 SF4 E 601 " - pdb=" SG CYS E 506 " pdb=" SF4 E 602 " pdb="FE4 SF4 E 602 " - pdb=" SG CYS E 194 " pdb="FE2 SF4 E 602 " - pdb=" SG CYS E 197 " pdb="FE3 SF4 E 602 " - pdb=" SG CYS E 158 " pdb="FE1 SF4 E 602 " - pdb=" SG CYS E 191 " pdb=" SF4 E 603 " pdb="FE3 SF4 E 603 " - pdb=" SG CYS E 201 " pdb="FE2 SF4 E 603 " - pdb=" SG CYS E 151 " pdb="FE4 SF4 E 603 " - pdb=" SG CYS E 148 " pdb="FE1 SF4 E 603 " - pdb=" SG CYS E 154 " pdb=" SF4 E 604 " pdb="FE4 SF4 E 604 " - pdb=" NE2 HIS E 96 " pdb="FE1 SF4 E 604 " - pdb=" SG CYS E 109 " pdb="FE2 SF4 E 604 " - pdb=" SG CYS E 100 " pdb="FE3 SF4 E 604 " - pdb=" SG CYS E 103 " pdb=" SF4 F 603 " pdb="FE3 SF4 F 603 " - pdb=" SG CYS F 503 " pdb="FE1 SF4 F 603 " - pdb=" SG CYS F 457 " pdb="FE4 SF4 F 603 " - pdb=" SG CYS F 460 " pdb="FE2 SF4 F 603 " - pdb=" SG CYS F 463 " pdb=" SF4 F 604 " pdb="FE1 SF4 F 604 " - pdb=" SG CYS F 587 " pdb="FE4 SF4 F 604 " - pdb=" SG CYS F 584 " pdb="FE2 SF4 F 604 " - pdb=" SG CYS F 561 " pdb="FE3 SF4 F 604 " - pdb=" SG CYS F 581 " pdb=" SF4 F 605 " pdb="FE1 SF4 F 605 " - pdb=" SG CYS F 551 " pdb="FE2 SF4 F 605 " - pdb=" SG CYS F 554 " pdb="FE3 SF4 F 605 " - pdb=" SG CYS F 557 " pdb="FE4 SF4 F 605 " - pdb=" SG CYS F 591 " Number of angles added : 193 Zn2+ tetrahedral coordination pdb=" ZN B 605 " pdb="ZN ZN B 605 " - pdb=" NE2 HIS B 527 " pdb="ZN ZN B 605 " - pdb=" SG CYS B 533 " pdb="ZN ZN B 605 " - pdb=" SG CYS B 440 " pdb="ZN ZN B 605 " - pdb=" SG CYS B 538 " pdb=" ZN F 601 " pdb="ZN ZN F 601 " - pdb=" NE2 HIS F 527 " pdb="ZN ZN F 601 " - pdb=" SG CYS F 440 " pdb="ZN ZN F 601 " - pdb=" SG CYS F 533 " pdb="ZN ZN F 601 " - pdb=" SG CYS F 538 " Number of angles added : 6 4704 Ramachandran restraints generated. 2352 Oldfield, 0 Emsley, 2352 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4272 Finding SS restraints... Secondary structure from input PDB file: 122 helices and 22 sheets defined 51.2% alpha, 10.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.19 Creating SS restraints... Processing helix chain 'A' and resid 20 through 28 Processing helix chain 'A' and resid 78 through 94 removed outlier: 3.516A pdb=" N SER A 94 " --> pdb=" O GLU A 90 " (cutoff:3.500A) Processing helix chain 'A' and resid 105 through 108 Processing helix chain 'A' and resid 109 through 119 Processing helix chain 'A' and resid 152 through 160 Processing helix chain 'A' and resid 172 through 176 Processing helix chain 'A' and resid 180 through 184 removed outlier: 3.850A pdb=" N ASN A 183 " --> pdb=" O PRO A 180 " (cutoff:3.500A) Processing helix chain 'A' and resid 185 through 189 Processing helix chain 'A' and resid 195 through 201 removed outlier: 3.826A pdb=" N CYS A 201 " --> pdb=" O CYS A 197 " (cutoff:3.500A) Processing helix chain 'A' and resid 211 through 220 Processing helix chain 'A' and resid 237 through 243 removed outlier: 3.570A pdb=" N GLY A 243 " --> pdb=" O GLU A 240 " (cutoff:3.500A) Processing helix chain 'A' and resid 250 through 261 Processing helix chain 'A' and resid 269 through 291 Processing helix chain 'A' and resid 301 through 312 removed outlier: 3.772A pdb=" N ILE A 305 " --> pdb=" O SER A 301 " (cutoff:3.500A) Processing helix chain 'A' and resid 313 through 319 Proline residue: A 317 - end of helix Processing helix chain 'A' and resid 324 through 342 removed outlier: 3.741A pdb=" N TYR A 337 " --> pdb=" O LEU A 333 " (cutoff:3.500A) removed outlier: 4.673A pdb=" N ALA A 338 " --> pdb=" O LYS A 334 " (cutoff:3.500A) Processing helix chain 'A' and resid 344 through 346 No H-bonds generated for 'chain 'A' and resid 344 through 346' Processing helix chain 'A' and resid 357 through 364 removed outlier: 4.234A pdb=" N TYR A 361 " --> pdb=" O THR A 357 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N GLN A 364 " --> pdb=" O LYS A 360 " (cutoff:3.500A) Processing helix chain 'A' and resid 381 through 393 Processing helix chain 'A' and resid 395 through 399 removed outlier: 3.570A pdb=" N LYS A 398 " --> pdb=" O LEU A 395 " (cutoff:3.500A) Processing helix chain 'A' and resid 412 through 417 Processing helix chain 'A' and resid 422 through 438 Processing helix chain 'A' and resid 475 through 489 Processing helix chain 'A' and resid 505 through 509 Processing helix chain 'A' and resid 517 through 523 Processing helix chain 'A' and resid 524 through 539 Processing helix chain 'A' and resid 549 through 559 Processing helix chain 'A' and resid 565 through 573 Processing helix chain 'B' and resid 131 through 136 Processing helix chain 'B' and resid 140 through 150 removed outlier: 3.814A pdb=" N GLU B 144 " --> pdb=" O TYR B 140 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N LEU B 148 " --> pdb=" O GLU B 144 " (cutoff:3.500A) Processing helix chain 'B' and resid 151 through 163 removed outlier: 3.620A pdb=" N ILE B 156 " --> pdb=" O PRO B 152 " (cutoff:3.500A) Processing helix chain 'B' and resid 173 through 184 removed outlier: 3.691A pdb=" N PHE B 180 " --> pdb=" O LEU B 176 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ALA B 181 " --> pdb=" O LYS B 177 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ALA B 184 " --> pdb=" O PHE B 180 " (cutoff:3.500A) Processing helix chain 'B' and resid 205 through 214 removed outlier: 3.786A pdb=" N LEU B 211 " --> pdb=" O ASP B 207 " (cutoff:3.500A) Processing helix chain 'B' and resid 214 through 230 removed outlier: 3.682A pdb=" N VAL B 218 " --> pdb=" O ASP B 214 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N MET B 222 " --> pdb=" O VAL B 218 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ALA B 223 " --> pdb=" O ILE B 219 " (cutoff:3.500A) Processing helix chain 'B' and resid 242 through 260 Processing helix chain 'B' and resid 265 through 269 Processing helix chain 'B' and resid 283 through 287 Processing helix chain 'B' and resid 288 through 298 removed outlier: 3.882A pdb=" N MET B 293 " --> pdb=" O GLU B 289 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ASN B 294 " --> pdb=" O THR B 290 " (cutoff:3.500A) Processing helix chain 'B' and resid 314 through 318 Processing helix chain 'B' and resid 325 through 330 removed outlier: 3.987A pdb=" N ASN B 330 " --> pdb=" O GLU B 326 " (cutoff:3.500A) Processing helix chain 'B' and resid 330 through 338 Processing helix chain 'B' and resid 338 through 344 removed outlier: 3.653A pdb=" N PHE B 342 " --> pdb=" O GLY B 338 " (cutoff:3.500A) Processing helix chain 'B' and resid 375 through 382 removed outlier: 3.746A pdb=" N ILE B 379 " --> pdb=" O THR B 375 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ILE B 380 " --> pdb=" O LEU B 376 " (cutoff:3.500A) Processing helix chain 'B' and resid 387 through 391 Processing helix chain 'B' and resid 400 through 403 Processing helix chain 'B' and resid 409 through 411 No H-bonds generated for 'chain 'B' and resid 409 through 411' Processing helix chain 'B' and resid 416 through 423 removed outlier: 3.628A pdb=" N LEU B 420 " --> pdb=" O ASP B 416 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ILE B 421 " --> pdb=" O TYR B 417 " (cutoff:3.500A) Processing helix chain 'B' and resid 440 through 455 removed outlier: 3.557A pdb=" N VAL B 444 " --> pdb=" O CYS B 440 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N THR B 452 " --> pdb=" O PHE B 448 " (cutoff:3.500A) Processing helix chain 'B' and resid 460 through 479 removed outlier: 4.594A pdb=" N THR B 467 " --> pdb=" O CYS B 463 " (cutoff:3.500A) removed outlier: 4.709A pdb=" N LYS B 468 " --> pdb=" O ARG B 464 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N ILE B 473 " --> pdb=" O ARG B 469 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N LEU B 474 " --> pdb=" O MET B 470 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N GLU B 475 " --> pdb=" O LEU B 471 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N ARG B 476 " --> pdb=" O GLU B 472 " (cutoff:3.500A) Processing helix chain 'B' and resid 485 through 499 removed outlier: 3.665A pdb=" N LEU B 493 " --> pdb=" O ARG B 489 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N GLY B 496 " --> pdb=" O GLU B 492 " (cutoff:3.500A) Processing helix chain 'B' and resid 503 through 508 removed outlier: 3.724A pdb=" N GLN B 507 " --> pdb=" O CYS B 503 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N THR B 508 " --> pdb=" O GLY B 504 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 503 through 508' Processing helix chain 'B' and resid 510 through 520 removed outlier: 3.664A pdb=" N PHE B 519 " --> pdb=" O SER B 515 " (cutoff:3.500A) Processing helix chain 'B' and resid 520 through 529 removed outlier: 4.253A pdb=" N TYR B 524 " --> pdb=" O PHE B 520 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N GLU B 525 " --> pdb=" O ARG B 521 " (cutoff:3.500A) Processing helix chain 'B' and resid 555 through 560 Processing helix chain 'B' and resid 585 through 591 removed outlier: 4.103A pdb=" N GLU B 589 " --> pdb=" O GLY B 585 " (cutoff:3.500A) Processing helix chain 'C' and resid 10 through 20 Processing helix chain 'C' and resid 25 through 39 removed outlier: 4.668A pdb=" N GLN C 29 " --> pdb=" O GLY C 25 " (cutoff:3.500A) Processing helix chain 'C' and resid 42 through 54 removed outlier: 3.858A pdb=" N GLN C 46 " --> pdb=" O PRO C 42 " (cutoff:3.500A) Processing helix chain 'C' and resid 56 through 67 removed outlier: 4.612A pdb=" N VAL C 60 " --> pdb=" O PRO C 56 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N TYR C 67 " --> pdb=" O VAL C 63 " (cutoff:3.500A) Processing helix chain 'C' and resid 85 through 91 removed outlier: 3.754A pdb=" N ARG C 91 " --> pdb=" O ALA C 87 " (cutoff:3.500A) Processing helix chain 'C' and resid 92 through 105 removed outlier: 4.041A pdb=" N ILE C 96 " --> pdb=" O GLY C 92 " (cutoff:3.500A) Processing helix chain 'E' and resid 20 through 28 removed outlier: 3.659A pdb=" N ALA E 24 " --> pdb=" O THR E 20 " (cutoff:3.500A) Processing helix chain 'E' and resid 78 through 93 Processing helix chain 'E' and resid 105 through 108 Processing helix chain 'E' and resid 109 through 119 Processing helix chain 'E' and resid 152 through 160 Processing helix chain 'E' and resid 172 through 176 Processing helix chain 'E' and resid 180 through 184 removed outlier: 4.199A pdb=" N ASN E 183 " --> pdb=" O PRO E 180 " (cutoff:3.500A) Processing helix chain 'E' and resid 185 through 189 Processing helix chain 'E' and resid 195 through 201 removed outlier: 3.913A pdb=" N CYS E 201 " --> pdb=" O CYS E 197 " (cutoff:3.500A) Processing helix chain 'E' and resid 211 through 220 Processing helix chain 'E' and resid 238 through 243 removed outlier: 3.659A pdb=" N GLY E 243 " --> pdb=" O GLU E 240 " (cutoff:3.500A) Processing helix chain 'E' and resid 250 through 261 Processing helix chain 'E' and resid 269 through 291 Processing helix chain 'E' and resid 301 through 312 removed outlier: 3.736A pdb=" N ILE E 305 " --> pdb=" O SER E 301 " (cutoff:3.500A) Processing helix chain 'E' and resid 313 through 319 Proline residue: E 317 - end of helix Processing helix chain 'E' and resid 324 through 342 removed outlier: 3.977A pdb=" N TYR E 337 " --> pdb=" O LEU E 333 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N ALA E 338 " --> pdb=" O LYS E 334 " (cutoff:3.500A) Processing helix chain 'E' and resid 344 through 346 No H-bonds generated for 'chain 'E' and resid 344 through 346' Processing helix chain 'E' and resid 357 through 364 removed outlier: 4.168A pdb=" N TYR E 361 " --> pdb=" O THR E 357 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N GLN E 364 " --> pdb=" O LYS E 360 " (cutoff:3.500A) Processing helix chain 'E' and resid 381 through 393 Processing helix chain 'E' and resid 395 through 399 Processing helix chain 'E' and resid 412 through 417 Processing helix chain 'E' and resid 422 through 438 Processing helix chain 'E' and resid 475 through 489 Processing helix chain 'E' and resid 505 through 509 Processing helix chain 'E' and resid 516 through 523 removed outlier: 3.969A pdb=" N ASP E 522 " --> pdb=" O LYS E 518 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ILE E 523 " --> pdb=" O ASP E 519 " (cutoff:3.500A) Processing helix chain 'E' and resid 524 through 539 Processing helix chain 'E' and resid 545 through 548 removed outlier: 3.630A pdb=" N GLN E 548 " --> pdb=" O LYS E 545 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 545 through 548' Processing helix chain 'E' and resid 549 through 559 Processing helix chain 'E' and resid 565 through 573 Processing helix chain 'F' and resid 131 through 136 Processing helix chain 'F' and resid 140 through 150 removed outlier: 3.561A pdb=" N GLU F 144 " --> pdb=" O TYR F 140 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N LEU F 148 " --> pdb=" O GLU F 144 " (cutoff:3.500A) Processing helix chain 'F' and resid 151 through 163 removed outlier: 3.634A pdb=" N ILE F 156 " --> pdb=" O PRO F 152 " (cutoff:3.500A) Processing helix chain 'F' and resid 173 through 184 removed outlier: 3.719A pdb=" N LYS F 177 " --> pdb=" O PRO F 173 " (cutoff:3.500A) Processing helix chain 'F' and resid 205 through 214 Processing helix chain 'F' and resid 214 through 230 removed outlier: 3.818A pdb=" N VAL F 218 " --> pdb=" O ASP F 214 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ALA F 221 " --> pdb=" O ALA F 217 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N MET F 222 " --> pdb=" O VAL F 218 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ALA F 223 " --> pdb=" O ILE F 219 " (cutoff:3.500A) Processing helix chain 'F' and resid 242 through 260 Processing helix chain 'F' and resid 265 through 269 Processing helix chain 'F' and resid 283 through 287 Processing helix chain 'F' and resid 288 through 298 removed outlier: 3.607A pdb=" N ASN F 294 " --> pdb=" O THR F 290 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N SER F 295 " --> pdb=" O ALA F 291 " (cutoff:3.500A) Processing helix chain 'F' and resid 314 through 318 Processing helix chain 'F' and resid 325 through 338 removed outlier: 3.600A pdb=" N ILE F 331 " --> pdb=" O THR F 327 " (cutoff:3.500A) Proline residue: F 332 - end of helix Processing helix chain 'F' and resid 338 through 344 removed outlier: 3.645A pdb=" N PHE F 342 " --> pdb=" O GLY F 338 " (cutoff:3.500A) Processing helix chain 'F' and resid 375 through 382 removed outlier: 3.639A pdb=" N ILE F 379 " --> pdb=" O THR F 375 " (cutoff:3.500A) Processing helix chain 'F' and resid 387 through 391 Processing helix chain 'F' and resid 400 through 403 Processing helix chain 'F' and resid 409 through 411 No H-bonds generated for 'chain 'F' and resid 409 through 411' Processing helix chain 'F' and resid 416 through 424 removed outlier: 3.655A pdb=" N LEU F 420 " --> pdb=" O ASP F 416 " (cutoff:3.500A) Processing helix chain 'F' and resid 440 through 456 removed outlier: 4.033A pdb=" N PHE F 451 " --> pdb=" O PHE F 447 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N THR F 452 " --> pdb=" O PHE F 448 " (cutoff:3.500A) Processing helix chain 'F' and resid 460 through 479 removed outlier: 5.021A pdb=" N THR F 467 " --> pdb=" O CYS F 463 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N LYS F 468 " --> pdb=" O ARG F 464 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ILE F 473 " --> pdb=" O ARG F 469 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N GLU F 475 " --> pdb=" O LEU F 471 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N ARG F 476 " --> pdb=" O GLU F 472 " (cutoff:3.500A) Processing helix chain 'F' and resid 485 through 499 removed outlier: 3.849A pdb=" N LEU F 493 " --> pdb=" O ARG F 489 " (cutoff:3.500A) Processing helix chain 'F' and resid 503 through 509 removed outlier: 3.815A pdb=" N GLN F 507 " --> pdb=" O CYS F 503 " (cutoff:3.500A) Processing helix chain 'F' and resid 510 through 520 removed outlier: 3.891A pdb=" N PHE F 519 " --> pdb=" O SER F 515 " (cutoff:3.500A) Processing helix chain 'F' and resid 521 through 529 removed outlier: 3.956A pdb=" N GLU F 525 " --> pdb=" O ARG F 521 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ALA F 526 " --> pdb=" O ASP F 522 " (cutoff:3.500A) Processing helix chain 'F' and resid 555 through 560 Processing helix chain 'F' and resid 585 through 591 removed outlier: 4.169A pdb=" N GLU F 589 " --> pdb=" O GLY F 585 " (cutoff:3.500A) Processing helix chain 'G' and resid 10 through 19 Processing helix chain 'G' and resid 25 through 39 removed outlier: 4.615A pdb=" N GLN G 29 " --> pdb=" O GLY G 25 " (cutoff:3.500A) Processing helix chain 'G' and resid 42 through 54 removed outlier: 3.907A pdb=" N GLN G 46 " --> pdb=" O PRO G 42 " (cutoff:3.500A) Processing helix chain 'G' and resid 56 through 67 removed outlier: 4.567A pdb=" N VAL G 60 " --> pdb=" O PRO G 56 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N TYR G 67 " --> pdb=" O VAL G 63 " (cutoff:3.500A) Processing helix chain 'G' and resid 85 through 90 Processing helix chain 'G' and resid 92 through 105 removed outlier: 3.929A pdb=" N ILE G 96 " --> pdb=" O GLY G 92 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 11 through 16 removed outlier: 9.846A pdb=" N VAL A 74 " --> pdb=" O THR A 5 " (cutoff:3.500A) removed outlier: 7.522A pdb=" N LYS A 7 " --> pdb=" O VAL A 74 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N GLN A 61 " --> pdb=" O VAL A 52 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 141 through 143 Processing sheet with id=AA3, first strand: chain 'A' and resid 168 through 170 Processing sheet with id=AA4, first strand: chain 'A' and resid 265 through 268 removed outlier: 8.771A pdb=" N ILE A 378 " --> pdb=" O MET A 348 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N VAL A 350 " --> pdb=" O ILE A 378 " (cutoff:3.500A) removed outlier: 8.004A pdb=" N ILE A 380 " --> pdb=" O VAL A 350 " (cutoff:3.500A) removed outlier: 6.124A pdb=" N SER A 352 " --> pdb=" O ILE A 380 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 296 through 297 removed outlier: 6.573A pdb=" N MET A 296 " --> pdb=" O ILE A 497 " (cutoff:3.500A) removed outlier: 7.852A pdb=" N LEU A 499 " --> pdb=" O MET A 296 " (cutoff:3.500A) removed outlier: 8.524A pdb=" N PHE A 496 " --> pdb=" O THR A 467 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N ASN A 469 " --> pdb=" O PHE A 496 " (cutoff:3.500A) removed outlier: 7.962A pdb=" N GLU A 498 " --> pdb=" O ASN A 469 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N VAL A 471 " --> pdb=" O GLU A 498 " (cutoff:3.500A) removed outlier: 8.545A pdb=" N MET A 500 " --> pdb=" O VAL A 471 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N ALA A 473 " --> pdb=" O MET A 500 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N LEU A 466 " --> pdb=" O VAL A 462 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N VAL A 468 " --> pdb=" O VAL A 460 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N VAL A 460 " --> pdb=" O VAL A 468 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 369 through 370 Processing sheet with id=AA7, first strand: chain 'B' and resid 274 through 280 removed outlier: 6.575A pdb=" N VAL B 193 " --> pdb=" O TYR B 235 " (cutoff:3.500A) removed outlier: 8.170A pdb=" N TYR B 237 " --> pdb=" O VAL B 193 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N CYS B 195 " --> pdb=" O TYR B 237 " (cutoff:3.500A) removed outlier: 8.673A pdb=" N ARG B 239 " --> pdb=" O CYS B 195 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ASN B 323 " --> pdb=" O ALA B 194 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 366 through 371 removed outlier: 4.036A pdb=" N GLY B 366 " --> pdb=" O LEU B 358 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N LEU B 432 " --> pdb=" O ALA B 357 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N ALA B 395 " --> pdb=" O MET B 435 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 543 through 546 Processing sheet with id=AB1, first strand: chain 'B' and resid 566 through 567 Processing sheet with id=AB2, first strand: chain 'C' and resid 78 through 81 removed outlier: 6.347A pdb=" N TYR C 78 " --> pdb=" O SER C 118 " (cutoff:3.500A) removed outlier: 7.654A pdb=" N ASP C 120 " --> pdb=" O TYR C 78 " (cutoff:3.500A) removed outlier: 6.210A pdb=" N ILE C 80 " --> pdb=" O ASP C 120 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'E' and resid 11 through 16 removed outlier: 9.750A pdb=" N VAL E 74 " --> pdb=" O THR E 5 " (cutoff:3.500A) removed outlier: 7.625A pdb=" N LYS E 7 " --> pdb=" O VAL E 74 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLN E 61 " --> pdb=" O VAL E 52 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 141 through 143 Processing sheet with id=AB5, first strand: chain 'E' and resid 168 through 170 Processing sheet with id=AB6, first strand: chain 'E' and resid 265 through 268 removed outlier: 6.078A pdb=" N THR E 225 " --> pdb=" O VAL E 349 " (cutoff:3.500A) removed outlier: 7.559A pdb=" N VAL E 351 " --> pdb=" O THR E 225 " (cutoff:3.500A) removed outlier: 6.178A pdb=" N ILE E 227 " --> pdb=" O VAL E 351 " (cutoff:3.500A) removed outlier: 7.816A pdb=" N ILE E 353 " --> pdb=" O ILE E 227 " (cutoff:3.500A) removed outlier: 7.120A pdb=" N GLN E 229 " --> pdb=" O ILE E 353 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ILE E 378 " --> pdb=" O VAL E 350 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 296 through 297 removed outlier: 6.745A pdb=" N MET E 296 " --> pdb=" O ILE E 497 " (cutoff:3.500A) removed outlier: 7.796A pdb=" N LEU E 499 " --> pdb=" O MET E 296 " (cutoff:3.500A) removed outlier: 8.493A pdb=" N PHE E 496 " --> pdb=" O THR E 467 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N ASN E 469 " --> pdb=" O PHE E 496 " (cutoff:3.500A) removed outlier: 8.083A pdb=" N GLU E 498 " --> pdb=" O ASN E 469 " (cutoff:3.500A) removed outlier: 7.051A pdb=" N VAL E 471 " --> pdb=" O GLU E 498 " (cutoff:3.500A) removed outlier: 8.424A pdb=" N MET E 500 " --> pdb=" O VAL E 471 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N ALA E 473 " --> pdb=" O MET E 500 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N LEU E 466 " --> pdb=" O VAL E 462 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N VAL E 468 " --> pdb=" O VAL E 460 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N VAL E 460 " --> pdb=" O VAL E 468 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 369 through 370 Processing sheet with id=AB9, first strand: chain 'F' and resid 277 through 280 removed outlier: 7.927A pdb=" N ARG F 278 " --> pdb=" O GLY F 234 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N VAL F 236 " --> pdb=" O ARG F 278 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N GLY F 280 " --> pdb=" O VAL F 236 " (cutoff:3.500A) removed outlier: 5.982A pdb=" N VAL F 238 " --> pdb=" O GLY F 280 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N VAL F 193 " --> pdb=" O TYR F 235 " (cutoff:3.500A) removed outlier: 8.134A pdb=" N TYR F 237 " --> pdb=" O VAL F 193 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N CYS F 195 " --> pdb=" O TYR F 237 " (cutoff:3.500A) removed outlier: 8.719A pdb=" N ARG F 239 " --> pdb=" O CYS F 195 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ASN F 323 " --> pdb=" O ALA F 194 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'F' and resid 368 through 371 removed outlier: 3.615A pdb=" N LEU F 368 " --> pdb=" O PHE F 356 " (cutoff:3.500A) removed outlier: 8.209A pdb=" N LEU F 432 " --> pdb=" O VAL F 355 " (cutoff:3.500A) removed outlier: 5.953A pdb=" N ALA F 357 " --> pdb=" O LEU F 432 " (cutoff:3.500A) removed outlier: 7.552A pdb=" N VAL F 434 " --> pdb=" O ALA F 357 " (cutoff:3.500A) removed outlier: 7.366A pdb=" N GLY F 359 " --> pdb=" O VAL F 434 " (cutoff:3.500A) removed outlier: 9.097A pdb=" N ASP F 436 " --> pdb=" O GLY F 359 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ALA F 395 " --> pdb=" O MET F 435 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'F' and resid 543 through 546 Processing sheet with id=AC3, first strand: chain 'F' and resid 566 through 567 Processing sheet with id=AC4, first strand: chain 'G' and resid 78 through 83 764 hydrogen bonds defined for protein. 2106 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: 5.47 Time building geometry restraints manager: 4.97 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.42: 7225 1.42 - 1.64: 10787 1.64 - 1.86: 200 1.86 - 2.08: 0 2.08 - 2.30: 184 Bond restraints: 18396 Sorted by residual: bond pdb=" C4 FMN F 602 " pdb=" C4A FMN F 602 " ideal model delta sigma weight residual 1.390 1.553 -0.163 2.00e-02 2.50e+03 6.67e+01 bond pdb=" C4 FMN B 601 " pdb=" C4A FMN B 601 " ideal model delta sigma weight residual 1.390 1.553 -0.163 2.00e-02 2.50e+03 6.65e+01 bond pdb=" C10 FMN B 601 " pdb=" C4A FMN B 601 " ideal model delta sigma weight residual 1.390 1.496 -0.106 2.00e-02 2.50e+03 2.83e+01 bond pdb=" C10 FMN F 602 " pdb=" C4A FMN F 602 " ideal model delta sigma weight residual 1.390 1.496 -0.106 2.00e-02 2.50e+03 2.83e+01 bond pdb=" C5A FMN F 602 " pdb=" C9A FMN F 602 " ideal model delta sigma weight residual 1.390 1.468 -0.078 2.00e-02 2.50e+03 1.52e+01 ... (remaining 18391 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.40: 24754 3.40 - 6.80: 215 6.80 - 10.20: 21 10.20 - 13.60: 2 13.60 - 17.00: 4 Bond angle restraints: 24996 Sorted by residual: angle pdb=" N VAL A 65 " pdb=" CA VAL A 65 " pdb=" C VAL A 65 " ideal model delta sigma weight residual 112.43 106.86 5.57 9.20e-01 1.18e+00 3.67e+01 angle pdb=" C4A FMN B 601 " pdb=" C10 FMN B 601 " pdb=" N1 FMN B 601 " ideal model delta sigma weight residual 120.00 103.00 17.00 3.00e+00 1.11e-01 3.21e+01 angle pdb=" C4A FMN F 602 " pdb=" C10 FMN F 602 " pdb=" N1 FMN F 602 " ideal model delta sigma weight residual 120.00 103.34 16.66 3.00e+00 1.11e-01 3.08e+01 angle pdb=" C10 FMN B 601 " pdb=" N1 FMN B 601 " pdb=" C2 FMN B 601 " ideal model delta sigma weight residual 120.00 134.64 -14.64 3.00e+00 1.11e-01 2.38e+01 angle pdb=" C10 FMN F 602 " pdb=" N1 FMN F 602 " pdb=" C2 FMN F 602 " ideal model delta sigma weight residual 120.00 134.62 -14.62 3.00e+00 1.11e-01 2.37e+01 ... (remaining 24991 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.20: 10880 35.20 - 70.39: 180 70.39 - 105.59: 21 105.59 - 140.78: 1 140.78 - 175.98: 2 Dihedral angle restraints: 11084 sinusoidal: 4386 harmonic: 6698 Sorted by residual: dihedral pdb=" C10 FMN F 602 " pdb=" C1' FMN F 602 " pdb=" N10 FMN F 602 " pdb=" C2' FMN F 602 " ideal model delta sinusoidal sigma weight residual 257.59 81.61 175.98 1 2.00e+01 2.50e-03 4.79e+01 dihedral pdb=" C10 FMN B 601 " pdb=" C1' FMN B 601 " pdb=" N10 FMN B 601 " pdb=" C2' FMN B 601 " ideal model delta sinusoidal sigma weight residual 257.59 84.54 173.06 1 2.00e+01 2.50e-03 4.78e+01 dihedral pdb=" CA ARG G 123 " pdb=" C ARG G 123 " pdb=" N CYS G 124 " pdb=" CA CYS G 124 " ideal model delta harmonic sigma weight residual 180.00 147.78 32.22 0 5.00e+00 4.00e-02 4.15e+01 ... (remaining 11081 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.087: 2560 0.087 - 0.173: 299 0.173 - 0.260: 11 0.260 - 0.347: 1 0.347 - 0.433: 1 Chirality restraints: 2872 Sorted by residual: chirality pdb=" CB ILE A 353 " pdb=" CA ILE A 353 " pdb=" CG1 ILE A 353 " pdb=" CG2 ILE A 353 " both_signs ideal model delta sigma weight residual False 2.64 2.21 0.43 2.00e-01 2.50e+01 4.69e+00 chirality pdb=" CG LEU E 284 " pdb=" CB LEU E 284 " pdb=" CD1 LEU E 284 " pdb=" CD2 LEU E 284 " both_signs ideal model delta sigma weight residual False -2.59 -2.29 -0.30 2.00e-01 2.50e+01 2.32e+00 chirality pdb=" CB ILE E 455 " pdb=" CA ILE E 455 " pdb=" CG1 ILE E 455 " pdb=" CG2 ILE E 455 " both_signs ideal model delta sigma weight residual False 2.64 2.43 0.21 2.00e-01 2.50e+01 1.10e+00 ... (remaining 2869 not shown) Planarity restraints: 3214 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR E 244 " 0.039 5.00e-02 4.00e+02 5.96e-02 5.69e+00 pdb=" N PRO E 245 " -0.103 5.00e-02 4.00e+02 pdb=" CA PRO E 245 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO E 245 " 0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 65 " 0.012 2.00e-02 2.50e+03 2.38e-02 5.65e+00 pdb=" C VAL A 65 " -0.041 2.00e-02 2.50e+03 pdb=" O VAL A 65 " 0.016 2.00e-02 2.50e+03 pdb=" N TYR A 66 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PRO F 461 " 0.034 5.00e-02 4.00e+02 5.08e-02 4.12e+00 pdb=" N PRO F 462 " -0.088 5.00e-02 4.00e+02 pdb=" CA PRO F 462 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO F 462 " 0.029 5.00e-02 4.00e+02 ... (remaining 3211 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 990 2.73 - 3.27: 18902 3.27 - 3.81: 29345 3.81 - 4.36: 34659 4.36 - 4.90: 57044 Nonbonded interactions: 140940 Sorted by model distance: nonbonded pdb=" OE2 GLU E 99 " pdb=" OG1 THR E 101 " model vdw 2.186 3.040 nonbonded pdb=" OD2 ASP B 443 " pdb=" OH TYR C 89 " model vdw 2.202 3.040 nonbonded pdb=" O LYS F 459 " pdb=" NH2 ARG F 464 " model vdw 2.256 3.120 nonbonded pdb=" O ALA B 281 " pdb=" NE2 GLN C 69 " model vdw 2.266 3.120 nonbonded pdb=" O ARG A 48 " pdb=" ND2 ASN A 88 " model vdw 2.271 3.120 ... (remaining 140935 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 'E' } ncs_group { reference = (chain 'B' and (resid 130 through 599 or resid 603 through 604)) selection = (chain 'F' and (resid 130 through 599 or resid 603 through 604)) } ncs_group { reference = chain 'C' selection = chain 'G' } 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: 0.700 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: 0.010 Extract box with map and model: 0.660 Check model and map are aligned: 0.130 Set scattering table: 0.160 Process input model: 45.730 Find NCS groups from input model: 0.670 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.790 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6876 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 0.163 18396 Z= 0.333 Angle : 0.844 17.002 24996 Z= 0.426 Chirality : 0.054 0.433 2872 Planarity : 0.005 0.060 3214 Dihedral : 13.847 175.981 6812 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.15 % Favored : 96.81 % Rotamer: Outliers : 0.52 % Allowed : 1.45 % Favored : 98.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.36 (0.17), residues: 2352 helix: -0.30 (0.16), residues: 898 sheet: 0.71 (0.38), residues: 166 loop : -0.20 (0.17), residues: 1288 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP A 304 HIS 0.017 0.002 HIS C 20 PHE 0.029 0.003 PHE A 418 TYR 0.017 0.002 TYR F 192 ARG 0.010 0.001 ARG A 393 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4704 Ramachandran restraints generated. 2352 Oldfield, 0 Emsley, 2352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4704 Ramachandran restraints generated. 2352 Oldfield, 0 Emsley, 2352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 1934 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 224 time to evaluate : 2.063 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 258 LEU cc_start: 0.7928 (mt) cc_final: 0.7575 (mt) REVERT: C 1 MET cc_start: -0.1107 (tpp) cc_final: -0.1337 (tpp) outliers start: 10 outliers final: 3 residues processed: 232 average time/residue: 0.2954 time to fit residues: 103.4883 Evaluate side-chains 135 residues out of total 1934 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 132 time to evaluate : 2.120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 250 GLN Chi-restraints excluded: chain B residue 576 ILE Chi-restraints excluded: chain F residue 576 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 197 optimal weight: 20.0000 chunk 177 optimal weight: 10.0000 chunk 98 optimal weight: 10.0000 chunk 60 optimal weight: 9.9990 chunk 119 optimal weight: 0.5980 chunk 94 optimal weight: 8.9990 chunk 183 optimal weight: 9.9990 chunk 70 optimal weight: 20.0000 chunk 111 optimal weight: 5.9990 chunk 136 optimal weight: 8.9990 chunk 212 optimal weight: 7.9990 overall best weight: 6.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 469 ASN B 507 GLN B 540 HIS ** C 20 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 35 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7113 moved from start: 0.2037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 18396 Z= 0.284 Angle : 0.696 9.930 24996 Z= 0.363 Chirality : 0.047 0.262 2872 Planarity : 0.005 0.060 3214 Dihedral : 7.552 173.113 2561 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 13.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 1.09 % Allowed : 9.15 % Favored : 89.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.11 (0.17), residues: 2352 helix: 0.09 (0.16), residues: 984 sheet: 0.80 (0.37), residues: 164 loop : -0.21 (0.18), residues: 1204 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP F 178 HIS 0.007 0.001 HIS A 474 PHE 0.023 0.002 PHE E 6 TYR 0.012 0.002 TYR G 61 ARG 0.006 0.001 ARG A 393 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4704 Ramachandran restraints generated. 2352 Oldfield, 0 Emsley, 2352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4704 Ramachandran restraints generated. 2352 Oldfield, 0 Emsley, 2352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1934 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 143 time to evaluate : 2.216 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 11 ASP cc_start: 0.7595 (p0) cc_final: 0.7385 (p0) outliers start: 21 outliers final: 16 residues processed: 156 average time/residue: 0.2586 time to fit residues: 66.0541 Evaluate side-chains 143 residues out of total 1934 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 127 time to evaluate : 2.021 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 300 CYS Chi-restraints excluded: chain A residue 322 CYS Chi-restraints excluded: chain A residue 382 THR Chi-restraints excluded: chain A residue 385 LEU Chi-restraints excluded: chain B residue 449 LEU Chi-restraints excluded: chain B residue 576 ILE Chi-restraints excluded: chain C residue 40 TYR Chi-restraints excluded: chain C residue 68 SER Chi-restraints excluded: chain E residue 111 LEU Chi-restraints excluded: chain E residue 186 LEU Chi-restraints excluded: chain E residue 199 ILE Chi-restraints excluded: chain E residue 382 THR Chi-restraints excluded: chain E residue 479 ILE Chi-restraints excluded: chain F residue 478 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 118 optimal weight: 30.0000 chunk 65 optimal weight: 50.0000 chunk 176 optimal weight: 30.0000 chunk 144 optimal weight: 30.0000 chunk 58 optimal weight: 0.0030 chunk 212 optimal weight: 5.9990 chunk 229 optimal weight: 30.0000 chunk 189 optimal weight: 8.9990 chunk 211 optimal weight: 5.9990 chunk 72 optimal weight: 40.0000 chunk 170 optimal weight: 40.0000 overall best weight: 10.2000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 11 GLN A 28 ASN ** A 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 179 GLN C 9 ASN ** C 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 569 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7279 moved from start: 0.3016 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.066 18396 Z= 0.393 Angle : 0.743 9.588 24996 Z= 0.393 Chirality : 0.051 0.292 2872 Planarity : 0.005 0.045 3214 Dihedral : 7.706 174.718 2556 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 18.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 1.86 % Allowed : 12.72 % Favored : 85.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.36 (0.17), residues: 2352 helix: -0.18 (0.16), residues: 1006 sheet: 0.60 (0.40), residues: 168 loop : -0.28 (0.18), residues: 1178 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP F 178 HIS 0.008 0.002 HIS A 474 PHE 0.022 0.002 PHE E 125 TYR 0.019 0.002 TYR A 37 ARG 0.007 0.001 ARG E 287 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4704 Ramachandran restraints generated. 2352 Oldfield, 0 Emsley, 2352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4704 Ramachandran restraints generated. 2352 Oldfield, 0 Emsley, 2352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1934 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 128 time to evaluate : 2.225 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 174 PHE cc_start: 0.7488 (OUTLIER) cc_final: 0.6848 (m-80) REVERT: A 246 MET cc_start: 0.7941 (mmp) cc_final: 0.7705 (mmp) outliers start: 36 outliers final: 26 residues processed: 156 average time/residue: 0.2668 time to fit residues: 66.8168 Evaluate side-chains 141 residues out of total 1934 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 114 time to evaluate : 2.027 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 CYS Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 174 PHE Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 199 ILE Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 300 CYS Chi-restraints excluded: chain A residue 382 THR Chi-restraints excluded: chain B residue 449 LEU Chi-restraints excluded: chain B residue 460 CYS Chi-restraints excluded: chain B residue 507 GLN Chi-restraints excluded: chain B residue 576 ILE Chi-restraints excluded: chain C residue 40 TYR Chi-restraints excluded: chain C residue 68 SER Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 124 CYS Chi-restraints excluded: chain E residue 111 LEU Chi-restraints excluded: chain E residue 186 LEU Chi-restraints excluded: chain E residue 199 ILE Chi-restraints excluded: chain E residue 203 VAL Chi-restraints excluded: chain E residue 382 THR Chi-restraints excluded: chain E residue 479 ILE Chi-restraints excluded: chain E residue 514 ILE Chi-restraints excluded: chain E residue 519 ASP Chi-restraints excluded: chain F residue 452 THR Chi-restraints excluded: chain G residue 68 SER Chi-restraints excluded: chain G residue 71 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 210 optimal weight: 20.0000 chunk 160 optimal weight: 7.9990 chunk 110 optimal weight: 30.0000 chunk 23 optimal weight: 20.0000 chunk 101 optimal weight: 20.0000 chunk 142 optimal weight: 0.9990 chunk 213 optimal weight: 4.9990 chunk 226 optimal weight: 9.9990 chunk 111 optimal weight: 7.9990 chunk 202 optimal weight: 9.9990 chunk 60 optimal weight: 30.0000 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 326 GLN ** C 20 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7241 moved from start: 0.3257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 18396 Z= 0.269 Angle : 0.652 8.536 24996 Z= 0.337 Chirality : 0.046 0.199 2872 Planarity : 0.004 0.047 3214 Dihedral : 7.423 173.604 2556 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 15.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 1.86 % Allowed : 14.58 % Favored : 83.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.23 (0.17), residues: 2352 helix: -0.04 (0.16), residues: 1010 sheet: 0.24 (0.37), residues: 188 loop : -0.17 (0.19), residues: 1154 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP F 178 HIS 0.005 0.001 HIS E 474 PHE 0.019 0.002 PHE E 125 TYR 0.015 0.002 TYR E 37 ARG 0.011 0.001 ARG A 48 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4704 Ramachandran restraints generated. 2352 Oldfield, 0 Emsley, 2352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4704 Ramachandran restraints generated. 2352 Oldfield, 0 Emsley, 2352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1934 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 131 time to evaluate : 2.020 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: C 91 ARG cc_start: 0.5646 (mpt180) cc_final: 0.4831 (mtm180) REVERT: E 246 MET cc_start: 0.8099 (mmp) cc_final: 0.7714 (mmp) REVERT: E 483 MET cc_start: 0.6835 (tmm) cc_final: 0.6434 (tmm) outliers start: 36 outliers final: 21 residues processed: 161 average time/residue: 0.2446 time to fit residues: 65.1413 Evaluate side-chains 144 residues out of total 1934 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 123 time to evaluate : 2.064 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 174 PHE Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 382 THR Chi-restraints excluded: chain B residue 449 LEU Chi-restraints excluded: chain B residue 460 CYS Chi-restraints excluded: chain B residue 576 ILE Chi-restraints excluded: chain C residue 40 TYR Chi-restraints excluded: chain C residue 68 SER Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 124 CYS Chi-restraints excluded: chain E residue 22 LEU Chi-restraints excluded: chain E residue 166 VAL Chi-restraints excluded: chain E residue 199 ILE Chi-restraints excluded: chain E residue 382 THR Chi-restraints excluded: chain E residue 479 ILE Chi-restraints excluded: chain E residue 519 ASP Chi-restraints excluded: chain F residue 460 CYS Chi-restraints excluded: chain G residue 68 SER Chi-restraints excluded: chain G residue 71 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 188 optimal weight: 30.0000 chunk 128 optimal weight: 8.9990 chunk 3 optimal weight: 9.9990 chunk 168 optimal weight: 9.9990 chunk 93 optimal weight: 9.9990 chunk 193 optimal weight: 9.9990 chunk 156 optimal weight: 6.9990 chunk 0 optimal weight: 20.0000 chunk 115 optimal weight: 8.9990 chunk 203 optimal weight: 40.0000 chunk 57 optimal weight: 50.0000 overall best weight: 8.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 28 ASN ** E 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 469 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7327 moved from start: 0.3886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 18396 Z= 0.349 Angle : 0.716 9.154 24996 Z= 0.374 Chirality : 0.049 0.228 2872 Planarity : 0.005 0.047 3214 Dihedral : 7.599 173.821 2556 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 19.75 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.93 % Favored : 95.03 % Rotamer: Outliers : 2.90 % Allowed : 15.51 % Favored : 81.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.49 (0.17), residues: 2352 helix: -0.18 (0.16), residues: 1000 sheet: -0.30 (0.35), residues: 208 loop : -0.31 (0.19), residues: 1144 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP F 178 HIS 0.006 0.002 HIS A 474 PHE 0.022 0.002 PHE E 125 TYR 0.017 0.002 TYR A 556 ARG 0.007 0.001 ARG A 48 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4704 Ramachandran restraints generated. 2352 Oldfield, 0 Emsley, 2352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4704 Ramachandran restraints generated. 2352 Oldfield, 0 Emsley, 2352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1934 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 125 time to evaluate : 2.025 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 246 MET cc_start: 0.7820 (mmp) cc_final: 0.7197 (mmp) REVERT: A 483 MET cc_start: 0.7125 (tmm) cc_final: 0.6922 (tmm) REVERT: C 61 TYR cc_start: 0.8049 (OUTLIER) cc_final: 0.7537 (t80) REVERT: C 91 ARG cc_start: 0.5822 (mpt180) cc_final: 0.4945 (mtm180) REVERT: E 246 MET cc_start: 0.8145 (mmp) cc_final: 0.7748 (mmp) REVERT: E 483 MET cc_start: 0.7122 (tmm) cc_final: 0.6778 (tmm) outliers start: 56 outliers final: 35 residues processed: 175 average time/residue: 0.2368 time to fit residues: 67.9607 Evaluate side-chains 150 residues out of total 1934 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 114 time to evaluate : 1.954 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 CYS Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 132 LYS Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 174 PHE Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 300 CYS Chi-restraints excluded: chain A residue 382 THR Chi-restraints excluded: chain B residue 289 GLU Chi-restraints excluded: chain B residue 358 LEU Chi-restraints excluded: chain B residue 437 GLU Chi-restraints excluded: chain B residue 449 LEU Chi-restraints excluded: chain B residue 460 CYS Chi-restraints excluded: chain B residue 507 GLN Chi-restraints excluded: chain B residue 576 ILE Chi-restraints excluded: chain C residue 9 ASN Chi-restraints excluded: chain C residue 61 TYR Chi-restraints excluded: chain C residue 68 SER Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 124 CYS Chi-restraints excluded: chain E residue 34 THR Chi-restraints excluded: chain E residue 101 THR Chi-restraints excluded: chain E residue 166 VAL Chi-restraints excluded: chain E residue 186 LEU Chi-restraints excluded: chain E residue 199 ILE Chi-restraints excluded: chain E residue 203 VAL Chi-restraints excluded: chain E residue 382 THR Chi-restraints excluded: chain E residue 479 ILE Chi-restraints excluded: chain E residue 519 ASP Chi-restraints excluded: chain F residue 460 CYS Chi-restraints excluded: chain F residue 525 GLU Chi-restraints excluded: chain G residue 68 SER Chi-restraints excluded: chain G residue 71 THR Chi-restraints excluded: chain G residue 88 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 76 optimal weight: 20.0000 chunk 203 optimal weight: 30.0000 chunk 44 optimal weight: 9.9990 chunk 132 optimal weight: 0.8980 chunk 55 optimal weight: 30.0000 chunk 226 optimal weight: 20.0000 chunk 187 optimal weight: 40.0000 chunk 104 optimal weight: 8.9990 chunk 18 optimal weight: 7.9990 chunk 74 optimal weight: 20.0000 chunk 118 optimal weight: 10.0000 overall best weight: 7.5790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 29 ASN ** C 20 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 28 ASN ** E 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7316 moved from start: 0.4125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 18396 Z= 0.298 Angle : 0.681 8.703 24996 Z= 0.351 Chirality : 0.047 0.210 2872 Planarity : 0.004 0.048 3214 Dihedral : 7.452 172.819 2556 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 17.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 2.59 % Allowed : 17.63 % Favored : 79.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.42 (0.17), residues: 2352 helix: -0.07 (0.16), residues: 988 sheet: -0.35 (0.33), residues: 228 loop : -0.30 (0.19), residues: 1136 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP F 178 HIS 0.005 0.001 HIS E 474 PHE 0.020 0.002 PHE E 125 TYR 0.015 0.002 TYR A 556 ARG 0.005 0.001 ARG A 48 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4704 Ramachandran restraints generated. 2352 Oldfield, 0 Emsley, 2352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4704 Ramachandran restraints generated. 2352 Oldfield, 0 Emsley, 2352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1934 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 123 time to evaluate : 2.089 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 483 MET cc_start: 0.7199 (tmm) cc_final: 0.6964 (tmm) REVERT: C 61 TYR cc_start: 0.7969 (OUTLIER) cc_final: 0.7481 (t80) REVERT: C 91 ARG cc_start: 0.5820 (mpt180) cc_final: 0.5005 (mtm180) REVERT: E 246 MET cc_start: 0.8075 (mmp) cc_final: 0.7563 (mmp) REVERT: E 483 MET cc_start: 0.7140 (tmm) cc_final: 0.6806 (tmm) outliers start: 50 outliers final: 34 residues processed: 167 average time/residue: 0.2536 time to fit residues: 69.6972 Evaluate side-chains 152 residues out of total 1934 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 117 time to evaluate : 2.046 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 78 SER Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 174 PHE Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 300 CYS Chi-restraints excluded: chain A residue 382 THR Chi-restraints excluded: chain A residue 424 VAL Chi-restraints excluded: chain B residue 289 GLU Chi-restraints excluded: chain B residue 358 LEU Chi-restraints excluded: chain B residue 437 GLU Chi-restraints excluded: chain B residue 449 LEU Chi-restraints excluded: chain B residue 460 CYS Chi-restraints excluded: chain B residue 507 GLN Chi-restraints excluded: chain C residue 9 ASN Chi-restraints excluded: chain C residue 61 TYR Chi-restraints excluded: chain C residue 68 SER Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 124 CYS Chi-restraints excluded: chain E residue 21 ILE Chi-restraints excluded: chain E residue 22 LEU Chi-restraints excluded: chain E residue 34 THR Chi-restraints excluded: chain E residue 166 VAL Chi-restraints excluded: chain E residue 183 ASN Chi-restraints excluded: chain E residue 186 LEU Chi-restraints excluded: chain E residue 199 ILE Chi-restraints excluded: chain E residue 382 THR Chi-restraints excluded: chain E residue 479 ILE Chi-restraints excluded: chain E residue 519 ASP Chi-restraints excluded: chain F residue 457 CYS Chi-restraints excluded: chain F residue 460 CYS Chi-restraints excluded: chain G residue 68 SER Chi-restraints excluded: chain G residue 71 THR Chi-restraints excluded: chain G residue 88 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 218 optimal weight: 8.9990 chunk 25 optimal weight: 8.9990 chunk 128 optimal weight: 8.9990 chunk 165 optimal weight: 6.9990 chunk 190 optimal weight: 40.0000 chunk 126 optimal weight: 4.9990 chunk 225 optimal weight: 8.9990 chunk 141 optimal weight: 20.0000 chunk 137 optimal weight: 2.9990 chunk 104 optimal weight: 1.9990 chunk 139 optimal weight: 0.0980 overall best weight: 3.4188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 35 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7239 moved from start: 0.4110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 18396 Z= 0.192 Angle : 0.638 10.143 24996 Z= 0.323 Chirality : 0.044 0.153 2872 Planarity : 0.004 0.048 3214 Dihedral : 7.202 172.053 2554 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 13.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 1.96 % Allowed : 19.08 % Favored : 78.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.18 (0.17), residues: 2352 helix: 0.13 (0.16), residues: 988 sheet: -0.30 (0.33), residues: 228 loop : -0.14 (0.19), residues: 1136 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP F 178 HIS 0.003 0.001 HIS A 474 PHE 0.015 0.001 PHE A 125 TYR 0.013 0.001 TYR A 556 ARG 0.005 0.000 ARG A 48 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4704 Ramachandran restraints generated. 2352 Oldfield, 0 Emsley, 2352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4704 Ramachandran restraints generated. 2352 Oldfield, 0 Emsley, 2352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1934 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 131 time to evaluate : 2.029 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 246 MET cc_start: 0.7600 (mmp) cc_final: 0.7095 (mmp) REVERT: A 483 MET cc_start: 0.7263 (tmm) cc_final: 0.7021 (tmm) REVERT: C 91 ARG cc_start: 0.5670 (mpt180) cc_final: 0.5126 (mtm180) REVERT: E 246 MET cc_start: 0.8146 (mmp) cc_final: 0.7749 (mmp) outliers start: 38 outliers final: 28 residues processed: 161 average time/residue: 0.2457 time to fit residues: 64.9301 Evaluate side-chains 150 residues out of total 1934 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 122 time to evaluate : 1.980 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 101 THR Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 174 PHE Chi-restraints excluded: chain A residue 382 THR Chi-restraints excluded: chain A residue 562 GLU Chi-restraints excluded: chain B residue 289 GLU Chi-restraints excluded: chain B residue 358 LEU Chi-restraints excluded: chain B residue 437 GLU Chi-restraints excluded: chain B residue 449 LEU Chi-restraints excluded: chain B residue 460 CYS Chi-restraints excluded: chain B residue 507 GLN Chi-restraints excluded: chain C residue 68 SER Chi-restraints excluded: chain C residue 124 CYS Chi-restraints excluded: chain E residue 22 LEU Chi-restraints excluded: chain E residue 34 THR Chi-restraints excluded: chain E residue 166 VAL Chi-restraints excluded: chain E residue 174 PHE Chi-restraints excluded: chain E residue 193 ASN Chi-restraints excluded: chain E residue 296 MET Chi-restraints excluded: chain E residue 382 THR Chi-restraints excluded: chain E residue 519 ASP Chi-restraints excluded: chain F residue 457 CYS Chi-restraints excluded: chain F residue 460 CYS Chi-restraints excluded: chain G residue 28 MET Chi-restraints excluded: chain G residue 68 SER Chi-restraints excluded: chain G residue 71 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 90 optimal weight: 9.9990 chunk 134 optimal weight: 8.9990 chunk 67 optimal weight: 5.9990 chunk 44 optimal weight: 10.0000 chunk 43 optimal weight: 20.0000 chunk 143 optimal weight: 20.0000 chunk 153 optimal weight: 0.9980 chunk 111 optimal weight: 0.9990 chunk 21 optimal weight: 7.9990 chunk 177 optimal weight: 50.0000 chunk 205 optimal weight: 0.0870 overall best weight: 3.2164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7224 moved from start: 0.4207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 18396 Z= 0.187 Angle : 0.648 15.634 24996 Z= 0.325 Chirality : 0.044 0.148 2872 Planarity : 0.004 0.047 3214 Dihedral : 7.046 172.390 2554 Min Nonbonded Distance : 2.302 Molprobity Statistics. All-atom Clashscore : 13.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 1.65 % Allowed : 19.96 % Favored : 78.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.07 (0.17), residues: 2352 helix: 0.19 (0.16), residues: 988 sheet: -0.08 (0.35), residues: 208 loop : -0.09 (0.19), residues: 1156 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP F 178 HIS 0.003 0.001 HIS A 474 PHE 0.013 0.001 PHE E 125 TYR 0.011 0.001 TYR E 408 ARG 0.003 0.000 ARG G 123 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4704 Ramachandran restraints generated. 2352 Oldfield, 0 Emsley, 2352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4704 Ramachandran restraints generated. 2352 Oldfield, 0 Emsley, 2352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1934 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 126 time to evaluate : 2.185 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 246 MET cc_start: 0.7691 (mmp) cc_final: 0.7212 (mmp) REVERT: A 483 MET cc_start: 0.7288 (tmm) cc_final: 0.7049 (tmm) REVERT: C 91 ARG cc_start: 0.5915 (mpt180) cc_final: 0.5322 (mtm180) REVERT: E 246 MET cc_start: 0.8162 (mmp) cc_final: 0.7769 (mmp) REVERT: E 483 MET cc_start: 0.7289 (tmm) cc_final: 0.7058 (tmm) outliers start: 32 outliers final: 29 residues processed: 149 average time/residue: 0.2396 time to fit residues: 59.4464 Evaluate side-chains 147 residues out of total 1934 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 118 time to evaluate : 1.992 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 THR Chi-restraints excluded: chain A residue 49 MET Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 101 THR Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 193 ASN Chi-restraints excluded: chain A residue 362 GLU Chi-restraints excluded: chain A residue 382 THR Chi-restraints excluded: chain A residue 562 GLU Chi-restraints excluded: chain B residue 437 GLU Chi-restraints excluded: chain B residue 449 LEU Chi-restraints excluded: chain B residue 460 CYS Chi-restraints excluded: chain B residue 507 GLN Chi-restraints excluded: chain C residue 68 SER Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 124 CYS Chi-restraints excluded: chain E residue 34 THR Chi-restraints excluded: chain E residue 93 LEU Chi-restraints excluded: chain E residue 166 VAL Chi-restraints excluded: chain E residue 174 PHE Chi-restraints excluded: chain E residue 296 MET Chi-restraints excluded: chain E residue 382 THR Chi-restraints excluded: chain E residue 519 ASP Chi-restraints excluded: chain F residue 457 CYS Chi-restraints excluded: chain F residue 460 CYS Chi-restraints excluded: chain G residue 28 MET Chi-restraints excluded: chain G residue 68 SER Chi-restraints excluded: chain G residue 71 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 216 optimal weight: 20.0000 chunk 197 optimal weight: 50.0000 chunk 210 optimal weight: 8.9990 chunk 126 optimal weight: 6.9990 chunk 91 optimal weight: 6.9990 chunk 165 optimal weight: 20.0000 chunk 64 optimal weight: 0.7980 chunk 189 optimal weight: 30.0000 chunk 198 optimal weight: 10.0000 chunk 209 optimal weight: 10.0000 chunk 138 optimal weight: 0.7980 overall best weight: 4.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7262 moved from start: 0.4385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 18396 Z= 0.224 Angle : 0.654 13.713 24996 Z= 0.333 Chirality : 0.044 0.150 2872 Planarity : 0.004 0.046 3214 Dihedral : 7.074 173.409 2554 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 14.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 1.81 % Allowed : 19.86 % Favored : 78.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.07 (0.17), residues: 2352 helix: 0.20 (0.16), residues: 988 sheet: -0.22 (0.33), residues: 228 loop : -0.07 (0.20), residues: 1136 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP F 178 HIS 0.004 0.001 HIS A 474 PHE 0.015 0.001 PHE E 125 TYR 0.013 0.001 TYR A 37 ARG 0.004 0.000 ARG B 476 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4704 Ramachandran restraints generated. 2352 Oldfield, 0 Emsley, 2352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4704 Ramachandran restraints generated. 2352 Oldfield, 0 Emsley, 2352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1934 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 120 time to evaluate : 2.161 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 CYS cc_start: 0.8948 (OUTLIER) cc_final: 0.8603 (p) REVERT: A 246 MET cc_start: 0.7770 (mmp) cc_final: 0.7281 (mmp) REVERT: A 418 PHE cc_start: 0.5061 (t80) cc_final: 0.4662 (t80) REVERT: A 483 MET cc_start: 0.7315 (tmm) cc_final: 0.7063 (tmm) REVERT: C 91 ARG cc_start: 0.6245 (mpt180) cc_final: 0.5602 (mtm180) REVERT: E 246 MET cc_start: 0.8170 (mmp) cc_final: 0.7834 (mmp) REVERT: E 483 MET cc_start: 0.7331 (tmm) cc_final: 0.7063 (tmm) REVERT: F 222 MET cc_start: 0.7128 (mpp) cc_final: 0.6837 (mpp) outliers start: 35 outliers final: 31 residues processed: 148 average time/residue: 0.2642 time to fit residues: 65.1542 Evaluate side-chains 146 residues out of total 1934 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 114 time to evaluate : 2.005 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 THR Chi-restraints excluded: chain A residue 47 CYS Chi-restraints excluded: chain A residue 49 MET Chi-restraints excluded: chain A residue 101 THR Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 174 PHE Chi-restraints excluded: chain A residue 362 GLU Chi-restraints excluded: chain A residue 382 THR Chi-restraints excluded: chain A residue 562 GLU Chi-restraints excluded: chain B residue 289 GLU Chi-restraints excluded: chain B residue 437 GLU Chi-restraints excluded: chain B residue 449 LEU Chi-restraints excluded: chain B residue 460 CYS Chi-restraints excluded: chain B residue 507 GLN Chi-restraints excluded: chain C residue 68 SER Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 124 CYS Chi-restraints excluded: chain E residue 34 THR Chi-restraints excluded: chain E residue 93 LEU Chi-restraints excluded: chain E residue 101 THR Chi-restraints excluded: chain E residue 166 VAL Chi-restraints excluded: chain E residue 174 PHE Chi-restraints excluded: chain E residue 193 ASN Chi-restraints excluded: chain E residue 382 THR Chi-restraints excluded: chain E residue 519 ASP Chi-restraints excluded: chain F residue 372 MET Chi-restraints excluded: chain F residue 457 CYS Chi-restraints excluded: chain F residue 460 CYS Chi-restraints excluded: chain G residue 68 SER Chi-restraints excluded: chain G residue 71 THR Chi-restraints excluded: chain G residue 88 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 222 optimal weight: 6.9990 chunk 135 optimal weight: 0.6980 chunk 105 optimal weight: 0.0470 chunk 154 optimal weight: 20.0000 chunk 233 optimal weight: 30.0000 chunk 214 optimal weight: 20.0000 chunk 185 optimal weight: 5.9990 chunk 19 optimal weight: 6.9990 chunk 143 optimal weight: 5.9990 chunk 113 optimal weight: 30.0000 chunk 147 optimal weight: 5.9990 overall best weight: 3.7484 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7233 moved from start: 0.4458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 18396 Z= 0.191 Angle : 0.664 13.088 24996 Z= 0.333 Chirality : 0.044 0.183 2872 Planarity : 0.004 0.047 3214 Dihedral : 6.954 172.883 2554 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 13.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 1.76 % Allowed : 20.27 % Favored : 77.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.01 (0.18), residues: 2352 helix: 0.24 (0.16), residues: 990 sheet: -0.10 (0.35), residues: 208 loop : -0.05 (0.19), residues: 1154 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP F 178 HIS 0.003 0.001 HIS A 474 PHE 0.014 0.001 PHE A 125 TYR 0.011 0.001 TYR A 556 ARG 0.004 0.000 ARG G 123 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4704 Ramachandran restraints generated. 2352 Oldfield, 0 Emsley, 2352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4704 Ramachandran restraints generated. 2352 Oldfield, 0 Emsley, 2352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1934 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 123 time to evaluate : 1.925 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 246 MET cc_start: 0.7693 (mmp) cc_final: 0.7300 (mmp) REVERT: A 418 PHE cc_start: 0.4952 (t80) cc_final: 0.4601 (t80) REVERT: A 483 MET cc_start: 0.7261 (tmm) cc_final: 0.7011 (tmm) REVERT: C 91 ARG cc_start: 0.6158 (mpt180) cc_final: 0.5537 (mtm180) REVERT: E 246 MET cc_start: 0.8087 (mmp) cc_final: 0.7790 (mmp) REVERT: E 483 MET cc_start: 0.7334 (tmm) cc_final: 0.7060 (tmm) REVERT: F 222 MET cc_start: 0.7218 (mpp) cc_final: 0.6991 (mpp) outliers start: 34 outliers final: 31 residues processed: 149 average time/residue: 0.2351 time to fit residues: 58.6413 Evaluate side-chains 151 residues out of total 1934 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 120 time to evaluate : 2.002 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 THR Chi-restraints excluded: chain A residue 49 MET Chi-restraints excluded: chain A residue 101 THR Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 193 ASN Chi-restraints excluded: chain A residue 362 GLU Chi-restraints excluded: chain A residue 382 THR Chi-restraints excluded: chain A residue 562 GLU Chi-restraints excluded: chain B residue 358 LEU Chi-restraints excluded: chain B residue 437 GLU Chi-restraints excluded: chain B residue 449 LEU Chi-restraints excluded: chain B residue 460 CYS Chi-restraints excluded: chain B residue 507 GLN Chi-restraints excluded: chain C residue 9 ASN Chi-restraints excluded: chain C residue 68 SER Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 124 CYS Chi-restraints excluded: chain E residue 34 THR Chi-restraints excluded: chain E residue 93 LEU Chi-restraints excluded: chain E residue 101 THR Chi-restraints excluded: chain E residue 166 VAL Chi-restraints excluded: chain E residue 174 PHE Chi-restraints excluded: chain E residue 193 ASN Chi-restraints excluded: chain E residue 296 MET Chi-restraints excluded: chain E residue 382 THR Chi-restraints excluded: chain F residue 457 CYS Chi-restraints excluded: chain F residue 460 CYS Chi-restraints excluded: chain G residue 28 MET Chi-restraints excluded: chain G residue 68 SER Chi-restraints excluded: chain G residue 71 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 197 optimal weight: 50.0000 chunk 56 optimal weight: 7.9990 chunk 171 optimal weight: 0.0070 chunk 27 optimal weight: 5.9990 chunk 51 optimal weight: 5.9990 chunk 185 optimal weight: 20.0000 chunk 77 optimal weight: 30.0000 chunk 190 optimal weight: 9.9990 chunk 23 optimal weight: 6.9990 chunk 34 optimal weight: 20.0000 chunk 163 optimal weight: 30.0000 overall best weight: 5.4006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 183 ASN ** E 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.054212 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2851 r_free = 0.2851 target = 0.034944 restraints weight = 100295.980| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2888 r_free = 0.2888 target = 0.036246 restraints weight = 64212.178| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.2907 r_free = 0.2907 target = 0.037022 restraints weight = 48859.832| |-----------------------------------------------------------------------------| r_work (final): 0.2798 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8606 moved from start: 0.4640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 18396 Z= 0.237 Angle : 0.682 13.413 24996 Z= 0.346 Chirality : 0.045 0.185 2872 Planarity : 0.004 0.046 3214 Dihedral : 7.014 173.908 2554 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 15.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 1.96 % Allowed : 20.17 % Favored : 77.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.05 (0.17), residues: 2352 helix: 0.22 (0.16), residues: 986 sheet: -0.17 (0.33), residues: 238 loop : -0.07 (0.20), residues: 1128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP F 178 HIS 0.004 0.001 HIS A 474 PHE 0.016 0.001 PHE E 125 TYR 0.013 0.001 TYR A 37 ARG 0.004 0.000 ARG B 476 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2846.41 seconds wall clock time: 52 minutes 52.21 seconds (3172.21 seconds total)