Starting phenix.real_space_refine on Sun Mar 17 14:57:53 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7q4w_13819/03_2024/7q4w_13819_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7q4w_13819/03_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_13819/03_2024/7q4w_13819.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7q4w_13819/03_2024/7q4w_13819.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7q4w_13819/03_2024/7q4w_13819_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7q4w_13819/03_2024/7q4w_13819_neut_updated.pdb" } 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 Residue "A GLU 23": "OE1" <-> "OE2" Residue "A GLU 99": "OE1" <-> "OE2" Residue "A GLU 107": "OE1" <-> "OE2" Residue "A PHE 174": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 217": "OD1" <-> "OD2" Residue "B GLU 289": "OE1" <-> "OE2" Residue "B GLU 297": "OE1" <-> "OE2" Residue "B PHE 342": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 437": "OE1" <-> "OE2" Residue "B ASP 450": "OD1" <-> "OD2" Residue "B GLU 455": "OE1" <-> "OE2" Residue "B GLU 472": "OE1" <-> "OE2" Residue "C GLU 44": "OE1" <-> "OE2" Residue "E GLU 110": "OE1" <-> "OE2" Residue "E PHE 125": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 144": "OD1" <-> "OD2" Residue "E PHE 174": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 182": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 217": "OD1" <-> "OD2" Residue "F TYR 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 273": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 297": "OE1" <-> "OE2" Residue "F PHE 342": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 418": "OD1" <-> "OD2" Residue "F GLU 455": "OE1" <-> "OE2" Residue "F GLU 472": "OE1" <-> "OE2" Residue "F GLU 589": "OE1" <-> "OE2" Residue "G GLU 19": "OE1" <-> "OE2" Residue "G TYR 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 44": "OE1" <-> "OE2" Residue "G GLU 52": "OE1" <-> "OE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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: 9.53, per 1000 atoms: 0.53 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 7.01 Conformation dependent library (CDL) restraints added in 3.5 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... running ksdssp... Secondary structure from input PDB file: 118 helices and 19 sheets defined 42.6% alpha, 8.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.75 Creating SS restraints... Processing helix chain 'A' and resid 21 through 27 Processing helix chain 'A' and resid 79 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 106 through 108 No H-bonds generated for 'chain 'A' and resid 106 through 108' Processing helix chain 'A' and resid 110 through 118 Processing helix chain 'A' and resid 153 through 160 Processing helix chain 'A' and resid 173 through 175 No H-bonds generated for 'chain 'A' and resid 173 through 175' Processing helix chain 'A' and resid 181 through 183 No H-bonds generated for 'chain 'A' and resid 181 through 183' Processing helix chain 'A' and resid 186 through 188 No H-bonds generated for 'chain 'A' and resid 186 through 188' Processing helix chain 'A' and resid 196 through 200 Processing helix chain 'A' and resid 212 through 219 Processing helix chain 'A' and resid 238 through 242 Processing helix chain 'A' and resid 251 through 260 Processing helix chain 'A' and resid 270 through 290 Processing helix chain 'A' and resid 302 through 311 Processing helix chain 'A' and resid 313 through 318 Proline residue: A 317 - end of helix Processing helix chain 'A' and resid 325 through 341 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 345 through 347 No H-bonds generated for 'chain 'A' and resid 345 through 347' Processing helix chain 'A' and resid 358 through 363 Processing helix chain 'A' and resid 382 through 392 Processing helix chain 'A' and resid 396 through 398 No H-bonds generated for 'chain 'A' and resid 396 through 398' Processing helix chain 'A' and resid 413 through 418 removed outlier: 4.721A pdb=" N PHE A 418 " --> pdb=" O ALA A 414 " (cutoff:3.500A) Processing helix chain 'A' and resid 423 through 437 Processing helix chain 'A' and resid 476 through 488 Processing helix chain 'A' and resid 506 through 508 No H-bonds generated for 'chain 'A' and resid 506 through 508' Processing helix chain 'A' and resid 518 through 522 Processing helix chain 'A' and resid 525 through 538 Processing helix chain 'A' and resid 550 through 558 Processing helix chain 'A' and resid 566 through 572 Processing helix chain 'B' and resid 131 through 137 removed outlier: 3.519A pdb=" N PHE B 137 " --> pdb=" O GLU B 133 " (cutoff:3.500A) Processing helix chain 'B' and resid 141 through 149 removed outlier: 3.915A pdb=" N LEU B 148 " --> pdb=" O GLU B 144 " (cutoff:3.500A) Processing helix chain 'B' and resid 152 through 162 removed outlier: 3.620A pdb=" N ILE B 156 " --> pdb=" O PRO B 152 " (cutoff:3.500A) Processing helix chain 'B' and resid 174 through 183 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) Processing helix chain 'B' and resid 206 through 229 removed outlier: 3.786A pdb=" N LEU B 211 " --> pdb=" O ASP B 207 " (cutoff:3.500A) Proline residue: B 215 - end of helix 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 243 through 259 Processing helix chain 'B' and resid 266 through 268 No H-bonds generated for 'chain 'B' and resid 266 through 268' Processing helix chain 'B' and resid 284 through 287 Processing helix chain 'B' and resid 289 through 297 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 315 through 317 No H-bonds generated for 'chain 'B' and resid 315 through 317' Processing helix chain 'B' and resid 325 through 329 Processing helix chain 'B' and resid 331 through 337 Processing helix chain 'B' and resid 339 through 344 Processing helix chain 'B' and resid 376 through 381 removed outlier: 3.503A pdb=" N ILE B 380 " --> pdb=" O LEU B 376 " (cutoff:3.500A) Processing helix chain 'B' and resid 388 through 390 No H-bonds generated for 'chain 'B' and resid 388 through 390' Processing helix chain 'B' and resid 400 through 402 No H-bonds generated for 'chain 'B' and resid 400 through 402' Processing helix chain 'B' and resid 408 through 410 No H-bonds generated for 'chain 'B' and resid 408 through 410' Processing helix chain 'B' and resid 417 through 422 removed outlier: 3.536A pdb=" N ILE B 421 " --> pdb=" O TYR B 417 " (cutoff:3.500A) Processing helix chain 'B' and resid 441 through 454 removed outlier: 3.545A pdb=" N THR B 452 " --> pdb=" O PHE B 448 " (cutoff:3.500A) Processing helix chain 'B' and resid 461 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 486 through 498 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 504 through 519 removed outlier: 3.737A pdb=" N THR B 508 " --> pdb=" O GLY B 504 " (cutoff:3.500A) Proline residue: B 510 - end of helix removed outlier: 4.898A pdb=" N VAL B 513 " --> pdb=" O ALA B 509 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N PHE B 519 " --> pdb=" O SER B 515 " (cutoff:3.500A) Processing helix chain 'B' and resid 521 through 528 removed outlier: 3.673A pdb=" N GLU B 525 " --> pdb=" O ARG B 521 " (cutoff:3.500A) Processing helix chain 'B' and resid 556 through 559 No H-bonds generated for 'chain 'B' and resid 556 through 559' Processing helix chain 'B' and resid 586 through 590 Processing helix chain 'C' and resid 11 through 19 Processing helix chain 'C' and resid 26 through 38 Processing helix chain 'C' and resid 43 through 53 Processing helix chain 'C' and resid 57 through 66 Processing helix chain 'C' and resid 86 through 90 Processing helix chain 'C' and resid 93 through 104 Processing helix chain 'E' and resid 21 through 27 Processing helix chain 'E' and resid 79 through 94 removed outlier: 3.596A pdb=" N SER E 94 " --> pdb=" O GLU E 90 " (cutoff:3.500A) Processing helix chain 'E' and resid 106 through 108 No H-bonds generated for 'chain 'E' and resid 106 through 108' Processing helix chain 'E' and resid 110 through 118 Processing helix chain 'E' and resid 153 through 160 Processing helix chain 'E' and resid 173 through 175 No H-bonds generated for 'chain 'E' and resid 173 through 175' Processing helix chain 'E' and resid 181 through 183 No H-bonds generated for 'chain 'E' and resid 181 through 183' Processing helix chain 'E' and resid 186 through 188 No H-bonds generated for 'chain 'E' and resid 186 through 188' Processing helix chain 'E' and resid 196 through 199 No H-bonds generated for 'chain 'E' and resid 196 through 199' Processing helix chain 'E' and resid 212 through 219 Processing helix chain 'E' and resid 239 through 242 Processing helix chain 'E' and resid 251 through 261 Processing helix chain 'E' and resid 270 through 290 Processing helix chain 'E' and resid 302 through 311 Processing helix chain 'E' and resid 313 through 318 Proline residue: E 317 - end of helix Processing helix chain 'E' and resid 325 through 341 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 345 through 347 No H-bonds generated for 'chain 'E' and resid 345 through 347' Processing helix chain 'E' and resid 358 through 364 removed outlier: 3.632A pdb=" N GLN E 364 " --> pdb=" O LYS E 360 " (cutoff:3.500A) Processing helix chain 'E' and resid 382 through 392 Processing helix chain 'E' and resid 396 through 398 No H-bonds generated for 'chain 'E' and resid 396 through 398' Processing helix chain 'E' and resid 413 through 418 removed outlier: 4.540A pdb=" N PHE E 418 " --> pdb=" O ALA E 414 " (cutoff:3.500A) Processing helix chain 'E' and resid 423 through 437 Processing helix chain 'E' and resid 476 through 488 Processing helix chain 'E' and resid 506 through 508 No H-bonds generated for 'chain 'E' and resid 506 through 508' Processing helix chain 'E' and resid 517 through 522 removed outlier: 3.969A pdb=" N ASP E 522 " --> pdb=" O LYS E 518 " (cutoff:3.500A) Processing helix chain 'E' and resid 525 through 538 Processing helix chain 'E' and resid 550 through 558 Processing helix chain 'E' and resid 566 through 572 Processing helix chain 'F' and resid 131 through 137 removed outlier: 3.582A pdb=" N PHE F 137 " --> pdb=" O GLU F 133 " (cutoff:3.500A) Processing helix chain 'F' and resid 141 through 149 removed outlier: 3.883A pdb=" N LEU F 148 " --> pdb=" O GLU F 144 " (cutoff:3.500A) Processing helix chain 'F' and resid 152 through 162 removed outlier: 3.634A pdb=" N ILE F 156 " --> pdb=" O PRO F 152 " (cutoff:3.500A) Processing helix chain 'F' and resid 174 through 183 Processing helix chain 'F' and resid 206 through 229 Proline residue: F 215 - end of helix 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 243 through 259 Processing helix chain 'F' and resid 266 through 268 No H-bonds generated for 'chain 'F' and resid 266 through 268' Processing helix chain 'F' and resid 284 through 287 Processing helix chain 'F' and resid 289 through 297 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 315 through 317 No H-bonds generated for 'chain 'F' and resid 315 through 317' Processing helix chain 'F' and resid 325 through 337 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 339 through 343 Processing helix chain 'F' and resid 376 through 381 Processing helix chain 'F' and resid 388 through 390 No H-bonds generated for 'chain 'F' and resid 388 through 390' Processing helix chain 'F' and resid 400 through 402 No H-bonds generated for 'chain 'F' and resid 400 through 402' Processing helix chain 'F' and resid 408 through 410 No H-bonds generated for 'chain 'F' and resid 408 through 410' Processing helix chain 'F' and resid 417 through 423 Processing helix chain 'F' and resid 441 through 455 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 461 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 486 through 498 removed outlier: 3.849A pdb=" N LEU F 493 " --> pdb=" O ARG F 489 " (cutoff:3.500A) Processing helix chain 'F' and resid 504 through 508 Processing helix chain 'F' and resid 511 through 519 removed outlier: 3.891A pdb=" N PHE F 519 " --> pdb=" O SER F 515 " (cutoff:3.500A) Processing helix chain 'F' and resid 522 through 528 removed outlier: 3.693A pdb=" N ALA F 526 " --> pdb=" O ASP F 522 " (cutoff:3.500A) Processing helix chain 'F' and resid 556 through 559 No H-bonds generated for 'chain 'F' and resid 556 through 559' Processing helix chain 'F' and resid 586 through 590 Processing helix chain 'G' and resid 11 through 18 Processing helix chain 'G' and resid 26 through 38 Processing helix chain 'G' and resid 43 through 53 Processing helix chain 'G' and resid 57 through 66 Processing helix chain 'G' and resid 86 through 89 No H-bonds generated for 'chain 'G' and resid 86 through 89' Processing helix chain 'G' and resid 93 through 104 Processing sheet with id= A, first strand: chain 'A' and resid 3 through 8 Processing sheet with id= B, first strand: chain 'A' and resid 141 through 143 Processing sheet with id= C, first strand: chain 'A' and resid 168 through 170 Processing sheet with id= D, first strand: chain 'A' and resid 265 through 268 removed outlier: 7.109A pdb=" N ILE A 378 " --> pdb=" O SER A 352 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 455 through 460 removed outlier: 3.877A pdb=" N VAL A 460 " --> pdb=" O VAL A 468 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N VAL A 468 " --> pdb=" O VAL A 460 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N PHE A 496 " --> pdb=" O VAL A 471 " (cutoff:3.500A) removed outlier: 7.904A pdb=" N ALA A 473 " --> pdb=" O PHE A 496 " (cutoff:3.500A) removed outlier: 6.018A pdb=" N GLU A 498 " --> pdb=" O ALA A 473 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 320 through 324 removed outlier: 7.368A pdb=" N TYR B 192 " --> pdb=" O VAL B 321 " (cutoff:3.500A) removed outlier: 8.863A pdb=" N ASN B 323 " --> pdb=" O TYR B 192 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N ALA B 194 " --> pdb=" O ASN B 323 " (cutoff:3.500A) removed outlier: 7.131A pdb=" N LYS B 233 " --> pdb=" O VAL B 193 " (cutoff:3.500A) removed outlier: 8.877A pdb=" N CYS B 195 " --> pdb=" O LYS B 233 " (cutoff:3.500A) removed outlier: 7.056A pdb=" N TYR B 235 " --> pdb=" O CYS B 195 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N ASP B 274 " --> pdb=" O GLY B 234 " (cutoff:3.500A) removed outlier: 7.594A pdb=" N VAL B 236 " --> pdb=" O ASP B 274 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N GLU B 276 " --> pdb=" O VAL B 236 " (cutoff:3.500A) removed outlier: 7.781A pdb=" N VAL B 238 " --> pdb=" O GLU B 276 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N ARG B 278 " --> pdb=" O VAL B 238 " (cutoff:3.500A) No H-bonds generated for sheet with id= F Processing sheet with id= G, 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) Processing sheet with id= H, first strand: chain 'B' and resid 543 through 546 Processing sheet with id= I, first strand: chain 'C' and resid 78 through 81 Processing sheet with id= J, first strand: chain 'E' and resid 3 through 8 Processing sheet with id= K, first strand: chain 'E' and resid 141 through 143 Processing sheet with id= L, first strand: chain 'E' and resid 168 through 170 Processing sheet with id= M, first strand: chain 'E' and resid 265 through 268 removed outlier: 6.811A pdb=" N ILE E 378 " --> pdb=" O SER E 352 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'E' and resid 455 through 460 removed outlier: 4.247A pdb=" N VAL E 460 " --> pdb=" O VAL E 468 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N VAL E 468 " --> pdb=" O VAL E 460 " (cutoff:3.500A) removed outlier: 6.180A pdb=" N PHE E 496 " --> pdb=" O VAL E 471 " (cutoff:3.500A) removed outlier: 7.678A pdb=" N ALA E 473 " --> pdb=" O PHE E 496 " (cutoff:3.500A) removed outlier: 5.857A pdb=" N GLU E 498 " --> pdb=" O ALA E 473 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'F' and resid 322 through 324 removed outlier: 9.078A pdb=" N ASN F 323 " --> pdb=" O TYR F 192 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N ALA F 194 " --> pdb=" O ASN F 323 " (cutoff:3.500A) removed outlier: 7.228A pdb=" N LYS F 233 " --> pdb=" O VAL F 193 " (cutoff:3.500A) removed outlier: 8.952A pdb=" N CYS F 195 " --> pdb=" O LYS F 233 " (cutoff:3.500A) removed outlier: 7.041A pdb=" N TYR F 235 " --> pdb=" O CYS F 195 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'F' and resid 353 through 356 removed outlier: 3.615A pdb=" N LEU F 368 " --> pdb=" O PHE F 356 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'F' and resid 357 through 360 removed outlier: 3.586A pdb=" N ALA F 395 " --> pdb=" O MET F 435 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'F' and resid 543 through 546 Processing sheet with id= S, first strand: chain 'G' and resid 78 through 83 587 hydrogen bonds defined for protein. 1704 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: 5.66 Time building geometry restraints manager: 7.29 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: 73.01 - 85.34: 176 85.34 - 97.66: 0 97.66 - 109.99: 2911 109.99 - 122.32: 19258 122.32 - 134.64: 2651 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: 1019 2.73 - 3.27: 19013 3.27 - 3.81: 29564 3.81 - 4.36: 34958 4.36 - 4.90: 57094 Nonbonded interactions: 141648 Sorted by model distance: nonbonded pdb=" OE2 GLU E 99 " pdb=" OG1 THR E 101 " model vdw 2.186 2.440 nonbonded pdb=" OD2 ASP B 443 " pdb=" OH TYR C 89 " model vdw 2.202 2.440 nonbonded pdb=" O LYS F 459 " pdb=" NH2 ARG F 464 " model vdw 2.256 2.520 nonbonded pdb=" O ALA B 281 " pdb=" NE2 GLN C 69 " model vdw 2.266 2.520 nonbonded pdb=" O ARG A 48 " pdb=" ND2 ASN A 88 " model vdw 2.271 2.520 ... (remaining 141643 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain '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: 0.340 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: 2.700 Check model and map are aligned: 0.270 Set scattering table: 0.160 Process input model: 54.290 Find NCS groups from input model: 1.070 Set up NCS constraints: 0.130 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:2.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 61.770 ------------------------------------------------------------------------------- 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= 0.325 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 : 2.133 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: 0.3081 time to fit residues: 108.0542 Evaluate side-chains 135 residues out of total 1934 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 132 time to evaluate : 2.046 ------------------------------------------------------------------------------- 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: 8.9990 chunk 177 optimal weight: 0.2980 chunk 98 optimal weight: 7.9990 chunk 60 optimal weight: 3.9990 chunk 119 optimal weight: 1.9990 chunk 94 optimal weight: 10.0000 chunk 183 optimal weight: 9.9990 chunk 70 optimal weight: 20.0000 chunk 111 optimal weight: 9.9990 chunk 136 optimal weight: 10.0000 chunk 212 optimal weight: 8.9990 overall best weight: 4.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 11 GLN ** A 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 507 GLN E 196 GLN ** 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: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7073 moved from start: 0.1788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 18396 Z= 0.221 Angle : 0.623 10.437 24996 Z= 0.320 Chirality : 0.045 0.265 2872 Planarity : 0.004 0.056 3214 Dihedral : 7.452 172.325 2561 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 14.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 0.83 % Allowed : 9.67 % Favored : 89.50 % 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: -0.09 (0.17), residues: 2352 helix: 0.08 (0.16), residues: 988 sheet: 0.85 (0.37), residues: 166 loop : -0.19 (0.18), residues: 1198 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP F 178 HIS 0.005 0.001 HIS A 474 PHE 0.020 0.002 PHE E 6 TYR 0.011 0.001 TYR G 61 ARG 0.007 0.001 ARG E 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 159 residues out of total 1934 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 143 time to evaluate : 2.052 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 246 MET cc_start: 0.7638 (mmp) cc_final: 0.7417 (mmp) outliers start: 16 outliers final: 12 residues processed: 151 average time/residue: 0.2592 time to fit residues: 63.3931 Evaluate side-chains 134 residues out of total 1934 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 122 time to evaluate : 2.181 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 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 478 CYS Chi-restraints excluded: chain F residue 522 ASP 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: 20.0000 chunk 212 optimal weight: 5.9990 chunk 229 optimal weight: 9.9990 chunk 189 optimal weight: 20.0000 chunk 211 optimal weight: 1.9990 chunk 72 optimal weight: 30.0000 chunk 170 optimal weight: 30.0000 overall best weight: 11.5994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 157 ASN B 179 GLN ** B 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 9 ASN ** 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: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7338 moved from start: 0.3229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.086 18396 Z= 0.444 Angle : 0.792 10.679 24996 Z= 0.422 Chirality : 0.053 0.282 2872 Planarity : 0.006 0.063 3214 Dihedral : 7.953 175.059 2554 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 27.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 2.22 % Allowed : 13.50 % Favored : 84.28 % 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: -0.54 (0.17), residues: 2352 helix: -0.32 (0.16), residues: 982 sheet: 0.85 (0.39), residues: 168 loop : -0.45 (0.18), residues: 1202 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP F 178 HIS 0.008 0.002 HIS E 474 PHE 0.024 0.003 PHE E 125 TYR 0.023 0.002 TYR E 312 ARG 0.009 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 167 residues out of total 1934 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 124 time to evaluate : 2.049 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 23 GLU cc_start: 0.8089 (OUTLIER) cc_final: 0.7687 (pp20) REVERT: A 47 CYS cc_start: 0.8012 (OUTLIER) cc_final: 0.7714 (p) REVERT: A 49 MET cc_start: 0.6482 (mmm) cc_final: 0.6191 (mmm) REVERT: E 246 MET cc_start: 0.8064 (mmp) cc_final: 0.7354 (mmp) outliers start: 43 outliers final: 33 residues processed: 156 average time/residue: 0.2673 time to fit residues: 68.2153 Evaluate side-chains 148 residues out of total 1934 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 113 time to evaluate : 2.111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 GLU Chi-restraints excluded: chain A residue 47 CYS Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 178 VAL 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 283 GLU Chi-restraints excluded: chain A residue 300 CYS Chi-restraints excluded: chain A residue 382 THR Chi-restraints excluded: chain A residue 385 LEU Chi-restraints excluded: chain B residue 441 MET Chi-restraints excluded: chain B residue 449 LEU Chi-restraints excluded: chain B residue 450 ASP Chi-restraints excluded: chain B residue 460 CYS Chi-restraints excluded: chain B residue 507 GLN Chi-restraints excluded: chain B residue 584 CYS Chi-restraints excluded: chain C residue 9 ASN Chi-restraints excluded: chain C residue 40 TYR Chi-restraints excluded: chain C residue 51 ASP Chi-restraints excluded: chain C residue 68 SER Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain E residue 47 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 348 MET 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 478 CYS Chi-restraints excluded: chain F residue 522 ASP Chi-restraints excluded: chain G residue 28 MET 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: 0.0670 chunk 160 optimal weight: 20.0000 chunk 110 optimal weight: 5.9990 chunk 23 optimal weight: 7.9990 chunk 101 optimal weight: 20.0000 chunk 142 optimal weight: 5.9990 chunk 213 optimal weight: 7.9990 chunk 226 optimal weight: 5.9990 chunk 111 optimal weight: 5.9990 chunk 202 optimal weight: 6.9990 chunk 60 optimal weight: 0.0570 overall best weight: 3.6242 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 469 ASN B 157 ASN C 9 ASN E 326 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7201 moved from start: 0.3077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 18396 Z= 0.186 Angle : 0.587 9.836 24996 Z= 0.300 Chirality : 0.043 0.206 2872 Planarity : 0.004 0.050 3214 Dihedral : 7.369 172.840 2554 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 16.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 1.86 % Allowed : 15.10 % Favored : 83.04 % 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: 0.04 (0.16), residues: 992 sheet: 0.83 (0.36), residues: 184 loop : -0.29 (0.18), residues: 1176 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP F 178 HIS 0.003 0.001 HIS E 474 PHE 0.016 0.001 PHE E 125 TYR 0.013 0.001 TYR E 312 ARG 0.004 0.000 ARG E 287 *********************** 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 173 residues out of total 1934 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 137 time to evaluate : 2.046 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 483 MET cc_start: 0.6811 (tmm) cc_final: 0.6424 (tmm) REVERT: C 91 ARG cc_start: 0.5570 (mpt180) cc_final: 0.4868 (mtm180) REVERT: E 397 ASN cc_start: 0.8731 (OUTLIER) cc_final: 0.8135 (p0) outliers start: 36 outliers final: 19 residues processed: 164 average time/residue: 0.2494 time to fit residues: 66.6387 Evaluate side-chains 144 residues out of total 1934 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 124 time to evaluate : 1.737 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 382 THR Chi-restraints excluded: chain A residue 500 MET Chi-restraints excluded: chain B residue 449 LEU Chi-restraints excluded: chain B residue 460 CYS 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 111 LEU Chi-restraints excluded: chain E residue 199 ILE Chi-restraints excluded: chain E residue 348 MET Chi-restraints excluded: chain E residue 382 THR Chi-restraints excluded: chain E residue 397 ASN 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 28 MET 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: 10.0000 chunk 128 optimal weight: 0.7980 chunk 3 optimal weight: 0.0970 chunk 168 optimal weight: 20.0000 chunk 93 optimal weight: 8.9990 chunk 193 optimal weight: 10.0000 chunk 156 optimal weight: 6.9990 chunk 0 optimal weight: 20.0000 chunk 115 optimal weight: 50.0000 chunk 203 optimal weight: 1.9990 chunk 57 optimal weight: 40.0000 overall best weight: 3.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 9 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7205 moved from start: 0.3241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 18396 Z= 0.184 Angle : 0.569 8.305 24996 Z= 0.291 Chirality : 0.043 0.207 2872 Planarity : 0.004 0.050 3214 Dihedral : 7.202 172.567 2554 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 16.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 2.22 % Allowed : 16.34 % Favored : 81.44 % 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 (0.17), residues: 2352 helix: 0.16 (0.16), residues: 980 sheet: 0.81 (0.39), residues: 164 loop : -0.14 (0.18), residues: 1208 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP F 178 HIS 0.003 0.001 HIS E 474 PHE 0.013 0.001 PHE E 125 TYR 0.013 0.001 TYR E 408 ARG 0.005 0.000 ARG E 26 *********************** 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 174 residues out of total 1934 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 131 time to evaluate : 2.055 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 23 GLU cc_start: 0.7919 (OUTLIER) cc_final: 0.7672 (pp20) REVERT: A 483 MET cc_start: 0.6882 (tmm) cc_final: 0.6606 (tmm) REVERT: C 61 TYR cc_start: 0.7761 (OUTLIER) cc_final: 0.7317 (t80) REVERT: C 91 ARG cc_start: 0.5530 (mpt180) cc_final: 0.4742 (mtm180) REVERT: E 246 MET cc_start: 0.8002 (mmp) cc_final: 0.7401 (mmp) REVERT: E 397 ASN cc_start: 0.8738 (OUTLIER) cc_final: 0.8134 (p0) REVERT: E 483 MET cc_start: 0.6923 (tmm) cc_final: 0.6676 (tmm) outliers start: 43 outliers final: 27 residues processed: 163 average time/residue: 0.2394 time to fit residues: 64.7428 Evaluate side-chains 153 residues out of total 1934 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 123 time to evaluate : 2.076 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 GLU Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 132 LYS 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 A residue 424 VAL Chi-restraints excluded: chain A residue 500 MET Chi-restraints excluded: chain B residue 449 LEU Chi-restraints excluded: chain B residue 460 CYS 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 E residue 47 CYS Chi-restraints excluded: chain E residue 199 ILE Chi-restraints excluded: chain E residue 382 THR Chi-restraints excluded: chain E residue 397 ASN Chi-restraints excluded: chain E residue 479 ILE Chi-restraints excluded: chain E residue 519 ASP Chi-restraints excluded: chain F residue 372 MET Chi-restraints excluded: chain F residue 437 GLU Chi-restraints excluded: chain F residue 460 CYS Chi-restraints excluded: chain F residue 478 CYS Chi-restraints excluded: chain F residue 522 ASP Chi-restraints excluded: chain G residue 28 MET 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: 8.9990 chunk 203 optimal weight: 5.9990 chunk 44 optimal weight: 30.0000 chunk 132 optimal weight: 0.8980 chunk 55 optimal weight: 10.0000 chunk 226 optimal weight: 20.0000 chunk 187 optimal weight: 30.0000 chunk 104 optimal weight: 40.0000 chunk 18 optimal weight: 0.1980 chunk 74 optimal weight: 6.9990 chunk 118 optimal weight: 30.0000 overall best weight: 4.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 9 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7229 moved from start: 0.3454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 18396 Z= 0.202 Angle : 0.581 8.819 24996 Z= 0.297 Chirality : 0.043 0.186 2872 Planarity : 0.004 0.050 3214 Dihedral : 7.137 172.548 2554 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 17.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 2.69 % Allowed : 17.32 % Favored : 79.99 % 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 (0.17), residues: 2352 helix: 0.17 (0.16), residues: 980 sheet: 0.78 (0.39), residues: 164 loop : -0.13 (0.18), residues: 1208 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP F 178 HIS 0.004 0.001 HIS E 474 PHE 0.013 0.001 PHE A 125 TYR 0.013 0.001 TYR A 408 ARG 0.004 0.000 ARG E 287 *********************** 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 177 residues out of total 1934 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 125 time to evaluate : 1.777 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 23 GLU cc_start: 0.7933 (OUTLIER) cc_final: 0.7652 (pp20) REVERT: A 397 ASN cc_start: 0.8614 (OUTLIER) cc_final: 0.8085 (p0) REVERT: A 483 MET cc_start: 0.6995 (tmm) cc_final: 0.6749 (tmm) REVERT: C 91 ARG cc_start: 0.5531 (mpt180) cc_final: 0.4779 (mtm180) REVERT: E 246 MET cc_start: 0.8018 (mmp) cc_final: 0.7389 (mmp) REVERT: E 397 ASN cc_start: 0.8722 (OUTLIER) cc_final: 0.8118 (p0) outliers start: 52 outliers final: 34 residues processed: 166 average time/residue: 0.2414 time to fit residues: 66.4956 Evaluate side-chains 160 residues out of total 1934 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 123 time to evaluate : 2.040 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 GLU Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 93 LEU 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 282 THR Chi-restraints excluded: chain A residue 382 THR Chi-restraints excluded: chain A residue 397 ASN Chi-restraints excluded: chain A residue 500 MET Chi-restraints excluded: chain B residue 358 LEU 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 E residue 34 THR Chi-restraints excluded: chain E residue 40 ASP Chi-restraints excluded: chain E residue 47 CYS Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain E residue 166 VAL Chi-restraints excluded: chain E residue 199 ILE Chi-restraints excluded: chain E residue 356 CYS Chi-restraints excluded: chain E residue 382 THR Chi-restraints excluded: chain E residue 397 ASN Chi-restraints excluded: chain E residue 479 ILE Chi-restraints excluded: chain E residue 519 ASP Chi-restraints excluded: chain F residue 372 MET Chi-restraints excluded: chain F residue 437 GLU Chi-restraints excluded: chain F residue 460 CYS Chi-restraints excluded: chain F residue 478 CYS Chi-restraints excluded: chain F residue 522 ASP Chi-restraints excluded: chain G residue 28 MET 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: 7.9990 chunk 25 optimal weight: 0.8980 chunk 128 optimal weight: 6.9990 chunk 165 optimal weight: 5.9990 chunk 190 optimal weight: 50.0000 chunk 126 optimal weight: 9.9990 chunk 225 optimal weight: 30.0000 chunk 141 optimal weight: 20.0000 chunk 137 optimal weight: 10.0000 chunk 104 optimal weight: 3.9990 chunk 139 optimal weight: 10.0000 overall best weight: 5.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 469 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7255 moved from start: 0.3721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 18396 Z= 0.223 Angle : 0.597 9.477 24996 Z= 0.306 Chirality : 0.043 0.168 2872 Planarity : 0.004 0.051 3214 Dihedral : 7.106 172.985 2554 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 18.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 2.84 % Allowed : 18.05 % Favored : 79.11 % 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: -0.02 (0.17), residues: 2352 helix: 0.13 (0.16), residues: 980 sheet: 0.78 (0.37), residues: 184 loop : -0.13 (0.19), residues: 1188 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP F 178 HIS 0.004 0.001 HIS E 474 PHE 0.013 0.001 PHE A 125 TYR 0.014 0.001 TYR A 37 ARG 0.004 0.000 ARG G 123 *********************** 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 179 residues out of total 1934 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 124 time to evaluate : 2.015 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 23 GLU cc_start: 0.7919 (OUTLIER) cc_final: 0.7659 (pp20) REVERT: A 397 ASN cc_start: 0.8641 (OUTLIER) cc_final: 0.8097 (p0) REVERT: A 483 MET cc_start: 0.7149 (tmm) cc_final: 0.6897 (tmm) REVERT: C 91 ARG cc_start: 0.5522 (mpt180) cc_final: 0.4852 (mtm180) REVERT: E 397 ASN cc_start: 0.8696 (OUTLIER) cc_final: 0.8125 (p0) outliers start: 55 outliers final: 40 residues processed: 164 average time/residue: 0.2401 time to fit residues: 66.1406 Evaluate side-chains 161 residues out of total 1934 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 118 time to evaluate : 1.932 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 GLU Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 99 GLU 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 A residue 385 LEU Chi-restraints excluded: chain A residue 397 ASN Chi-restraints excluded: chain A residue 500 MET Chi-restraints excluded: chain B residue 358 LEU Chi-restraints excluded: chain B residue 441 MET 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 E residue 34 THR Chi-restraints excluded: chain E residue 40 ASP Chi-restraints excluded: chain E residue 47 CYS Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain E residue 166 VAL Chi-restraints excluded: chain E residue 199 ILE Chi-restraints excluded: chain E residue 348 MET Chi-restraints excluded: chain E residue 356 CYS Chi-restraints excluded: chain E residue 369 CYS Chi-restraints excluded: chain E residue 382 THR Chi-restraints excluded: chain E residue 397 ASN Chi-restraints excluded: chain E residue 479 ILE Chi-restraints excluded: chain E residue 519 ASP Chi-restraints excluded: chain F residue 372 MET Chi-restraints excluded: chain F residue 437 GLU Chi-restraints excluded: chain F residue 460 CYS Chi-restraints excluded: chain F residue 475 GLU Chi-restraints excluded: chain F residue 478 CYS Chi-restraints excluded: chain F residue 522 ASP Chi-restraints excluded: chain F residue 525 GLU Chi-restraints excluded: chain G residue 28 MET 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 90 optimal weight: 20.0000 chunk 134 optimal weight: 7.9990 chunk 67 optimal weight: 5.9990 chunk 44 optimal weight: 5.9990 chunk 43 optimal weight: 8.9990 chunk 143 optimal weight: 7.9990 chunk 153 optimal weight: 8.9990 chunk 111 optimal weight: 6.9990 chunk 21 optimal weight: 8.9990 chunk 177 optimal weight: 0.8980 chunk 205 optimal weight: 5.9990 overall best weight: 5.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 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: 0.3936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 18396 Z= 0.222 Angle : 0.596 11.530 24996 Z= 0.305 Chirality : 0.043 0.184 2872 Planarity : 0.004 0.051 3214 Dihedral : 7.085 172.799 2554 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 19.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 2.43 % Allowed : 18.87 % Favored : 78.70 % 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: -0.00 (0.17), residues: 2352 helix: 0.14 (0.16), residues: 970 sheet: 0.80 (0.37), residues: 184 loop : -0.12 (0.19), residues: 1198 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP F 178 HIS 0.004 0.001 HIS E 474 PHE 0.013 0.001 PHE E 125 TYR 0.013 0.001 TYR A 37 ARG 0.004 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 169 residues out of total 1934 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 122 time to evaluate : 2.248 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 397 ASN cc_start: 0.8635 (OUTLIER) cc_final: 0.8087 (p0) REVERT: A 418 PHE cc_start: 0.5115 (t80) cc_final: 0.4620 (t80) REVERT: A 483 MET cc_start: 0.7111 (tmm) cc_final: 0.6851 (tmm) REVERT: C 91 ARG cc_start: 0.5728 (mpt180) cc_final: 0.5053 (mtm180) REVERT: E 246 MET cc_start: 0.7975 (mmp) cc_final: 0.7352 (mmp) REVERT: E 397 ASN cc_start: 0.8697 (OUTLIER) cc_final: 0.8116 (p0) outliers start: 47 outliers final: 37 residues processed: 155 average time/residue: 0.2435 time to fit residues: 63.4574 Evaluate side-chains 156 residues out of total 1934 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 117 time to evaluate : 2.057 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 93 LEU 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 A residue 397 ASN Chi-restraints excluded: chain A residue 500 MET Chi-restraints excluded: chain B residue 358 LEU Chi-restraints excluded: chain B residue 441 MET 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 E residue 34 THR Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain E residue 166 VAL Chi-restraints excluded: chain E residue 199 ILE Chi-restraints excluded: chain E residue 348 MET Chi-restraints excluded: chain E residue 356 CYS Chi-restraints excluded: chain E residue 369 CYS Chi-restraints excluded: chain E residue 382 THR Chi-restraints excluded: chain E residue 397 ASN Chi-restraints excluded: chain E residue 479 ILE Chi-restraints excluded: chain E residue 519 ASP Chi-restraints excluded: chain F residue 372 MET Chi-restraints excluded: chain F residue 437 GLU Chi-restraints excluded: chain F residue 460 CYS Chi-restraints excluded: chain F residue 475 GLU Chi-restraints excluded: chain F residue 478 CYS Chi-restraints excluded: chain F residue 522 ASP Chi-restraints excluded: chain F residue 525 GLU Chi-restraints excluded: chain G residue 28 MET 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 216 optimal weight: 20.0000 chunk 197 optimal weight: 30.0000 chunk 210 optimal weight: 9.9990 chunk 126 optimal weight: 10.0000 chunk 91 optimal weight: 0.6980 chunk 165 optimal weight: 0.0470 chunk 64 optimal weight: 0.0060 chunk 189 optimal weight: 5.9990 chunk 198 optimal weight: 20.0000 chunk 209 optimal weight: 10.0000 chunk 138 optimal weight: 6.9990 overall best weight: 2.7498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7202 moved from start: 0.3953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 18396 Z= 0.165 Angle : 0.585 12.019 24996 Z= 0.293 Chirality : 0.043 0.283 2872 Planarity : 0.004 0.051 3214 Dihedral : 6.911 171.760 2554 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 16.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 1.76 % Allowed : 19.49 % Favored : 78.75 % 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: 0.15 (0.17), residues: 2352 helix: 0.31 (0.17), residues: 954 sheet: 0.88 (0.37), residues: 184 loop : -0.07 (0.19), residues: 1214 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP F 178 HIS 0.002 0.001 HIS E 474 PHE 0.013 0.001 PHE B 342 TYR 0.010 0.001 TYR A 556 ARG 0.003 0.000 ARG G 123 *********************** 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 161 residues out of total 1934 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 127 time to evaluate : 2.075 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 397 ASN cc_start: 0.8559 (OUTLIER) cc_final: 0.8001 (p0) REVERT: A 418 PHE cc_start: 0.5155 (t80) cc_final: 0.4707 (t80) REVERT: A 483 MET cc_start: 0.7124 (tmm) cc_final: 0.6867 (tmm) REVERT: C 91 ARG cc_start: 0.5671 (mpt180) cc_final: 0.5117 (mtm180) REVERT: E 246 MET cc_start: 0.7881 (mmp) cc_final: 0.7245 (mmp) REVERT: E 397 ASN cc_start: 0.8649 (OUTLIER) cc_final: 0.8094 (p0) outliers start: 34 outliers final: 31 residues processed: 150 average time/residue: 0.2400 time to fit residues: 60.0301 Evaluate side-chains 152 residues out of total 1934 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 119 time to evaluate : 2.047 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 93 LEU 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 A residue 397 ASN Chi-restraints excluded: chain A residue 500 MET Chi-restraints excluded: chain B residue 358 LEU Chi-restraints excluded: chain B residue 449 LEU Chi-restraints excluded: chain B residue 460 CYS Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain E residue 34 THR Chi-restraints excluded: chain E residue 93 LEU Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain E residue 166 VAL Chi-restraints excluded: chain E residue 199 ILE Chi-restraints excluded: chain E residue 356 CYS Chi-restraints excluded: chain E residue 382 THR Chi-restraints excluded: chain E residue 397 ASN Chi-restraints excluded: chain E residue 497 ILE Chi-restraints excluded: chain E residue 519 ASP Chi-restraints excluded: chain F residue 437 GLU Chi-restraints excluded: chain F residue 460 CYS Chi-restraints excluded: chain F residue 475 GLU Chi-restraints excluded: chain F residue 478 CYS Chi-restraints excluded: chain F residue 522 ASP Chi-restraints excluded: chain G residue 28 MET 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: 30.0000 chunk 135 optimal weight: 7.9990 chunk 105 optimal weight: 7.9990 chunk 154 optimal weight: 1.9990 chunk 233 optimal weight: 30.0000 chunk 214 optimal weight: 6.9990 chunk 185 optimal weight: 20.0000 chunk 19 optimal weight: 9.9990 chunk 143 optimal weight: 20.0000 chunk 113 optimal weight: 40.0000 chunk 147 optimal weight: 6.9990 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 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7292 moved from start: 0.4247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 18396 Z= 0.260 Angle : 0.644 10.887 24996 Z= 0.328 Chirality : 0.045 0.318 2872 Planarity : 0.004 0.050 3214 Dihedral : 7.092 173.559 2554 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 21.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 2.17 % Allowed : 19.39 % Favored : 78.44 % 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: -0.06 (0.17), residues: 2352 helix: 0.08 (0.16), residues: 968 sheet: 0.73 (0.37), residues: 184 loop : -0.14 (0.19), residues: 1200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP F 178 HIS 0.004 0.001 HIS A 474 PHE 0.015 0.002 PHE E 125 TYR 0.015 0.001 TYR E 37 ARG 0.005 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 158 residues out of total 1934 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 116 time to evaluate : 2.113 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 397 ASN cc_start: 0.8597 (OUTLIER) cc_final: 0.8028 (p0) REVERT: A 418 PHE cc_start: 0.5393 (t80) cc_final: 0.5017 (t80) REVERT: C 91 ARG cc_start: 0.5836 (mpt180) cc_final: 0.5193 (mtm180) REVERT: E 246 MET cc_start: 0.8014 (mmp) cc_final: 0.7432 (mmp) REVERT: E 397 ASN cc_start: 0.8701 (OUTLIER) cc_final: 0.8115 (p0) outliers start: 42 outliers final: 35 residues processed: 144 average time/residue: 0.2409 time to fit residues: 58.7638 Evaluate side-chains 152 residues out of total 1934 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 115 time to evaluate : 2.178 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 LEU 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 A residue 397 ASN Chi-restraints excluded: chain A residue 500 MET Chi-restraints excluded: chain B residue 358 LEU Chi-restraints excluded: chain B residue 441 MET 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 E residue 34 THR Chi-restraints excluded: chain E residue 93 LEU Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain E residue 166 VAL Chi-restraints excluded: chain E residue 199 ILE Chi-restraints excluded: chain E residue 348 MET Chi-restraints excluded: chain E residue 356 CYS Chi-restraints excluded: chain E residue 369 CYS Chi-restraints excluded: chain E residue 382 THR Chi-restraints excluded: chain E residue 397 ASN Chi-restraints excluded: chain E residue 497 ILE Chi-restraints excluded: chain E residue 519 ASP Chi-restraints excluded: chain F residue 372 MET Chi-restraints excluded: chain F residue 437 GLU Chi-restraints excluded: chain F residue 460 CYS Chi-restraints excluded: chain F residue 475 GLU Chi-restraints excluded: chain F residue 478 CYS Chi-restraints excluded: chain F residue 522 ASP Chi-restraints excluded: chain G residue 28 MET 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 197 optimal weight: 40.0000 chunk 56 optimal weight: 6.9990 chunk 171 optimal weight: 30.0000 chunk 27 optimal weight: 5.9990 chunk 51 optimal weight: 8.9990 chunk 185 optimal weight: 20.0000 chunk 77 optimal weight: 10.0000 chunk 190 optimal weight: 20.0000 chunk 23 optimal weight: 20.0000 chunk 34 optimal weight: 20.0000 chunk 163 optimal weight: 30.0000 overall best weight: 10.3994 ------------------------------------------------------------------------------- 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 290 ASN ** A 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 469 ASN B 157 ASN E 290 ASN ** G 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.053406 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2842 r_free = 0.2842 target = 0.034606 restraints weight = 103800.485| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.2877 r_free = 0.2877 target = 0.035808 restraints weight = 68781.912| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2895 r_free = 0.2895 target = 0.036543 restraints weight = 52639.095| |-----------------------------------------------------------------------------| r_work (final): 0.2774 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8650 moved from start: 0.4923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.061 18396 Z= 0.399 Angle : 0.782 11.054 24996 Z= 0.412 Chirality : 0.051 0.379 2872 Planarity : 0.005 0.053 3214 Dihedral : 7.655 175.189 2554 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 29.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.91 % Favored : 94.09 % Rotamer: Outliers : 2.12 % Allowed : 19.60 % Favored : 78.28 % 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: -0.67 (0.17), residues: 2352 helix: -0.45 (0.16), residues: 962 sheet: 0.16 (0.36), residues: 202 loop : -0.41 (0.18), residues: 1188 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP F 178 HIS 0.007 0.002 HIS E 495 PHE 0.023 0.003 PHE E 125 TYR 0.021 0.002 TYR F 140 ARG 0.008 0.001 ARG E 287 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2854.72 seconds wall clock time: 53 minutes 22.77 seconds (3202.77 seconds total)