Starting phenix.real_space_refine on Tue Nov 19 13:21:06 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7q4v_13818/11_2024/7q4v_13818_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7q4v_13818/11_2024/7q4v_13818.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7q4v_13818/11_2024/7q4v_13818.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7q4v_13818/11_2024/7q4v_13818.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7q4v_13818/11_2024/7q4v_13818_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7q4v_13818/11_2024/7q4v_13818_neut.cif" } resolution = 4.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 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 66 7.16 5 Zn 2 6.06 5 P 4 5.49 5 S 224 5.16 5 C 12049 2.51 5 N 3247 2.21 5 O 3711 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 43 residue(s): 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 19303 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: 4510 Number of conformers: 1 Conformer: "" Number of residues, atoms: 599, 4510 Classifications: {'peptide': 599} Link IDs: {'PCIS': 4, 'PTRANS': 26, 'TRANS': 568} Chain: "C" Number of atoms: 1188 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1188 Classifications: {'peptide': 156} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 148} 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: 968 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 968 Classifications: {'peptide': 129} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 122} Chain breaks: 1 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: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 60 Unusual residues: {' ZN': 1, 'FES': 1, 'FMN': 1, 'SF4': 3} Classifications: {'undetermined': 6} Link IDs: {None: 5} 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: 100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 100 Unusual residues: {' ZN': 1, 'FMN': 1, 'NAD': 1, 'SF4': 3} Classifications: {'undetermined': 6} Link IDs: {None: 5} 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 1485 SG CYS A 197 70.799 91.196 81.836 1.00114.62 S ATOM 1466 SG CYS A 194 71.092 94.046 85.545 1.00116.20 S ATOM 1204 SG CYS A 158 67.194 96.742 81.275 1.00105.56 S ATOM 1444 SG CYS A 191 73.838 95.843 79.905 1.00128.70 S ATOM 1178 SG CYS A 154 64.154 89.680 78.163 1.00 69.55 S ATOM 1152 SG CYS A 151 61.636 85.936 79.356 1.00 60.00 S ATOM 1515 SG CYS A 201 66.391 83.672 79.654 1.00 87.71 S ATOM 1130 SG CYS A 148 64.018 85.289 73.798 1.00 70.72 S ATOM 790 SG CYS A 103 71.148 75.565 77.957 1.00115.02 S ATOM 770 SG CYS A 100 67.501 71.551 75.898 1.00 96.97 S ATOM 770 SG CYS A 100 67.501 71.551 75.898 1.00 96.97 S ATOM 838 SG CYS A 109 65.503 74.712 80.128 1.00 97.73 S ATOM 388 SG CYS A 50 48.990 80.433 83.418 1.00142.31 S ATOM 483 SG CYS A 64 48.422 84.133 83.937 1.00157.42 S ATOM 278 SG CYS A 36 52.843 83.344 82.937 1.00119.08 S ATOM 363 SG CYS A 47 52.829 80.534 81.077 1.00122.36 S ATOM 3802 SG CYS A 502 73.343 93.657 93.673 1.00158.69 S ATOM 2683 SG CYS A 356 78.767 92.887 93.347 1.00161.42 S ATOM 2683 SG CYS A 356 78.767 92.887 93.347 1.00161.42 S ATOM 4532 SG CYS B 11 27.502 106.296 44.948 1.00482.94 S ATOM 4557 SG CYS B 16 29.690 105.471 42.423 1.00505.00 S ATOM 4798 SG CYS B 48 27.021 102.447 48.119 1.00439.72 S ATOM 4827 SG CYS B 52 29.580 101.368 45.457 1.00441.51 S ATOM 8830 SG CYS B 581 56.750 72.617 31.765 1.00356.24 S ATOM 8868 SG CYS B 587 53.659 76.720 27.427 1.00356.64 S ATOM 8680 SG CYS B 561 59.481 75.496 27.259 1.00385.72 S ATOM 8853 SG CYS B 584 56.942 79.370 31.882 1.00336.56 S ATOM 8614 SG CYS B 551 49.989 72.987 17.593 1.00411.99 S ATOM 8633 SG CYS B 554 52.305 78.816 15.379 1.00429.49 S ATOM 8651 SG CYS B 557 54.018 76.203 21.176 1.00441.33 S ATOM 8896 SG CYS B 591 48.235 78.512 20.115 1.00388.68 S ATOM 7754 SG CYS B 440 42.575 73.507 44.414 1.00229.29 S ATOM 8480 SG CYS B 533 43.848 72.587 41.006 1.00238.07 S ATOM 8509 SG CYS B 538 46.387 73.384 43.725 1.00244.76 S ATOM 7933 SG CYS B 463 47.529 84.586 66.184 1.00108.71 S ATOM 7894 SG CYS B 457 48.184 89.756 69.169 1.00126.70 S ATOM 7913 SG CYS B 460 48.122 83.004 71.033 1.00107.95 S ATOM 8237 SG CYS B 503 44.760 88.554 68.682 1.00120.75 S ATOM 9600 SG CYS C 83 42.046 95.787 47.172 1.00369.74 S ATOM 9630 SG CYS C 88 40.605 93.884 44.354 1.00321.96 S ATOM 9600 SG CYS C 83 42.046 95.787 47.172 1.00369.74 S ATOM 9900 SG CYS C 124 40.889 94.436 51.174 1.00332.85 S ATOM 9922 SG CYS C 128 37.894 95.554 48.814 1.00357.46 S ATOM 11606 SG CYS E 194 66.735 41.064 84.318 1.00 86.56 S ATOM 11584 SG CYS E 191 63.762 38.863 79.672 1.00117.23 S ATOM 11344 SG CYS E 158 70.228 38.276 81.148 1.00126.73 S ATOM 11606 SG CYS E 194 66.735 41.064 84.318 1.00 86.56 S ATOM 11625 SG CYS E 197 65.863 43.644 81.909 1.00 86.39 S ATOM 11318 SG CYS E 154 73.026 45.099 77.895 1.00101.23 S ATOM 11292 SG CYS E 151 76.715 49.899 79.648 1.00 83.64 S ATOM 11655 SG CYS E 201 70.817 50.931 79.182 1.00 92.09 S ATOM 11270 SG CYS E 148 73.644 50.276 73.762 1.00 94.22 S ATOM 10978 SG CYS E 109 71.845 60.071 80.542 1.00111.20 S ATOM 10930 SG CYS E 103 67.189 61.207 76.132 1.00103.92 S ATOM 10910 SG CYS E 100 69.659 64.737 76.057 1.00 98.54 S ATOM 10930 SG CYS E 103 67.189 61.207 76.132 1.00103.92 S ATOM 10418 SG CYS E 36 85.018 52.094 83.051 1.00133.43 S ATOM 10528 SG CYS E 50 88.376 54.327 83.584 1.00178.99 S ATOM 10623 SG CYS E 64 88.236 50.562 84.699 1.00178.45 S ATOM 10418 SG CYS E 36 85.018 52.094 83.051 1.00133.43 S ATOM 10503 SG CYS E 47 84.361 54.606 80.960 1.00139.83 S ATOM 10528 SG CYS E 50 88.376 54.327 83.584 1.00178.99 S ATOM 13942 SG CYS E 502 63.853 40.742 94.292 1.00162.85 S ATOM 12823 SG CYS E 356 58.710 42.337 93.067 1.00163.54 S ATOM 12823 SG CYS E 356 58.710 42.337 93.067 1.00163.54 S ATOM 13963 SG CYS E 506 59.949 41.094 96.427 1.00150.14 S ATOM 17823 SG CYS F 561 77.834 59.548 27.194 1.00334.23 S ATOM 18011 SG CYS F 587 83.935 58.778 27.591 1.00331.25 S ATOM 17996 SG CYS F 584 80.345 56.290 32.290 1.00311.46 S ATOM 17973 SG CYS F 581 80.523 63.047 30.126 1.00319.19 S ATOM 17776 SG CYS F 554 85.422 56.183 16.459 1.00368.00 S ATOM 18039 SG CYS F 591 89.247 57.170 20.580 1.00364.96 S ATOM 17794 SG CYS F 557 83.270 58.936 21.772 1.00364.31 S ATOM 17757 SG CYS F 551 88.195 61.586 17.798 1.00341.27 S ATOM 16897 SG CYS F 440 94.068 61.551 44.758 1.00248.55 S ATOM 17623 SG CYS F 533 93.210 63.031 41.366 1.00269.77 S ATOM 17652 SG CYS F 538 90.259 62.250 43.844 1.00276.58 S ATOM 17380 SG CYS F 503 92.781 47.339 68.700 1.00172.63 S ATOM 17076 SG CYS F 463 90.045 50.533 66.202 1.00163.03 S ATOM 17056 SG CYS F 460 89.153 52.070 71.104 1.00147.81 S ATOM 17037 SG CYS F 457 88.395 45.178 69.565 1.00157.98 S ATOM 18743 SG CYS G 83 86.905 39.189 39.642 1.00739.93 S ATOM 18773 SG CYS G 88 88.065 41.996 38.126 1.00747.26 S ATOM 18986 SG CYS G 124 92.328 38.672 41.510 1.00682.29 S ATOM 19008 SG CYS G 128 93.679 39.734 38.665 1.00759.78 S Time building chain proxies: 12.69, per 1000 atoms: 0.66 Number of scatterers: 19303 At special positions: 0 Unit cell: (138.43, 138.43, 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 66 26.01 S 224 16.00 P 4 15.00 O 3711 8.00 N 3247 7.00 C 12049 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 5.23 Conformation dependent library (CDL) restraints added in 2.8 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" FES A 604 " pdb="FE2 FES A 604 " - pdb=" SG CYS A 47 " pdb="FE1 FES A 604 " - pdb=" SG CYS A 50 " pdb="FE2 FES A 604 " - pdb=" SG CYS A 36 " pdb="FE1 FES A 604 " - pdb=" SG CYS A 64 " pdb=" FES B 601 " pdb="FE1 FES B 601 " - pdb=" SG CYS B 16 " pdb="FE2 FES B 601 " - pdb=" SG CYS B 48 " pdb="FE2 FES B 601 " - pdb=" SG CYS B 52 " pdb="FE1 FES B 601 " - pdb=" SG CYS B 11 " pdb=" FES C 201 " pdb="FE1 FES C 201 " - pdb=" SG CYS C 88 " pdb="FE2 FES C 201 " - pdb=" SG CYS C 128 " pdb="FE1 FES C 201 " - pdb=" SG CYS C 83 " pdb="FE2 FES C 201 " - pdb=" SG CYS C 124 " pdb=" FES E 604 " pdb="FE2 FES E 604 " - pdb=" SG CYS E 47 " pdb="FE1 FES E 604 " - pdb=" SG CYS E 50 " pdb="FE2 FES E 604 " - pdb=" SG CYS E 36 " pdb="FE1 FES E 604 " - pdb=" SG CYS E 64 " pdb=" FES G 201 " pdb="FE2 FES G 201 " - pdb=" SG CYS G 124 " pdb="FE1 FES G 201 " - pdb=" SG CYS G 88 " pdb="FE2 FES G 201 " - pdb=" SG CYS G 128 " pdb="FE1 FES G 201 " - pdb=" SG CYS G 83 " pdb=" SF4 A 601 " pdb="FE2 SF4 A 601 " - pdb=" SG CYS A 194 " pdb="FE1 SF4 A 601 " - pdb=" SG CYS A 197 " pdb="FE3 SF4 A 601 " - pdb=" SG CYS A 158 " pdb="FE4 SF4 A 601 " - pdb=" SG CYS A 191 " pdb=" SF4 A 602 " pdb="FE2 SF4 A 602 " - pdb=" SG CYS A 151 " pdb="FE4 SF4 A 602 " - pdb=" SG CYS A 148 " pdb="FE1 SF4 A 602 " - pdb=" SG CYS A 154 " pdb="FE3 SF4 A 602 " - pdb=" SG CYS A 201 " pdb=" SF4 A 603 " pdb="FE2 SF4 A 603 " - pdb=" SG CYS A 100 " pdb="FE4 SF4 A 603 " - pdb=" SG CYS A 109 " pdb="FE1 SF4 A 603 " - pdb=" SG CYS A 103 " pdb="FE3 SF4 A 603 " - pdb=" NE2 HIS A 96 " pdb=" SF4 A 605 " pdb="FE2 SF4 A 605 " - pdb=" SG CYS A 356 " pdb="FE1 SF4 A 605 " - pdb=" SG CYS A 502 " pdb="FE3 SF4 A 605 " - pdb=" SG CYS A 506 " pdb=" SF4 B 602 " pdb="FE4 SF4 B 602 " - pdb=" SG CYS B 584 " pdb="FE3 SF4 B 602 " - pdb=" SG CYS B 561 " pdb="FE2 SF4 B 602 " - pdb=" SG CYS B 587 " pdb="FE1 SF4 B 602 " - pdb=" SG CYS B 581 " pdb=" SF4 B 603 " pdb="FE1 SF4 B 603 " - pdb=" SG CYS B 551 " pdb="FE2 SF4 B 603 " - pdb=" SG CYS B 554 " pdb="FE3 SF4 B 603 " - pdb=" SG CYS B 557 " pdb="FE4 SF4 B 603 " - pdb=" SG CYS B 591 " pdb=" SF4 B 606 " pdb="FE1 SF4 B 606 " - pdb=" SG CYS B 463 " pdb="FE2 SF4 B 606 " - pdb=" SG CYS B 457 " pdb="FE3 SF4 B 606 " - pdb=" SG CYS B 460 " pdb="FE4 SF4 B 606 " - pdb=" SG CYS B 503 " pdb=" SF4 E 601 " pdb="FE1 SF4 E 601 " - pdb=" SG CYS E 194 " pdb="FE2 SF4 E 601 " - pdb=" SG CYS E 191 " pdb="FE3 SF4 E 601 " - pdb=" SG CYS E 158 " pdb="FE4 SF4 E 601 " - pdb=" SG CYS E 197 " pdb=" SF4 E 602 " pdb="FE2 SF4 E 602 " - pdb=" SG CYS E 151 " pdb="FE4 SF4 E 602 " - pdb=" SG CYS E 148 " pdb="FE1 SF4 E 602 " - pdb=" SG CYS E 154 " pdb="FE3 SF4 E 602 " - pdb=" SG CYS E 201 " pdb=" SF4 E 603 " pdb="FE3 SF4 E 603 " - pdb=" SG CYS E 103 " pdb="FE4 SF4 E 603 " - pdb=" SG CYS E 100 " pdb="FE2 SF4 E 603 " - pdb=" SG CYS E 109 " pdb="FE1 SF4 E 603 " - pdb=" NE2 HIS E 96 " pdb=" SF4 E 605 " pdb="FE1 SF4 E 605 " - pdb=" SG CYS E 502 " pdb="FE2 SF4 E 605 " - pdb=" SG CYS E 356 " pdb="FE3 SF4 E 605 " - pdb=" SG CYS E 506 " pdb=" SF4 F 601 " pdb="FE2 SF4 F 601 " - pdb=" SG CYS F 587 " pdb="FE1 SF4 F 601 " - pdb=" SG CYS F 561 " pdb="FE3 SF4 F 601 " - pdb=" SG CYS F 584 " pdb="FE4 SF4 F 601 " - pdb=" SG CYS F 581 " pdb=" SF4 F 602 " pdb="FE1 SF4 F 602 " - pdb=" SG CYS F 554 " pdb="FE4 SF4 F 602 " - pdb=" SG CYS F 551 " pdb="FE3 SF4 F 602 " - pdb=" SG CYS F 557 " pdb="FE2 SF4 F 602 " - pdb=" SG CYS F 591 " pdb=" SF4 F 606 " pdb="FE4 SF4 F 606 " - pdb=" SG CYS F 457 " pdb="FE1 SF4 F 606 " - pdb=" SG CYS F 503 " pdb="FE3 SF4 F 606 " - pdb=" SG CYS F 460 " pdb="FE2 SF4 F 606 " - pdb=" SG CYS F 463 " Number of angles added : 196 Zn2+ tetrahedral coordination pdb=" ZN B 604 " pdb="ZN ZN B 604 " - pdb=" NE2 HIS B 527 " pdb="ZN ZN B 604 " - pdb=" SG CYS B 533 " pdb="ZN ZN B 604 " - pdb=" SG CYS B 440 " pdb="ZN ZN B 604 " - pdb=" SG CYS B 538 " pdb=" ZN F 603 " pdb="ZN ZN F 603 " - pdb=" NE2 HIS F 527 " pdb="ZN ZN F 603 " - pdb=" SG CYS F 533 " pdb="ZN ZN F 603 " - pdb=" SG CYS F 440 " pdb="ZN ZN F 603 " - pdb=" SG CYS F 538 " Number of angles added : 6 5012 Ramachandran restraints generated. 2506 Oldfield, 0 Emsley, 2506 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4556 Finding SS restraints... Secondary structure from input PDB file: 128 helices and 25 sheets defined 48.1% alpha, 9.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.43 Creating SS restraints... Processing helix chain 'A' and resid 20 through 28 Processing helix chain 'A' and resid 78 through 94 removed outlier: 3.604A pdb=" N ARG A 82 " --> pdb=" O SER A 78 " (cutoff:3.500A) Processing helix chain 'A' and resid 109 through 119 Processing helix chain 'A' and resid 152 through 160 Processing helix chain 'A' and resid 172 through 176 Processing helix chain 'A' and resid 180 through 184 removed outlier: 3.945A pdb=" N ASN A 183 " --> pdb=" O PRO A 180 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LYS A 184 " --> pdb=" O VAL A 181 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 180 through 184' Processing helix chain 'A' and resid 185 through 189 Processing helix chain 'A' and resid 195 through 201 removed outlier: 3.592A pdb=" N CYS A 201 " --> pdb=" O CYS A 197 " (cutoff:3.500A) Processing helix chain 'A' and resid 211 through 221 Processing helix chain 'A' and resid 238 through 243 Processing helix chain 'A' and resid 250 through 260 Processing helix chain 'A' and resid 269 through 291 Processing helix chain 'A' and resid 301 through 311 removed outlier: 3.698A pdb=" N ILE A 305 " --> pdb=" O SER A 301 " (cutoff:3.500A) Processing helix chain 'A' and resid 312 through 319 removed outlier: 3.929A pdb=" N ALA A 315 " --> pdb=" O TYR A 312 " (cutoff:3.500A) Proline residue: A 317 - end of helix Processing helix chain 'A' and resid 324 through 342 removed outlier: 3.809A pdb=" N TYR A 337 " --> pdb=" O LEU A 333 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N ALA A 338 " --> pdb=" O LYS A 334 " (cutoff:3.500A) Processing helix chain 'A' and resid 357 through 363 removed outlier: 4.197A pdb=" N TYR A 361 " --> pdb=" O THR A 357 " (cutoff:3.500A) Processing helix chain 'A' and resid 381 through 393 Processing helix chain 'A' and resid 395 through 399 Processing helix chain 'A' and resid 412 through 417 Processing helix chain 'A' and resid 422 through 437 Processing helix chain 'A' and resid 475 through 489 Processing helix chain 'A' and resid 505 through 509 removed outlier: 3.606A pdb=" N ASN A 508 " --> pdb=" O GLY A 505 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N GLY A 509 " --> pdb=" O CYS A 506 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 505 through 509' Processing helix chain 'A' and resid 516 through 523 removed outlier: 3.675A pdb=" N ILE A 523 " --> pdb=" O ASP A 519 " (cutoff:3.500A) Processing helix chain 'A' and resid 524 through 539 removed outlier: 3.762A pdb=" N GLU A 528 " --> pdb=" O ASP A 524 " (cutoff:3.500A) Processing helix chain 'A' and resid 549 through 559 Processing helix chain 'A' and resid 565 through 572 Processing helix chain 'B' and resid 13 through 19 Processing helix chain 'B' and resid 20 through 35 removed outlier: 3.504A pdb=" N LEU B 24 " --> pdb=" O GLY B 20 " (cutoff:3.500A) Processing helix chain 'B' and resid 71 through 73 No H-bonds generated for 'chain 'B' and resid 71 through 73' Processing helix chain 'B' and resid 74 through 82 removed outlier: 3.704A pdb=" N MET B 78 " --> pdb=" O ASP B 74 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N VAL B 79 " --> pdb=" O ILE B 75 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLU B 80 " --> pdb=" O PRO B 76 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N HIS B 82 " --> pdb=" O MET B 78 " (cutoff:3.500A) Processing helix chain 'B' and resid 105 through 109 Processing helix chain 'B' and resid 130 through 136 removed outlier: 4.044A pdb=" N TYR B 134 " --> pdb=" O ASN B 130 " (cutoff:3.500A) Processing helix chain 'B' and resid 141 through 147 removed outlier: 3.744A pdb=" N LYS B 145 " --> pdb=" O LEU B 141 " (cutoff:3.500A) Processing helix chain 'B' and resid 151 through 163 removed outlier: 4.204A pdb=" N ILE B 156 " --> pdb=" O PRO B 152 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ASN B 157 " --> pdb=" O VAL B 153 " (cutoff:3.500A) Processing helix chain 'B' and resid 173 through 183 removed outlier: 3.796A pdb=" N LYS B 177 " --> pdb=" O PRO B 173 " (cutoff:3.500A) Processing helix chain 'B' and resid 208 through 214 Processing helix chain 'B' and resid 214 through 230 removed outlier: 4.148A pdb=" N VAL B 218 " --> pdb=" O ASP B 214 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N VAL B 229 " --> pdb=" O ALA B 225 " (cutoff:3.500A) Processing helix chain 'B' and resid 242 through 260 removed outlier: 3.774A pdb=" N ASN B 247 " --> pdb=" O PRO B 243 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ARG B 248 " --> pdb=" O ILE B 244 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N GLN B 250 " --> pdb=" O VAL B 246 " (cutoff:3.500A) Processing helix chain 'B' and resid 283 through 288 Processing helix chain 'B' and resid 292 through 297 Processing helix chain 'B' and resid 324 through 330 removed outlier: 3.605A pdb=" N TYR B 328 " --> pdb=" O ASN B 324 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N ASN B 330 " --> pdb=" O GLU B 326 " (cutoff:3.500A) Processing helix chain 'B' and resid 330 through 338 Processing helix chain 'B' and resid 338 through 344 removed outlier: 3.742A pdb=" N PHE B 342 " --> pdb=" O GLY B 338 " (cutoff:3.500A) Processing helix chain 'B' and resid 375 through 382 removed outlier: 3.850A pdb=" N ILE B 379 " --> pdb=" O THR B 375 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ILE B 380 " --> pdb=" O LEU B 376 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N TYR B 381 " --> pdb=" O ARG B 377 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N GLU B 382 " --> pdb=" O GLU B 378 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 375 through 382' Processing helix chain 'B' and resid 387 through 391 removed outlier: 3.941A pdb=" N GLY B 390 " --> pdb=" O ILE B 387 " (cutoff:3.500A) Processing helix chain 'B' and resid 400 through 403 Processing helix chain 'B' and resid 409 through 411 No H-bonds generated for 'chain 'B' and resid 409 through 411' Processing helix chain 'B' and resid 416 through 421 removed outlier: 3.714A pdb=" N LEU B 420 " --> pdb=" O ASP B 416 " (cutoff:3.500A) Processing helix chain 'B' and resid 442 through 456 removed outlier: 3.661A pdb=" N ARG B 446 " --> pdb=" O VAL B 442 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N THR B 452 " --> pdb=" O PHE B 448 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N GLN B 453 " --> pdb=" O LEU B 449 " (cutoff:3.500A) Processing helix chain 'B' and resid 460 through 479 removed outlier: 5.106A pdb=" N THR B 467 " --> pdb=" O CYS B 463 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N LYS B 468 " --> pdb=" O ARG B 464 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N GLU B 472 " --> pdb=" O LYS B 468 " (cutoff:3.500A) removed outlier: 4.903A pdb=" N ILE B 473 " --> pdb=" O ARG B 469 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N LEU B 474 " --> pdb=" O MET B 470 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ILE B 477 " --> pdb=" O ILE B 473 " (cutoff:3.500A) Processing helix chain 'B' and resid 485 through 499 removed outlier: 3.547A pdb=" N GLU B 492 " --> pdb=" O GLU B 488 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N LEU B 493 " --> pdb=" O ARG B 489 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N VAL B 495 " --> pdb=" O GLU B 491 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N GLY B 496 " --> pdb=" O GLU B 492 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N LYS B 498 " --> pdb=" O ALA B 494 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N SER B 499 " --> pdb=" O VAL B 495 " (cutoff:3.500A) Processing helix chain 'B' and resid 503 through 509 removed outlier: 3.987A pdb=" N GLN B 507 " --> pdb=" O CYS B 503 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N THR B 508 " --> pdb=" O GLY B 504 " (cutoff:3.500A) Processing helix chain 'B' and resid 510 through 518 removed outlier: 3.502A pdb=" N THR B 516 " --> pdb=" O PRO B 512 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ILE B 517 " --> pdb=" O VAL B 513 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N ARG B 518 " --> pdb=" O LEU B 514 " (cutoff:3.500A) Processing helix chain 'B' and resid 520 through 529 removed outlier: 3.907A pdb=" N TYR B 524 " --> pdb=" O PHE B 520 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N GLU B 525 " --> pdb=" O ARG B 521 " (cutoff:3.500A) Processing helix chain 'B' and resid 538 through 542 removed outlier: 3.507A pdb=" N LEU B 542 " --> pdb=" O LYS B 539 " (cutoff:3.500A) Processing helix chain 'B' and resid 555 through 560 removed outlier: 3.532A pdb=" N LYS B 559 " --> pdb=" O GLY B 555 " (cutoff:3.500A) Processing helix chain 'B' and resid 585 through 591 removed outlier: 4.596A pdb=" N GLU B 589 " --> pdb=" O GLY B 585 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N ALA B 590 " --> pdb=" O ALA B 586 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N CYS B 591 " --> pdb=" O CYS B 587 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 585 through 591' Processing helix chain 'C' and resid 10 through 20 Processing helix chain 'C' and resid 26 through 39 Processing helix chain 'C' and resid 42 through 54 removed outlier: 3.641A pdb=" N GLN C 46 " --> pdb=" O PRO C 42 " (cutoff:3.500A) Processing helix chain 'C' and resid 56 through 67 removed outlier: 4.470A pdb=" N VAL C 60 " --> pdb=" O PRO C 56 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N TYR C 67 " --> pdb=" O VAL C 63 " (cutoff:3.500A) Processing helix chain 'C' and resid 85 through 90 Processing helix chain 'C' and resid 92 through 105 removed outlier: 3.872A pdb=" N ILE C 96 " --> pdb=" O GLY C 92 " (cutoff:3.500A) Processing helix chain 'C' and resid 127 through 131 removed outlier: 3.549A pdb=" N LEU C 130 " --> pdb=" O ALA C 127 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ALA C 131 " --> pdb=" O CYS C 128 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 127 through 131' Processing helix chain 'C' and resid 148 through 154 Processing helix chain 'E' and resid 20 through 28 Processing helix chain 'E' and resid 78 through 94 removed outlier: 3.815A pdb=" N SER E 94 " --> pdb=" O GLU E 90 " (cutoff:3.500A) Processing helix chain 'E' and resid 105 through 108 removed outlier: 3.634A pdb=" N ASN E 108 " --> pdb=" O ARG E 105 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 105 through 108' Processing helix chain 'E' and resid 109 through 118 removed outlier: 3.633A pdb=" N THR E 113 " --> pdb=" O CYS E 109 " (cutoff:3.500A) Processing helix chain 'E' and resid 152 through 160 Processing helix chain 'E' and resid 172 through 176 Processing helix chain 'E' and resid 182 through 184 No H-bonds generated for 'chain 'E' and resid 182 through 184' Processing helix chain 'E' and resid 195 through 200 removed outlier: 3.801A pdb=" N ASN E 200 " --> pdb=" O GLN E 196 " (cutoff:3.500A) Processing helix chain 'E' and resid 212 through 221 Processing helix chain 'E' and resid 233 through 236 removed outlier: 4.025A pdb=" N ALA E 236 " --> pdb=" O ALA E 233 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 233 through 236' Processing helix chain 'E' and resid 237 through 242 removed outlier: 3.973A pdb=" N GLU E 241 " --> pdb=" O ALA E 237 " (cutoff:3.500A) Processing helix chain 'E' and resid 250 through 261 Processing helix chain 'E' and resid 269 through 290 Processing helix chain 'E' and resid 301 through 312 removed outlier: 3.937A pdb=" N ILE E 305 " --> pdb=" O SER E 301 " (cutoff:3.500A) Processing helix chain 'E' and resid 313 through 319 removed outlier: 3.686A pdb=" N ILE E 316 " --> pdb=" O PRO E 313 " (cutoff:3.500A) Proline residue: E 317 - end of helix No H-bonds generated for 'chain 'E' and resid 313 through 319' Processing helix chain 'E' and resid 324 through 342 removed outlier: 3.811A pdb=" N TYR E 337 " --> pdb=" O LEU E 333 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N ALA E 338 " --> pdb=" O LYS E 334 " (cutoff:3.500A) Processing helix chain 'E' and resid 344 through 346 No H-bonds generated for 'chain 'E' and resid 344 through 346' Processing helix chain 'E' and resid 358 through 365 removed outlier: 3.666A pdb=" N GLU E 362 " --> pdb=" O ALA E 358 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N GLN E 364 " --> pdb=" O LYS E 360 " (cutoff:3.500A) Processing helix chain 'E' and resid 381 through 393 Processing helix chain 'E' and resid 395 through 399 removed outlier: 3.668A pdb=" N LYS E 398 " --> pdb=" O LEU E 395 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N LEU E 399 " --> pdb=" O PHE E 396 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 395 through 399' Processing helix chain 'E' and resid 412 through 416 Processing helix chain 'E' and resid 422 through 437 Processing helix chain 'E' and resid 475 through 488 Processing helix chain 'E' and resid 505 through 509 Processing helix chain 'E' and resid 516 through 523 removed outlier: 4.045A pdb=" N ASP E 522 " --> pdb=" O LYS E 518 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N ILE E 523 " --> pdb=" O ASP E 519 " (cutoff:3.500A) Processing helix chain 'E' and resid 524 through 539 removed outlier: 3.995A pdb=" N GLU E 528 " --> pdb=" O ASP E 524 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ASN E 539 " --> pdb=" O ASP E 535 " (cutoff:3.500A) Processing helix chain 'E' and resid 549 through 559 removed outlier: 3.874A pdb=" N ILE E 553 " --> pdb=" O ASN E 549 " (cutoff:3.500A) Processing helix chain 'E' and resid 565 through 572 Processing helix chain 'F' and resid 131 through 136 Processing helix chain 'F' and resid 140 through 147 removed outlier: 3.778A pdb=" N GLU F 144 " --> pdb=" O TYR F 140 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N LYS F 145 " --> pdb=" O LEU F 141 " (cutoff:3.500A) Processing helix chain 'F' and resid 151 through 163 removed outlier: 3.638A pdb=" N VAL F 155 " --> pdb=" O SER F 151 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N ILE F 156 " --> pdb=" O PRO F 152 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N VAL F 159 " --> pdb=" O VAL F 155 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LYS F 160 " --> pdb=" O ILE F 156 " (cutoff:3.500A) Processing helix chain 'F' and resid 173 through 184 removed outlier: 3.784A pdb=" N LYS F 177 " --> pdb=" O PRO F 173 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N TRP F 178 " --> pdb=" O THR F 174 " (cutoff:3.500A) Processing helix chain 'F' and resid 205 through 214 removed outlier: 4.002A pdb=" N SER F 209 " --> pdb=" O PHE F 205 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N VAL F 210 " --> pdb=" O MET F 206 " (cutoff:3.500A) Processing helix chain 'F' and resid 215 through 230 removed outlier: 3.714A pdb=" N MET F 222 " --> pdb=" O VAL F 218 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ALA F 223 " --> pdb=" O ILE F 219 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N VAL F 229 " --> pdb=" O ALA F 225 " (cutoff:3.500A) Processing helix chain 'F' and resid 242 through 260 removed outlier: 3.553A pdb=" N VAL F 246 " --> pdb=" O TYR F 242 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N ASN F 247 " --> pdb=" O PRO F 243 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N ARG F 248 " --> pdb=" O ILE F 244 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLN F 250 " --> pdb=" O VAL F 246 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ILE F 251 " --> pdb=" O ASN F 247 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N GLU F 258 " --> pdb=" O ASP F 254 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N TYR F 259 " --> pdb=" O GLN F 255 " (cutoff:3.500A) Processing helix chain 'F' and resid 283 through 287 removed outlier: 3.605A pdb=" N GLY F 287 " --> pdb=" O PHE F 284 " (cutoff:3.500A) Processing helix chain 'F' and resid 288 through 298 removed outlier: 3.950A pdb=" N MET F 293 " --> pdb=" O GLU F 289 " (cutoff:3.500A) Processing helix chain 'F' and resid 314 through 318 Processing helix chain 'F' and resid 325 through 330 removed outlier: 4.040A pdb=" N ASN F 330 " --> pdb=" O GLU F 326 " (cutoff:3.500A) Processing helix chain 'F' and resid 330 through 338 Processing helix chain 'F' and resid 338 through 343 removed outlier: 3.951A pdb=" N PHE F 342 " --> pdb=" O GLY F 338 " (cutoff:3.500A) Processing helix chain 'F' and resid 375 through 382 removed outlier: 3.717A pdb=" N TYR F 381 " --> pdb=" O ARG F 377 " (cutoff:3.500A) Processing helix chain 'F' and resid 387 through 391 removed outlier: 3.919A pdb=" N GLY F 390 " --> pdb=" O ILE F 387 " (cutoff:3.500A) Processing helix chain 'F' and resid 400 through 403 Processing helix chain 'F' and resid 409 through 411 No H-bonds generated for 'chain 'F' and resid 409 through 411' Processing helix chain 'F' and resid 416 through 424 removed outlier: 3.671A pdb=" N ILE F 421 " --> pdb=" O TYR F 417 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ALA F 422 " --> pdb=" O ASP F 418 " (cutoff:3.500A) Processing helix chain 'F' and resid 440 through 454 removed outlier: 3.787A pdb=" N PHE F 448 " --> pdb=" O VAL F 444 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N LEU F 449 " --> pdb=" O ALA F 445 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N PHE F 451 " --> pdb=" O PHE F 447 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N ASP F 454 " --> pdb=" O ASP F 450 " (cutoff:3.500A) Processing helix chain 'F' and resid 460 through 480 removed outlier: 4.916A pdb=" N THR F 467 " --> pdb=" O CYS F 463 " (cutoff:3.500A) removed outlier: 4.711A pdb=" N LYS F 468 " --> pdb=" O ARG F 464 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ARG F 469 " --> pdb=" O ILE F 465 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N MET F 470 " --> pdb=" O GLY F 466 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N LEU F 471 " --> pdb=" O THR F 467 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ILE F 473 " --> pdb=" O ARG F 469 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LEU F 474 " --> pdb=" O MET F 470 " (cutoff:3.500A) Processing helix chain 'F' and resid 488 through 500 removed outlier: 4.225A pdb=" N GLU F 492 " --> pdb=" O GLU F 488 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N LEU F 493 " --> pdb=" O ARG F 489 " (cutoff:3.500A) Processing helix chain 'F' and resid 504 through 509 removed outlier: 3.708A pdb=" N THR F 508 " --> pdb=" O GLY F 504 " (cutoff:3.500A) Processing helix chain 'F' and resid 510 through 520 removed outlier: 3.516A pdb=" N ILE F 517 " --> pdb=" O VAL F 513 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N PHE F 519 " --> pdb=" O SER F 515 " (cutoff:3.500A) Processing helix chain 'F' and resid 521 through 523 No H-bonds generated for 'chain 'F' and resid 521 through 523' Processing helix chain 'F' and resid 524 through 529 Processing helix chain 'F' and resid 538 through 542 removed outlier: 4.269A pdb=" N LEU F 541 " --> pdb=" O CYS F 538 " (cutoff:3.500A) Processing helix chain 'F' and resid 555 through 561 removed outlier: 3.519A pdb=" N LYS F 559 " --> pdb=" O GLY F 555 " (cutoff:3.500A) Processing helix chain 'F' and resid 585 through 591 removed outlier: 4.533A pdb=" N GLU F 589 " --> pdb=" O GLY F 585 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ALA F 590 " --> pdb=" O ALA F 586 " (cutoff:3.500A) Processing helix chain 'G' and resid 5 through 16 removed outlier: 3.513A pdb=" N ILE G 16 " --> pdb=" O VAL G 12 " (cutoff:3.500A) Processing helix chain 'G' and resid 25 through 38 removed outlier: 3.670A pdb=" N GLN G 29 " --> pdb=" O GLY G 25 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N GLU G 33 " --> pdb=" O GLN G 29 " (cutoff:3.500A) Processing helix chain 'G' and resid 45 through 54 Processing helix chain 'G' and resid 57 through 67 Processing helix chain 'G' and resid 85 through 92 Processing helix chain 'G' and resid 93 through 102 Processing helix chain 'G' and resid 127 through 131 removed outlier: 3.649A pdb=" N LEU G 130 " --> pdb=" O ALA G 127 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N ALA G 131 " --> pdb=" O CYS G 128 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 127 through 131' Processing sheet with id=AA1, first strand: chain 'A' and resid 11 through 16 removed outlier: 9.644A pdb=" N VAL A 74 " --> pdb=" O THR A 5 " (cutoff:3.500A) removed outlier: 7.252A pdb=" N LYS A 7 " --> pdb=" O VAL A 74 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N LEU A 75 " --> pdb=" O GLU A 53 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N GLU A 53 " --> pdb=" O LEU A 75 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N GLN A 61 " --> pdb=" O VAL A 52 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 141 through 143 Processing sheet with id=AA3, first strand: chain 'A' and resid 168 through 170 Processing sheet with id=AA4, first strand: chain 'A' and resid 265 through 268 removed outlier: 9.191A pdb=" N ILE A 378 " --> pdb=" O MET A 348 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N VAL A 350 " --> pdb=" O ILE A 378 " (cutoff:3.500A) removed outlier: 8.052A pdb=" N ILE A 380 " --> pdb=" O VAL A 350 " (cutoff:3.500A) removed outlier: 6.208A pdb=" N SER A 352 " --> pdb=" O ILE A 380 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 296 through 297 removed outlier: 6.753A pdb=" N MET A 296 " --> pdb=" O ILE A 497 " (cutoff:3.500A) removed outlier: 8.066A pdb=" N LEU A 499 " --> pdb=" O MET A 296 " (cutoff:3.500A) removed outlier: 8.675A pdb=" N PHE A 496 " --> pdb=" O THR A 467 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N ASN A 469 " --> pdb=" O PHE A 496 " (cutoff:3.500A) removed outlier: 7.903A pdb=" N GLU A 498 " --> pdb=" O ASN A 469 " (cutoff:3.500A) removed outlier: 7.108A pdb=" N VAL A 471 " --> pdb=" O GLU A 498 " (cutoff:3.500A) removed outlier: 8.098A pdb=" N MET A 500 " --> pdb=" O VAL A 471 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N ALA A 473 " --> pdb=" O MET A 500 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N VAL A 468 " --> pdb=" O VAL A 460 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N VAL A 460 " --> pdb=" O VAL A 468 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 369 through 370 Processing sheet with id=AA7, first strand: chain 'B' and resid 41 through 46 removed outlier: 3.615A pdb=" N ILE B 59 " --> pdb=" O LEU B 9 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N VAL B 58 " --> pdb=" O TYR B 67 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N VAL B 60 " --> pdb=" O THR B 65 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N THR B 65 " --> pdb=" O VAL B 60 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 192 through 193 removed outlier: 6.344A pdb=" N VAL B 193 " --> pdb=" O TYR B 235 " (cutoff:3.500A) removed outlier: 8.188A pdb=" N TYR B 237 " --> pdb=" O VAL B 193 " (cutoff:3.500A) removed outlier: 7.235A pdb=" N GLY B 234 " --> pdb=" O GLU B 276 " (cutoff:3.500A) removed outlier: 7.725A pdb=" N ARG B 278 " --> pdb=" O GLY B 234 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N VAL B 236 " --> pdb=" O ARG B 278 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N GLY B 280 " --> pdb=" O VAL B 236 " (cutoff:3.500A) removed outlier: 5.848A pdb=" N VAL B 238 " --> pdb=" O GLY B 280 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'B' and resid 367 through 371 removed outlier: 8.405A pdb=" N LEU B 432 " --> pdb=" O VAL B 355 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N ALA B 357 " --> pdb=" O LEU B 432 " (cutoff:3.500A) removed outlier: 8.233A pdb=" N VAL B 434 " --> pdb=" O ALA B 357 " (cutoff:3.500A) removed outlier: 7.243A pdb=" N GLY B 359 " --> pdb=" O VAL B 434 " (cutoff:3.500A) removed outlier: 9.086A pdb=" N ASP B 436 " --> pdb=" O GLY B 359 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N ALA B 395 " --> pdb=" O MET B 435 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 544 through 546 Processing sheet with id=AB2, first strand: chain 'B' and resid 566 through 567 removed outlier: 3.522A pdb=" N SER B 567 " --> pdb=" O ASN B 575 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 117 through 119 Processing sheet with id=AB4, first strand: chain 'E' and resid 11 through 16 removed outlier: 9.878A pdb=" N VAL E 74 " --> pdb=" O THR E 5 " (cutoff:3.500A) removed outlier: 7.441A pdb=" N LYS E 7 " --> pdb=" O VAL E 74 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N GLN E 61 " --> pdb=" O VAL E 52 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 141 through 143 Processing sheet with id=AB6, first strand: chain 'E' and resid 167 through 170 Processing sheet with id=AB7, first strand: chain 'E' and resid 265 through 268 removed outlier: 5.929A pdb=" N THR E 225 " --> pdb=" O VAL E 349 " (cutoff:3.500A) removed outlier: 7.456A pdb=" N VAL E 351 " --> pdb=" O THR E 225 " (cutoff:3.500A) removed outlier: 5.809A pdb=" N ILE E 227 " --> pdb=" O VAL E 351 " (cutoff:3.500A) removed outlier: 7.888A pdb=" N ILE E 353 " --> pdb=" O ILE E 227 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N GLN E 229 " --> pdb=" O ILE E 353 " (cutoff:3.500A) removed outlier: 8.658A pdb=" N ILE E 378 " --> pdb=" O MET E 348 " (cutoff:3.500A) removed outlier: 6.055A pdb=" N VAL E 350 " --> pdb=" O ILE E 378 " (cutoff:3.500A) removed outlier: 7.773A pdb=" N ILE E 380 " --> pdb=" O VAL E 350 " (cutoff:3.500A) removed outlier: 5.947A pdb=" N SER E 352 " --> pdb=" O ILE E 380 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 296 through 297 removed outlier: 7.033A pdb=" N MET E 296 " --> pdb=" O ILE E 497 " (cutoff:3.500A) removed outlier: 8.108A pdb=" N LEU E 499 " --> pdb=" O MET E 296 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 369 through 370 Processing sheet with id=AC1, first strand: chain 'F' and resid 194 through 196 removed outlier: 3.653A pdb=" N ASN F 323 " --> pdb=" O ALA F 194 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'F' and resid 233 through 239 removed outlier: 6.716A pdb=" N GLY F 234 " --> pdb=" O GLU F 276 " (cutoff:3.500A) removed outlier: 7.342A pdb=" N ARG F 278 " --> pdb=" O GLY F 234 " (cutoff:3.500A) removed outlier: 5.772A pdb=" N VAL F 236 " --> pdb=" O ARG F 278 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N GLY F 280 " --> pdb=" O VAL F 236 " (cutoff:3.500A) removed outlier: 5.549A pdb=" N VAL F 238 " --> pdb=" O GLY F 280 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 Processing sheet with id=AC3, first strand: chain 'F' and resid 353 through 357 removed outlier: 3.579A pdb=" N LYS F 354 " --> pdb=" O ILE F 370 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ILE F 370 " --> pdb=" O LYS F 354 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N PHE F 356 " --> pdb=" O LEU F 368 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N LEU F 368 " --> pdb=" O PHE F 356 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC3 Processing sheet with id=AC4, first strand: chain 'F' and resid 404 through 407 Processing sheet with id=AC5, first strand: chain 'F' and resid 543 through 546 Processing sheet with id=AC6, first strand: chain 'F' and resid 566 through 567 Processing sheet with id=AC7, first strand: chain 'G' and resid 121 through 122 removed outlier: 4.598A pdb=" N THR G 122 " --> pdb=" O ILE G 82 " (cutoff:3.500A) 691 hydrogen bonds defined for protein. 1923 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: 6.88 Time building geometry restraints manager: 5.90 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.41: 7604 1.41 - 1.63: 11662 1.63 - 1.85: 219 1.85 - 2.07: 0 2.07 - 2.28: 188 Bond restraints: 19673 Sorted by residual: bond pdb=" CA HIS A 573 " pdb=" C HIS A 573 " ideal model delta sigma weight residual 1.522 1.626 -0.104 1.18e-02 7.18e+03 7.76e+01 bond pdb=" C4 FMN B 605 " pdb=" C4A FMN B 605 " ideal model delta sigma weight residual 1.390 1.554 -0.164 2.00e-02 2.50e+03 6.75e+01 bond pdb=" C4 FMN F 604 " pdb=" C4A FMN F 604 " ideal model delta sigma weight residual 1.390 1.552 -0.162 2.00e-02 2.50e+03 6.60e+01 bond pdb=" CG PRO A 245 " pdb=" CD PRO A 245 " ideal model delta sigma weight residual 1.503 1.232 0.271 3.40e-02 8.65e+02 6.34e+01 bond pdb=" CA ASN A 549 " pdb=" C ASN A 549 " ideal model delta sigma weight residual 1.524 1.614 -0.090 1.26e-02 6.30e+03 5.07e+01 ... (remaining 19668 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.69: 26276 3.69 - 7.38: 386 7.38 - 11.07: 51 11.07 - 14.76: 10 14.76 - 18.45: 4 Bond angle restraints: 26727 Sorted by residual: angle pdb=" CA PRO A 245 " pdb=" N PRO A 245 " pdb=" CD PRO A 245 " ideal model delta sigma weight residual 112.00 95.75 16.25 1.40e+00 5.10e-01 1.35e+02 angle pdb=" N PRO A 245 " pdb=" CD PRO A 245 " pdb=" CG PRO A 245 " ideal model delta sigma weight residual 103.20 89.79 13.41 1.50e+00 4.44e-01 7.99e+01 angle pdb=" N THR A 574 " pdb=" CA THR A 574 " pdb=" C THR A 574 " ideal model delta sigma weight residual 109.65 123.39 -13.74 1.56e+00 4.11e-01 7.75e+01 angle pdb=" CA HIS A 96 " pdb=" CB HIS A 96 " pdb=" CG HIS A 96 " ideal model delta sigma weight residual 113.80 105.92 7.88 1.00e+00 1.00e+00 6.21e+01 angle pdb=" N HIS A 573 " pdb=" CA HIS A 573 " pdb=" CB HIS A 573 " ideal model delta sigma weight residual 110.84 100.85 9.99 1.52e+00 4.33e-01 4.32e+01 ... (remaining 26722 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.13: 11648 35.13 - 70.26: 221 70.26 - 105.39: 27 105.39 - 140.52: 0 140.52 - 175.65: 2 Dihedral angle restraints: 11898 sinusoidal: 4756 harmonic: 7142 Sorted by residual: dihedral pdb=" CA VAL G 23 " pdb=" C VAL G 23 " pdb=" N PRO G 24 " pdb=" CA PRO G 24 " ideal model delta harmonic sigma weight residual 180.00 141.11 38.89 0 5.00e+00 4.00e-02 6.05e+01 dihedral pdb=" C10 FMN B 605 " pdb=" C1' FMN B 605 " pdb=" N10 FMN B 605 " pdb=" C2' FMN B 605 " ideal model delta sinusoidal sigma weight residual 257.59 81.94 175.65 1 2.00e+01 2.50e-03 4.79e+01 dihedral pdb=" C10 FMN F 604 " pdb=" C1' FMN F 604 " pdb=" N10 FMN F 604 " pdb=" C2' FMN F 604 " ideal model delta sinusoidal sigma weight residual 257.59 86.59 171.00 1 2.00e+01 2.50e-03 4.77e+01 ... (remaining 11895 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.114: 2922 0.114 - 0.228: 130 0.228 - 0.342: 12 0.342 - 0.456: 6 0.456 - 0.570: 4 Chirality restraints: 3074 Sorted by residual: chirality pdb=" CA VAL E 228 " pdb=" N VAL E 228 " pdb=" C VAL E 228 " pdb=" CB VAL E 228 " both_signs ideal model delta sigma weight residual False 2.44 1.87 0.57 2.00e-01 2.50e+01 8.11e+00 chirality pdb=" CA VAL G 13 " pdb=" N VAL G 13 " pdb=" C VAL G 13 " pdb=" CB VAL G 13 " both_signs ideal model delta sigma weight residual False 2.44 1.95 0.49 2.00e-01 2.50e+01 5.93e+00 chirality pdb=" CB ILE G 136 " pdb=" CA ILE G 136 " pdb=" CG1 ILE G 136 " pdb=" CG2 ILE G 136 " both_signs ideal model delta sigma weight residual False 2.64 2.17 0.48 2.00e-01 2.50e+01 5.65e+00 ... (remaining 3071 not shown) Planarity restraints: 3429 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1D NAD F 605 " -0.050 2.00e-02 2.50e+03 1.09e-01 2.37e+02 pdb=" C2N NAD F 605 " 0.182 2.00e-02 2.50e+03 pdb=" C3N NAD F 605 " 0.082 2.00e-02 2.50e+03 pdb=" C4N NAD F 605 " 0.088 2.00e-02 2.50e+03 pdb=" C5N NAD F 605 " -0.033 2.00e-02 2.50e+03 pdb=" C6N NAD F 605 " -0.098 2.00e-02 2.50e+03 pdb=" C7N NAD F 605 " -0.184 2.00e-02 2.50e+03 pdb=" N1N NAD F 605 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS A 96 " -0.105 2.00e-02 2.50e+03 8.45e-02 1.07e+02 pdb=" CG HIS A 96 " 0.163 2.00e-02 2.50e+03 pdb=" ND1 HIS A 96 " 0.035 2.00e-02 2.50e+03 pdb=" CD2 HIS A 96 " -0.013 2.00e-02 2.50e+03 pdb=" CE1 HIS A 96 " -0.057 2.00e-02 2.50e+03 pdb=" NE2 HIS A 96 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS E 573 " -0.044 2.00e-02 2.50e+03 5.65e-02 4.78e+01 pdb=" CG HIS E 573 " -0.003 2.00e-02 2.50e+03 pdb=" ND1 HIS E 573 " 0.094 2.00e-02 2.50e+03 pdb=" CD2 HIS E 573 " 0.038 2.00e-02 2.50e+03 pdb=" CE1 HIS E 573 " -0.083 2.00e-02 2.50e+03 pdb=" NE2 HIS E 573 " -0.002 2.00e-02 2.50e+03 ... (remaining 3426 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.68: 450 2.68 - 3.24: 18605 3.24 - 3.79: 30411 3.79 - 4.35: 39385 4.35 - 4.90: 60824 Nonbonded interactions: 149675 Sorted by model distance: nonbonded pdb=" O ILE G 5 " pdb=" OD1 ASN G 9 " model vdw 2.129 3.040 nonbonded pdb=" O LEU G 31 " pdb=" OG1 THR G 34 " model vdw 2.174 3.040 nonbonded pdb=" CB GLU G 3 " pdb=" OE2 GLU G 8 " model vdw 2.184 3.440 nonbonded pdb=" O CYS A 103 " pdb=" OG SER A 106 " model vdw 2.207 3.040 nonbonded pdb=" OG1 THR A 382 " pdb=" O GLY A 511 " model vdw 2.217 3.040 ... (remaining 149670 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'E' } 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: 0.830 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.810 Check model and map are aligned: 0.140 Set scattering table: 0.180 Process input model: 55.200 Find NCS groups from input model: 0.470 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 60.570 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7640 moved from start: 0.0000 Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_fail.pdb'. Return code: -15 Dumping stderr: