Starting phenix.real_space_refine on Sat Mar 16 22:15:12 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xse_33424/03_2024/7xse_33424.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xse_33424/03_2024/7xse_33424.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xse_33424/03_2024/7xse_33424.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xse_33424/03_2024/7xse_33424.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xse_33424/03_2024/7xse_33424.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xse_33424/03_2024/7xse_33424.pdb" } resolution = 3.6 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= 0.001 sd= 0.005 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 Zn 10 6.06 5 P 275 5.49 5 Mg 1 5.21 5 S 294 5.16 5 C 46616 2.51 5 N 13218 2.21 5 O 14815 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "d TYR 118": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.15s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 75229 Number of models: 1 Model: "" Number of chains: 41 Chain: "A" Number of atoms: 11064 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1404, 11064 Classifications: {'peptide': 1404} Link IDs: {'PCIS': 3, 'PTRANS': 63, 'TRANS': 1337} Chain breaks: 5 Chain: "B" Number of atoms: 9284 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1164, 9284 Classifications: {'peptide': 1164} Link IDs: {'PTRANS': 52, 'TRANS': 1111} Chain breaks: 4 Chain: "C" Number of atoms: 2098 Number of conformers: 1 Conformer: "" Number of residues, atoms: 263, 2098 Classifications: {'peptide': 263} Link IDs: {'PTRANS': 12, 'TRANS': 250} Chain: "D" Number of atoms: 1349 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 1349 Classifications: {'peptide': 174} Link IDs: {'PTRANS': 4, 'TRANS': 169} Chain breaks: 1 Chain: "E" Number of atoms: 1741 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1741 Classifications: {'peptide': 213} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 202} Chain: "F" Number of atoms: 677 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 677 Classifications: {'peptide': 84} Link IDs: {'PTRANS': 5, 'TRANS': 78} Chain: "G" Number of atoms: 1325 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1325 Classifications: {'peptide': 171} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 160} Chain: "H" Number of atoms: 1053 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 1053 Classifications: {'peptide': 133} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 128} Chain breaks: 1 Chain: "I" Number of atoms: 917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 917 Classifications: {'peptide': 111} Link IDs: {'PTRANS': 5, 'TRANS': 105} Chain: "J" Number of atoms: 554 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 554 Classifications: {'peptide': 67} Link IDs: {'PTRANS': 2, 'TRANS': 64} Chain: "K" Number of atoms: 932 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 932 Classifications: {'peptide': 113} Link IDs: {'PTRANS': 8, 'TRANS': 104} Chain: "L" Number of atoms: 359 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 359 Classifications: {'peptide': 45} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 43} Chain: "M" Number of atoms: 505 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 505 Classifications: {'peptide': 64} Link IDs: {'PTRANS': 2, 'TRANS': 61} Chain: "N" Number of atoms: 2527 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 2527 Classifications: {'DNA': 123} Link IDs: {'rna3p': 122} Chain breaks: 1 Chain: "P" Number of atoms: 404 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 404 Classifications: {'RNA': 19} Modifications used: {'rna2p_pyr': 4, 'rna3p_pur': 8, 'rna3p_pyr': 7} Link IDs: {'rna2p': 4, 'rna3p': 14} Chain: "T" Number of atoms: 2735 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 2735 Classifications: {'DNA': 134} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 133} Chain: "V" Number of atoms: 824 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 824 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 5, 'TRANS': 100} Chain: "W" Number of atoms: 4232 Number of conformers: 1 Conformer: "" Number of residues, atoms: 533, 4232 Classifications: {'peptide': 533} Link IDs: {'PTRANS': 18, 'TRANS': 514} Chain breaks: 2 Chain: "a" Number of atoms: 746 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 746 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 2, 'TRANS': 89} Chain: "b" Number of atoms: 662 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 662 Classifications: {'peptide': 83} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 81} Chain: "c" Number of atoms: 796 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 796 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 5, 'TRANS': 97} Chain: "d" Number of atoms: 735 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 735 Classifications: {'peptide': 94} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 91} Chain: "e" Number of atoms: 795 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 795 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 3, 'TRANS': 93} Chain: "f" Number of atoms: 619 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 619 Classifications: {'peptide': 78} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 76} Chain: "g" Number of atoms: 757 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 757 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 4, 'TRANS': 93} Chain: "h" Number of atoms: 725 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 725 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 2, 'TRANS': 90} Chain: "m" Number of atoms: 9730 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1187, 9730 Classifications: {'peptide': 1187} Link IDs: {'PTRANS': 45, 'TRANS': 1141} Chain breaks: 3 Chain: "n" Number of atoms: 1115 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 1115 Classifications: {'peptide': 139} Link IDs: {'PTRANS': 8, 'TRANS': 130} Chain: "q" Number of atoms: 7552 Number of conformers: 1 Conformer: "" Number of residues, atoms: 930, 7552 Classifications: {'peptide': 930} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 910} Chain: "r" Number of atoms: 2139 Number of conformers: 1 Conformer: "" Number of residues, atoms: 266, 2139 Classifications: {'peptide': 266} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 259} Chain breaks: 2 Chain: "u" Number of atoms: 1707 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 1707 Classifications: {'peptide': 208} Link IDs: {'PTRANS': 9, 'TRANS': 198} Chain: "v" Number of atoms: 2878 Number of conformers: 1 Conformer: "" Number of residues, atoms: 349, 2878 Classifications: {'peptide': 349} Link IDs: {'PTRANS': 22, 'TRANS': 326} Chain breaks: 3 Chain: "x" Number of atoms: 1682 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1682 Classifications: {'peptide': 205} Link IDs: {'PTRANS': 9, 'TRANS': 195} Chain breaks: 1 Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 1, ' ZN': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "J" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "L" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "M" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "V" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 527 SG CYS A 67 79.727 92.189 143.448 1.00 51.82 S ATOM 549 SG CYS A 70 83.321 91.092 144.062 1.00 40.45 S ATOM 594 SG CYS A 77 82.285 94.695 144.786 1.00 38.51 S ATOM 829 SG CYS A 107 82.605 117.197 102.048 1.00 79.64 S ATOM 851 SG CYS A 110 84.570 114.156 100.873 1.00 94.41 S ATOM 1157 SG CYS A 148 84.872 117.437 99.054 1.00113.90 S ATOM 1229 SG CYS A 168 81.461 115.571 98.992 1.00133.42 S ATOM 19880 SG CYS B1163 93.273 92.316 130.660 1.00 37.49 S ATOM 19898 SG CYS B1166 91.321 95.511 130.316 1.00 36.59 S ATOM 20021 SG CYS B1182 89.472 92.241 130.977 1.00 47.95 S ATOM 20044 SG CYS B1185 91.123 92.983 127.581 1.00 49.50 S ATOM 20989 SG CYS C 85 94.542 103.690 210.886 1.00 75.22 S ATOM 21002 SG CYS C 87 91.160 102.502 209.634 1.00 84.49 S ATOM 21037 SG CYS C 91 91.340 104.357 212.763 1.00 72.84 S ATOM 21060 SG CYS C 94 92.088 106.353 209.670 1.00 63.30 S ATOM 29206 SG CYS I 78 86.122 197.614 154.956 1.00218.19 S ATOM 29422 SG CYS I 103 86.860 193.244 154.349 1.00208.11 S ATOM 28659 SG CYS I 10 63.394 177.280 115.085 1.00116.00 S ATOM 28822 SG CYS I 29 67.365 177.772 112.903 1.00118.65 S ATOM 28847 SG CYS I 32 65.532 179.441 112.319 1.00116.68 S ATOM 29563 SG CYS J 7 95.271 137.120 199.888 1.00 62.00 S ATOM 29586 SG CYS J 10 97.984 136.260 202.507 1.00 42.50 S ATOM 29862 SG CYS J 44 98.364 139.289 200.117 1.00 67.14 S ATOM 29868 SG CYS J 45 96.043 139.206 203.081 1.00 57.61 S ATOM 31039 SG CYS L 33 55.010 122.806 188.362 1.00 67.03 S ATOM 31054 SG CYS L 36 53.122 123.290 191.650 1.00 84.12 S ATOM 31164 SG CYS L 50 52.113 120.498 189.245 1.00 78.30 S ATOM 31188 SG CYS L 53 51.635 124.142 188.233 1.00 86.83 S ATOM 31445 SG CYS M 25 55.317 139.473 104.229 1.00228.43 S ATOM 31470 SG CYS M 28 55.480 135.739 104.366 1.00249.61 S ATOM 31628 SG CYS M 49 58.399 137.658 102.859 1.00207.97 S ATOM 31652 SG CYS M 52 54.932 137.341 101.073 1.00221.89 S ATOM 37566 SG CYS V 12 26.852 107.125 117.650 1.00194.10 S ATOM 37588 SG CYS V 15 27.925 110.225 115.907 1.00191.11 S ATOM 37690 SG CYS V 29 24.387 110.092 116.751 1.00186.67 S ATOM 37711 SG CYS V 32 25.690 107.856 114.010 1.00200.50 S Time building chain proxies: 28.17, per 1000 atoms: 0.37 Number of scatterers: 75229 At special positions: 0 Unit cell: (216.664, 221.116, 264.152, 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 10 29.99 S 294 16.00 P 275 15.00 Mg 1 11.99 O 14815 8.00 N 13218 7.00 C 46616 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: 23.65 Conformation dependent library (CDL) restraints added in 9.3 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1801 " pdb="ZN ZN A1801 " - pdb=" NE2 HIS A 80 " pdb="ZN ZN A1801 " - pdb=" SG CYS A 70 " pdb="ZN ZN A1801 " - pdb=" SG CYS A 67 " pdb="ZN ZN A1801 " - pdb=" SG CYS A 77 " pdb=" ZN A1802 " pdb="ZN ZN A1802 " - pdb=" SG CYS A 107 " pdb="ZN ZN A1802 " - pdb=" SG CYS A 148 " pdb="ZN ZN A1802 " - pdb=" SG CYS A 168 " pdb="ZN ZN A1802 " - pdb=" SG CYS A 110 " pdb=" ZN B1301 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1166 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1163 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1185 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1182 " pdb=" ZN C 401 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 91 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 85 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 87 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 94 " pdb=" ZN I 201 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 78 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 103 " pdb=" ZN I 202 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 32 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 29 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 10 " pdb=" ZN J 101 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 45 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 10 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 44 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 7 " pdb=" ZN L 101 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 33 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 53 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 50 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 36 " pdb=" ZN M 201 " pdb="ZN ZN M 201 " - pdb=" SG CYS M 28 " pdb="ZN ZN M 201 " - pdb=" SG CYS M 25 " pdb="ZN ZN M 201 " - pdb=" SG CYS M 52 " pdb="ZN ZN M 201 " - pdb=" SG CYS M 49 " pdb=" ZN V 300 " pdb="ZN ZN V 300 " - pdb=" SG CYS V 15 " pdb="ZN ZN V 300 " - pdb=" SG CYS V 29 " pdb="ZN ZN V 300 " - pdb=" SG CYS V 32 " pdb="ZN ZN V 300 " - pdb=" SG CYS V 12 " Number of angles added : 45 17126 Ramachandran restraints generated. 8563 Oldfield, 0 Emsley, 8563 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 16438 Finding SS restraints... Secondary structure from input PDB file: 359 helices and 80 sheets defined 50.4% alpha, 13.3% beta 133 base pairs and 234 stacking pairs defined. Time for finding SS restraints: 19.12 Creating SS restraints... Processing helix chain 'A' and resid 23 through 31 Processing helix chain 'A' and resid 55 through 59 Processing helix chain 'A' and resid 95 through 106 Processing helix chain 'A' and resid 119 through 128 removed outlier: 3.723A pdb=" N ILE A 128 " --> pdb=" O GLN A 124 " (cutoff:3.500A) Processing helix chain 'A' and resid 130 through 145 removed outlier: 4.492A pdb=" N THR A 144 " --> pdb=" O GLN A 140 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N LYS A 145 " --> pdb=" O LEU A 141 " (cutoff:3.500A) Processing helix chain 'A' and resid 204 through 213 Processing helix chain 'A' and resid 216 through 223 Processing helix chain 'A' and resid 231 through 234 Processing helix chain 'A' and resid 261 through 284 Processing helix chain 'A' and resid 286 through 306 removed outlier: 3.701A pdb=" N MET A 305 " --> pdb=" O VAL A 301 " (cutoff:3.500A) Processing helix chain 'A' and resid 325 through 331 removed outlier: 3.711A pdb=" N LEU A 330 " --> pdb=" O ILE A 326 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N LYS A 331 " --> pdb=" O ARG A 327 " (cutoff:3.500A) Processing helix chain 'A' and resid 335 through 341 removed outlier: 3.525A pdb=" N LEU A 341 " --> pdb=" O LEU A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 369 through 375 Processing helix chain 'A' and resid 385 through 396 Processing helix chain 'A' and resid 421 through 425 Processing helix chain 'A' and resid 452 through 454 No H-bonds generated for 'chain 'A' and resid 452 through 454' Processing helix chain 'A' and resid 473 through 477 removed outlier: 3.891A pdb=" N SER A 477 " --> pdb=" O SER A 474 " (cutoff:3.500A) Processing helix chain 'A' and resid 495 through 506 Processing helix chain 'A' and resid 507 through 512 removed outlier: 3.679A pdb=" N ILE A 512 " --> pdb=" O PRO A 509 " (cutoff:3.500A) Processing helix chain 'A' and resid 526 through 536 Processing helix chain 'A' and resid 543 through 553 removed outlier: 3.505A pdb=" N ASN A 549 " --> pdb=" O GLU A 545 " (cutoff:3.500A) Processing helix chain 'A' and resid 575 through 583 removed outlier: 3.769A pdb=" N ALA A 582 " --> pdb=" O LEU A 578 " (cutoff:3.500A) Processing helix chain 'A' and resid 619 through 624 Processing helix chain 'A' and resid 629 through 639 Processing helix chain 'A' and resid 639 through 662 removed outlier: 3.582A pdb=" N PHE A 647 " --> pdb=" O CYS A 643 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N GLY A 648 " --> pdb=" O ALA A 644 " (cutoff:3.500A) Processing helix chain 'A' and resid 666 through 671 removed outlier: 3.726A pdb=" N ILE A 671 " --> pdb=" O GLY A 668 " (cutoff:3.500A) Processing helix chain 'A' and resid 673 through 700 removed outlier: 3.617A pdb=" N GLU A 679 " --> pdb=" O SER A 675 " (cutoff:3.500A) Processing helix chain 'A' and resid 710 through 738 Processing helix chain 'A' and resid 742 through 750 Processing helix chain 'A' and resid 755 through 764 Processing helix chain 'A' and resid 794 through 798 Processing helix chain 'A' and resid 810 through 847 removed outlier: 4.728A pdb=" N ALA A 833 " --> pdb=" O ALA A 829 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N GLU A 834 " --> pdb=" O VAL A 830 " (cutoff:3.500A) Processing helix chain 'A' and resid 868 through 872 Processing helix chain 'A' and resid 890 through 899 Processing helix chain 'A' and resid 924 through 947 Processing helix chain 'A' and resid 961 through 974 Processing helix chain 'A' and resid 984 through 996 Processing helix chain 'A' and resid 1006 through 1017 removed outlier: 3.684A pdb=" N THR A1017 " --> pdb=" O GLN A1013 " (cutoff:3.500A) Processing helix chain 'A' and resid 1017 through 1028 Processing helix chain 'A' and resid 1029 through 1036 Processing helix chain 'A' and resid 1040 through 1058 Processing helix chain 'A' and resid 1065 through 1079 Proline residue: A1077 - end of helix Processing helix chain 'A' and resid 1099 through 1109 Processing helix chain 'A' and resid 1123 through 1128 removed outlier: 3.569A pdb=" N LEU A1128 " --> pdb=" O ARG A1124 " (cutoff:3.500A) Processing helix chain 'A' and resid 1129 through 1141 Processing helix chain 'A' and resid 1145 through 1148 No H-bonds generated for 'chain 'A' and resid 1145 through 1148' Processing helix chain 'A' and resid 1168 through 1177 Processing helix chain 'A' and resid 1200 through 1207 Processing helix chain 'A' and resid 1210 through 1223 Processing helix chain 'A' and resid 1259 through 1274 Processing helix chain 'A' and resid 1315 through 1321 removed outlier: 3.625A pdb=" N ALA A1321 " --> pdb=" O ALA A1317 " (cutoff:3.500A) Processing helix chain 'A' and resid 1334 through 1343 removed outlier: 3.637A pdb=" N GLY A1343 " --> pdb=" O LEU A1339 " (cutoff:3.500A) Processing helix chain 'A' and resid 1344 through 1361 Processing helix chain 'A' and resid 1367 through 1379 removed outlier: 3.986A pdb=" N MET A1371 " --> pdb=" O ASN A1367 " (cutoff:3.500A) Processing helix chain 'A' and resid 1388 through 1393 Processing helix chain 'A' and resid 1398 through 1404 removed outlier: 3.514A pdb=" N SER A1404 " --> pdb=" O LEU A1400 " (cutoff:3.500A) Processing helix chain 'A' and resid 1407 through 1418 Processing helix chain 'A' and resid 1426 through 1433 removed outlier: 3.811A pdb=" N ASN A1430 " --> pdb=" O GLY A1426 " (cutoff:3.500A) Processing helix chain 'A' and resid 1439 through 1442 Processing helix chain 'A' and resid 1451 through 1455 Processing helix chain 'B' and resid 13 through 28 Processing helix chain 'B' and resid 31 through 44 Processing helix chain 'B' and resid 44 through 52 Processing helix chain 'B' and resid 100 through 108 Processing helix chain 'B' and resid 177 through 183 removed outlier: 3.662A pdb=" N TYR B 181 " --> pdb=" O GLU B 177 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LYS B 182 " --> pdb=" O VAL B 178 " (cutoff:3.500A) Processing helix chain 'B' and resid 274 through 282 Processing helix chain 'B' and resid 285 through 294 Processing helix chain 'B' and resid 299 through 314 Proline residue: B 308 - end of helix Processing helix chain 'B' and resid 318 through 329 removed outlier: 3.647A pdb=" N ARG B 329 " --> pdb=" O PHE B 325 " (cutoff:3.500A) Processing helix chain 'B' and resid 337 through 351 Processing helix chain 'B' and resid 364 through 383 Processing helix chain 'B' and resid 393 through 395 No H-bonds generated for 'chain 'B' and resid 393 through 395' Processing helix chain 'B' and resid 401 through 430 removed outlier: 4.198A pdb=" N GLU B 430 " --> pdb=" O GLN B 426 " (cutoff:3.500A) Processing helix chain 'B' and resid 443 through 457 removed outlier: 3.618A pdb=" N THR B 447 " --> pdb=" O SER B 443 " (cutoff:3.500A) Processing helix chain 'B' and resid 461 through 465 Processing helix chain 'B' and resid 480 through 488 Processing helix chain 'B' and resid 501 through 506 removed outlier: 4.207A pdb=" N ARG B 505 " --> pdb=" O LEU B 501 " (cutoff:3.500A) Processing helix chain 'B' and resid 508 through 512 Processing helix chain 'B' and resid 522 through 526 removed outlier: 4.346A pdb=" N ALA B 525 " --> pdb=" O GLU B 522 " (cutoff:3.500A) Processing helix chain 'B' and resid 544 through 554 Processing helix chain 'B' and resid 560 through 562 No H-bonds generated for 'chain 'B' and resid 560 through 562' Processing helix chain 'B' and resid 585 through 599 removed outlier: 3.575A pdb=" N LEU B 589 " --> pdb=" O ASP B 585 " (cutoff:3.500A) Processing helix chain 'B' and resid 648 through 658 Processing helix chain 'B' and resid 677 through 684 Processing helix chain 'B' and resid 693 through 698 removed outlier: 3.501A pdb=" N GLU B 696 " --> pdb=" O GLU B 693 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ILE B 698 " --> pdb=" O GLU B 695 " (cutoff:3.500A) Processing helix chain 'B' and resid 703 through 708 removed outlier: 3.620A pdb=" N GLN B 708 " --> pdb=" O GLU B 705 " (cutoff:3.500A) Processing helix chain 'B' and resid 744 through 749 removed outlier: 3.745A pdb=" N LEU B 749 " --> pdb=" O SER B 746 " (cutoff:3.500A) Processing helix chain 'B' and resid 751 through 755 removed outlier: 3.552A pdb=" N ILE B 755 " --> pdb=" O ALA B 752 " (cutoff:3.500A) Processing helix chain 'B' and resid 758 through 762 removed outlier: 3.536A pdb=" N ASN B 762 " --> pdb=" O PRO B 759 " (cutoff:3.500A) Processing helix chain 'B' and resid 763 through 774 Processing helix chain 'B' and resid 775 through 777 No H-bonds generated for 'chain 'B' and resid 775 through 777' Processing helix chain 'B' and resid 806 through 811 removed outlier: 3.507A pdb=" N TYR B 811 " --> pdb=" O ALA B 808 " (cutoff:3.500A) Processing helix chain 'B' and resid 843 through 848 Processing helix chain 'B' and resid 921 through 926 removed outlier: 4.145A pdb=" N GLU B 924 " --> pdb=" O ASP B 921 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLY B 926 " --> pdb=" O GLU B 923 " (cutoff:3.500A) Processing helix chain 'B' and resid 995 through 999 removed outlier: 3.655A pdb=" N MET B 999 " --> pdb=" O HIS B 996 " (cutoff:3.500A) Processing helix chain 'B' and resid 1015 through 1021 removed outlier: 4.632A pdb=" N SER B1019 " --> pdb=" O HIS B1015 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N ARG B1020 " --> pdb=" O ALA B1016 " (cutoff:3.500A) Processing helix chain 'B' and resid 1022 through 1039 removed outlier: 3.961A pdb=" N LEU B1026 " --> pdb=" O THR B1022 " (cutoff:3.500A) Processing helix chain 'B' and resid 1051 through 1062 removed outlier: 3.532A pdb=" N VAL B1055 " --> pdb=" O THR B1051 " (cutoff:3.500A) Processing helix chain 'B' and resid 1098 through 1102 Processing helix chain 'B' and resid 1131 through 1142 Processing helix chain 'B' and resid 1143 through 1152 Processing helix chain 'B' and resid 1198 through 1210 Processing helix chain 'C' and resid 25 through 39 Processing helix chain 'C' and resid 58 through 68 Processing helix chain 'C' and resid 81 through 85 Processing helix chain 'C' and resid 116 through 118 No H-bonds generated for 'chain 'C' and resid 116 through 118' Processing helix chain 'C' and resid 167 through 171 Processing helix chain 'C' and resid 206 through 210 removed outlier: 3.611A pdb=" N GLU C 210 " --> pdb=" O ALA C 207 " (cutoff:3.500A) Processing helix chain 'C' and resid 239 through 266 removed outlier: 3.981A pdb=" N ARG C 266 " --> pdb=" O LEU C 262 " (cutoff:3.500A) Processing helix chain 'D' and resid 31 through 35 Processing helix chain 'D' and resid 52 through 72 Processing helix chain 'D' and resid 85 through 93 removed outlier: 3.996A pdb=" N THR D 93 " --> pdb=" O LEU D 89 " (cutoff:3.500A) Processing helix chain 'D' and resid 95 through 112 Processing helix chain 'D' and resid 117 through 131 removed outlier: 3.605A pdb=" N SER D 131 " --> pdb=" O LEU D 127 " (cutoff:3.500A) Processing helix chain 'D' and resid 132 through 136 removed outlier: 3.670A pdb=" N VAL D 136 " --> pdb=" O ASP D 133 " (cutoff:3.500A) Processing helix chain 'D' and resid 138 through 149 removed outlier: 3.716A pdb=" N GLY D 149 " --> pdb=" O LEU D 145 " (cutoff:3.500A) Processing helix chain 'D' and resid 152 through 160 Processing helix chain 'D' and resid 161 through 166 removed outlier: 4.193A pdb=" N ALA D 165 " --> pdb=" O PRO D 161 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N LYS D 166 " --> pdb=" O SER D 162 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 161 through 166' Processing helix chain 'D' and resid 170 through 182 Processing helix chain 'E' and resid 3 through 25 Processing helix chain 'E' and resid 30 through 35 Processing helix chain 'E' and resid 37 through 46 Processing helix chain 'E' and resid 53 through 57 Processing helix chain 'E' and resid 64 through 71 Processing helix chain 'E' and resid 88 through 102 Processing helix chain 'E' and resid 116 through 122 removed outlier: 3.589A pdb=" N MET E 122 " --> pdb=" O SER E 118 " (cutoff:3.500A) Processing helix chain 'E' and resid 137 through 140 removed outlier: 3.585A pdb=" N VAL E 140 " --> pdb=" O SER E 137 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 137 through 140' Processing helix chain 'E' and resid 142 through 146 Processing helix chain 'E' and resid 156 through 168 Processing helix chain 'E' and resid 170 through 174 removed outlier: 3.641A pdb=" N LEU E 174 " --> pdb=" O GLU E 171 " (cutoff:3.500A) Processing helix chain 'E' and resid 181 through 188 Processing helix chain 'F' and resid 75 through 79 removed outlier: 3.709A pdb=" N ARG F 79 " --> pdb=" O LYS F 76 " (cutoff:3.500A) Processing helix chain 'F' and resid 86 through 103 Processing helix chain 'F' and resid 116 through 127 Processing helix chain 'G' and resid 14 through 18 Processing helix chain 'G' and resid 19 through 20 No H-bonds generated for 'chain 'G' and resid 19 through 20' Processing helix chain 'G' and resid 21 through 35 Processing helix chain 'G' and resid 113 through 115 No H-bonds generated for 'chain 'G' and resid 113 through 115' Processing helix chain 'H' and resid 87 through 92 removed outlier: 3.529A pdb=" N ASP H 91 " --> pdb=" O LEU H 88 " (cutoff:3.500A) Processing helix chain 'H' and resid 127 through 132 Processing helix chain 'H' and resid 133 through 135 No H-bonds generated for 'chain 'H' and resid 133 through 135' Processing helix chain 'I' and resid 61 through 65 removed outlier: 3.573A pdb=" N ASP I 65 " --> pdb=" O ILE I 62 " (cutoff:3.500A) Processing helix chain 'J' and resid 17 through 27 Processing helix chain 'J' and resid 30 through 38 Processing helix chain 'J' and resid 42 through 51 removed outlier: 3.891A pdb=" N MET J 48 " --> pdb=" O CYS J 44 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N VAL J 49 " --> pdb=" O CYS J 45 " (cutoff:3.500A) Processing helix chain 'J' and resid 55 through 60 Processing helix chain 'K' and resid 5 through 10 Processing helix chain 'K' and resid 39 through 51 removed outlier: 3.816A pdb=" N LEU K 45 " --> pdb=" O THR K 41 " (cutoff:3.500A) Processing helix chain 'K' and resid 82 through 113 Processing helix chain 'M' and resid 65 through 78 Processing helix chain 'V' and resid 20 through 28 Processing helix chain 'V' and resid 31 through 35 removed outlier: 4.046A pdb=" N SER V 34 " --> pdb=" O ASN V 31 " (cutoff:3.500A) Processing helix chain 'V' and resid 42 through 49 Processing helix chain 'V' and resid 66 through 72 Processing helix chain 'V' and resid 91 through 101 Processing helix chain 'W' and resid 235 through 251 Processing helix chain 'W' and resid 278 through 287 Processing helix chain 'W' and resid 304 through 310 removed outlier: 4.207A pdb=" N ASP W 308 " --> pdb=" O VAL W 304 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N LEU W 310 " --> pdb=" O TYR W 306 " (cutoff:3.500A) Processing helix chain 'W' and resid 395 through 403 Processing helix chain 'W' and resid 443 through 452 Processing helix chain 'W' and resid 453 through 455 No H-bonds generated for 'chain 'W' and resid 453 through 455' Processing helix chain 'W' and resid 461 through 475 Processing helix chain 'W' and resid 515 through 520 Processing helix chain 'W' and resid 692 through 695 Processing helix chain 'W' and resid 760 through 764 removed outlier: 4.298A pdb=" N TYR W 763 " --> pdb=" O GLN W 760 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N LYS W 764 " --> pdb=" O GLY W 761 " (cutoff:3.500A) No H-bonds generated for 'chain 'W' and resid 760 through 764' Processing helix chain 'W' and resid 792 through 794 No H-bonds generated for 'chain 'W' and resid 792 through 794' Processing helix chain 'a' and resid 44 through 56 removed outlier: 3.714A pdb=" N LEU a 48 " --> pdb=" O GLY a 44 " (cutoff:3.500A) Processing helix chain 'a' and resid 63 through 76 Processing helix chain 'a' and resid 85 through 114 Processing helix chain 'a' and resid 120 through 132 Processing helix chain 'b' and resid 25 through 29 Processing helix chain 'b' and resid 30 through 41 Processing helix chain 'b' and resid 49 through 76 removed outlier: 3.840A pdb=" N ASP b 68 " --> pdb=" O ASN b 64 " (cutoff:3.500A) Processing helix chain 'b' and resid 82 through 93 removed outlier: 3.554A pdb=" N GLN b 93 " --> pdb=" O ALA b 89 " (cutoff:3.500A) Processing helix chain 'c' and resid 17 through 21 removed outlier: 3.509A pdb=" N ALA c 21 " --> pdb=" O ARG c 17 " (cutoff:3.500A) No H-bonds generated for 'chain 'c' and resid 17 through 21' Processing helix chain 'c' and resid 26 through 36 removed outlier: 3.855A pdb=" N VAL c 30 " --> pdb=" O PRO c 26 " (cutoff:3.500A) Processing helix chain 'c' and resid 45 through 73 removed outlier: 4.411A pdb=" N VAL c 49 " --> pdb=" O ALA c 45 " (cutoff:3.500A) Processing helix chain 'c' and resid 79 through 90 Processing helix chain 'c' and resid 90 through 97 Processing helix chain 'c' and resid 112 through 116 Processing helix chain 'd' and resid 34 through 46 Processing helix chain 'd' and resid 52 through 81 Processing helix chain 'd' and resid 87 through 99 Processing helix chain 'd' and resid 100 through 121 removed outlier: 3.537A pdb=" N ALA d 121 " --> pdb=" O LYS d 117 " (cutoff:3.500A) Processing helix chain 'e' and resid 44 through 57 Processing helix chain 'e' and resid 63 through 76 Processing helix chain 'e' and resid 85 through 114 Processing helix chain 'e' and resid 120 through 131 Processing helix chain 'f' and resid 25 through 29 removed outlier: 3.612A pdb=" N ILE f 29 " --> pdb=" O ILE f 26 " (cutoff:3.500A) Processing helix chain 'f' and resid 30 through 41 Processing helix chain 'f' and resid 49 through 77 Processing helix chain 'f' and resid 82 through 94 Processing helix chain 'g' and resid 16 through 21 Processing helix chain 'g' and resid 26 through 36 Processing helix chain 'g' and resid 46 through 73 removed outlier: 3.622A pdb=" N LEU g 65 " --> pdb=" O GLU g 61 " (cutoff:3.500A) Processing helix chain 'g' and resid 79 through 90 Processing helix chain 'g' and resid 90 through 97 Processing helix chain 'h' and resid 34 through 46 Processing helix chain 'h' and resid 52 through 81 Processing helix chain 'h' and resid 87 through 99 Processing helix chain 'h' and resid 100 through 121 Processing helix chain 'm' and resid 230 through 242 Processing helix chain 'm' and resid 244 through 259 removed outlier: 4.415A pdb=" N TRP m 249 " --> pdb=" O THR m 245 " (cutoff:3.500A) removed outlier: 5.694A pdb=" N THR m 250 " --> pdb=" O ASP m 246 " (cutoff:3.500A) Processing helix chain 'm' and resid 279 through 284 Processing helix chain 'm' and resid 285 through 293 Processing helix chain 'm' and resid 295 through 304 Processing helix chain 'm' and resid 307 through 314 Processing helix chain 'm' and resid 323 through 342 Processing helix chain 'm' and resid 342 through 353 Processing helix chain 'm' and resid 358 through 377 Processing helix chain 'm' and resid 380 through 388 Processing helix chain 'm' and resid 388 through 393 removed outlier: 3.934A pdb=" N ALA m 392 " --> pdb=" O ARG m 388 " (cutoff:3.500A) Processing helix chain 'm' and resid 410 through 442 removed outlier: 3.945A pdb=" N ASP m 429 " --> pdb=" O HIS m 425 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N LYS m 430 " --> pdb=" O SER m 426 " (cutoff:3.500A) Processing helix chain 'm' and resid 447 through 456 removed outlier: 3.603A pdb=" N SER m 456 " --> pdb=" O GLU m 452 " (cutoff:3.500A) Processing helix chain 'm' and resid 459 through 474 Processing helix chain 'm' and resid 474 through 484 Processing helix chain 'm' and resid 518 through 527 Processing helix chain 'm' and resid 529 through 537 removed outlier: 4.044A pdb=" N ALA m 537 " --> pdb=" O VAL m 533 " (cutoff:3.500A) Processing helix chain 'm' and resid 538 through 549 Processing helix chain 'm' and resid 561 through 573 Processing helix chain 'm' and resid 581 through 599 Processing helix chain 'm' and resid 600 through 615 removed outlier: 3.503A pdb=" N ARG m 604 " --> pdb=" O GLU m 600 " (cutoff:3.500A) Processing helix chain 'm' and resid 622 through 629 removed outlier: 3.520A pdb=" N ILE m 629 " --> pdb=" O GLY m 625 " (cutoff:3.500A) Processing helix chain 'm' and resid 633 through 639 removed outlier: 3.719A pdb=" N ASP m 637 " --> pdb=" O PRO m 634 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LYS m 639 " --> pdb=" O PHE m 636 " (cutoff:3.500A) Processing helix chain 'm' and resid 648 through 651 Processing helix chain 'm' and resid 652 through 665 removed outlier: 3.908A pdb=" N TYR m 656 " --> pdb=" O THR m 652 " (cutoff:3.500A) Processing helix chain 'm' and resid 676 through 689 Processing helix chain 'm' and resid 694 through 748 Proline residue: m 717 - end of helix Processing helix chain 'm' and resid 802 through 815 removed outlier: 3.567A pdb=" N SER m 806 " --> pdb=" O SER m 802 " (cutoff:3.500A) Processing helix chain 'm' and resid 830 through 847 removed outlier: 4.059A pdb=" N LYS m 834 " --> pdb=" O ILE m 830 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N LEU m 835 " --> pdb=" O HIS m 831 " (cutoff:3.500A) Processing helix chain 'm' and resid 878 through 887 removed outlier: 3.749A pdb=" N HIS m 886 " --> pdb=" O ARG m 882 " (cutoff:3.500A) Processing helix chain 'm' and resid 887 through 894 removed outlier: 3.690A pdb=" N SER m 891 " --> pdb=" O SER m 887 " (cutoff:3.500A) Processing helix chain 'm' and resid 898 through 913 Processing helix chain 'm' and resid 913 through 921 Processing helix chain 'm' and resid 922 through 928 removed outlier: 4.124A pdb=" N MET m 925 " --> pdb=" O ASP m 922 " (cutoff:3.500A) Processing helix chain 'm' and resid 938 through 958 Processing helix chain 'm' and resid 961 through 967 Processing helix chain 'm' and resid 967 through 972 Processing helix chain 'm' and resid 973 through 977 Processing helix chain 'm' and resid 981 through 996 Processing helix chain 'm' and resid 1003 through 1008 Processing helix chain 'm' and resid 1012 through 1020 Processing helix chain 'm' and resid 1030 through 1034 removed outlier: 3.950A pdb=" N ARG m1033 " --> pdb=" O ASP m1030 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N ASN m1034 " --> pdb=" O VAL m1031 " (cutoff:3.500A) No H-bonds generated for 'chain 'm' and resid 1030 through 1034' Processing helix chain 'm' and resid 1040 through 1045 Processing helix chain 'm' and resid 1048 through 1050 No H-bonds generated for 'chain 'm' and resid 1048 through 1050' Processing helix chain 'm' and resid 1051 through 1064 Processing helix chain 'm' and resid 1072 through 1085 Processing helix chain 'm' and resid 1097 through 1103 Processing helix chain 'm' and resid 1104 through 1117 removed outlier: 3.557A pdb=" N TYR m1108 " --> pdb=" O ILE m1104 " (cutoff:3.500A) Processing helix chain 'm' and resid 1120 through 1133 Processing helix chain 'm' and resid 1146 through 1156 Processing helix chain 'm' and resid 1194 through 1198 removed outlier: 4.376A pdb=" N LEU m1198 " --> pdb=" O ARG m1194 " (cutoff:3.500A) No H-bonds generated for 'chain 'm' and resid 1194 through 1198' Processing helix chain 'm' and resid 1205 through 1210 Processing helix chain 'm' and resid 1235 through 1240 Processing helix chain 'm' and resid 1256 through 1273 Processing helix chain 'm' and resid 1290 through 1300 removed outlier: 3.706A pdb=" N ALA m1300 " --> pdb=" O ASP m1296 " (cutoff:3.500A) Processing helix chain 'm' and resid 1358 through 1380 removed outlier: 3.929A pdb=" N ASN m1368 " --> pdb=" O VAL m1364 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N ASN m1369 " --> pdb=" O GLU m1365 " (cutoff:3.500A) Processing helix chain 'm' and resid 1387 through 1402 Processing helix chain 'm' and resid 1453 through 1469 Processing helix chain 'n' and resid 153 through 180 Processing helix chain 'n' and resid 185 through 200 Proline residue: n 192 - end of helix removed outlier: 3.549A pdb=" N ARG n 200 " --> pdb=" O ASP n 196 " (cutoff:3.500A) Processing helix chain 'n' and resid 203 through 211 Processing helix chain 'n' and resid 212 through 221 Processing helix chain 'n' and resid 230 through 244 Processing helix chain 'n' and resid 247 through 255 Processing helix chain 'n' and resid 255 through 266 removed outlier: 4.553A pdb=" N VAL n 259 " --> pdb=" O GLY n 255 " (cutoff:3.500A) Processing helix chain 'n' and resid 270 through 289 Proline residue: n 287 - end of helix Processing helix chain 'q' and resid 5 through 13 removed outlier: 3.878A pdb=" N TYR q 9 " --> pdb=" O ASP q 5 " (cutoff:3.500A) Processing helix chain 'q' and resid 14 through 20 removed outlier: 3.750A pdb=" N GLU q 20 " --> pdb=" O ASP q 16 " (cutoff:3.500A) Processing helix chain 'q' and resid 21 through 23 No H-bonds generated for 'chain 'q' and resid 21 through 23' Processing helix chain 'q' and resid 46 through 58 Processing helix chain 'q' and resid 60 through 74 removed outlier: 3.663A pdb=" N TRP q 64 " --> pdb=" O ARG q 60 " (cutoff:3.500A) Processing helix chain 'q' and resid 76 through 89 Processing helix chain 'q' and resid 90 through 96 Processing helix chain 'q' and resid 97 through 120 removed outlier: 3.873A pdb=" N THR q 101 " --> pdb=" O SER q 97 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N THR q 119 " --> pdb=" O GLU q 115 " (cutoff:3.500A) Processing helix chain 'q' and resid 122 through 141 Processing helix chain 'q' and resid 144 through 158 removed outlier: 3.690A pdb=" N GLY q 148 " --> pdb=" O LEU q 144 " (cutoff:3.500A) Processing helix chain 'q' and resid 160 through 175 Processing helix chain 'q' and resid 178 through 192 Processing helix chain 'q' and resid 194 through 209 removed outlier: 3.534A pdb=" N LEU q 201 " --> pdb=" O GLN q 197 " (cutoff:3.500A) Processing helix chain 'q' and resid 215 through 227 removed outlier: 4.129A pdb=" N GLY q 219 " --> pdb=" O ASP q 215 " (cutoff:3.500A) Processing helix chain 'q' and resid 229 through 244 Processing helix chain 'q' and resid 248 through 267 removed outlier: 3.878A pdb=" N LYS q 252 " --> pdb=" O ASN q 248 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N SER q 267 " --> pdb=" O CYS q 263 " (cutoff:3.500A) Processing helix chain 'q' and resid 269 through 289 Processing helix chain 'q' and resid 294 through 308 removed outlier: 3.601A pdb=" N SER q 303 " --> pdb=" O MET q 299 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N TYR q 304 " --> pdb=" O VAL q 300 " (cutoff:3.500A) Processing helix chain 'q' and resid 310 through 325 Processing helix chain 'q' and resid 328 through 347 removed outlier: 3.552A pdb=" N VAL q 332 " --> pdb=" O ASN q 328 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N HIS q 345 " --> pdb=" O ARG q 341 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N LYS q 346 " --> pdb=" O VAL q 342 " (cutoff:3.500A) Processing helix chain 'q' and resid 348 through 363 Processing helix chain 'q' and resid 366 through 380 removed outlier: 3.544A pdb=" N LYS q 370 " --> pdb=" O ASN q 366 " (cutoff:3.500A) Processing helix chain 'q' and resid 382 through 397 Processing helix chain 'q' and resid 402 through 417 Processing helix chain 'q' and resid 419 through 438 Processing helix chain 'q' and resid 442 through 454 removed outlier: 3.802A pdb=" N TYR q 446 " --> pdb=" O LEU q 442 " (cutoff:3.500A) Processing helix chain 'q' and resid 457 through 473 Processing helix chain 'q' and resid 474 through 476 No H-bonds generated for 'chain 'q' and resid 474 through 476' Processing helix chain 'q' and resid 477 through 491 Processing helix chain 'q' and resid 493 through 508 Processing helix chain 'q' and resid 509 through 511 No H-bonds generated for 'chain 'q' and resid 509 through 511' Processing helix chain 'q' and resid 512 through 535 removed outlier: 4.231A pdb=" N GLU q 517 " --> pdb=" O PRO q 513 " (cutoff:3.500A) removed outlier: 5.131A pdb=" N ALA q 518 " --> pdb=" O GLN q 514 " (cutoff:3.500A) Processing helix chain 'q' and resid 535 through 550 removed outlier: 3.533A pdb=" N ALA q 539 " --> pdb=" O ASN q 535 " (cutoff:3.500A) Processing helix chain 'q' and resid 553 through 569 removed outlier: 4.101A pdb=" N LYS q 557 " --> pdb=" O TYR q 553 " (cutoff:3.500A) Processing helix chain 'q' and resid 572 through 583 Processing helix chain 'q' and resid 586 through 605 removed outlier: 6.251A pdb=" N ARG q 602 " --> pdb=" O LYS q 598 " (cutoff:3.500A) removed outlier: 5.805A pdb=" N LYS q 603 " --> pdb=" O ARG q 599 " (cutoff:3.500A) Processing helix chain 'q' and resid 609 through 622 Processing helix chain 'q' and resid 626 through 644 Processing helix chain 'q' and resid 648 through 673 Processing helix chain 'q' and resid 676 through 690 removed outlier: 3.546A pdb=" N ALA q 680 " --> pdb=" O ASN q 676 " (cutoff:3.500A) Processing helix chain 'q' and resid 692 through 707 Processing helix chain 'q' and resid 709 through 723 Processing helix chain 'q' and resid 725 through 740 Processing helix chain 'q' and resid 745 through 764 removed outlier: 3.789A pdb=" N LEU q 749 " --> pdb=" O ASP q 745 " (cutoff:3.500A) Processing helix chain 'q' and resid 765 through 784 removed outlier: 3.670A pdb=" N TYR q 769 " --> pdb=" O SER q 765 " (cutoff:3.500A) Processing helix chain 'q' and resid 785 through 806 Processing helix chain 'q' and resid 807 through 811 Processing helix chain 'q' and resid 812 through 835 Processing helix chain 'q' and resid 842 through 856 removed outlier: 3.535A pdb=" N THR q 856 " --> pdb=" O MET q 852 " (cutoff:3.500A) Processing helix chain 'q' and resid 856 through 930 removed outlier: 3.780A pdb=" N ARG q 883 " --> pdb=" O LEU q 879 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N ARG q 884 " --> pdb=" O ARG q 880 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N LYS q 885 " --> pdb=" O THR q 881 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N GLU q 917 " --> pdb=" O ILE q 913 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N LEU q 918 " --> pdb=" O LYS q 914 " (cutoff:3.500A) Processing helix chain 'r' and resid 197 through 204 removed outlier: 3.803A pdb=" N ILE r 204 " --> pdb=" O ASP r 200 " (cutoff:3.500A) Processing helix chain 'r' and resid 207 through 215 Processing helix chain 'r' and resid 219 through 225 Processing helix chain 'r' and resid 287 through 289 No H-bonds generated for 'chain 'r' and resid 287 through 289' Processing helix chain 'r' and resid 295 through 310 Processing helix chain 'r' and resid 315 through 332 Processing helix chain 'r' and resid 335 through 350 Processing helix chain 'r' and resid 353 through 374 Processing helix chain 'r' and resid 378 through 391 removed outlier: 3.610A pdb=" N ARG r 382 " --> pdb=" O GLU r 378 " (cutoff:3.500A) Processing helix chain 'r' and resid 398 through 433 removed outlier: 3.828A pdb=" N ARG r 420 " --> pdb=" O ASN r 416 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N GLU r 428 " --> pdb=" O MET r 424 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N LYS r 429 " --> pdb=" O ALA r 425 " (cutoff:3.500A) Processing helix chain 'r' and resid 486 through 490 Processing helix chain 'r' and resid 492 through 497 Processing helix chain 'r' and resid 498 through 505 Processing helix chain 'u' and resid 122 through 129 Processing helix chain 'u' and resid 135 through 149 Processing helix chain 'u' and resid 228 through 242 removed outlier: 3.624A pdb=" N GLN u 242 " --> pdb=" O LEU u 238 " (cutoff:3.500A) Processing helix chain 'u' and resid 258 through 282 Processing helix chain 'v' and resid 32 through 35 Processing helix chain 'v' and resid 36 through 45 Processing helix chain 'v' and resid 47 through 58 Processing helix chain 'v' and resid 64 through 71 removed outlier: 3.574A pdb=" N ASP v 68 " --> pdb=" O GLU v 65 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N GLY v 69 " --> pdb=" O THR v 66 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ASP v 71 " --> pdb=" O ASP v 68 " (cutoff:3.500A) Processing helix chain 'v' and resid 73 through 77 removed outlier: 3.609A pdb=" N ILE v 77 " --> pdb=" O TYR v 74 " (cutoff:3.500A) Processing helix chain 'v' and resid 85 through 94 Processing helix chain 'v' and resid 103 through 109 Processing helix chain 'v' and resid 158 through 172 Processing helix chain 'v' and resid 178 through 185 Processing helix chain 'v' and resid 218 through 221 Processing helix chain 'v' and resid 225 through 233 Processing helix chain 'v' and resid 244 through 249 Processing helix chain 'v' and resid 271 through 284 Processing helix chain 'v' and resid 345 through 347 No H-bonds generated for 'chain 'v' and resid 345 through 347' Processing helix chain 'v' and resid 348 through 353 Processing helix chain 'v' and resid 368 through 380 Processing helix chain 'x' and resid 136 through 145 Processing helix chain 'x' and resid 153 through 157 removed outlier: 4.066A pdb=" N LEU x 156 " --> pdb=" O ASN x 153 " (cutoff:3.500A) Processing helix chain 'x' and resid 164 through 175 Processing helix chain 'x' and resid 224 through 230 Processing helix chain 'x' and resid 275 through 280 removed outlier: 3.548A pdb=" N TYR x 278 " --> pdb=" O LYS x 275 " (cutoff:3.500A) Processing helix chain 'x' and resid 290 through 295 removed outlier: 3.646A pdb=" N GLN x 293 " --> pdb=" O LYS x 290 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N LYS x 295 " --> pdb=" O TRP x 292 " (cutoff:3.500A) Processing helix chain 'x' and resid 301 through 309 Processing helix chain 'x' and resid 322 through 327 Processing helix chain 'x' and resid 341 through 361 removed outlier: 4.390A pdb=" N GLN x 345 " --> pdb=" O PHE x 341 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 1421 through 1422 Processing sheet with id=AA2, first strand: chain 'A' and resid 82 through 91 removed outlier: 6.778A pdb=" N THR A 238 " --> pdb=" O LEU A 86 " (cutoff:3.500A) removed outlier: 10.601A pdb=" N LYS A 88 " --> pdb=" O ILE A 236 " (cutoff:3.500A) removed outlier: 10.190A pdb=" N ILE A 236 " --> pdb=" O LYS A 88 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 174 through 178 Processing sheet with id=AA4, first strand: chain 'A' and resid 251 through 252 Processing sheet with id=AA5, first strand: chain 'A' and resid 344 through 346 removed outlier: 3.613A pdb=" N LYS A 344 " --> pdb=" O PHE B1130 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N LEU B1128 " --> pdb=" O VAL A 346 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 1104 through 1106 removed outlier: 3.691A pdb=" N THR A 352 " --> pdb=" O MET A 488 " (cutoff:3.500A) removed outlier: 6.080A pdb=" N VAL A 365 " --> pdb=" O LYS A 462 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N MET A 464 " --> pdb=" O VAL A 365 " (cutoff:3.500A) removed outlier: 5.433A pdb=" N VAL A 367 " --> pdb=" O MET A 464 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 376 through 380 removed outlier: 3.967A pdb=" N TYR A 405 " --> pdb=" O GLU A 434 " (cutoff:3.500A) removed outlier: 6.174A pdb=" N HIS A 436 " --> pdb=" O ALA A 403 " (cutoff:3.500A) removed outlier: 7.072A pdb=" N ALA A 403 " --> pdb=" O HIS A 436 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 541 through 542 Processing sheet with id=AA9, first strand: chain 'A' and resid 566 through 568 removed outlier: 6.329A pdb=" N VAL H 95 " --> pdb=" O LEU A 567 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ILE H 29 " --> pdb=" O THR H 11 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N ILE H 27 " --> pdb=" O GLN H 13 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N VAL H 15 " --> pdb=" O ARG H 25 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N ARG H 25 " --> pdb=" O VAL H 15 " (cutoff:3.500A) removed outlier: 5.556A pdb=" N LEU H 121 " --> pdb=" O ASP H 41 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N LYS H 102 " --> pdb=" O TYR H 114 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N SER H 116 " --> pdb=" O VAL H 100 " (cutoff:3.500A) removed outlier: 5.781A pdb=" N VAL H 100 " --> pdb=" O SER H 116 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 589 through 591 removed outlier: 6.953A pdb=" N LEU A 607 " --> pdb=" O MET A 614 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 767 through 768 Processing sheet with id=AB3, first strand: chain 'A' and resid 850 through 851 removed outlier: 6.740A pdb=" N THR A 857 " --> pdb=" O ILE A 865 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 879 through 883 Processing sheet with id=AB5, first strand: chain 'A' and resid 1284 through 1295 removed outlier: 3.969A pdb=" N LYS A1284 " --> pdb=" O ASP A1312 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N LEU A1118 " --> pdb=" O THR A1311 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 1143 through 1144 Processing sheet with id=AB7, first strand: chain 'A' and resid 1226 through 1230 removed outlier: 4.335A pdb=" N LEU A1238 " --> pdb=" O LEU A1199 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N VAL A1244 " --> pdb=" O TRP A1193 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N TRP A1193 " --> pdb=" O VAL A1244 " (cutoff:3.500A) removed outlier: 7.219A pdb=" N TYR A1156 " --> pdb=" O LYS I 42 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N LYS I 42 " --> pdb=" O TYR A1156 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 1444 through 1448 Processing sheet with id=AB9, first strand: chain 'B' and resid 55 through 62 removed outlier: 4.938A pdb=" N ASP B 118 " --> pdb=" O GLY B 80 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N ILE B 82 " --> pdb=" O TYR B 116 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N TYR B 116 " --> pdb=" O ILE B 82 " (cutoff:3.500A) removed outlier: 4.976A pdb=" N LEU B 84 " --> pdb=" O PRO B 114 " (cutoff:3.500A) removed outlier: 5.553A pdb=" N SER B 113 " --> pdb=" O LYS B 160 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N LYS B 160 " --> pdb=" O SER B 113 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N VAL B 115 " --> pdb=" O ILE B 158 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 88 through 90 Processing sheet with id=AC2, first strand: chain 'B' and resid 194 through 196 Processing sheet with id=AC3, first strand: chain 'B' and resid 397 through 400 Processing sheet with id=AC4, first strand: chain 'B' and resid 215 through 218 removed outlier: 3.950A pdb=" N HIS B 227 " --> pdb=" O LEU B 249 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N SER B 243 " --> pdb=" O SER B 233 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N GLN B 246 " --> pdb=" O THR B 264 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 537 through 538 removed outlier: 3.967A pdb=" N GLU B 644 " --> pdb=" O GLU B 634 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 644 through 645 current: chain 'B' and resid 740 through 741 Processing sheet with id=AC6, first strand: chain 'B' and resid 557 through 558 removed outlier: 5.660A pdb=" N TRP B 579 " --> pdb=" O VAL B 575 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N VAL B 575 " --> pdb=" O TRP B 579 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N GLY B 581 " --> pdb=" O ILE B 573 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N ARG B 572 " --> pdb=" O PHE B 617 " (cutoff:3.500A) removed outlier: 8.016A pdb=" N ILE B 619 " --> pdb=" O ARG B 572 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N PHE B 574 " --> pdb=" O ILE B 619 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 792 through 796 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 853 through 862 current: chain 'B' and resid 947 through 956 removed outlier: 8.660A pdb=" N GLY B 947 " --> pdb=" O THR B 971 " (cutoff:3.500A) removed outlier: 8.591A pdb=" N THR B 971 " --> pdb=" O GLY B 947 " (cutoff:3.500A) removed outlier: 5.334A pdb=" N VAL B 949 " --> pdb=" O ARG B 969 " (cutoff:3.500A) removed outlier: 6.050A pdb=" N ARG B 969 " --> pdb=" O VAL B 949 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 962 through 972 current: chain 'L' and resid 39 through 42 Processing sheet with id=AC8, first strand: chain 'B' and resid 804 through 805 Processing sheet with id=AC9, first strand: chain 'B' and resid 1069 through 1070 removed outlier: 7.004A pdb=" N MET B 839 " --> pdb=" O GLY B 991 " (cutoff:3.500A) removed outlier: 6.225A pdb=" N THR B 993 " --> pdb=" O MET B 839 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N MET B 841 " --> pdb=" O THR B 993 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N PHE B1086 " --> pdb=" O ILE B 827 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 873 through 874 removed outlier: 7.424A pdb=" N LEU B 883 " --> pdb=" O ASP B 936 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 910 through 912 removed outlier: 3.538A pdb=" N ILE B 912 " --> pdb=" O THR B 939 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 1001 through 1002 Processing sheet with id=AD4, first strand: chain 'B' and resid 1157 through 1163 Processing sheet with id=AD5, first strand: chain 'C' and resid 6 through 12 removed outlier: 6.590A pdb=" N GLU C 18 " --> pdb=" O ILE C 10 " (cutoff:3.500A) removed outlier: 4.702A pdb=" N ALA C 12 " --> pdb=" O GLU C 16 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N GLU C 16 " --> pdb=" O ALA C 12 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N GLU C 233 " --> pdb=" O ALA C 175 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N ALA C 175 " --> pdb=" O GLU C 233 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 119 through 122 removed outlier: 6.730A pdb=" N VAL C 97 " --> pdb=" O VAL C 121 " (cutoff:3.500A) removed outlier: 7.078A pdb=" N ARG C 156 " --> pdb=" O ILE C 50 " (cutoff:3.500A) removed outlier: 5.363A pdb=" N ILE C 50 " --> pdb=" O ARG C 156 " (cutoff:3.500A) removed outlier: 7.255A pdb=" N ILE C 158 " --> pdb=" O VAL C 48 " (cutoff:3.500A) removed outlier: 5.699A pdb=" N VAL C 48 " --> pdb=" O ILE C 158 " (cutoff:3.500A) removed outlier: 7.209A pdb=" N LYS C 160 " --> pdb=" O ASP C 46 " (cutoff:3.500A) removed outlier: 6.069A pdb=" N ASP C 46 " --> pdb=" O LYS C 160 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N GLY C 162 " --> pdb=" O ALA C 44 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N ALA C 44 " --> pdb=" O GLY C 162 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 71 through 73 removed outlier: 4.671A pdb=" N GLU C 131 " --> pdb=" O VAL C 72 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 111 through 114 removed outlier: 6.475A pdb=" N THR C 111 " --> pdb=" O LYS C 146 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N LYS C 146 " --> pdb=" O THR C 111 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N VAL C 113 " --> pdb=" O LEU C 144 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'D' and resid 5 through 6 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 5 through 6 current: chain 'G' and resid 2 through 13 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 2 through 13 current: chain 'G' and resid 43 through 48 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 43 through 48 current: chain 'G' and resid 68 through 79 No H-bonds generated for sheet with id=AD9 Processing sheet with id=AE1, first strand: chain 'D' and resid 37 through 39 Processing sheet with id=AE2, first strand: chain 'E' and resid 59 through 61 removed outlier: 6.470A pdb=" N TRP E 78 " --> pdb=" O ILE E 108 " (cutoff:3.500A) removed outlier: 7.714A pdb=" N ILE E 110 " --> pdb=" O TRP E 78 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N GLU E 80 " --> pdb=" O ILE E 110 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'E' and resid 86 through 87 removed outlier: 3.522A pdb=" N VAL E 87 " --> pdb=" O ASN E 114 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE3 Processing sheet with id=AE4, first strand: chain 'E' and resid 151 through 154 removed outlier: 4.117A pdb=" N LYS E 151 " --> pdb=" O ILE E 198 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ILE E 198 " --> pdb=" O LYS E 151 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'G' and resid 169 through 170 removed outlier: 5.590A pdb=" N VAL G 147 " --> pdb=" O SER G 162 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N SER G 162 " --> pdb=" O VAL G 147 " (cutoff:3.500A) removed outlier: 5.255A pdb=" N ASN G 107 " --> pdb=" O ILE G 157 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N ALA G 159 " --> pdb=" O ASN G 107 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLY G 161 " --> pdb=" O PHE G 109 " (cutoff:3.500A) removed outlier: 4.846A pdb=" N SER G 111 " --> pdb=" O GLY G 161 " (cutoff:3.500A) removed outlier: 7.051A pdb=" N GLY G 98 " --> pdb=" O VAL G 94 " (cutoff:3.500A) removed outlier: 5.165A pdb=" N VAL G 94 " --> pdb=" O GLY G 98 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N PHE G 100 " --> pdb=" O SER G 92 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'G' and resid 120 through 122 Processing sheet with id=AE7, first strand: chain 'I' and resid 15 through 19 removed outlier: 3.737A pdb=" N ARG I 24 " --> pdb=" O ASP I 19 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'I' and resid 70 through 71 Processing sheet with id=AE9, first strand: chain 'K' and resid 19 through 23 Processing sheet with id=AF1, first strand: chain 'M' and resid 16 through 21 removed outlier: 3.901A pdb=" N VAL M 34 " --> pdb=" O THR M 21 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'V' and resid 18 through 19 Processing sheet with id=AF3, first strand: chain 'V' and resid 81 through 86 removed outlier: 6.968A pdb=" N GLY V 56 " --> pdb=" O VAL V 84 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N VAL V 86 " --> pdb=" O PHE V 54 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N PHE V 54 " --> pdb=" O VAL V 86 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'W' and resid 337 through 339 Processing sheet with id=AF5, first strand: chain 'W' and resid 349 through 354 removed outlier: 4.663A pdb=" N GLU W 420 " --> pdb=" O TYR W 427 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'W' and resid 522 through 526 removed outlier: 7.775A pdb=" N ILE W 506 " --> pdb=" O VAL W 501 " (cutoff:3.500A) removed outlier: 5.411A pdb=" N VAL W 501 " --> pdb=" O ILE W 506 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N SER W 508 " --> pdb=" O SER W 499 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'W' and resid 572 through 576 removed outlier: 6.041A pdb=" N ILE W 565 " --> pdb=" O ILE W 554 " (cutoff:3.500A) removed outlier: 5.914A pdb=" N ILE W 554 " --> pdb=" O ILE W 565 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'W' and resid 601 through 603 removed outlier: 6.872A pdb=" N ASP W 621 " --> pdb=" O ILE W 613 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'W' and resid 650 through 651 removed outlier: 3.560A pdb=" N ALA W 650 " --> pdb=" O VAL W 658 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'W' and resid 697 through 701 removed outlier: 6.908A pdb=" N PHE W 683 " --> pdb=" O VAL W 679 " (cutoff:3.500A) removed outlier: 4.715A pdb=" N VAL W 679 " --> pdb=" O PHE W 683 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N PHE W 685 " --> pdb=" O LEU W 677 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'W' and resid 787 through 791 removed outlier: 4.573A pdb=" N LYS W 787 " --> pdb=" O LEU W 782 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N ARG W 779 " --> pdb=" O LYS W 771 " (cutoff:3.500A) removed outlier: 6.059A pdb=" N THR W 755 " --> pdb=" O GLU W 799 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'a' and resid 83 through 84 removed outlier: 6.932A pdb=" N ARG a 83 " --> pdb=" O VAL b 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG3 Processing sheet with id=AG4, first strand: chain 'a' and resid 118 through 119 Processing sheet with id=AG5, first strand: chain 'b' and resid 96 through 98 removed outlier: 6.610A pdb=" N THR b 96 " --> pdb=" O THR g 101 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG5 Processing sheet with id=AG6, first strand: chain 'c' and resid 42 through 43 removed outlier: 7.626A pdb=" N ARG c 42 " --> pdb=" O ILE d 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG6 Processing sheet with id=AG7, first strand: chain 'c' and resid 77 through 78 Processing sheet with id=AG8, first strand: chain 'c' and resid 101 through 102 removed outlier: 7.019A pdb=" N THR c 101 " --> pdb=" O TYR f 98 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG8 Processing sheet with id=AG9, first strand: chain 'e' and resid 83 through 84 removed outlier: 6.688A pdb=" N ARG e 83 " --> pdb=" O VAL f 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG9 Processing sheet with id=AH1, first strand: chain 'e' and resid 118 through 119 Processing sheet with id=AH2, first strand: chain 'g' and resid 42 through 43 removed outlier: 7.381A pdb=" N ARG g 42 " --> pdb=" O ILE h 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AH2 Processing sheet with id=AH3, first strand: chain 'g' and resid 77 through 78 Processing sheet with id=AH4, first strand: chain 'm' and resid 396 through 397 Processing sheet with id=AH5, first strand: chain 'm' and resid 644 through 645 Processing sheet with id=AH6, first strand: chain 'm' and resid 790 through 796 removed outlier: 3.832A pdb=" N SER m 792 " --> pdb=" O PHE m 783 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N LEU m 766 " --> pdb=" O GLY m 824 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'm' and resid 959 through 960 removed outlier: 6.876A pdb=" N VAL m 959 " --> pdb=" O TYR m1024 " (cutoff:3.500A) No H-bonds generated for sheet with id=AH7 Processing sheet with id=AH8, first strand: chain 'm' and resid 1167 through 1175 removed outlier: 6.712A pdb=" N SER m1181 " --> pdb=" O ARG m1173 " (cutoff:3.500A) removed outlier: 5.371A pdb=" N VAL m1175 " --> pdb=" O TYR m1179 " (cutoff:3.500A) removed outlier: 7.189A pdb=" N TYR m1179 " --> pdb=" O VAL m1175 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N CYS m1230 " --> pdb=" O ALA m1189 " (cutoff:3.500A) removed outlier: 5.301A pdb=" N GLN m1193 " --> pdb=" O LEU m1232 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N SER m1233 " --> pdb=" O ILE m1220 " (cutoff:3.500A) removed outlier: 5.749A pdb=" N ILE m1220 " --> pdb=" O SER m1233 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'm' and resid 1306 through 1310 removed outlier: 6.746A pdb=" N LEU m1328 " --> pdb=" O VAL m1324 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'm' and resid 1407 through 1412 Processing sheet with id=AI2, first strand: chain 'q' and resid 25 through 29 Processing sheet with id=AI3, first strand: chain 'r' and resid 228 through 232 removed outlier: 4.020A pdb=" N LEU r 229 " --> pdb=" O VAL r 246 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N VAL r 246 " --> pdb=" O LEU r 229 " (cutoff:3.500A) removed outlier: 5.753A pdb=" N VAL r 248 " --> pdb=" O ALA r 275 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N ALA r 275 " --> pdb=" O VAL r 248 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'r' and resid 259 through 260 Processing sheet with id=AI5, first strand: chain 'u' and resid 87 through 91 WARNING: can't find start of bonding for strands! previous: chain 'u' and resid 87 through 91 current: chain 'u' and resid 178 through 182 removed outlier: 4.923A pdb=" N TYR u 178 " --> pdb=" O MET u 189 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'u' and resid 185 through 193 current: chain 'u' and resid 208 through 223 WARNING: can't find start of bonding for strands! previous: chain 'u' and resid 208 through 223 current: chain 'v' and resid 263 through 268 removed outlier: 6.449A pdb=" N ILE v 264 " --> pdb=" O ASP v 302 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N ASP v 302 " --> pdb=" O ILE v 264 " (cutoff:3.500A) removed outlier: 7.103A pdb=" N LEU v 266 " --> pdb=" O ILE v 300 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'v' and resid 295 through 309 current: chain 'v' and resid 327 through 333 Processing sheet with id=AI6, first strand: chain 'u' and resid 116 through 120 removed outlier: 4.467A pdb=" N TRP u 152 " --> pdb=" O ASN u 117 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N GLU u 119 " --> pdb=" O TRP u 152 " (cutoff:3.500A) removed outlier: 8.193A pdb=" N TYR u 154 " --> pdb=" O GLU u 119 " (cutoff:3.500A) Processing sheet with id=AI7, first strand: chain 'v' and resid 29 through 30 Processing sheet with id=AI8, first strand: chain 'x' and resid 247 through 252 removed outlier: 5.934A pdb=" N ILE x 210 " --> pdb=" O VAL x 266 " (cutoff:3.500A) removed outlier: 7.679A pdb=" N ILE x 209 " --> pdb=" O VAL x 283 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N ILE x 285 " --> pdb=" O ILE x 209 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N VAL x 211 " --> pdb=" O ILE x 285 " (cutoff:3.500A) removed outlier: 8.059A pdb=" N PHE x 312 " --> pdb=" O VAL x 283 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N ILE x 285 " --> pdb=" O PHE x 312 " (cutoff:3.500A) removed outlier: 7.915A pdb=" N PHE x 314 " --> pdb=" O ILE x 285 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N GLY x 311 " --> pdb=" O LYS x 331 " (cutoff:3.500A) removed outlier: 7.781A pdb=" N LEU x 333 " --> pdb=" O GLY x 311 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N TYR x 313 " --> pdb=" O LEU x 333 " (cutoff:3.500A) removed outlier: 7.604A pdb=" N ILE x 335 " --> pdb=" O TYR x 313 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N LYS x 315 " --> pdb=" O ILE x 335 " (cutoff:3.500A) 3453 hydrogen bonds defined for protein. 9843 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 339 hydrogen bonds 678 hydrogen bond angles 0 basepair planarities 133 basepair parallelities 234 stacking parallelities Total time for adding SS restraints: 39.10 Time building geometry restraints manager: 25.92 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 17554 1.33 - 1.45: 16366 1.45 - 1.57: 42212 1.57 - 1.69: 547 1.69 - 1.81: 480 Bond restraints: 77159 Sorted by residual: bond pdb=" C1' DA T 34 " pdb=" N9 DA T 34 " ideal model delta sigma weight residual 1.460 1.381 0.079 2.00e-02 2.50e+03 1.57e+01 bond pdb=" C1' DA T 53 " pdb=" N9 DA T 53 " ideal model delta sigma weight residual 1.460 1.385 0.075 2.00e-02 2.50e+03 1.42e+01 bond pdb=" C1' DA T 32 " pdb=" N9 DA T 32 " ideal model delta sigma weight residual 1.460 1.387 0.073 2.00e-02 2.50e+03 1.34e+01 bond pdb=" C1' DA T 59 " pdb=" N9 DA T 59 " ideal model delta sigma weight residual 1.460 1.388 0.072 2.00e-02 2.50e+03 1.28e+01 bond pdb=" C1' DG T 47 " pdb=" N9 DG T 47 " ideal model delta sigma weight residual 1.460 1.389 0.071 2.00e-02 2.50e+03 1.28e+01 ... (remaining 77154 not shown) Histogram of bond angle deviations from ideal: 97.29 - 104.83: 2109 104.83 - 112.37: 39959 112.37 - 119.90: 28350 119.90 - 127.44: 33788 127.44 - 134.98: 1139 Bond angle restraints: 105345 Sorted by residual: angle pdb=" N VAL A1001 " pdb=" CA VAL A1001 " pdb=" C VAL A1001 " ideal model delta sigma weight residual 112.96 107.24 5.72 1.00e+00 1.00e+00 3.27e+01 angle pdb=" O3' G P 10 " pdb=" P U P 11 " pdb=" OP1 U P 11 " ideal model delta sigma weight residual 108.00 124.07 -16.07 3.00e+00 1.11e-01 2.87e+01 angle pdb=" O5' DC T 19 " pdb=" C5' DC T 19 " pdb=" C4' DC T 19 " ideal model delta sigma weight residual 110.80 117.85 -7.05 1.50e+00 4.44e-01 2.21e+01 angle pdb=" C3' DT N -17 " pdb=" O3' DT N -17 " pdb=" P DT N -16 " ideal model delta sigma weight residual 120.20 127.09 -6.89 1.50e+00 4.44e-01 2.11e+01 angle pdb=" C3' DC N -25 " pdb=" O3' DC N -25 " pdb=" P DT N -24 " ideal model delta sigma weight residual 120.20 126.62 -6.42 1.50e+00 4.44e-01 1.83e+01 ... (remaining 105340 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.17: 44674 34.17 - 68.34: 1840 68.34 - 102.51: 83 102.51 - 136.68: 1 136.68 - 170.85: 3 Dihedral angle restraints: 46601 sinusoidal: 21236 harmonic: 25365 Sorted by residual: dihedral pdb=" O4' U P -3 " pdb=" C1' U P -3 " pdb=" N1 U P -3 " pdb=" C2 U P -3 " ideal model delta sinusoidal sigma weight residual 200.00 57.43 142.57 1 1.50e+01 4.44e-03 7.65e+01 dihedral pdb=" O4' C P -4 " pdb=" C1' C P -4 " pdb=" N1 C P -4 " pdb=" C2 C P -4 " ideal model delta sinusoidal sigma weight residual 232.00 61.15 170.85 1 1.70e+01 3.46e-03 6.60e+01 dihedral pdb=" C3' G P -2 " pdb=" C4' G P -2 " pdb=" O4' G P -2 " pdb=" C1' G P -2 " ideal model delta sinusoidal sigma weight residual 20.00 -19.02 39.02 1 8.00e+00 1.56e-02 3.35e+01 ... (remaining 46598 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.100: 11303 0.100 - 0.199: 451 0.199 - 0.299: 9 0.299 - 0.398: 1 0.398 - 0.498: 1 Chirality restraints: 11765 Sorted by residual: chirality pdb=" P U P 11 " pdb=" OP1 U P 11 " pdb=" OP2 U P 11 " pdb=" O5' U P 11 " both_signs ideal model delta sigma weight residual True 2.41 -2.91 -0.50 2.00e-01 2.50e+01 6.19e+00 chirality pdb=" C3' DT N -17 " pdb=" C4' DT N -17 " pdb=" O3' DT N -17 " pdb=" C2' DT N -17 " both_signs ideal model delta sigma weight residual False -2.66 -2.35 -0.31 2.00e-01 2.50e+01 2.48e+00 chirality pdb=" CA ASP e 81 " pdb=" N ASP e 81 " pdb=" C ASP e 81 " pdb=" CB ASP e 81 " both_signs ideal model delta sigma weight residual False 2.51 2.22 0.29 2.00e-01 2.50e+01 2.15e+00 ... (remaining 11762 not shown) Planarity restraints: 12665 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DT N -17 " 0.155 2.00e-02 2.50e+03 7.03e-02 1.23e+02 pdb=" N1 DT N -17 " -0.066 2.00e-02 2.50e+03 pdb=" C2 DT N -17 " -0.044 2.00e-02 2.50e+03 pdb=" O2 DT N -17 " -0.020 2.00e-02 2.50e+03 pdb=" N3 DT N -17 " -0.037 2.00e-02 2.50e+03 pdb=" C4 DT N -17 " 0.007 2.00e-02 2.50e+03 pdb=" O4 DT N -17 " 0.106 2.00e-02 2.50e+03 pdb=" C5 DT N -17 " -0.033 2.00e-02 2.50e+03 pdb=" C7 DT N -17 " 0.002 2.00e-02 2.50e+03 pdb=" C6 DT N -17 " -0.071 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DG N -18 " 0.150 2.00e-02 2.50e+03 6.01e-02 1.08e+02 pdb=" N9 DG N -18 " -0.031 2.00e-02 2.50e+03 pdb=" C8 DG N -18 " -0.046 2.00e-02 2.50e+03 pdb=" N7 DG N -18 " -0.047 2.00e-02 2.50e+03 pdb=" C5 DG N -18 " -0.027 2.00e-02 2.50e+03 pdb=" C6 DG N -18 " 0.028 2.00e-02 2.50e+03 pdb=" O6 DG N -18 " 0.072 2.00e-02 2.50e+03 pdb=" N1 DG N -18 " 0.044 2.00e-02 2.50e+03 pdb=" C2 DG N -18 " -0.002 2.00e-02 2.50e+03 pdb=" N2 DG N -18 " -0.032 2.00e-02 2.50e+03 pdb=" N3 DG N -18 " -0.057 2.00e-02 2.50e+03 pdb=" C4 DG N -18 " -0.052 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DG N -19 " 0.073 2.00e-02 2.50e+03 5.52e-02 9.15e+01 pdb=" N9 DG N -19 " 0.009 2.00e-02 2.50e+03 pdb=" C8 DG N -19 " -0.099 2.00e-02 2.50e+03 pdb=" N7 DG N -19 " -0.067 2.00e-02 2.50e+03 pdb=" C5 DG N -19 " 0.018 2.00e-02 2.50e+03 pdb=" C6 DG N -19 " 0.045 2.00e-02 2.50e+03 pdb=" O6 DG N -19 " 0.043 2.00e-02 2.50e+03 pdb=" N1 DG N -19 " 0.015 2.00e-02 2.50e+03 pdb=" C2 DG N -19 " 0.007 2.00e-02 2.50e+03 pdb=" N2 DG N -19 " -0.104 2.00e-02 2.50e+03 pdb=" N3 DG N -19 " 0.029 2.00e-02 2.50e+03 pdb=" C4 DG N -19 " 0.031 2.00e-02 2.50e+03 ... (remaining 12662 not shown) Histogram of nonbonded interaction distances: 2.02 - 2.60: 582 2.60 - 3.17: 62110 3.17 - 3.75: 119940 3.75 - 4.32: 165334 4.32 - 4.90: 269215 Nonbonded interactions: 617181 Sorted by model distance: nonbonded pdb=" OD1 ASP A 484 " pdb="MG MG A1803 " model vdw 2.019 2.170 nonbonded pdb=" OG1 THR K 57 " pdb=" OE1 GLN K 76 " model vdw 2.168 2.440 nonbonded pdb=" O ILE u 145 " pdb=" OG1 THR u 149 " model vdw 2.173 2.440 nonbonded pdb=" OD2 ASP E 47 " pdb=" NE2 GLN E 53 " model vdw 2.189 2.520 nonbonded pdb=" O VAL m1170 " pdb=" OG1 THR m1215 " model vdw 2.193 2.440 ... (remaining 617176 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' and resid 43 through 134) } ncs_group { reference = (chain 'b' and resid 25 through 102) selection = chain 'f' } ncs_group { reference = (chain 'c' and resid 16 through 111) selection = (chain 'g' and resid 16 through 111) } ncs_group { reference = (chain 'd' and resid 29 through 121) selection = chain 'h' } 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: 0.690 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: 0.070 Extract box with map and model: 6.560 Check model and map are aligned: 0.820 Set scattering table: 0.520 Process input model: 183.160 Find NCS groups from input model: 1.870 Set up NCS constraints: 0.290 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:2.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 196.760 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7110 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 0.079 77159 Z= 0.289 Angle : 0.564 16.068 105345 Z= 0.326 Chirality : 0.043 0.498 11765 Planarity : 0.004 0.074 12665 Dihedral : 16.540 170.848 30163 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.01 % Allowed : 2.25 % Favored : 97.73 % Rotamer: Outliers : 0.00 % Allowed : 0.09 % Favored : 99.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.42 (0.09), residues: 8563 helix: 1.96 (0.08), residues: 3933 sheet: 0.30 (0.15), residues: 1163 loop : 0.06 (0.11), residues: 3467 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 170 HIS 0.012 0.001 HIS b 75 PHE 0.017 0.001 PHE B 363 TYR 0.019 0.001 TYR m 530 ARG 0.008 0.000 ARG a 69 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17126 Ramachandran restraints generated. 8563 Oldfield, 0 Emsley, 8563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17126 Ramachandran restraints generated. 8563 Oldfield, 0 Emsley, 8563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 814 residues out of total 7692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 814 time to evaluate : 6.407 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 347 ASP cc_start: 0.7980 (m-30) cc_final: 0.7767 (m-30) REVERT: A 457 MET cc_start: 0.8785 (mtm) cc_final: 0.8486 (mtp) REVERT: A 488 MET cc_start: 0.8963 (mtp) cc_final: 0.8543 (mtm) REVERT: A 614 MET cc_start: 0.8293 (mmt) cc_final: 0.8070 (mmt) REVERT: A 747 MET cc_start: 0.9095 (mtm) cc_final: 0.8240 (mtp) REVERT: B 839 MET cc_start: 0.8861 (ptp) cc_final: 0.8410 (ptp) REVERT: B 1152 MET cc_start: 0.8321 (mmm) cc_final: 0.7980 (mmm) REVERT: G 93 ASN cc_start: 0.7962 (t0) cc_final: 0.7707 (t0) REVERT: M 22 GLN cc_start: 0.8420 (mp10) cc_final: 0.7547 (mm110) REVERT: V 48 GLU cc_start: 0.6835 (mm-30) cc_final: 0.6463 (mm-30) REVERT: V 89 ARG cc_start: 0.7517 (mtm-85) cc_final: 0.7238 (mpp-170) REVERT: W 504 SER cc_start: 0.6031 (t) cc_final: 0.5346 (m) REVERT: b 84 MET cc_start: 0.4291 (mmt) cc_final: 0.4002 (ttp) REVERT: g 91 GLU cc_start: 0.3984 (tt0) cc_final: 0.3722 (pm20) REVERT: m 257 MET cc_start: 0.1886 (mtm) cc_final: 0.0140 (tpt) REVERT: m 422 LEU cc_start: 0.5701 (mt) cc_final: 0.5416 (tp) REVERT: m 518 TYR cc_start: 0.3336 (m-80) cc_final: 0.2887 (m-80) REVERT: m 564 ASP cc_start: 0.5365 (m-30) cc_final: 0.5128 (t0) REVERT: m 667 LEU cc_start: 0.7530 (mt) cc_final: 0.6417 (mt) REVERT: m 1030 ASP cc_start: 0.6561 (t0) cc_final: 0.6335 (m-30) REVERT: n 239 ASP cc_start: 0.8866 (m-30) cc_final: 0.8656 (t70) REVERT: n 262 PHE cc_start: 0.6385 (t80) cc_final: 0.6157 (t80) REVERT: n 264 GLN cc_start: 0.8309 (tm-30) cc_final: 0.8011 (tp40) REVERT: n 286 ARG cc_start: 0.7669 (mtt-85) cc_final: 0.7115 (tpm170) REVERT: q 43 GLU cc_start: 0.3365 (mt-10) cc_final: 0.2995 (mm-30) REVERT: q 110 TRP cc_start: 0.3149 (m100) cc_final: 0.2596 (m100) REVERT: q 715 ASN cc_start: 0.6070 (m-40) cc_final: 0.5652 (m-40) REVERT: q 808 ASN cc_start: 0.7708 (m-40) cc_final: 0.6507 (p0) REVERT: q 891 GLU cc_start: 0.8217 (mt-10) cc_final: 0.7955 (pt0) REVERT: r 279 GLN cc_start: 0.1570 (mt0) cc_final: -0.0241 (tp40) REVERT: r 329 MET cc_start: -0.0252 (tmm) cc_final: -0.1006 (ttt) REVERT: r 404 MET cc_start: 0.8935 (mtt) cc_final: 0.8628 (mtp) REVERT: r 507 ASP cc_start: 0.7313 (m-30) cc_final: 0.5787 (p0) REVERT: u 210 MET cc_start: 0.2393 (tpt) cc_final: 0.1864 (tpt) REVERT: u 262 ARG cc_start: 0.7337 (ptp90) cc_final: 0.7116 (tpt170) REVERT: v 8 GLN cc_start: 0.6186 (mp10) cc_final: 0.5069 (pm20) REVERT: v 85 LYS cc_start: 0.4765 (mttt) cc_final: 0.4541 (tptp) REVERT: v 305 GLN cc_start: 0.6695 (pp30) cc_final: 0.5289 (tm-30) REVERT: v 340 LYS cc_start: 0.4684 (mtmm) cc_final: 0.4261 (tmtt) REVERT: x 230 GLN cc_start: 0.8623 (tt0) cc_final: 0.8192 (tt0) REVERT: x 345 GLN cc_start: 0.8957 (tt0) cc_final: 0.8529 (tm-30) outliers start: 0 outliers final: 0 residues processed: 814 average time/residue: 0.7893 time to fit residues: 1049.3787 Evaluate side-chains 375 residues out of total 7692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 375 time to evaluate : 6.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 879 random chunks: chunk 742 optimal weight: 40.0000 chunk 666 optimal weight: 40.0000 chunk 369 optimal weight: 2.9990 chunk 227 optimal weight: 20.0000 chunk 449 optimal weight: 50.0000 chunk 355 optimal weight: 6.9990 chunk 688 optimal weight: 50.0000 chunk 266 optimal weight: 10.0000 chunk 418 optimal weight: 5.9990 chunk 512 optimal weight: 40.0000 chunk 798 optimal weight: 3.9990 overall best weight: 5.9992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 287 GLN A 291 ASN A 436 HIS ** B 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 356 HIS B 506 GLN B 958 GLN G 41 GLN ** G 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 11 ASN I 12 ASN K 85 GLN V 43 GLN W 283 ASN ** W 433 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 644 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 784 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 93 GLN ** c 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 68 ASN d 46 HIS ** f 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** m 425 HIS m 480 ASN m 816 ASN m 896 ASN ** n 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** q 577 GLN ** q 681 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 818 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** v 212 HIS ** x 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7212 moved from start: 0.1903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.093 77159 Z= 0.362 Angle : 0.598 10.398 105345 Z= 0.318 Chirality : 0.042 0.242 11765 Planarity : 0.004 0.074 12665 Dihedral : 17.424 172.114 12605 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 9.65 Ramachandran Plot: Outliers : 0.01 % Allowed : 2.66 % Favored : 97.33 % Rotamer: Outliers : 0.69 % Allowed : 5.20 % Favored : 94.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.46 (0.09), residues: 8563 helix: 2.00 (0.08), residues: 3963 sheet: 0.18 (0.15), residues: 1127 loop : 0.12 (0.11), residues: 3473 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP m 708 HIS 0.013 0.001 HIS m 358 PHE 0.017 0.002 PHE G 3 TYR 0.023 0.002 TYR E 207 ARG 0.008 0.001 ARG J 47 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17126 Ramachandran restraints generated. 8563 Oldfield, 0 Emsley, 8563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17126 Ramachandran restraints generated. 8563 Oldfield, 0 Emsley, 8563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 443 residues out of total 7692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 390 time to evaluate : 6.405 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 347 ASP cc_start: 0.8157 (m-30) cc_final: 0.7877 (m-30) REVERT: A 457 MET cc_start: 0.8811 (mtm) cc_final: 0.8610 (mtp) REVERT: A 488 MET cc_start: 0.9048 (mtp) cc_final: 0.8425 (mtm) REVERT: A 614 MET cc_start: 0.8323 (mmt) cc_final: 0.8005 (mmt) REVERT: A 747 MET cc_start: 0.9206 (mtm) cc_final: 0.8171 (mtp) REVERT: V 89 ARG cc_start: 0.7750 (mtm-85) cc_final: 0.7436 (mpp-170) REVERT: W 504 SER cc_start: 0.5522 (t) cc_final: 0.4991 (m) REVERT: f 84 MET cc_start: 0.3925 (mmp) cc_final: 0.3436 (ptm) REVERT: g 91 GLU cc_start: 0.3608 (tt0) cc_final: 0.3261 (pm20) REVERT: g 92 GLU cc_start: 0.4757 (mm-30) cc_final: 0.3940 (mt-10) REVERT: h 59 MET cc_start: -0.0420 (mmm) cc_final: -0.0736 (mtt) REVERT: m 257 MET cc_start: 0.2110 (mtm) cc_final: 0.0020 (tpt) REVERT: m 422 LEU cc_start: 0.6274 (mt) cc_final: 0.5793 (tp) REVERT: m 511 MET cc_start: 0.4798 (ptt) cc_final: 0.3897 (ptt) REVERT: m 564 ASP cc_start: 0.5818 (m-30) cc_final: 0.5463 (t0) REVERT: m 1019 MET cc_start: 0.4703 (ptt) cc_final: 0.4445 (ppp) REVERT: m 1030 ASP cc_start: 0.6555 (t0) cc_final: 0.6347 (m-30) REVERT: n 260 MET cc_start: 0.7485 (mmp) cc_final: 0.7205 (mmm) REVERT: n 264 GLN cc_start: 0.8274 (tm-30) cc_final: 0.7995 (tp40) REVERT: n 286 ARG cc_start: 0.7896 (mtt-85) cc_final: 0.7141 (tpm170) REVERT: q 43 GLU cc_start: 0.3695 (mt-10) cc_final: 0.3478 (mm-30) REVERT: q 110 TRP cc_start: 0.3224 (m100) cc_final: 0.2843 (m100) REVERT: q 380 ARG cc_start: 0.5280 (mtp180) cc_final: 0.4512 (tpt90) REVERT: q 577 GLN cc_start: 0.4341 (OUTLIER) cc_final: 0.4109 (mm110) REVERT: q 928 MET cc_start: 0.2431 (ptt) cc_final: 0.2092 (ptt) REVERT: r 279 GLN cc_start: 0.1411 (mt0) cc_final: -0.0198 (tp40) REVERT: r 329 MET cc_start: -0.0377 (tmm) cc_final: -0.1374 (ttt) REVERT: r 404 MET cc_start: 0.8987 (mtt) cc_final: 0.8657 (mtp) REVERT: r 507 ASP cc_start: 0.7355 (m-30) cc_final: 0.5734 (p0) REVERT: u 154 TYR cc_start: 0.3646 (m-80) cc_final: 0.3372 (m-10) REVERT: u 210 MET cc_start: 0.2571 (tpt) cc_final: 0.2318 (tpt) REVERT: x 230 GLN cc_start: 0.8684 (tt0) cc_final: 0.8237 (tt0) REVERT: x 235 LEU cc_start: 0.6481 (mp) cc_final: 0.5716 (pp) REVERT: x 345 GLN cc_start: 0.9025 (tt0) cc_final: 0.8410 (tm-30) outliers start: 53 outliers final: 33 residues processed: 424 average time/residue: 0.7144 time to fit residues: 517.6068 Evaluate side-chains 367 residues out of total 7692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 333 time to evaluate : 6.229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 ARG Chi-restraints excluded: chain A residue 238 THR Chi-restraints excluded: chain A residue 827 ASP Chi-restraints excluded: chain A residue 1140 ILE Chi-restraints excluded: chain A residue 1222 PHE Chi-restraints excluded: chain A residue 1350 SER Chi-restraints excluded: chain A residue 1401 MET Chi-restraints excluded: chain A residue 1408 THR Chi-restraints excluded: chain A residue 1414 GLU Chi-restraints excluded: chain B residue 232 ARG Chi-restraints excluded: chain B residue 425 MET Chi-restraints excluded: chain B residue 510 THR Chi-restraints excluded: chain B residue 864 LYS Chi-restraints excluded: chain C residue 20 MET Chi-restraints excluded: chain I residue 50 THR Chi-restraints excluded: chain J residue 56 ILE Chi-restraints excluded: chain K residue 14 ASP Chi-restraints excluded: chain K residue 15 ASP Chi-restraints excluded: chain M residue 37 THR Chi-restraints excluded: chain W residue 401 VAL Chi-restraints excluded: chain W residue 543 ILE Chi-restraints excluded: chain W residue 787 LYS Chi-restraints excluded: chain b residue 49 LEU Chi-restraints excluded: chain b residue 93 GLN Chi-restraints excluded: chain m residue 563 MET Chi-restraints excluded: chain m residue 660 ILE Chi-restraints excluded: chain m residue 1097 THR Chi-restraints excluded: chain m residue 1104 ILE Chi-restraints excluded: chain q residue 577 GLN Chi-restraints excluded: chain r residue 405 LEU Chi-restraints excluded: chain x residue 210 ILE Chi-restraints excluded: chain x residue 211 VAL Chi-restraints excluded: chain x residue 321 VAL Chi-restraints excluded: chain x residue 335 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 879 random chunks: chunk 443 optimal weight: 50.0000 chunk 247 optimal weight: 1.9990 chunk 664 optimal weight: 40.0000 chunk 543 optimal weight: 6.9990 chunk 220 optimal weight: 5.9990 chunk 799 optimal weight: 30.0000 chunk 863 optimal weight: 50.0000 chunk 712 optimal weight: 50.0000 chunk 793 optimal weight: 30.0000 chunk 272 optimal weight: 3.9990 chunk 641 optimal weight: 9.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 359 ASN A 590 GLN A1021 GLN ** B 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 301 GLN H 44 ASN V 100 GLN ** W 433 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 644 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 93 GLN c 24 GLN d 64 ASN ** f 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 92 GLN m 526 GLN m 554 GLN m1271 GLN ** n 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** q 363 GLN q 577 GLN ** q 681 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 818 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** v 381 GLN ** x 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7235 moved from start: 0.2442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.079 77159 Z= 0.341 Angle : 0.548 9.013 105345 Z= 0.293 Chirality : 0.041 0.186 11765 Planarity : 0.004 0.047 12665 Dihedral : 17.421 172.664 12605 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 9.61 Ramachandran Plot: Outliers : 0.01 % Allowed : 2.55 % Favored : 97.44 % Rotamer: Outliers : 0.88 % Allowed : 7.31 % Favored : 91.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.49 (0.09), residues: 8563 helix: 2.07 (0.08), residues: 3979 sheet: 0.12 (0.15), residues: 1135 loop : 0.09 (0.11), residues: 3449 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 554 HIS 0.008 0.001 HIS q 758 PHE 0.022 0.001 PHE x 273 TYR 0.024 0.001 TYR m 518 ARG 0.008 0.000 ARG A1369 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17126 Ramachandran restraints generated. 8563 Oldfield, 0 Emsley, 8563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17126 Ramachandran restraints generated. 8563 Oldfield, 0 Emsley, 8563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 415 residues out of total 7692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 347 time to evaluate : 6.363 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 347 ASP cc_start: 0.8150 (m-30) cc_final: 0.7846 (m-30) REVERT: A 488 MET cc_start: 0.9035 (mtp) cc_final: 0.8457 (mtm) REVERT: A 614 MET cc_start: 0.8348 (mmt) cc_final: 0.8065 (mmt) REVERT: A 747 MET cc_start: 0.9198 (mtm) cc_final: 0.8161 (mtp) REVERT: B 277 VAL cc_start: 0.9247 (OUTLIER) cc_final: 0.8887 (p) REVERT: B 302 MET cc_start: 0.7043 (ptt) cc_final: 0.6383 (ptt) REVERT: b 49 LEU cc_start: 0.6108 (OUTLIER) cc_final: 0.5109 (tp) REVERT: c 71 ARG cc_start: 0.4866 (ttp-170) cc_final: 0.4554 (mmt-90) REVERT: g 91 GLU cc_start: 0.3864 (tt0) cc_final: 0.3498 (pm20) REVERT: g 92 GLU cc_start: 0.4992 (mm-30) cc_final: 0.3865 (mt-10) REVERT: h 59 MET cc_start: -0.0216 (mmm) cc_final: -0.0544 (mtt) REVERT: m 257 MET cc_start: 0.1963 (mtm) cc_final: -0.0060 (tpt) REVERT: m 422 LEU cc_start: 0.6257 (mt) cc_final: 0.5768 (tp) REVERT: m 1030 ASP cc_start: 0.6468 (t0) cc_final: 0.6189 (m-30) REVERT: n 264 GLN cc_start: 0.8273 (tm-30) cc_final: 0.8001 (tp40) REVERT: n 275 ARG cc_start: 0.6350 (OUTLIER) cc_final: 0.6083 (mmt180) REVERT: n 286 ARG cc_start: 0.7901 (mtt-85) cc_final: 0.7182 (tpm170) REVERT: q 110 TRP cc_start: 0.2907 (m100) cc_final: 0.2421 (m100) REVERT: q 380 ARG cc_start: 0.4979 (mtp180) cc_final: 0.4123 (tpt90) REVERT: q 852 MET cc_start: 0.7503 (tmm) cc_final: 0.6971 (ptt) REVERT: q 871 TYR cc_start: 0.7509 (m-80) cc_final: 0.7244 (m-80) REVERT: r 279 GLN cc_start: 0.1399 (mt0) cc_final: -0.0207 (tp40) REVERT: r 329 MET cc_start: -0.0417 (tmm) cc_final: -0.1362 (ttt) REVERT: r 404 MET cc_start: 0.9246 (mtt) cc_final: 0.9034 (mtp) REVERT: r 507 ASP cc_start: 0.7352 (m-30) cc_final: 0.5713 (p0) REVERT: u 210 MET cc_start: 0.2964 (tpt) cc_final: 0.2687 (tpt) REVERT: v 167 GLU cc_start: 0.7844 (OUTLIER) cc_final: 0.7411 (mm-30) REVERT: x 230 GLN cc_start: 0.8742 (tt0) cc_final: 0.8197 (tt0) REVERT: x 235 LEU cc_start: 0.6542 (mp) cc_final: 0.5742 (pp) REVERT: x 345 GLN cc_start: 0.9013 (tt0) cc_final: 0.8755 (tm-30) outliers start: 68 outliers final: 38 residues processed: 391 average time/residue: 0.7034 time to fit residues: 474.6869 Evaluate side-chains 364 residues out of total 7692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 322 time to evaluate : 6.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 ARG Chi-restraints excluded: chain A residue 238 THR Chi-restraints excluded: chain A residue 827 ASP Chi-restraints excluded: chain A residue 850 MET Chi-restraints excluded: chain A residue 960 VAL Chi-restraints excluded: chain A residue 1140 ILE Chi-restraints excluded: chain A residue 1350 SER Chi-restraints excluded: chain A residue 1401 MET Chi-restraints excluded: chain A residue 1408 THR Chi-restraints excluded: chain A residue 1414 GLU Chi-restraints excluded: chain B residue 277 VAL Chi-restraints excluded: chain B residue 425 MET Chi-restraints excluded: chain B residue 503 LYS Chi-restraints excluded: chain B residue 593 MET Chi-restraints excluded: chain B residue 806 THR Chi-restraints excluded: chain B residue 864 LYS Chi-restraints excluded: chain C residue 20 MET Chi-restraints excluded: chain C residue 155 ILE Chi-restraints excluded: chain C residue 157 CYS Chi-restraints excluded: chain I residue 50 THR Chi-restraints excluded: chain I residue 59 VAL Chi-restraints excluded: chain K residue 14 ASP Chi-restraints excluded: chain K residue 15 ASP Chi-restraints excluded: chain K residue 72 VAL Chi-restraints excluded: chain M residue 63 LEU Chi-restraints excluded: chain V residue 100 GLN Chi-restraints excluded: chain W residue 401 VAL Chi-restraints excluded: chain W residue 543 ILE Chi-restraints excluded: chain W residue 578 ASN Chi-restraints excluded: chain W residue 689 ARG Chi-restraints excluded: chain W residue 787 LYS Chi-restraints excluded: chain b residue 49 LEU Chi-restraints excluded: chain m residue 563 MET Chi-restraints excluded: chain m residue 1104 ILE Chi-restraints excluded: chain n residue 259 VAL Chi-restraints excluded: chain n residue 275 ARG Chi-restraints excluded: chain q residue 766 MET Chi-restraints excluded: chain r residue 405 LEU Chi-restraints excluded: chain v residue 167 GLU Chi-restraints excluded: chain v residue 324 ILE Chi-restraints excluded: chain x residue 210 ILE Chi-restraints excluded: chain x residue 321 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 879 random chunks: chunk 790 optimal weight: 50.0000 chunk 601 optimal weight: 50.0000 chunk 415 optimal weight: 40.0000 chunk 88 optimal weight: 0.3980 chunk 381 optimal weight: 5.9990 chunk 536 optimal weight: 30.0000 chunk 802 optimal weight: 6.9990 chunk 849 optimal weight: 40.0000 chunk 419 optimal weight: 6.9990 chunk 760 optimal weight: 30.0000 chunk 228 optimal weight: 4.9990 overall best weight: 5.0788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1390 HIS ** B 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 436 ASN B 761 HIS H 44 ASN ** W 644 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** e 93 GLN ** f 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** m 710 GLN m 998 ASN ** n 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 681 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 818 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** v 381 GLN ** x 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7239 moved from start: 0.2815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 77159 Z= 0.302 Angle : 0.526 9.912 105345 Z= 0.281 Chirality : 0.040 0.182 11765 Planarity : 0.004 0.048 12665 Dihedral : 17.425 173.320 12605 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.01 % Allowed : 2.71 % Favored : 97.28 % Rotamer: Outliers : 1.13 % Allowed : 8.46 % Favored : 90.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.53 (0.09), residues: 8563 helix: 2.15 (0.08), residues: 3986 sheet: 0.05 (0.15), residues: 1110 loop : 0.09 (0.11), residues: 3467 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP q 338 HIS 0.006 0.001 HIS m 358 PHE 0.019 0.001 PHE n 262 TYR 0.021 0.001 TYR q 155 ARG 0.005 0.000 ARG A 47 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17126 Ramachandran restraints generated. 8563 Oldfield, 0 Emsley, 8563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17126 Ramachandran restraints generated. 8563 Oldfield, 0 Emsley, 8563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 420 residues out of total 7692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 333 time to evaluate : 6.447 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 253 MET cc_start: 0.6991 (tmm) cc_final: 0.6240 (tmm) REVERT: A 282 MET cc_start: 0.8094 (ppp) cc_final: 0.7869 (ppp) REVERT: A 347 ASP cc_start: 0.8201 (m-30) cc_final: 0.7922 (m-30) REVERT: A 488 MET cc_start: 0.9037 (mtp) cc_final: 0.8433 (mtm) REVERT: A 614 MET cc_start: 0.8352 (mmt) cc_final: 0.8079 (mmt) REVERT: A 747 MET cc_start: 0.9179 (mtm) cc_final: 0.8137 (mtp) REVERT: A 1270 MET cc_start: 0.7286 (mmp) cc_final: 0.6514 (mmp) REVERT: A 1378 MET cc_start: 0.8954 (mtp) cc_final: 0.8731 (mtp) REVERT: B 277 VAL cc_start: 0.9232 (OUTLIER) cc_final: 0.8875 (p) REVERT: B 1152 MET cc_start: 0.8438 (mmm) cc_final: 0.8189 (mmm) REVERT: E 49 MET cc_start: 0.5735 (pmm) cc_final: 0.5383 (pmm) REVERT: b 49 LEU cc_start: 0.6352 (OUTLIER) cc_final: 0.5376 (tp) REVERT: c 71 ARG cc_start: 0.4862 (ttp-170) cc_final: 0.4547 (mmt-90) REVERT: f 63 GLU cc_start: 0.5810 (tp30) cc_final: 0.5547 (tp30) REVERT: g 91 GLU cc_start: 0.3553 (tt0) cc_final: 0.3320 (pm20) REVERT: g 92 GLU cc_start: 0.5033 (mm-30) cc_final: 0.4110 (mt-10) REVERT: h 59 MET cc_start: -0.0154 (mmm) cc_final: -0.0488 (mtt) REVERT: m 257 MET cc_start: 0.1921 (mtm) cc_final: -0.0055 (tpt) REVERT: m 291 GLU cc_start: 0.3409 (OUTLIER) cc_final: 0.3057 (pt0) REVERT: m 570 MET cc_start: -0.1742 (mmm) cc_final: -0.2168 (mtt) REVERT: m 1030 ASP cc_start: 0.6511 (t0) cc_final: 0.6205 (m-30) REVERT: m 1384 MET cc_start: 0.3805 (mmm) cc_final: 0.2742 (ptm) REVERT: n 264 GLN cc_start: 0.8254 (tm-30) cc_final: 0.7972 (tp40) REVERT: n 286 ARG cc_start: 0.7917 (mtt-85) cc_final: 0.7244 (tpm170) REVERT: q 110 TRP cc_start: 0.2935 (m100) cc_final: 0.2409 (m100) REVERT: q 852 MET cc_start: 0.7487 (tmm) cc_final: 0.6747 (ptp) REVERT: q 914 LYS cc_start: 0.4084 (OUTLIER) cc_final: 0.3505 (pttm) REVERT: q 928 MET cc_start: 0.2725 (OUTLIER) cc_final: 0.2501 (ptt) REVERT: r 279 GLN cc_start: 0.1669 (mt0) cc_final: 0.0064 (tp40) REVERT: r 329 MET cc_start: -0.0440 (tmm) cc_final: -0.1298 (ttt) REVERT: r 404 MET cc_start: 0.9231 (mtt) cc_final: 0.9010 (mtp) REVERT: r 507 ASP cc_start: 0.7334 (m-30) cc_final: 0.5716 (p0) REVERT: u 210 MET cc_start: 0.2945 (tpt) cc_final: 0.2577 (tpt) REVERT: v 167 GLU cc_start: 0.7836 (OUTLIER) cc_final: 0.7427 (mm-30) REVERT: x 230 GLN cc_start: 0.8804 (tt0) cc_final: 0.8323 (tt0) REVERT: x 235 LEU cc_start: 0.6628 (mp) cc_final: 0.5908 (pp) REVERT: x 239 LYS cc_start: 0.8520 (tptt) cc_final: 0.8238 (tptp) REVERT: x 307 GLN cc_start: 0.4253 (OUTLIER) cc_final: 0.3000 (mt0) REVERT: x 345 GLN cc_start: 0.9184 (tt0) cc_final: 0.8697 (tm-30) outliers start: 87 outliers final: 46 residues processed: 397 average time/residue: 0.7033 time to fit residues: 484.5433 Evaluate side-chains 370 residues out of total 7692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 317 time to evaluate : 6.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 ARG Chi-restraints excluded: chain A residue 84 MET Chi-restraints excluded: chain A residue 238 THR Chi-restraints excluded: chain A residue 827 ASP Chi-restraints excluded: chain A residue 850 MET Chi-restraints excluded: chain A residue 1009 ILE Chi-restraints excluded: chain A residue 1140 ILE Chi-restraints excluded: chain A residue 1240 ILE Chi-restraints excluded: chain A residue 1350 SER Chi-restraints excluded: chain A residue 1408 THR Chi-restraints excluded: chain A residue 1414 GLU Chi-restraints excluded: chain B residue 277 VAL Chi-restraints excluded: chain B residue 425 MET Chi-restraints excluded: chain B residue 510 THR Chi-restraints excluded: chain B residue 593 MET Chi-restraints excluded: chain B residue 864 LYS Chi-restraints excluded: chain B residue 933 THR Chi-restraints excluded: chain B residue 944 THR Chi-restraints excluded: chain B residue 971 THR Chi-restraints excluded: chain C residue 20 MET Chi-restraints excluded: chain C residue 155 ILE Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 111 ILE Chi-restraints excluded: chain G residue 52 MET Chi-restraints excluded: chain I residue 50 THR Chi-restraints excluded: chain I residue 59 VAL Chi-restraints excluded: chain J residue 56 ILE Chi-restraints excluded: chain K residue 14 ASP Chi-restraints excluded: chain K residue 15 ASP Chi-restraints excluded: chain K residue 59 VAL Chi-restraints excluded: chain K residue 72 VAL Chi-restraints excluded: chain M residue 63 LEU Chi-restraints excluded: chain V residue 40 ASP Chi-restraints excluded: chain W residue 304 VAL Chi-restraints excluded: chain W residue 401 VAL Chi-restraints excluded: chain W residue 543 ILE Chi-restraints excluded: chain W residue 578 ASN Chi-restraints excluded: chain W residue 593 SER Chi-restraints excluded: chain W residue 787 LYS Chi-restraints excluded: chain b residue 49 LEU Chi-restraints excluded: chain m residue 291 GLU Chi-restraints excluded: chain m residue 1083 MET Chi-restraints excluded: chain m residue 1104 ILE Chi-restraints excluded: chain n residue 178 ILE Chi-restraints excluded: chain n residue 239 ASP Chi-restraints excluded: chain n residue 259 VAL Chi-restraints excluded: chain q residue 766 MET Chi-restraints excluded: chain q residue 914 LYS Chi-restraints excluded: chain q residue 928 MET Chi-restraints excluded: chain v residue 167 GLU Chi-restraints excluded: chain x residue 210 ILE Chi-restraints excluded: chain x residue 307 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 879 random chunks: chunk 707 optimal weight: 40.0000 chunk 482 optimal weight: 7.9990 chunk 12 optimal weight: 20.0000 chunk 632 optimal weight: 50.0000 chunk 350 optimal weight: 8.9990 chunk 725 optimal weight: 0.4980 chunk 587 optimal weight: 30.0000 chunk 1 optimal weight: 7.9990 chunk 433 optimal weight: 30.0000 chunk 762 optimal weight: 50.0000 chunk 214 optimal weight: 3.9990 overall best weight: 5.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1021 GLN ** B 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 317 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1141 HIS ** G 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 44 ASN V 43 GLN ** W 644 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 64 ASN ** n 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 681 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 818 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** q 855 ASN q 886 GLN v 381 GLN ** x 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7263 moved from start: 0.3210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.088 77159 Z= 0.347 Angle : 0.549 9.694 105345 Z= 0.291 Chirality : 0.041 0.265 11765 Planarity : 0.004 0.049 12665 Dihedral : 17.397 173.724 12605 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 10.36 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.98 % Favored : 97.00 % Rotamer: Outliers : 1.29 % Allowed : 9.54 % Favored : 89.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.46 (0.09), residues: 8563 helix: 2.12 (0.08), residues: 3965 sheet: -0.05 (0.15), residues: 1135 loop : 0.04 (0.11), residues: 3463 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.001 TRP q 338 HIS 0.007 0.001 HIS B 996 PHE 0.018 0.002 PHE M 23 TYR 0.030 0.001 TYR r 494 ARG 0.007 0.000 ARG q 380 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17126 Ramachandran restraints generated. 8563 Oldfield, 0 Emsley, 8563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17126 Ramachandran restraints generated. 8563 Oldfield, 0 Emsley, 8563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 432 residues out of total 7692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 333 time to evaluate : 6.418 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 253 MET cc_start: 0.7381 (tmm) cc_final: 0.6802 (tmm) REVERT: A 488 MET cc_start: 0.9052 (mtp) cc_final: 0.8451 (mtm) REVERT: A 614 MET cc_start: 0.8363 (mmt) cc_final: 0.8080 (mmt) REVERT: A 747 MET cc_start: 0.9152 (mtm) cc_final: 0.8283 (mtp) REVERT: A 1378 MET cc_start: 0.8948 (mtp) cc_final: 0.8623 (mtp) REVERT: B 277 VAL cc_start: 0.9224 (OUTLIER) cc_final: 0.8872 (p) REVERT: B 1082 MET cc_start: 0.9060 (tpp) cc_final: 0.8677 (tpp) REVERT: B 1169 MET cc_start: 0.6767 (mtm) cc_final: 0.6450 (mtm) REVERT: E 49 MET cc_start: 0.5796 (pmm) cc_final: 0.5510 (pmm) REVERT: b 49 LEU cc_start: 0.6311 (OUTLIER) cc_final: 0.5359 (tp) REVERT: c 71 ARG cc_start: 0.4694 (ttp-170) cc_final: 0.4477 (mmt-90) REVERT: g 91 GLU cc_start: 0.3519 (tt0) cc_final: 0.3190 (pm20) REVERT: g 92 GLU cc_start: 0.4984 (mm-30) cc_final: 0.4128 (mt-10) REVERT: h 59 MET cc_start: -0.0229 (mmm) cc_final: -0.0521 (mtt) REVERT: m 257 MET cc_start: 0.1913 (mtm) cc_final: -0.0045 (tpt) REVERT: m 291 GLU cc_start: 0.3632 (OUTLIER) cc_final: 0.3393 (pt0) REVERT: m 1009 GLN cc_start: 0.4146 (mm110) cc_final: 0.3675 (tm-30) REVERT: m 1030 ASP cc_start: 0.6260 (t0) cc_final: 0.5928 (m-30) REVERT: m 1384 MET cc_start: 0.3627 (mmm) cc_final: 0.2724 (ptm) REVERT: n 260 MET cc_start: 0.7265 (mmm) cc_final: 0.7041 (mmp) REVERT: n 264 GLN cc_start: 0.8204 (tm-30) cc_final: 0.7984 (tp40) REVERT: n 286 ARG cc_start: 0.7926 (mtt-85) cc_final: 0.7238 (tpm170) REVERT: q 110 TRP cc_start: 0.2715 (m100) cc_final: 0.2110 (m100) REVERT: q 193 GLN cc_start: 0.6472 (mt0) cc_final: 0.6267 (mp10) REVERT: q 852 MET cc_start: 0.7484 (tmm) cc_final: 0.6862 (ptp) REVERT: q 893 ARG cc_start: 0.7120 (mpt-90) cc_final: 0.6535 (mmp80) REVERT: q 914 LYS cc_start: 0.3461 (OUTLIER) cc_final: 0.2901 (pttm) REVERT: r 279 GLN cc_start: 0.1629 (mt0) cc_final: -0.0115 (tp40) REVERT: r 329 MET cc_start: -0.0553 (tmm) cc_final: -0.1340 (ttt) REVERT: r 404 MET cc_start: 0.9223 (mtt) cc_final: 0.9008 (mtp) REVERT: r 507 ASP cc_start: 0.7311 (m-30) cc_final: 0.5770 (p0) REVERT: u 210 MET cc_start: 0.3091 (tpt) cc_final: 0.2711 (tpt) REVERT: v 167 GLU cc_start: 0.7815 (OUTLIER) cc_final: 0.7329 (mm-30) REVERT: x 230 GLN cc_start: 0.8792 (tt0) cc_final: 0.8235 (tt0) REVERT: x 235 LEU cc_start: 0.6672 (mp) cc_final: 0.5905 (pp) REVERT: x 239 LYS cc_start: 0.8511 (tptt) cc_final: 0.8218 (tptp) REVERT: x 345 GLN cc_start: 0.9162 (tt0) cc_final: 0.8701 (tm-30) outliers start: 99 outliers final: 64 residues processed: 407 average time/residue: 0.7009 time to fit residues: 494.3513 Evaluate side-chains 382 residues out of total 7692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 313 time to evaluate : 6.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 ARG Chi-restraints excluded: chain A residue 84 MET Chi-restraints excluded: chain A residue 238 THR Chi-restraints excluded: chain A residue 285 SER Chi-restraints excluded: chain A residue 369 ILE Chi-restraints excluded: chain A residue 547 VAL Chi-restraints excluded: chain A residue 691 VAL Chi-restraints excluded: chain A residue 827 ASP Chi-restraints excluded: chain A residue 850 MET Chi-restraints excluded: chain A residue 960 VAL Chi-restraints excluded: chain A residue 1140 ILE Chi-restraints excluded: chain A residue 1152 THR Chi-restraints excluded: chain A residue 1240 ILE Chi-restraints excluded: chain A residue 1350 SER Chi-restraints excluded: chain A residue 1408 THR Chi-restraints excluded: chain A residue 1414 GLU Chi-restraints excluded: chain B residue 70 ASN Chi-restraints excluded: chain B residue 88 THR Chi-restraints excluded: chain B residue 277 VAL Chi-restraints excluded: chain B residue 425 MET Chi-restraints excluded: chain B residue 503 LYS Chi-restraints excluded: chain B residue 510 THR Chi-restraints excluded: chain B residue 593 MET Chi-restraints excluded: chain B residue 806 THR Chi-restraints excluded: chain B residue 864 LYS Chi-restraints excluded: chain B residue 871 VAL Chi-restraints excluded: chain B residue 933 THR Chi-restraints excluded: chain B residue 944 THR Chi-restraints excluded: chain B residue 971 THR Chi-restraints excluded: chain C residue 20 MET Chi-restraints excluded: chain C residue 126 ASN Chi-restraints excluded: chain C residue 155 ILE Chi-restraints excluded: chain C residue 157 CYS Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain F residue 111 ILE Chi-restraints excluded: chain F residue 153 VAL Chi-restraints excluded: chain G residue 52 MET Chi-restraints excluded: chain I residue 50 THR Chi-restraints excluded: chain I residue 59 VAL Chi-restraints excluded: chain J residue 56 ILE Chi-restraints excluded: chain K residue 14 ASP Chi-restraints excluded: chain K residue 15 ASP Chi-restraints excluded: chain K residue 59 VAL Chi-restraints excluded: chain K residue 72 VAL Chi-restraints excluded: chain V residue 40 ASP Chi-restraints excluded: chain W residue 304 VAL Chi-restraints excluded: chain W residue 543 ILE Chi-restraints excluded: chain W residue 578 ASN Chi-restraints excluded: chain W residue 593 SER Chi-restraints excluded: chain W residue 675 THR Chi-restraints excluded: chain W residue 787 LYS Chi-restraints excluded: chain b residue 49 LEU Chi-restraints excluded: chain m residue 291 GLU Chi-restraints excluded: chain m residue 821 ASP Chi-restraints excluded: chain m residue 1026 VAL Chi-restraints excluded: chain m residue 1083 MET Chi-restraints excluded: chain m residue 1104 ILE Chi-restraints excluded: chain n residue 178 ILE Chi-restraints excluded: chain n residue 259 VAL Chi-restraints excluded: chain n residue 275 ARG Chi-restraints excluded: chain q residue 766 MET Chi-restraints excluded: chain q residue 914 LYS Chi-restraints excluded: chain r residue 227 MET Chi-restraints excluded: chain r residue 405 LEU Chi-restraints excluded: chain u residue 107 VAL Chi-restraints excluded: chain v residue 167 GLU Chi-restraints excluded: chain v residue 324 ILE Chi-restraints excluded: chain x residue 210 ILE Chi-restraints excluded: chain x residue 321 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 879 random chunks: chunk 285 optimal weight: 8.9990 chunk 765 optimal weight: 40.0000 chunk 167 optimal weight: 5.9990 chunk 498 optimal weight: 7.9990 chunk 209 optimal weight: 2.9990 chunk 850 optimal weight: 50.0000 chunk 705 optimal weight: 50.0000 chunk 393 optimal weight: 40.0000 chunk 70 optimal weight: 0.7980 chunk 281 optimal weight: 0.0570 chunk 446 optimal weight: 2.9990 overall best weight: 2.5704 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 63 GLN B 887 HIS ** G 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 44 ASN ** V 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 544 HIS ** W 644 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 784 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** e 93 GLN ** f 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** m 526 GLN ** n 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 681 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 818 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** v 381 GLN ** x 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7219 moved from start: 0.3302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 77159 Z= 0.180 Angle : 0.482 10.253 105345 Z= 0.257 Chirality : 0.039 0.205 11765 Planarity : 0.003 0.048 12665 Dihedral : 17.314 174.506 12605 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 9.63 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.48 % Favored : 97.50 % Rotamer: Outliers : 0.96 % Allowed : 10.30 % Favored : 88.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.64 (0.09), residues: 8563 helix: 2.28 (0.08), residues: 3971 sheet: 0.05 (0.15), residues: 1113 loop : 0.11 (0.11), residues: 3479 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP q 64 HIS 0.005 0.001 HIS m 358 PHE 0.017 0.001 PHE n 262 TYR 0.026 0.001 TYR r 494 ARG 0.006 0.000 ARG n 217 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17126 Ramachandran restraints generated. 8563 Oldfield, 0 Emsley, 8563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17126 Ramachandran restraints generated. 8563 Oldfield, 0 Emsley, 8563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 409 residues out of total 7692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 335 time to evaluate : 6.445 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 253 MET cc_start: 0.7413 (tmm) cc_final: 0.6791 (tmm) REVERT: A 347 ASP cc_start: 0.8132 (m-30) cc_final: 0.7894 (m-30) REVERT: A 488 MET cc_start: 0.8989 (mtp) cc_final: 0.8439 (mtm) REVERT: A 614 MET cc_start: 0.8325 (mmt) cc_final: 0.8010 (mmt) REVERT: A 747 MET cc_start: 0.9099 (mtm) cc_final: 0.8733 (mtp) REVERT: A 1378 MET cc_start: 0.8891 (mtp) cc_final: 0.8652 (mtp) REVERT: B 277 VAL cc_start: 0.9174 (OUTLIER) cc_final: 0.8838 (p) REVERT: B 836 GLU cc_start: 0.7975 (OUTLIER) cc_final: 0.7606 (mm-30) REVERT: B 1082 MET cc_start: 0.8999 (tpp) cc_final: 0.8695 (tpt) REVERT: B 1152 MET cc_start: 0.8419 (mmm) cc_final: 0.8152 (mmm) REVERT: E 49 MET cc_start: 0.5853 (pmm) cc_final: 0.5644 (pmm) REVERT: G 133 ASN cc_start: 0.6980 (p0) cc_final: 0.6605 (p0) REVERT: V 89 ARG cc_start: 0.7817 (mtm-85) cc_final: 0.7432 (tpp80) REVERT: b 49 LEU cc_start: 0.6249 (OUTLIER) cc_final: 0.5335 (tp) REVERT: c 71 ARG cc_start: 0.4681 (ttp-170) cc_final: 0.4441 (mmp80) REVERT: f 63 GLU cc_start: 0.5492 (tp30) cc_final: 0.5123 (tp30) REVERT: g 91 GLU cc_start: 0.3508 (tt0) cc_final: 0.3181 (pm20) REVERT: g 92 GLU cc_start: 0.4962 (mm-30) cc_final: 0.4072 (mt-10) REVERT: h 59 MET cc_start: -0.0226 (mmm) cc_final: -0.0464 (mtt) REVERT: m 257 MET cc_start: 0.1851 (mtm) cc_final: -0.0051 (tpt) REVERT: m 291 GLU cc_start: 0.3538 (OUTLIER) cc_final: 0.3171 (pt0) REVERT: m 1009 GLN cc_start: 0.4169 (mm110) cc_final: 0.3706 (tm-30) REVERT: m 1030 ASP cc_start: 0.6267 (t0) cc_final: 0.5929 (m-30) REVERT: m 1384 MET cc_start: 0.3344 (mmm) cc_final: 0.2481 (ptm) REVERT: n 286 ARG cc_start: 0.7914 (mtt-85) cc_final: 0.7191 (tpm170) REVERT: q 110 TRP cc_start: 0.2731 (m100) cc_final: 0.2109 (m100) REVERT: q 193 GLN cc_start: 0.6459 (mt0) cc_final: 0.6240 (mp10) REVERT: q 852 MET cc_start: 0.7621 (tmm) cc_final: 0.6908 (ptp) REVERT: q 893 ARG cc_start: 0.7134 (mpt-90) cc_final: 0.6534 (mmp80) REVERT: r 279 GLN cc_start: 0.1614 (mt0) cc_final: -0.0114 (tp40) REVERT: r 329 MET cc_start: -0.0747 (tmm) cc_final: -0.1452 (ttt) REVERT: r 404 MET cc_start: 0.9058 (mtt) cc_final: 0.8837 (mtp) REVERT: r 507 ASP cc_start: 0.7058 (m-30) cc_final: 0.5872 (p0) REVERT: u 210 MET cc_start: 0.2997 (tpt) cc_final: 0.2673 (tpt) REVERT: v 167 GLU cc_start: 0.7797 (OUTLIER) cc_final: 0.7334 (mm-30) REVERT: v 362 MET cc_start: 0.6549 (OUTLIER) cc_final: 0.6292 (ttt) REVERT: x 230 GLN cc_start: 0.8773 (tt0) cc_final: 0.8221 (tt0) REVERT: x 235 LEU cc_start: 0.6877 (mp) cc_final: 0.6114 (pp) REVERT: x 239 LYS cc_start: 0.8528 (tptt) cc_final: 0.8245 (tptp) REVERT: x 307 GLN cc_start: 0.2934 (OUTLIER) cc_final: 0.2247 (mt0) REVERT: x 345 GLN cc_start: 0.9161 (tt0) cc_final: 0.8703 (tm-30) outliers start: 74 outliers final: 47 residues processed: 389 average time/residue: 0.7683 time to fit residues: 519.8756 Evaluate side-chains 377 residues out of total 7692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 323 time to evaluate : 6.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 ARG Chi-restraints excluded: chain A residue 84 MET Chi-restraints excluded: chain A residue 220 CYS Chi-restraints excluded: chain A residue 238 THR Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 337 LEU Chi-restraints excluded: chain A residue 369 ILE Chi-restraints excluded: chain A residue 827 ASP Chi-restraints excluded: chain A residue 850 MET Chi-restraints excluded: chain A residue 1009 ILE Chi-restraints excluded: chain A residue 1140 ILE Chi-restraints excluded: chain A residue 1350 SER Chi-restraints excluded: chain A residue 1408 THR Chi-restraints excluded: chain A residue 1414 GLU Chi-restraints excluded: chain B residue 70 ASN Chi-restraints excluded: chain B residue 88 THR Chi-restraints excluded: chain B residue 277 VAL Chi-restraints excluded: chain B residue 425 MET Chi-restraints excluded: chain B residue 446 ILE Chi-restraints excluded: chain B residue 503 LYS Chi-restraints excluded: chain B residue 836 GLU Chi-restraints excluded: chain B residue 933 THR Chi-restraints excluded: chain D residue 119 GLU Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 111 ILE Chi-restraints excluded: chain G residue 52 MET Chi-restraints excluded: chain I residue 50 THR Chi-restraints excluded: chain J residue 56 ILE Chi-restraints excluded: chain K residue 15 ASP Chi-restraints excluded: chain K residue 59 VAL Chi-restraints excluded: chain K residue 72 VAL Chi-restraints excluded: chain K residue 84 LYS Chi-restraints excluded: chain V residue 40 ASP Chi-restraints excluded: chain W residue 304 VAL Chi-restraints excluded: chain W residue 543 ILE Chi-restraints excluded: chain W residue 787 LYS Chi-restraints excluded: chain b residue 49 LEU Chi-restraints excluded: chain m residue 255 GLU Chi-restraints excluded: chain m residue 291 GLU Chi-restraints excluded: chain m residue 1026 VAL Chi-restraints excluded: chain m residue 1083 MET Chi-restraints excluded: chain m residue 1104 ILE Chi-restraints excluded: chain n residue 178 ILE Chi-restraints excluded: chain n residue 239 ASP Chi-restraints excluded: chain n residue 259 VAL Chi-restraints excluded: chain q residue 766 MET Chi-restraints excluded: chain u residue 107 VAL Chi-restraints excluded: chain v residue 167 GLU Chi-restraints excluded: chain v residue 362 MET Chi-restraints excluded: chain v residue 381 GLN Chi-restraints excluded: chain x residue 210 ILE Chi-restraints excluded: chain x residue 307 GLN Chi-restraints excluded: chain x residue 321 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 879 random chunks: chunk 819 optimal weight: 6.9990 chunk 95 optimal weight: 7.9990 chunk 484 optimal weight: 30.0000 chunk 621 optimal weight: 50.0000 chunk 481 optimal weight: 1.9990 chunk 715 optimal weight: 30.0000 chunk 474 optimal weight: 30.0000 chunk 847 optimal weight: 30.0000 chunk 530 optimal weight: 50.0000 chunk 516 optimal weight: 50.0000 chunk 391 optimal weight: 30.0000 overall best weight: 15.3994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 400 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 518 ASN ** A 737 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 927 GLN A1021 GLN B 47 GLN B 301 GLN B 506 GLN ** B1084 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 126 ASN C 150 HIS ** G 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 44 ASN W 445 ASN ** W 567 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 644 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 784 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 104 GLN ** f 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 31 HIS ** h 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** m 591 GLN m 831 HIS m 962 ASN m1193 GLN ** n 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** q 58 ASN ** q 667 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 818 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 887 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** x 310 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7375 moved from start: 0.4175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.013 0.186 77159 Z= 0.854 Angle : 0.891 13.103 105345 Z= 0.458 Chirality : 0.050 0.207 11765 Planarity : 0.006 0.095 12665 Dihedral : 17.698 171.511 12605 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 16.51 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.40 % Favored : 95.57 % Rotamer: Outliers : 1.65 % Allowed : 11.38 % Favored : 86.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.47 (0.09), residues: 8563 helix: 1.27 (0.08), residues: 3960 sheet: -0.50 (0.15), residues: 1139 loop : -0.43 (0.11), residues: 3464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.003 TRP F 146 HIS 0.014 0.002 HIS B 996 PHE 0.032 0.003 PHE B 24 TYR 0.034 0.003 TYR m 926 ARG 0.021 0.001 ARG A1369 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17126 Ramachandran restraints generated. 8563 Oldfield, 0 Emsley, 8563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17126 Ramachandran restraints generated. 8563 Oldfield, 0 Emsley, 8563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 431 residues out of total 7692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 127 poor density : 304 time to evaluate : 6.354 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 253 MET cc_start: 0.7347 (tmm) cc_final: 0.6834 (tmm) REVERT: A 488 MET cc_start: 0.9159 (mtp) cc_final: 0.8609 (mtm) REVERT: A 709 MET cc_start: 0.7511 (OUTLIER) cc_final: 0.7144 (tmm) REVERT: A 747 MET cc_start: 0.9146 (mtm) cc_final: 0.8551 (mtp) REVERT: A 1378 MET cc_start: 0.9062 (mtp) cc_final: 0.8749 (mtp) REVERT: B 1152 MET cc_start: 0.8573 (mmm) cc_final: 0.8334 (mmm) REVERT: I 61 ASP cc_start: 0.8374 (t0) cc_final: 0.8128 (t0) REVERT: L 53 CYS cc_start: 0.8893 (OUTLIER) cc_final: 0.8594 (p) REVERT: V 13 MET cc_start: 0.7737 (tpt) cc_final: 0.7494 (tpp) REVERT: V 40 ASP cc_start: 0.6508 (OUTLIER) cc_final: 0.5134 (t70) REVERT: V 42 ASP cc_start: 0.6965 (OUTLIER) cc_final: 0.6764 (m-30) REVERT: b 49 LEU cc_start: 0.5589 (OUTLIER) cc_final: 0.4702 (tp) REVERT: c 71 ARG cc_start: 0.4837 (ttp-170) cc_final: 0.4483 (mmt-90) REVERT: g 91 GLU cc_start: 0.4072 (tt0) cc_final: 0.3676 (pm20) REVERT: g 92 GLU cc_start: 0.4928 (mm-30) cc_final: 0.3681 (mt-10) REVERT: m 257 MET cc_start: 0.1435 (mtm) cc_final: -0.0358 (tpt) REVERT: m 291 GLU cc_start: 0.3576 (OUTLIER) cc_final: 0.3286 (pt0) REVERT: m 659 MET cc_start: 0.6345 (ptp) cc_final: 0.5442 (mpp) REVERT: m 1030 ASP cc_start: 0.6437 (t0) cc_final: 0.5996 (m-30) REVERT: m 1166 MET cc_start: 0.5471 (ppp) cc_final: 0.4940 (ppp) REVERT: m 1384 MET cc_start: 0.3743 (mmm) cc_final: 0.2741 (ptm) REVERT: n 286 ARG cc_start: 0.7754 (mtt-85) cc_final: 0.7218 (tpt170) REVERT: q 110 TRP cc_start: 0.2232 (m100) cc_final: 0.1483 (m100) REVERT: q 852 MET cc_start: 0.7669 (tmm) cc_final: 0.6950 (ptt) REVERT: r 329 MET cc_start: -0.0997 (tmm) cc_final: -0.1650 (ttt) REVERT: r 404 MET cc_start: 0.9226 (mtt) cc_final: 0.9004 (mtp) REVERT: r 507 ASP cc_start: 0.6963 (m-30) cc_final: 0.5849 (p0) REVERT: u 178 TYR cc_start: 0.6029 (m-80) cc_final: 0.5778 (m-80) REVERT: u 210 MET cc_start: 0.3563 (tpt) cc_final: 0.2822 (tpp) REVERT: v 167 GLU cc_start: 0.7875 (OUTLIER) cc_final: 0.7464 (mm-30) REVERT: v 230 GLU cc_start: 0.5266 (tp30) cc_final: 0.5004 (pt0) REVERT: x 230 GLN cc_start: 0.8863 (tt0) cc_final: 0.8269 (tt0) REVERT: x 235 LEU cc_start: 0.6967 (mp) cc_final: 0.6187 (pp) REVERT: x 307 GLN cc_start: 0.3454 (OUTLIER) cc_final: 0.2048 (mt0) REVERT: x 345 GLN cc_start: 0.9181 (tt0) cc_final: 0.8903 (tm-30) outliers start: 127 outliers final: 86 residues processed: 407 average time/residue: 0.6707 time to fit residues: 480.5662 Evaluate side-chains 381 residues out of total 7692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 287 time to evaluate : 6.185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 ARG Chi-restraints excluded: chain A residue 84 MET Chi-restraints excluded: chain A residue 220 CYS Chi-restraints excluded: chain A residue 238 THR Chi-restraints excluded: chain A residue 290 ILE Chi-restraints excluded: chain A residue 337 LEU Chi-restraints excluded: chain A residue 369 ILE Chi-restraints excluded: chain A residue 540 THR Chi-restraints excluded: chain A residue 547 VAL Chi-restraints excluded: chain A residue 579 LEU Chi-restraints excluded: chain A residue 691 VAL Chi-restraints excluded: chain A residue 709 MET Chi-restraints excluded: chain A residue 827 ASP Chi-restraints excluded: chain A residue 850 MET Chi-restraints excluded: chain A residue 884 ILE Chi-restraints excluded: chain A residue 960 VAL Chi-restraints excluded: chain A residue 1009 ILE Chi-restraints excluded: chain A residue 1140 ILE Chi-restraints excluded: chain A residue 1152 THR Chi-restraints excluded: chain A residue 1322 VAL Chi-restraints excluded: chain A residue 1401 MET Chi-restraints excluded: chain A residue 1408 THR Chi-restraints excluded: chain A residue 1414 GLU Chi-restraints excluded: chain B residue 70 ASN Chi-restraints excluded: chain B residue 88 THR Chi-restraints excluded: chain B residue 179 ASP Chi-restraints excluded: chain B residue 277 VAL Chi-restraints excluded: chain B residue 425 MET Chi-restraints excluded: chain B residue 441 VAL Chi-restraints excluded: chain B residue 446 ILE Chi-restraints excluded: chain B residue 480 THR Chi-restraints excluded: chain B residue 503 LYS Chi-restraints excluded: chain B residue 510 THR Chi-restraints excluded: chain B residue 806 THR Chi-restraints excluded: chain B residue 864 LYS Chi-restraints excluded: chain B residue 871 VAL Chi-restraints excluded: chain B residue 889 THR Chi-restraints excluded: chain B residue 933 THR Chi-restraints excluded: chain B residue 944 THR Chi-restraints excluded: chain B residue 953 LEU Chi-restraints excluded: chain B residue 971 THR Chi-restraints excluded: chain C residue 20 MET Chi-restraints excluded: chain C residue 155 ILE Chi-restraints excluded: chain C residue 157 CYS Chi-restraints excluded: chain C residue 251 LEU Chi-restraints excluded: chain C residue 258 VAL Chi-restraints excluded: chain D residue 119 GLU Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 155 LEU Chi-restraints excluded: chain E residue 200 ARG Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 111 ILE Chi-restraints excluded: chain F residue 153 VAL Chi-restraints excluded: chain H residue 23 VAL Chi-restraints excluded: chain H residue 84 THR Chi-restraints excluded: chain H residue 91 ASP Chi-restraints excluded: chain H residue 93 ASP Chi-restraints excluded: chain H residue 138 ASN Chi-restraints excluded: chain H residue 141 ILE Chi-restraints excluded: chain I residue 50 THR Chi-restraints excluded: chain I residue 59 VAL Chi-restraints excluded: chain J residue 56 ILE Chi-restraints excluded: chain K residue 15 ASP Chi-restraints excluded: chain K residue 59 VAL Chi-restraints excluded: chain K residue 72 VAL Chi-restraints excluded: chain L residue 53 CYS Chi-restraints excluded: chain M residue 37 THR Chi-restraints excluded: chain V residue 40 ASP Chi-restraints excluded: chain V residue 42 ASP Chi-restraints excluded: chain W residue 304 VAL Chi-restraints excluded: chain W residue 543 ILE Chi-restraints excluded: chain W residue 575 VAL Chi-restraints excluded: chain W residue 578 ASN Chi-restraints excluded: chain W residue 593 SER Chi-restraints excluded: chain W residue 675 THR Chi-restraints excluded: chain W residue 689 ARG Chi-restraints excluded: chain W residue 787 LYS Chi-restraints excluded: chain b residue 49 LEU Chi-restraints excluded: chain m residue 255 GLU Chi-restraints excluded: chain m residue 291 GLU Chi-restraints excluded: chain m residue 821 ASP Chi-restraints excluded: chain m residue 1083 MET Chi-restraints excluded: chain m residue 1104 ILE Chi-restraints excluded: chain n residue 178 ILE Chi-restraints excluded: chain n residue 259 VAL Chi-restraints excluded: chain u residue 107 VAL Chi-restraints excluded: chain v residue 167 GLU Chi-restraints excluded: chain v residue 324 ILE Chi-restraints excluded: chain v residue 362 MET Chi-restraints excluded: chain x residue 210 ILE Chi-restraints excluded: chain x residue 296 ASN Chi-restraints excluded: chain x residue 307 GLN Chi-restraints excluded: chain x residue 321 VAL Chi-restraints excluded: chain x residue 353 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 879 random chunks: chunk 524 optimal weight: 30.0000 chunk 338 optimal weight: 40.0000 chunk 505 optimal weight: 9.9990 chunk 255 optimal weight: 0.9980 chunk 166 optimal weight: 5.9990 chunk 164 optimal weight: 6.9990 chunk 538 optimal weight: 10.0000 chunk 577 optimal weight: 8.9990 chunk 418 optimal weight: 3.9990 chunk 78 optimal weight: 1.9990 chunk 665 optimal weight: 0.7980 overall best weight: 2.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 736 HIS ** G 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 44 ASN V 43 GLN ** V 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 567 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 644 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 784 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 113 HIS e 93 GLN f 25 ASN m 962 ASN ** n 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** q 135 GLN q 187 GLN ** q 667 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 681 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 818 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** u 103 GLN ** x 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7252 moved from start: 0.4019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 77159 Z= 0.218 Angle : 0.524 10.870 105345 Z= 0.280 Chirality : 0.040 0.209 11765 Planarity : 0.004 0.054 12665 Dihedral : 17.514 172.914 12605 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 10.86 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.38 % Favored : 97.59 % Rotamer: Outliers : 0.94 % Allowed : 12.31 % Favored : 86.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.18 (0.09), residues: 8563 helix: 1.93 (0.08), residues: 3951 sheet: -0.26 (0.15), residues: 1122 loop : -0.11 (0.11), residues: 3490 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP q 595 HIS 0.006 0.001 HIS A 491 PHE 0.017 0.001 PHE A1222 TYR 0.031 0.001 TYR q 155 ARG 0.006 0.000 ARG A 47 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17126 Ramachandran restraints generated. 8563 Oldfield, 0 Emsley, 8563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17126 Ramachandran restraints generated. 8563 Oldfield, 0 Emsley, 8563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 382 residues out of total 7692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 310 time to evaluate : 6.480 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 253 MET cc_start: 0.7432 (tmm) cc_final: 0.7094 (tmm) REVERT: A 488 MET cc_start: 0.9061 (mtp) cc_final: 0.8483 (mtm) REVERT: A 614 MET cc_start: 0.8408 (mmt) cc_final: 0.8020 (mmt) REVERT: A 747 MET cc_start: 0.9123 (mtm) cc_final: 0.8394 (mtp) REVERT: A 1378 MET cc_start: 0.8800 (mtp) cc_final: 0.8436 (mtp) REVERT: B 277 VAL cc_start: 0.9286 (OUTLIER) cc_final: 0.8911 (p) REVERT: B 1082 MET cc_start: 0.9033 (tpp) cc_final: 0.8831 (tpp) REVERT: B 1152 MET cc_start: 0.8400 (mmm) cc_final: 0.8127 (mmm) REVERT: L 53 CYS cc_start: 0.8363 (OUTLIER) cc_final: 0.8160 (p) REVERT: V 13 MET cc_start: 0.7526 (tpt) cc_final: 0.7224 (tpp) REVERT: V 25 MET cc_start: 0.6359 (ptp) cc_final: 0.6131 (ptm) REVERT: b 49 LEU cc_start: 0.6040 (OUTLIER) cc_final: 0.5205 (tp) REVERT: c 71 ARG cc_start: 0.5041 (ttp-170) cc_final: 0.4587 (mmp80) REVERT: m 257 MET cc_start: 0.1902 (mtm) cc_final: -0.0020 (tpt) REVERT: m 1030 ASP cc_start: 0.6589 (t0) cc_final: 0.6170 (m-30) REVERT: m 1384 MET cc_start: 0.3784 (mmm) cc_final: 0.2704 (ptm) REVERT: n 286 ARG cc_start: 0.7861 (mtt-85) cc_final: 0.7278 (tpt170) REVERT: q 110 TRP cc_start: 0.2310 (m100) cc_final: 0.1601 (m100) REVERT: q 852 MET cc_start: 0.7647 (tmm) cc_final: 0.6938 (ptt) REVERT: r 279 GLN cc_start: 0.1233 (mt0) cc_final: -0.0502 (tp40) REVERT: r 329 MET cc_start: -0.1046 (tmm) cc_final: -0.1618 (ttt) REVERT: r 404 MET cc_start: 0.9041 (mtt) cc_final: 0.8816 (mtp) REVERT: r 507 ASP cc_start: 0.6860 (m-30) cc_final: 0.5868 (p0) REVERT: u 210 MET cc_start: 0.3866 (tpt) cc_final: 0.3487 (tpt) REVERT: v 167 GLU cc_start: 0.7767 (OUTLIER) cc_final: 0.7323 (mm-30) REVERT: v 230 GLU cc_start: 0.5632 (tp30) cc_final: 0.5310 (pt0) REVERT: v 306 MET cc_start: 0.6931 (mpp) cc_final: 0.6628 (mtm) REVERT: v 362 MET cc_start: 0.6545 (OUTLIER) cc_final: 0.6250 (ttt) REVERT: x 230 GLN cc_start: 0.8830 (tt0) cc_final: 0.8236 (tt0) REVERT: x 235 LEU cc_start: 0.7073 (mp) cc_final: 0.6321 (pp) REVERT: x 307 GLN cc_start: 0.3660 (OUTLIER) cc_final: 0.2280 (mt0) REVERT: x 345 GLN cc_start: 0.9177 (tt0) cc_final: 0.8751 (tm-30) outliers start: 72 outliers final: 56 residues processed: 364 average time/residue: 0.7211 time to fit residues: 462.5740 Evaluate side-chains 356 residues out of total 7692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 294 time to evaluate : 6.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 ARG Chi-restraints excluded: chain A residue 84 MET Chi-restraints excluded: chain A residue 220 CYS Chi-restraints excluded: chain A residue 238 THR Chi-restraints excluded: chain A residue 337 LEU Chi-restraints excluded: chain A residue 369 ILE Chi-restraints excluded: chain A residue 547 VAL Chi-restraints excluded: chain A residue 827 ASP Chi-restraints excluded: chain A residue 850 MET Chi-restraints excluded: chain A residue 960 VAL Chi-restraints excluded: chain A residue 1009 ILE Chi-restraints excluded: chain A residue 1140 ILE Chi-restraints excluded: chain A residue 1240 ILE Chi-restraints excluded: chain A residue 1408 THR Chi-restraints excluded: chain A residue 1414 GLU Chi-restraints excluded: chain B residue 70 ASN Chi-restraints excluded: chain B residue 125 THR Chi-restraints excluded: chain B residue 277 VAL Chi-restraints excluded: chain B residue 425 MET Chi-restraints excluded: chain B residue 441 VAL Chi-restraints excluded: chain B residue 503 LYS Chi-restraints excluded: chain B residue 871 VAL Chi-restraints excluded: chain B residue 918 ILE Chi-restraints excluded: chain B residue 933 THR Chi-restraints excluded: chain B residue 944 THR Chi-restraints excluded: chain B residue 971 THR Chi-restraints excluded: chain C residue 155 ILE Chi-restraints excluded: chain D residue 119 GLU Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 111 ILE Chi-restraints excluded: chain F residue 153 VAL Chi-restraints excluded: chain G residue 52 MET Chi-restraints excluded: chain H residue 23 VAL Chi-restraints excluded: chain I residue 50 THR Chi-restraints excluded: chain I residue 59 VAL Chi-restraints excluded: chain J residue 56 ILE Chi-restraints excluded: chain K residue 15 ASP Chi-restraints excluded: chain K residue 59 VAL Chi-restraints excluded: chain K residue 72 VAL Chi-restraints excluded: chain L residue 53 CYS Chi-restraints excluded: chain V residue 40 ASP Chi-restraints excluded: chain W residue 543 ILE Chi-restraints excluded: chain W residue 575 VAL Chi-restraints excluded: chain W residue 578 ASN Chi-restraints excluded: chain W residue 593 SER Chi-restraints excluded: chain W residue 689 ARG Chi-restraints excluded: chain W residue 787 LYS Chi-restraints excluded: chain b residue 49 LEU Chi-restraints excluded: chain m residue 255 GLU Chi-restraints excluded: chain m residue 1083 MET Chi-restraints excluded: chain m residue 1104 ILE Chi-restraints excluded: chain n residue 167 MET Chi-restraints excluded: chain n residue 178 ILE Chi-restraints excluded: chain n residue 259 VAL Chi-restraints excluded: chain n residue 275 ARG Chi-restraints excluded: chain u residue 107 VAL Chi-restraints excluded: chain v residue 167 GLU Chi-restraints excluded: chain v residue 362 MET Chi-restraints excluded: chain x residue 210 ILE Chi-restraints excluded: chain x residue 307 GLN Chi-restraints excluded: chain x residue 321 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 879 random chunks: chunk 770 optimal weight: 20.0000 chunk 811 optimal weight: 30.0000 chunk 740 optimal weight: 40.0000 chunk 789 optimal weight: 50.0000 chunk 475 optimal weight: 30.0000 chunk 343 optimal weight: 40.0000 chunk 619 optimal weight: 9.9990 chunk 242 optimal weight: 5.9990 chunk 713 optimal weight: 40.0000 chunk 746 optimal weight: 40.0000 chunk 786 optimal weight: 50.0000 overall best weight: 19.1996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 400 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 700 HIS ** A 737 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1021 GLN ** B 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1084 GLN D 99 ASN G 41 GLN ** G 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 44 ASN ** I 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 37 ASN ** W 567 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 603 GLN ** W 644 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 784 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 39 HIS ** e 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 612 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** m 962 ASN m1018 ASN ** n 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** q 105 HIS q 381 ASN q 483 ASN q 667 HIS ** q 715 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 818 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 887 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** r 262 ASN r 493 ASN ** v 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7412 moved from start: 0.4973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.016 0.199 77159 Z= 1.013 Angle : 1.009 14.719 105345 Z= 0.521 Chirality : 0.055 0.252 11765 Planarity : 0.007 0.097 12665 Dihedral : 17.947 169.814 12605 Min Nonbonded Distance : 1.890 Molprobity Statistics. All-atom Clashscore : 20.64 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.45 % Favored : 94.49 % Rotamer: Outliers : 1.48 % Allowed : 12.53 % Favored : 85.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.29 (0.09), residues: 8563 helix: 0.65 (0.08), residues: 3978 sheet: -0.86 (0.15), residues: 1124 loop : -0.85 (0.10), residues: 3461 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.004 TRP G 79 HIS 0.016 0.003 HIS B 996 PHE 0.036 0.004 PHE K 71 TYR 0.034 0.003 TYR m 530 ARG 0.019 0.001 ARG A1369 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17126 Ramachandran restraints generated. 8563 Oldfield, 0 Emsley, 8563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17126 Ramachandran restraints generated. 8563 Oldfield, 0 Emsley, 8563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 408 residues out of total 7692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 114 poor density : 294 time to evaluate : 6.355 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 253 MET cc_start: 0.7137 (tmm) cc_final: 0.6696 (tmm) REVERT: A 488 MET cc_start: 0.9148 (mtp) cc_final: 0.8588 (mtm) REVERT: A 747 MET cc_start: 0.9120 (mtm) cc_final: 0.8665 (mtp) REVERT: A 1378 MET cc_start: 0.9086 (mtp) cc_final: 0.8736 (mtp) REVERT: B 123 MET cc_start: 0.5417 (ppp) cc_final: 0.5188 (ppp) REVERT: V 40 ASP cc_start: 0.6988 (OUTLIER) cc_final: 0.5698 (t70) REVERT: W 543 ILE cc_start: 0.7801 (OUTLIER) cc_final: 0.7498 (mm) REVERT: b 49 LEU cc_start: 0.5567 (OUTLIER) cc_final: 0.4641 (tp) REVERT: m 257 MET cc_start: 0.1529 (mtm) cc_final: -0.0279 (tpt) REVERT: m 659 MET cc_start: 0.6630 (ptp) cc_final: 0.5220 (mpp) REVERT: m 1166 MET cc_start: 0.5731 (ppp) cc_final: 0.5482 (ppp) REVERT: m 1384 MET cc_start: 0.4125 (mmm) cc_final: 0.2840 (ptm) REVERT: n 223 LEU cc_start: 0.4402 (OUTLIER) cc_final: 0.4032 (mp) REVERT: n 286 ARG cc_start: 0.7678 (mtt-85) cc_final: 0.7178 (tpt170) REVERT: q 105 HIS cc_start: 0.5648 (m90) cc_final: 0.5443 (m-70) REVERT: q 110 TRP cc_start: 0.2282 (m100) cc_final: 0.1422 (m100) REVERT: q 852 MET cc_start: 0.8116 (tmm) cc_final: 0.7189 (ptt) REVERT: r 282 MET cc_start: 0.2144 (mmt) cc_final: 0.1848 (mmp) REVERT: r 329 MET cc_start: -0.1110 (tmm) cc_final: -0.1712 (ttt) REVERT: r 507 ASP cc_start: 0.7016 (m-30) cc_final: 0.5882 (p0) REVERT: u 178 TYR cc_start: 0.5705 (m-80) cc_final: 0.5384 (m-80) REVERT: u 210 MET cc_start: 0.4555 (tpt) cc_final: 0.4261 (tpp) REVERT: v 167 GLU cc_start: 0.7903 (OUTLIER) cc_final: 0.7412 (pt0) REVERT: v 230 GLU cc_start: 0.4966 (tp30) cc_final: 0.4665 (mt-10) REVERT: x 235 LEU cc_start: 0.7090 (mp) cc_final: 0.6411 (pp) REVERT: x 307 GLN cc_start: 0.3962 (OUTLIER) cc_final: 0.2608 (mt0) REVERT: x 345 GLN cc_start: 0.9225 (tt0) cc_final: 0.8983 (tm-30) outliers start: 114 outliers final: 90 residues processed: 389 average time/residue: 0.7203 time to fit residues: 494.8848 Evaluate side-chains 377 residues out of total 7692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 281 time to evaluate : 6.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 ARG Chi-restraints excluded: chain A residue 84 MET Chi-restraints excluded: chain A residue 220 CYS Chi-restraints excluded: chain A residue 238 THR Chi-restraints excluded: chain A residue 285 SER Chi-restraints excluded: chain A residue 290 ILE Chi-restraints excluded: chain A residue 337 LEU Chi-restraints excluded: chain A residue 369 ILE Chi-restraints excluded: chain A residue 540 THR Chi-restraints excluded: chain A residue 547 VAL Chi-restraints excluded: chain A residue 827 ASP Chi-restraints excluded: chain A residue 850 MET Chi-restraints excluded: chain A residue 884 ILE Chi-restraints excluded: chain A residue 960 VAL Chi-restraints excluded: chain A residue 1009 ILE Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain A residue 1140 ILE Chi-restraints excluded: chain A residue 1152 THR Chi-restraints excluded: chain A residue 1240 ILE Chi-restraints excluded: chain A residue 1408 THR Chi-restraints excluded: chain A residue 1414 GLU Chi-restraints excluded: chain B residue 70 ASN Chi-restraints excluded: chain B residue 125 THR Chi-restraints excluded: chain B residue 277 VAL Chi-restraints excluded: chain B residue 425 MET Chi-restraints excluded: chain B residue 441 VAL Chi-restraints excluded: chain B residue 446 ILE Chi-restraints excluded: chain B residue 480 THR Chi-restraints excluded: chain B residue 503 LYS Chi-restraints excluded: chain B residue 510 THR Chi-restraints excluded: chain B residue 606 VAL Chi-restraints excluded: chain B residue 806 THR Chi-restraints excluded: chain B residue 871 VAL Chi-restraints excluded: chain B residue 889 THR Chi-restraints excluded: chain B residue 933 THR Chi-restraints excluded: chain B residue 944 THR Chi-restraints excluded: chain B residue 971 THR Chi-restraints excluded: chain B residue 1119 VAL Chi-restraints excluded: chain B residue 1184 SER Chi-restraints excluded: chain C residue 20 MET Chi-restraints excluded: chain C residue 126 ASN Chi-restraints excluded: chain C residue 155 ILE Chi-restraints excluded: chain C residue 157 CYS Chi-restraints excluded: chain C residue 230 MET Chi-restraints excluded: chain D residue 60 ILE Chi-restraints excluded: chain D residue 119 GLU Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 133 THR Chi-restraints excluded: chain E residue 200 ARG Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 111 ILE Chi-restraints excluded: chain F residue 153 VAL Chi-restraints excluded: chain G residue 16 SER Chi-restraints excluded: chain G residue 33 ASP Chi-restraints excluded: chain G residue 46 VAL Chi-restraints excluded: chain G residue 52 MET Chi-restraints excluded: chain H residue 23 VAL Chi-restraints excluded: chain H residue 49 VAL Chi-restraints excluded: chain H residue 138 ASN Chi-restraints excluded: chain I residue 50 THR Chi-restraints excluded: chain I residue 59 VAL Chi-restraints excluded: chain J residue 56 ILE Chi-restraints excluded: chain K residue 15 ASP Chi-restraints excluded: chain K residue 33 ILE Chi-restraints excluded: chain K residue 59 VAL Chi-restraints excluded: chain K residue 72 VAL Chi-restraints excluded: chain K residue 84 LYS Chi-restraints excluded: chain L residue 53 CYS Chi-restraints excluded: chain V residue 40 ASP Chi-restraints excluded: chain W residue 401 VAL Chi-restraints excluded: chain W residue 543 ILE Chi-restraints excluded: chain W residue 575 VAL Chi-restraints excluded: chain W residue 578 ASN Chi-restraints excluded: chain W residue 593 SER Chi-restraints excluded: chain W residue 689 ARG Chi-restraints excluded: chain W residue 787 LYS Chi-restraints excluded: chain b residue 49 LEU Chi-restraints excluded: chain m residue 255 GLU Chi-restraints excluded: chain m residue 637 ASP Chi-restraints excluded: chain m residue 786 ASP Chi-restraints excluded: chain m residue 821 ASP Chi-restraints excluded: chain m residue 1083 MET Chi-restraints excluded: chain m residue 1104 ILE Chi-restraints excluded: chain n residue 178 ILE Chi-restraints excluded: chain n residue 223 LEU Chi-restraints excluded: chain n residue 259 VAL Chi-restraints excluded: chain q residue 16 ASP Chi-restraints excluded: chain u residue 107 VAL Chi-restraints excluded: chain v residue 167 GLU Chi-restraints excluded: chain v residue 324 ILE Chi-restraints excluded: chain v residue 362 MET Chi-restraints excluded: chain x residue 210 ILE Chi-restraints excluded: chain x residue 296 ASN Chi-restraints excluded: chain x residue 307 GLN Chi-restraints excluded: chain x residue 321 VAL Chi-restraints excluded: chain x residue 353 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 879 random chunks: chunk 518 optimal weight: 8.9990 chunk 834 optimal weight: 20.0000 chunk 509 optimal weight: 30.0000 chunk 396 optimal weight: 50.0000 chunk 580 optimal weight: 50.0000 chunk 875 optimal weight: 20.0000 chunk 805 optimal weight: 50.0000 chunk 697 optimal weight: 10.0000 chunk 72 optimal weight: 4.9990 chunk 538 optimal weight: 20.0000 chunk 427 optimal weight: 40.0000 overall best weight: 12.7996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 157 HIS ** B 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 317 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 72 ASN ** G 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 644 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 643 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** m 947 GLN ** n 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** q 147 ASN ** q 818 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 887 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** r 278 ASN ** v 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7365 moved from start: 0.5132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.157 77159 Z= 0.694 Angle : 0.778 11.494 105345 Z= 0.406 Chirality : 0.047 0.228 11765 Planarity : 0.005 0.060 12665 Dihedral : 17.898 168.069 12605 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 16.34 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.71 % Favored : 95.26 % Rotamer: Outliers : 1.29 % Allowed : 13.17 % Favored : 85.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.11 (0.09), residues: 8563 helix: 0.88 (0.08), residues: 3953 sheet: -0.95 (0.15), residues: 1131 loop : -0.77 (0.10), residues: 3479 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.003 TRP q 925 HIS 0.012 0.002 HIS B 996 PHE 0.022 0.002 PHE H 117 TYR 0.032 0.002 TYR q 155 ARG 0.010 0.001 ARG C 266 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17126 Ramachandran restraints generated. 8563 Oldfield, 0 Emsley, 8563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17126 Ramachandran restraints generated. 8563 Oldfield, 0 Emsley, 8563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 390 residues out of total 7692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 291 time to evaluate : 6.369 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 253 MET cc_start: 0.7012 (tmm) cc_final: 0.6642 (tmm) REVERT: A 488 MET cc_start: 0.9166 (mtp) cc_final: 0.8703 (mtm) REVERT: A 614 MET cc_start: 0.8478 (mmt) cc_final: 0.8073 (mmt) REVERT: A 770 MET cc_start: 0.8380 (OUTLIER) cc_final: 0.8136 (mtm) REVERT: A 1378 MET cc_start: 0.8978 (mtp) cc_final: 0.8669 (mtp) REVERT: B 1082 MET cc_start: 0.9154 (tpp) cc_final: 0.8933 (tpp) REVERT: V 40 ASP cc_start: 0.7130 (OUTLIER) cc_final: 0.5953 (t70) REVERT: V 99 GLU cc_start: 0.8214 (mt-10) cc_final: 0.7793 (mm-30) REVERT: m 257 MET cc_start: 0.1600 (mtm) cc_final: -0.0227 (tpt) REVERT: m 1384 MET cc_start: 0.4333 (mmm) cc_final: 0.3094 (ptm) REVERT: n 286 ARG cc_start: 0.7763 (mtt-85) cc_final: 0.7239 (tpt170) REVERT: q 852 MET cc_start: 0.8144 (tmm) cc_final: 0.7082 (ptt) REVERT: r 282 MET cc_start: 0.2043 (mmt) cc_final: 0.1807 (mmp) REVERT: r 507 ASP cc_start: 0.7071 (m-30) cc_final: 0.6212 (p0) REVERT: u 178 TYR cc_start: 0.5703 (m-80) cc_final: 0.5335 (m-80) REVERT: u 210 MET cc_start: 0.4661 (tpt) cc_final: 0.4368 (tpt) REVERT: v 167 GLU cc_start: 0.8032 (OUTLIER) cc_final: 0.7505 (mm-30) REVERT: v 230 GLU cc_start: 0.5238 (tp30) cc_final: 0.4901 (pt0) REVERT: x 212 LEU cc_start: 0.8460 (mt) cc_final: 0.7830 (pp) REVERT: x 235 LEU cc_start: 0.6951 (mp) cc_final: 0.6360 (pp) REVERT: x 307 GLN cc_start: 0.4568 (OUTLIER) cc_final: 0.3325 (mt0) REVERT: x 345 GLN cc_start: 0.9240 (tt0) cc_final: 0.8993 (tm-30) outliers start: 99 outliers final: 82 residues processed: 374 average time/residue: 0.6829 time to fit residues: 449.2001 Evaluate side-chains 368 residues out of total 7692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 282 time to evaluate : 6.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 ARG Chi-restraints excluded: chain A residue 84 MET Chi-restraints excluded: chain A residue 220 CYS Chi-restraints excluded: chain A residue 238 THR Chi-restraints excluded: chain A residue 290 ILE Chi-restraints excluded: chain A residue 337 LEU Chi-restraints excluded: chain A residue 369 ILE Chi-restraints excluded: chain A residue 540 THR Chi-restraints excluded: chain A residue 547 VAL Chi-restraints excluded: chain A residue 579 LEU Chi-restraints excluded: chain A residue 770 MET Chi-restraints excluded: chain A residue 827 ASP Chi-restraints excluded: chain A residue 850 MET Chi-restraints excluded: chain A residue 960 VAL Chi-restraints excluded: chain A residue 1009 ILE Chi-restraints excluded: chain A residue 1128 LEU Chi-restraints excluded: chain A residue 1140 ILE Chi-restraints excluded: chain A residue 1152 THR Chi-restraints excluded: chain A residue 1408 THR Chi-restraints excluded: chain A residue 1414 GLU Chi-restraints excluded: chain B residue 70 ASN Chi-restraints excluded: chain B residue 125 THR Chi-restraints excluded: chain B residue 277 VAL Chi-restraints excluded: chain B residue 425 MET Chi-restraints excluded: chain B residue 441 VAL Chi-restraints excluded: chain B residue 446 ILE Chi-restraints excluded: chain B residue 480 THR Chi-restraints excluded: chain B residue 503 LYS Chi-restraints excluded: chain B residue 510 THR Chi-restraints excluded: chain B residue 606 VAL Chi-restraints excluded: chain B residue 806 THR Chi-restraints excluded: chain B residue 871 VAL Chi-restraints excluded: chain B residue 933 THR Chi-restraints excluded: chain B residue 944 THR Chi-restraints excluded: chain B residue 971 THR Chi-restraints excluded: chain B residue 1119 VAL Chi-restraints excluded: chain B residue 1218 THR Chi-restraints excluded: chain C residue 20 MET Chi-restraints excluded: chain C residue 157 CYS Chi-restraints excluded: chain C residue 230 MET Chi-restraints excluded: chain D residue 119 GLU Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 111 ILE Chi-restraints excluded: chain F residue 153 VAL Chi-restraints excluded: chain G residue 16 SER Chi-restraints excluded: chain G residue 33 ASP Chi-restraints excluded: chain G residue 46 VAL Chi-restraints excluded: chain G residue 52 MET Chi-restraints excluded: chain H residue 23 VAL Chi-restraints excluded: chain H residue 84 THR Chi-restraints excluded: chain H residue 138 ASN Chi-restraints excluded: chain I residue 50 THR Chi-restraints excluded: chain I residue 59 VAL Chi-restraints excluded: chain J residue 56 ILE Chi-restraints excluded: chain K residue 15 ASP Chi-restraints excluded: chain K residue 33 ILE Chi-restraints excluded: chain K residue 59 VAL Chi-restraints excluded: chain K residue 72 VAL Chi-restraints excluded: chain K residue 84 LYS Chi-restraints excluded: chain L residue 53 CYS Chi-restraints excluded: chain V residue 40 ASP Chi-restraints excluded: chain W residue 401 VAL Chi-restraints excluded: chain W residue 575 VAL Chi-restraints excluded: chain W residue 578 ASN Chi-restraints excluded: chain W residue 593 SER Chi-restraints excluded: chain W residue 689 ARG Chi-restraints excluded: chain W residue 787 LYS Chi-restraints excluded: chain b residue 26 ILE Chi-restraints excluded: chain b residue 49 LEU Chi-restraints excluded: chain m residue 255 GLU Chi-restraints excluded: chain m residue 637 ASP Chi-restraints excluded: chain m residue 786 ASP Chi-restraints excluded: chain m residue 821 ASP Chi-restraints excluded: chain m residue 1083 MET Chi-restraints excluded: chain m residue 1104 ILE Chi-restraints excluded: chain n residue 178 ILE Chi-restraints excluded: chain n residue 259 VAL Chi-restraints excluded: chain q residue 16 ASP Chi-restraints excluded: chain u residue 107 VAL Chi-restraints excluded: chain v residue 167 GLU Chi-restraints excluded: chain v residue 324 ILE Chi-restraints excluded: chain x residue 210 ILE Chi-restraints excluded: chain x residue 238 SER Chi-restraints excluded: chain x residue 307 GLN Chi-restraints excluded: chain x residue 321 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 879 random chunks: chunk 553 optimal weight: 40.0000 chunk 742 optimal weight: 50.0000 chunk 213 optimal weight: 1.9990 chunk 642 optimal weight: 9.9990 chunk 102 optimal weight: 1.9990 chunk 193 optimal weight: 1.9990 chunk 698 optimal weight: 8.9990 chunk 292 optimal weight: 10.0000 chunk 717 optimal weight: 8.9990 chunk 88 optimal weight: 3.9990 chunk 128 optimal weight: 4.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 700 HIS A1021 GLN B 63 GLN D 72 ASN ** G 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 44 ASN L 39 ASN ** V 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 644 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** q 147 ASN ** q 681 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 818 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** r 262 ASN ** v 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4526 r_free = 0.4526 target = 0.141637 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.101754 restraints weight = 317722.958| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.100186 restraints weight = 179476.979| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.100049 restraints weight = 154301.538| |-----------------------------------------------------------------------------| r_work (final): 0.3409 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7544 moved from start: 0.4972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.091 77159 Z= 0.224 Angle : 0.558 19.480 105345 Z= 0.296 Chirality : 0.041 0.209 11765 Planarity : 0.004 0.054 12665 Dihedral : 17.637 170.545 12605 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 12.04 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.19 % Favored : 96.78 % Rotamer: Outliers : 0.86 % Allowed : 13.66 % Favored : 85.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.64 (0.09), residues: 8563 helix: 1.53 (0.08), residues: 3961 sheet: -0.66 (0.15), residues: 1098 loop : -0.42 (0.11), residues: 3504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP q 595 HIS 0.007 0.001 HIS b 75 PHE 0.025 0.001 PHE q 126 TYR 0.030 0.001 TYR q 155 ARG 0.005 0.000 ARG A 47 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11390.71 seconds wall clock time: 205 minutes 31.29 seconds (12331.29 seconds total)