Starting phenix.real_space_refine on Tue Mar 26 00:07:38 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q6o_18191/03_2024/8q6o_18191.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q6o_18191/03_2024/8q6o_18191.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.14 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q6o_18191/03_2024/8q6o_18191.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q6o_18191/03_2024/8q6o_18191.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q6o_18191/03_2024/8q6o_18191.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q6o_18191/03_2024/8q6o_18191.pdb" } resolution = 3.14 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.058 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: 5 Type Number sf(0) Gaussians Zn 10 6.06 5 S 336 5.16 5 C 32944 2.51 5 N 9010 2.21 5 O 9683 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B PHE 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 218": "OD1" <-> "OD2" Residue "M ASP 57": "OD1" <-> "OD2" Residue "P TYR 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ASP 267": "OD1" <-> "OD2" Residue "P TYR 282": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 366": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 57": "OD1" <-> "OD2" Residue "J TYR 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 267": "OD1" <-> "OD2" Residue "J TYR 282": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 366": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 PHE 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 ASP 218": "OD1" <-> "OD2" Time to flip residues: 0.13s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 51983 Number of models: 1 Model: "" Number of chains: 34 Chain: "A" Number of atoms: 2141 Number of conformers: 1 Conformer: "" Number of residues, atoms: 267, 2141 Classifications: {'peptide': 267} Link IDs: {'PTRANS': 14, 'TRANS': 252} Chain: "B" Number of atoms: 2066 Number of conformers: 1 Conformer: "" Number of residues, atoms: 262, 2066 Classifications: {'peptide': 262} Link IDs: {'PTRANS': 11, 'TRANS': 250} Chain: "C" Number of atoms: 2112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 258, 2112 Classifications: {'peptide': 258} Link IDs: {'PTRANS': 15, 'TRANS': 242} Chain breaks: 1 Chain: "D" Number of atoms: 2059 Number of conformers: 1 Conformer: "" Number of residues, atoms: 256, 2059 Classifications: {'peptide': 256} Link IDs: {'PTRANS': 14, 'TRANS': 241} Chain breaks: 2 Chain: "E" Number of atoms: 1997 Number of conformers: 1 Conformer: "" Number of residues, atoms: 249, 1997 Classifications: {'peptide': 249} Link IDs: {'PTRANS': 11, 'TRANS': 237} Chain breaks: 1 Chain: "F" Number of atoms: 2227 Number of conformers: 1 Conformer: "" Number of residues, atoms: 275, 2227 Classifications: {'peptide': 275} Link IDs: {'PTRANS': 14, 'TRANS': 260} Chain breaks: 3 Chain: "M" Number of atoms: 1622 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1622 Classifications: {'peptide': 196} Link IDs: {'PTRANS': 6, 'TRANS': 189} Chain: "N" Number of atoms: 1418 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 1418 Classifications: {'peptide': 175} Link IDs: {'PTRANS': 11, 'TRANS': 163} Chain: "O" Number of atoms: 1621 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 1621 Classifications: {'peptide': 202} Link IDs: {'PTRANS': 11, 'TRANS': 190} Chain: "P" Number of atoms: 4233 Number of conformers: 1 Conformer: "" Number of residues, atoms: 523, 4233 Classifications: {'peptide': 523} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 13, 'TRANS': 509} Chain breaks: 1 Chain: "Q" Number of atoms: 1655 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 1655 Classifications: {'peptide': 203} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 13, 'TRANS': 189} Chain: "R" Number of atoms: 2835 Number of conformers: 1 Conformer: "" Number of residues, atoms: 361, 2835 Classifications: {'peptide': 361} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 21, 'TRANS': 339} Chain breaks: 4 Chain: "G" Number of atoms: 1623 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1623 Classifications: {'peptide': 196} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 189} Chain: "K" Number of atoms: 1655 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 1655 Classifications: {'peptide': 203} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 13, 'TRANS': 189} Chain: "H" Number of atoms: 1418 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 1418 Classifications: {'peptide': 175} Link IDs: {'PTRANS': 11, 'TRANS': 163} Chain: "I" Number of atoms: 1621 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 1621 Classifications: {'peptide': 202} Link IDs: {'PTRANS': 11, 'TRANS': 190} Chain: "J" Number of atoms: 4233 Number of conformers: 1 Conformer: "" Number of residues, atoms: 523, 4233 Classifications: {'peptide': 523} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 13, 'TRANS': 509} Chain breaks: 1 Chain: "2" Number of atoms: 2141 Number of conformers: 1 Conformer: "" Number of residues, atoms: 267, 2141 Classifications: {'peptide': 267} Link IDs: {'PTRANS': 14, 'TRANS': 252} Chain: "3" Number of atoms: 2066 Number of conformers: 1 Conformer: "" Number of residues, atoms: 262, 2066 Classifications: {'peptide': 262} Link IDs: {'PTRANS': 11, 'TRANS': 250} Chain: "4" Number of atoms: 2112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 258, 2112 Classifications: {'peptide': 258} Link IDs: {'PTRANS': 15, 'TRANS': 242} Chain breaks: 1 Chain: "5" Number of atoms: 2059 Number of conformers: 1 Conformer: "" Number of residues, atoms: 256, 2059 Classifications: {'peptide': 256} Link IDs: {'PTRANS': 14, 'TRANS': 241} Chain breaks: 2 Chain: "6" Number of atoms: 1997 Number of conformers: 1 Conformer: "" Number of residues, atoms: 249, 1997 Classifications: {'peptide': 249} Link IDs: {'PTRANS': 11, 'TRANS': 237} Chain breaks: 1 Chain: "7" Number of atoms: 2227 Number of conformers: 1 Conformer: "" Number of residues, atoms: 275, 2227 Classifications: {'peptide': 275} Link IDs: {'PTRANS': 14, 'TRANS': 260} Chain breaks: 3 Chain: "L" Number of atoms: 2835 Number of conformers: 1 Conformer: "" Number of residues, atoms: 361, 2835 Classifications: {'peptide': 361} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 21, 'TRANS': 339} Chain breaks: 4 Chain: "A" 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: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "2" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "4" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "5" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "6" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "7" 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 1222 SG CYS A 314 92.421 93.441 112.722 1.00221.82 S ATOM 1245 SG CYS A 317 88.674 92.775 112.095 1.00227.27 S ATOM 1404 SG CYS A 337 90.213 92.119 115.513 1.00239.21 S ATOM 1426 SG CYS A 340 90.900 89.852 112.670 1.00235.15 S ATOM 5376 SG CYS C 306 126.616 89.509 140.360 1.00220.02 S ATOM 5398 SG CYS C 309 127.453 87.157 143.277 1.00222.54 S ATOM 5545 SG CYS C 328 129.596 87.148 140.172 1.00226.54 S ATOM 5570 SG CYS C 331 126.079 85.784 139.976 1.00229.79 S ATOM 7521 SG CYS D 173 111.862 94.443 92.480 1.00149.44 S ATOM 7544 SG CYS D 176 110.127 91.480 90.891 1.00136.83 S ATOM 7711 SG CYS D 198 109.374 92.415 94.415 1.00131.99 S ATOM 7725 SG CYS D 208 112.703 90.892 93.787 1.00148.65 S ATOM 9504 SG CYS E 160 110.263 91.285 130.744 1.00248.99 S ATOM 9526 SG CYS E 163 109.109 88.933 133.403 1.00249.40 S ATOM 9685 SG CYS E 182 112.808 89.749 132.772 1.00251.85 S ATOM 9722 SG CYS E 187 110.657 87.286 130.558 1.00262.74 S ATOM 11697 SG CYS F 183 144.694 87.597 120.207 1.00233.52 S ATOM 11720 SG CYS F 186 146.930 85.699 117.790 1.00238.77 S ATOM 11866 SG CYS F 205 143.986 87.517 116.399 1.00240.66 S ATOM 11905 SG CYS F 210 143.289 84.540 118.586 1.00247.81 S ATOM 37758 SG CYS 2 314 108.944 88.961 112.718 1.00221.14 S ATOM 37781 SG CYS 2 317 112.693 89.641 112.089 1.00225.16 S ATOM 37940 SG CYS 2 337 111.148 90.286 115.507 1.00238.99 S ATOM 37962 SG CYS 2 340 110.454 92.554 112.666 1.00234.41 S ATOM 41912 SG CYS 4 306 74.751 92.868 140.334 1.00219.22 S ATOM 41934 SG CYS 4 309 73.917 95.202 143.268 1.00221.58 S ATOM 42081 SG CYS 4 328 71.785 95.236 140.159 1.00226.85 S ATOM 42106 SG CYS 4 331 75.305 96.595 139.975 1.00230.17 S ATOM 44057 SG CYS 5 173 89.518 87.956 92.460 1.00149.15 S ATOM 44080 SG CYS 5 176 91.256 90.919 90.881 1.00136.45 S ATOM 44247 SG CYS 5 198 92.004 89.976 94.406 1.00132.41 S ATOM 44261 SG CYS 5 208 88.680 91.507 93.775 1.00148.35 S ATOM 46040 SG CYS 6 160 91.112 91.105 130.716 1.00249.25 S ATOM 46062 SG CYS 6 163 92.265 93.452 133.383 1.00249.40 S ATOM 46221 SG CYS 6 182 88.568 92.647 132.742 1.00252.64 S ATOM 46258 SG CYS 6 187 90.711 95.108 130.532 1.00261.90 S ATOM 48233 SG CYS 7 183 56.670 94.774 120.195 1.00234.36 S ATOM 48256 SG CYS 7 186 54.432 96.672 117.778 1.00239.31 S ATOM 48402 SG CYS 7 205 57.381 94.854 116.387 1.00242.02 S ATOM 48441 SG CYS 7 210 58.073 97.830 118.571 1.00249.72 S Time building chain proxies: 25.60, per 1000 atoms: 0.49 Number of scatterers: 51983 At special positions: 0 Unit cell: (202.35, 183.35, 190, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 10 29.99 S 336 16.00 O 9683 8.00 N 9010 7.00 C 32944 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: 21.03 Conformation dependent library (CDL) restraints added in 9.8 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN 21000 " pdb="ZN ZN 21000 " - pdb=" SG CYS 2 337 " pdb="ZN ZN 21000 " - pdb=" SG CYS 2 340 " pdb="ZN ZN 21000 " - pdb=" SG CYS 2 317 " pdb="ZN ZN 21000 " - pdb=" SG CYS 2 314 " pdb=" ZN 41000 " pdb="ZN ZN 41000 " - pdb=" SG CYS 4 328 " pdb="ZN ZN 41000 " - pdb=" SG CYS 4 331 " pdb="ZN ZN 41000 " - pdb=" SG CYS 4 306 " pdb="ZN ZN 41000 " - pdb=" SG CYS 4 309 " pdb=" ZN 51000 " pdb="ZN ZN 51000 " - pdb=" SG CYS 5 198 " pdb="ZN ZN 51000 " - pdb=" SG CYS 5 176 " pdb="ZN ZN 51000 " - pdb=" SG CYS 5 173 " pdb="ZN ZN 51000 " - pdb=" SG CYS 5 208 " pdb=" ZN 61000 " pdb="ZN ZN 61000 " - pdb=" SG CYS 6 163 " pdb="ZN ZN 61000 " - pdb=" SG CYS 6 182 " pdb="ZN ZN 61000 " - pdb=" SG CYS 6 160 " pdb="ZN ZN 61000 " - pdb=" SG CYS 6 187 " pdb=" ZN 71000 " pdb="ZN ZN 71000 " - pdb=" SG CYS 7 183 " pdb="ZN ZN 71000 " - pdb=" SG CYS 7 205 " pdb="ZN ZN 71000 " - pdb=" SG CYS 7 210 " pdb="ZN ZN 71000 " - pdb=" SG CYS 7 186 " pdb=" ZN A1000 " pdb="ZN ZN A1000 " - pdb=" SG CYS A 337 " pdb="ZN ZN A1000 " - pdb=" SG CYS A 340 " pdb="ZN ZN A1000 " - pdb=" SG CYS A 317 " pdb="ZN ZN A1000 " - pdb=" SG CYS A 314 " pdb=" ZN C1000 " pdb="ZN ZN C1000 " - pdb=" SG CYS C 328 " pdb="ZN ZN C1000 " - pdb=" SG CYS C 331 " pdb="ZN ZN C1000 " - pdb=" SG CYS C 306 " pdb="ZN ZN C1000 " - pdb=" SG CYS C 309 " pdb=" ZN D1000 " pdb="ZN ZN D1000 " - pdb=" SG CYS D 198 " pdb="ZN ZN D1000 " - pdb=" SG CYS D 176 " pdb="ZN ZN D1000 " - pdb=" SG CYS D 173 " pdb="ZN ZN D1000 " - pdb=" SG CYS D 208 " pdb=" ZN E1000 " pdb="ZN ZN E1000 " - pdb=" SG CYS E 163 " pdb="ZN ZN E1000 " - pdb=" SG CYS E 182 " pdb="ZN ZN E1000 " - pdb=" SG CYS E 160 " pdb="ZN ZN E1000 " - pdb=" SG CYS E 187 " pdb=" ZN F1000 " pdb="ZN ZN F1000 " - pdb=" SG CYS F 205 " pdb="ZN ZN F1000 " - pdb=" SG CYS F 210 " pdb="ZN ZN F1000 " - pdb=" SG CYS F 183 " pdb="ZN ZN F1000 " - pdb=" SG CYS F 186 " Number of angles added : 60 12716 Ramachandran restraints generated. 6358 Oldfield, 0 Emsley, 6358 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 12336 Finding SS restraints... Secondary structure from input PDB file: 239 helices and 65 sheets defined 43.0% alpha, 20.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.96 Creating SS restraints... Processing helix chain 'A' and resid 166 through 172 Processing helix chain 'A' and resid 173 through 190 Processing helix chain 'A' and resid 198 through 210 removed outlier: 3.689A pdb=" N GLU A 202 " --> pdb=" O ASN A 198 " (cutoff:3.500A) Processing helix chain 'A' and resid 219 through 226 Processing helix chain 'A' and resid 226 through 233 Processing helix chain 'A' and resid 236 through 256 removed outlier: 3.542A pdb=" N LEU A 241 " --> pdb=" O PRO A 237 " (cutoff:3.500A) Processing helix chain 'A' and resid 278 through 282 removed outlier: 4.179A pdb=" N LEU A 282 " --> pdb=" O LEU A 279 " (cutoff:3.500A) Processing helix chain 'A' and resid 283 through 287 Processing helix chain 'A' and resid 386 through 388 No H-bonds generated for 'chain 'A' and resid 386 through 388' Processing helix chain 'A' and resid 408 through 416 Processing helix chain 'B' and resid 10 through 24 Processing helix chain 'B' and resid 31 through 42 Processing helix chain 'B' and resid 51 through 58 Processing helix chain 'B' and resid 58 through 68 Processing helix chain 'B' and resid 68 through 88 removed outlier: 3.991A pdb=" N GLU B 72 " --> pdb=" O ASP B 68 " (cutoff:3.500A) Processing helix chain 'B' and resid 88 through 95 removed outlier: 3.573A pdb=" N PHE B 95 " --> pdb=" O TYR B 91 " (cutoff:3.500A) Processing helix chain 'B' and resid 117 through 121 removed outlier: 3.877A pdb=" N LEU B 120 " --> pdb=" O THR B 117 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N LEU B 121 " --> pdb=" O ALA B 118 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 117 through 121' Processing helix chain 'B' and resid 187 through 191 Processing helix chain 'B' and resid 204 through 208 removed outlier: 3.740A pdb=" N ALA B 208 " --> pdb=" O PRO B 205 " (cutoff:3.500A) Processing helix chain 'B' and resid 222 through 226 Processing helix chain 'C' and resid 158 through 172 Processing helix chain 'C' and resid 192 through 204 removed outlier: 3.829A pdb=" N VAL C 202 " --> pdb=" O GLU C 198 " (cutoff:3.500A) Processing helix chain 'C' and resid 212 through 219 Processing helix chain 'C' and resid 219 through 229 Processing helix chain 'C' and resid 229 through 249 removed outlier: 3.548A pdb=" N VAL C 233 " --> pdb=" O TYR C 229 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ILE C 234 " --> pdb=" O PRO C 230 " (cutoff:3.500A) Proline residue: C 235 - end of helix Processing helix chain 'C' and resid 275 through 279 Processing helix chain 'C' and resid 377 through 379 No H-bonds generated for 'chain 'C' and resid 377 through 379' Processing helix chain 'D' and resid 28 through 43 Processing helix chain 'D' and resid 55 through 67 Processing helix chain 'D' and resid 75 through 82 Processing helix chain 'D' and resid 82 through 88 Processing helix chain 'D' and resid 92 through 112 removed outlier: 3.705A pdb=" N HIS D 96 " --> pdb=" O GLN D 92 " (cutoff:3.500A) Processing helix chain 'D' and resid 137 through 141 Processing helix chain 'D' and resid 253 through 255 No H-bonds generated for 'chain 'D' and resid 253 through 255' Processing helix chain 'E' and resid 23 through 39 Processing helix chain 'E' and resid 46 through 57 removed outlier: 3.942A pdb=" N SER E 50 " --> pdb=" O ASN E 46 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N GLU E 54 " --> pdb=" O SER E 50 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N ARG E 57 " --> pdb=" O GLU E 53 " (cutoff:3.500A) Processing helix chain 'E' and resid 67 through 74 Processing helix chain 'E' and resid 74 through 84 Processing helix chain 'E' and resid 84 through 104 Proline residue: E 90 - end of helix Processing helix chain 'F' and resid 5 through 18 Processing helix chain 'F' and resid 30 through 41 Processing helix chain 'F' and resid 51 through 58 Processing helix chain 'F' and resid 58 through 68 removed outlier: 3.684A pdb=" N VAL F 62 " --> pdb=" O ASP F 58 " (cutoff:3.500A) Processing helix chain 'F' and resid 70 through 84 removed outlier: 3.753A pdb=" N ASN F 74 " --> pdb=" O ARG F 70 " (cutoff:3.500A) Processing helix chain 'F' and resid 85 through 88 removed outlier: 3.605A pdb=" N LYS F 88 " --> pdb=" O PRO F 85 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 85 through 88' Processing helix chain 'F' and resid 96 through 111 Processing helix chain 'F' and resid 147 through 151 Processing helix chain 'F' and resid 152 through 156 removed outlier: 3.621A pdb=" N SER F 155 " --> pdb=" O LYS F 152 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N ILE F 156 " --> pdb=" O ALA F 153 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 152 through 156' Processing helix chain 'F' and resid 207 through 213 Processing helix chain 'F' and resid 259 through 261 No H-bonds generated for 'chain 'F' and resid 259 through 261' Processing helix chain 'M' and resid 3 through 16 removed outlier: 3.953A pdb=" N ALA M 16 " --> pdb=" O GLU M 12 " (cutoff:3.500A) Processing helix chain 'M' and resid 26 through 53 Processing helix chain 'M' and resid 55 through 57 No H-bonds generated for 'chain 'M' and resid 55 through 57' Processing helix chain 'M' and resid 58 through 94 removed outlier: 3.768A pdb=" N ALA M 89 " --> pdb=" O LEU M 85 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N LEU M 90 " --> pdb=" O ARG M 86 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N ARG M 91 " --> pdb=" O ILE M 87 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N TRP M 92 " --> pdb=" O ARG M 88 " (cutoff:3.500A) Processing helix chain 'M' and resid 99 through 105 removed outlier: 3.906A pdb=" N HIS M 105 " --> pdb=" O ALA M 101 " (cutoff:3.500A) Processing helix chain 'M' and resid 107 through 128 Processing helix chain 'M' and resid 178 through 181 removed outlier: 3.543A pdb=" N LYS M 181 " --> pdb=" O PRO M 178 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 178 through 181' Processing helix chain 'M' and resid 182 through 189 Processing helix chain 'N' and resid 2 through 11 Processing helix chain 'N' and resid 46 through 55 Processing helix chain 'N' and resid 67 through 79 Processing helix chain 'N' and resid 91 through 103 Processing helix chain 'N' and resid 109 through 139 removed outlier: 3.503A pdb=" N ILE N 113 " --> pdb=" O LYS N 109 " (cutoff:3.500A) Processing helix chain 'N' and resid 149 through 157 removed outlier: 3.871A pdb=" N ILE N 156 " --> pdb=" O GLU N 152 " (cutoff:3.500A) Processing helix chain 'N' and resid 159 through 172 Processing helix chain 'O' and resid 20 through 27 Processing helix chain 'O' and resid 42 through 46 Processing helix chain 'O' and resid 64 through 71 Processing helix chain 'O' and resid 83 through 86 Processing helix chain 'O' and resid 87 through 97 removed outlier: 3.585A pdb=" N VAL O 93 " --> pdb=" O GLY O 89 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ASP O 97 " --> pdb=" O VAL O 93 " (cutoff:3.500A) Processing helix chain 'O' and resid 109 through 117 removed outlier: 3.660A pdb=" N PHE O 113 " --> pdb=" O HIS O 109 " (cutoff:3.500A) Processing helix chain 'O' and resid 124 through 149 removed outlier: 3.500A pdb=" N LYS O 130 " --> pdb=" O PRO O 126 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N ARG O 141 " --> pdb=" O VAL O 137 " (cutoff:3.500A) removed outlier: 5.262A pdb=" N ARG O 142 " --> pdb=" O GLY O 138 " (cutoff:3.500A) Processing helix chain 'O' and resid 163 through 185 removed outlier: 3.526A pdb=" N ALA O 179 " --> pdb=" O ARG O 175 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N PHE O 180 " --> pdb=" O GLY O 176 " (cutoff:3.500A) Processing helix chain 'O' and resid 194 through 203 Processing helix chain 'P' and resid 26 through 43 Processing helix chain 'P' and resid 54 through 65 Processing helix chain 'P' and resid 82 through 88 removed outlier: 3.641A pdb=" N THR P 86 " --> pdb=" O ASP P 82 " (cutoff:3.500A) Processing helix chain 'P' and resid 105 through 110 Processing helix chain 'P' and resid 129 through 134 Processing helix chain 'P' and resid 180 through 190 Processing helix chain 'P' and resid 198 through 210 removed outlier: 3.528A pdb=" N MET P 202 " --> pdb=" O SER P 198 " (cutoff:3.500A) Processing helix chain 'P' and resid 214 through 231 Processing helix chain 'P' and resid 235 through 254 Processing helix chain 'P' and resid 286 through 294 Processing helix chain 'P' and resid 295 through 302 Processing helix chain 'P' and resid 305 through 320 Processing helix chain 'P' and resid 322 through 327 Processing helix chain 'P' and resid 329 through 333 removed outlier: 3.592A pdb=" N MET P 333 " --> pdb=" O PHE P 330 " (cutoff:3.500A) Processing helix chain 'P' and resid 335 through 339 removed outlier: 3.549A pdb=" N GLU P 339 " --> pdb=" O SER P 336 " (cutoff:3.500A) Processing helix chain 'P' and resid 340 through 352 Processing helix chain 'P' and resid 374 through 386 Processing helix chain 'P' and resid 393 through 404 Processing helix chain 'P' and resid 409 through 437 Processing helix chain 'P' and resid 458 through 462 Processing helix chain 'P' and resid 463 through 482 Processing helix chain 'P' and resid 486 through 490 removed outlier: 3.688A pdb=" N LEU P 490 " --> pdb=" O CYS P 487 " (cutoff:3.500A) Processing helix chain 'P' and resid 522 through 535 Processing helix chain 'P' and resid 554 through 567 Processing helix chain 'Q' and resid 20 through 37 Processing helix chain 'Q' and resid 45 through 66 removed outlier: 3.655A pdb=" N GLN Q 61 " --> pdb=" O ASN Q 57 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ALA Q 66 " --> pdb=" O ASN Q 62 " (cutoff:3.500A) Processing helix chain 'Q' and resid 70 through 101 removed outlier: 3.929A pdb=" N SER Q 74 " --> pdb=" O ASP Q 70 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N TYR Q 85 " --> pdb=" O GLU Q 81 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N MET Q 86 " --> pdb=" O ARG Q 82 " (cutoff:3.500A) Processing helix chain 'Q' and resid 101 through 111 Processing helix chain 'Q' and resid 121 through 143 Processing helix chain 'Q' and resid 144 through 147 Processing helix chain 'Q' and resid 209 through 215 Processing helix chain 'R' and resid 14 through 22 removed outlier: 3.555A pdb=" N LEU R 19 " --> pdb=" O PRO R 15 " (cutoff:3.500A) Processing helix chain 'R' and resid 177 through 181 Processing helix chain 'R' and resid 184 through 197 Processing helix chain 'R' and resid 209 through 212 Processing helix chain 'R' and resid 213 through 224 removed outlier: 3.643A pdb=" N ARG R 217 " --> pdb=" O SER R 213 " (cutoff:3.500A) Processing helix chain 'R' and resid 252 through 256 removed outlier: 3.506A pdb=" N SER R 255 " --> pdb=" O THR R 252 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N GLN R 256 " --> pdb=" O PRO R 253 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 252 through 256' Processing helix chain 'R' and resid 258 through 281 Processing helix chain 'R' and resid 302 through 306 removed outlier: 3.649A pdb=" N GLY R 305 " --> pdb=" O GLY R 302 " (cutoff:3.500A) Processing helix chain 'R' and resid 317 through 326 Processing helix chain 'R' and resid 396 through 408 removed outlier: 3.730A pdb=" N ASN R 406 " --> pdb=" O ARG R 402 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N GLU R 407 " --> pdb=" O LYS R 403 " (cutoff:3.500A) Processing helix chain 'R' and resid 413 through 417 removed outlier: 3.908A pdb=" N VAL R 417 " --> pdb=" O PRO R 414 " (cutoff:3.500A) Processing helix chain 'R' and resid 423 through 435 removed outlier: 4.022A pdb=" N THR R 427 " --> pdb=" O THR R 423 " (cutoff:3.500A) Processing helix chain 'R' and resid 494 through 509 removed outlier: 3.674A pdb=" N SER R 507 " --> pdb=" O MET R 503 " (cutoff:3.500A) Processing helix chain 'R' and resid 521 through 528 removed outlier: 5.052A pdb=" N VAL R 525 " --> pdb=" O PRO R 522 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N PHE R 526 " --> pdb=" O THR R 523 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ASN R 527 " --> pdb=" O ALA R 524 " (cutoff:3.500A) Processing helix chain 'R' and resid 548 through 556 Processing helix chain 'G' and resid 3 through 16 removed outlier: 3.956A pdb=" N ALA G 16 " --> pdb=" O GLU G 12 " (cutoff:3.500A) Processing helix chain 'G' and resid 26 through 53 Processing helix chain 'G' and resid 55 through 57 No H-bonds generated for 'chain 'G' and resid 55 through 57' Processing helix chain 'G' and resid 58 through 94 removed outlier: 3.769A pdb=" N ALA G 89 " --> pdb=" O LEU G 85 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N LEU G 90 " --> pdb=" O ARG G 86 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N ARG G 91 " --> pdb=" O ILE G 87 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N TRP G 92 " --> pdb=" O ARG G 88 " (cutoff:3.500A) Processing helix chain 'G' and resid 99 through 105 removed outlier: 3.924A pdb=" N HIS G 105 " --> pdb=" O ALA G 101 " (cutoff:3.500A) Processing helix chain 'G' and resid 107 through 128 Processing helix chain 'G' and resid 182 through 189 Processing helix chain 'K' and resid 20 through 37 Processing helix chain 'K' and resid 45 through 66 removed outlier: 3.681A pdb=" N GLN K 61 " --> pdb=" O ASN K 57 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N ALA K 66 " --> pdb=" O ASN K 62 " (cutoff:3.500A) Processing helix chain 'K' and resid 70 through 101 removed outlier: 3.938A pdb=" N SER K 74 " --> pdb=" O ASP K 70 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N TYR K 85 " --> pdb=" O GLU K 81 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N MET K 86 " --> pdb=" O ARG K 82 " (cutoff:3.500A) Processing helix chain 'K' and resid 101 through 111 Processing helix chain 'K' and resid 121 through 143 Processing helix chain 'K' and resid 144 through 147 Processing helix chain 'K' and resid 209 through 215 Processing helix chain 'H' and resid 2 through 11 Processing helix chain 'H' and resid 46 through 55 Processing helix chain 'H' and resid 67 through 79 Processing helix chain 'H' and resid 91 through 103 Processing helix chain 'H' and resid 109 through 139 removed outlier: 3.503A pdb=" N ILE H 113 " --> pdb=" O LYS H 109 " (cutoff:3.500A) Processing helix chain 'H' and resid 149 through 157 removed outlier: 3.869A pdb=" N ILE H 156 " --> pdb=" O GLU H 152 " (cutoff:3.500A) Processing helix chain 'H' and resid 159 through 172 Processing helix chain 'I' and resid 20 through 27 Processing helix chain 'I' and resid 42 through 46 Processing helix chain 'I' and resid 64 through 71 Processing helix chain 'I' and resid 83 through 86 Processing helix chain 'I' and resid 87 through 97 removed outlier: 3.584A pdb=" N VAL I 93 " --> pdb=" O GLY I 89 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ASP I 97 " --> pdb=" O VAL I 93 " (cutoff:3.500A) Processing helix chain 'I' and resid 109 through 117 removed outlier: 3.665A pdb=" N PHE I 113 " --> pdb=" O HIS I 109 " (cutoff:3.500A) Processing helix chain 'I' and resid 124 through 149 removed outlier: 3.502A pdb=" N LYS I 130 " --> pdb=" O PRO I 126 " (cutoff:3.500A) removed outlier: 4.682A pdb=" N ARG I 141 " --> pdb=" O VAL I 137 " (cutoff:3.500A) removed outlier: 5.244A pdb=" N ARG I 142 " --> pdb=" O GLY I 138 " (cutoff:3.500A) Processing helix chain 'I' and resid 163 through 185 removed outlier: 3.530A pdb=" N ALA I 179 " --> pdb=" O ARG I 175 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N PHE I 180 " --> pdb=" O GLY I 176 " (cutoff:3.500A) Processing helix chain 'I' and resid 194 through 203 Processing helix chain 'J' and resid 10 through 15 removed outlier: 3.729A pdb=" N ILE J 14 " --> pdb=" O PHE J 10 " (cutoff:3.500A) Processing helix chain 'J' and resid 26 through 43 Processing helix chain 'J' and resid 54 through 65 Processing helix chain 'J' and resid 82 through 88 removed outlier: 3.644A pdb=" N THR J 86 " --> pdb=" O ASP J 82 " (cutoff:3.500A) Processing helix chain 'J' and resid 105 through 110 Processing helix chain 'J' and resid 129 through 134 Processing helix chain 'J' and resid 180 through 190 Processing helix chain 'J' and resid 198 through 210 removed outlier: 3.516A pdb=" N MET J 202 " --> pdb=" O SER J 198 " (cutoff:3.500A) Processing helix chain 'J' and resid 214 through 231 Processing helix chain 'J' and resid 235 through 254 Processing helix chain 'J' and resid 286 through 294 Processing helix chain 'J' and resid 295 through 302 Processing helix chain 'J' and resid 305 through 320 Processing helix chain 'J' and resid 322 through 327 removed outlier: 3.526A pdb=" N LYS J 327 " --> pdb=" O LEU J 323 " (cutoff:3.500A) Processing helix chain 'J' and resid 329 through 333 removed outlier: 3.607A pdb=" N MET J 333 " --> pdb=" O PHE J 330 " (cutoff:3.500A) Processing helix chain 'J' and resid 335 through 339 removed outlier: 3.550A pdb=" N GLU J 339 " --> pdb=" O SER J 336 " (cutoff:3.500A) Processing helix chain 'J' and resid 340 through 352 Processing helix chain 'J' and resid 374 through 386 Processing helix chain 'J' and resid 393 through 404 Processing helix chain 'J' and resid 409 through 437 Processing helix chain 'J' and resid 458 through 462 Processing helix chain 'J' and resid 463 through 482 Processing helix chain 'J' and resid 486 through 490 removed outlier: 3.624A pdb=" N LEU J 490 " --> pdb=" O CYS J 487 " (cutoff:3.500A) Processing helix chain 'J' and resid 522 through 535 Processing helix chain 'J' and resid 554 through 567 Processing helix chain '2' and resid 167 through 172 Processing helix chain '2' and resid 173 through 190 Processing helix chain '2' and resid 198 through 210 removed outlier: 3.688A pdb=" N GLU 2 202 " --> pdb=" O ASN 2 198 " (cutoff:3.500A) Processing helix chain '2' and resid 219 through 226 Processing helix chain '2' and resid 226 through 233 Processing helix chain '2' and resid 236 through 256 removed outlier: 3.559A pdb=" N LEU 2 241 " --> pdb=" O PRO 2 237 " (cutoff:3.500A) Processing helix chain '2' and resid 278 through 282 removed outlier: 4.174A pdb=" N LEU 2 282 " --> pdb=" O LEU 2 279 " (cutoff:3.500A) Processing helix chain '2' and resid 283 through 287 Processing helix chain '2' and resid 386 through 388 No H-bonds generated for 'chain '2' and resid 386 through 388' Processing helix chain '2' and resid 408 through 416 Processing helix chain '3' and resid 10 through 24 Processing helix chain '3' and resid 31 through 42 Processing helix chain '3' and resid 51 through 58 Processing helix chain '3' and resid 58 through 68 Processing helix chain '3' and resid 68 through 88 removed outlier: 3.989A pdb=" N GLU 3 72 " --> pdb=" O ASP 3 68 " (cutoff:3.500A) Processing helix chain '3' and resid 88 through 95 removed outlier: 3.587A pdb=" N PHE 3 95 " --> pdb=" O TYR 3 91 " (cutoff:3.500A) Processing helix chain '3' and resid 117 through 121 removed outlier: 3.878A pdb=" N LEU 3 120 " --> pdb=" O THR 3 117 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N LEU 3 121 " --> pdb=" O ALA 3 118 " (cutoff:3.500A) No H-bonds generated for 'chain '3' and resid 117 through 121' Processing helix chain '3' and resid 188 through 191 Processing helix chain '3' and resid 204 through 208 removed outlier: 3.738A pdb=" N ALA 3 208 " --> pdb=" O PRO 3 205 " (cutoff:3.500A) Processing helix chain '3' and resid 222 through 226 Processing helix chain '4' and resid 158 through 172 Processing helix chain '4' and resid 192 through 204 removed outlier: 3.830A pdb=" N VAL 4 202 " --> pdb=" O GLU 4 198 " (cutoff:3.500A) Processing helix chain '4' and resid 212 through 219 Processing helix chain '4' and resid 219 through 229 Processing helix chain '4' and resid 229 through 249 removed outlier: 3.548A pdb=" N VAL 4 233 " --> pdb=" O TYR 4 229 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ILE 4 234 " --> pdb=" O PRO 4 230 " (cutoff:3.500A) Proline residue: 4 235 - end of helix Processing helix chain '4' and resid 275 through 279 Processing helix chain '4' and resid 377 through 379 No H-bonds generated for 'chain '4' and resid 377 through 379' Processing helix chain '5' and resid 28 through 43 Processing helix chain '5' and resid 55 through 67 Processing helix chain '5' and resid 75 through 82 Processing helix chain '5' and resid 82 through 88 Processing helix chain '5' and resid 92 through 112 removed outlier: 3.703A pdb=" N HIS 5 96 " --> pdb=" O GLN 5 92 " (cutoff:3.500A) Processing helix chain '5' and resid 253 through 255 No H-bonds generated for 'chain '5' and resid 253 through 255' Processing helix chain '6' and resid 23 through 39 Processing helix chain '6' and resid 46 through 57 removed outlier: 3.947A pdb=" N SER 6 50 " --> pdb=" O ASN 6 46 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N GLU 6 54 " --> pdb=" O SER 6 50 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N ARG 6 57 " --> pdb=" O GLU 6 53 " (cutoff:3.500A) Processing helix chain '6' and resid 67 through 74 Processing helix chain '6' and resid 74 through 84 Processing helix chain '6' and resid 84 through 104 Proline residue: 6 90 - end of helix Processing helix chain '7' and resid 5 through 18 Processing helix chain '7' and resid 30 through 41 Processing helix chain '7' and resid 51 through 58 Processing helix chain '7' and resid 58 through 68 removed outlier: 3.684A pdb=" N VAL 7 62 " --> pdb=" O ASP 7 58 " (cutoff:3.500A) Processing helix chain '7' and resid 70 through 84 removed outlier: 3.755A pdb=" N ASN 7 74 " --> pdb=" O ARG 7 70 " (cutoff:3.500A) Processing helix chain '7' and resid 85 through 88 removed outlier: 3.606A pdb=" N LYS 7 88 " --> pdb=" O PRO 7 85 " (cutoff:3.500A) No H-bonds generated for 'chain '7' and resid 85 through 88' Processing helix chain '7' and resid 96 through 111 Processing helix chain '7' and resid 147 through 151 Processing helix chain '7' and resid 152 through 156 removed outlier: 3.629A pdb=" N SER 7 155 " --> pdb=" O LYS 7 152 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ILE 7 156 " --> pdb=" O ALA 7 153 " (cutoff:3.500A) No H-bonds generated for 'chain '7' and resid 152 through 156' Processing helix chain '7' and resid 207 through 213 Processing helix chain '7' and resid 259 through 261 No H-bonds generated for 'chain '7' and resid 259 through 261' Processing helix chain 'L' and resid 14 through 22 removed outlier: 3.576A pdb=" N LEU L 19 " --> pdb=" O PRO L 15 " (cutoff:3.500A) Processing helix chain 'L' and resid 177 through 181 Processing helix chain 'L' and resid 184 through 197 Processing helix chain 'L' and resid 209 through 212 Processing helix chain 'L' and resid 213 through 224 removed outlier: 3.621A pdb=" N ARG L 217 " --> pdb=" O SER L 213 " (cutoff:3.500A) Processing helix chain 'L' and resid 252 through 256 removed outlier: 3.610A pdb=" N GLN L 256 " --> pdb=" O PRO L 253 " (cutoff:3.500A) Processing helix chain 'L' and resid 258 through 281 Processing helix chain 'L' and resid 302 through 306 removed outlier: 3.648A pdb=" N GLY L 305 " --> pdb=" O GLY L 302 " (cutoff:3.500A) Processing helix chain 'L' and resid 317 through 326 Processing helix chain 'L' and resid 396 through 408 removed outlier: 3.737A pdb=" N ASN L 406 " --> pdb=" O ARG L 402 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N GLU L 407 " --> pdb=" O LYS L 403 " (cutoff:3.500A) Processing helix chain 'L' and resid 413 through 417 removed outlier: 3.903A pdb=" N VAL L 417 " --> pdb=" O PRO L 414 " (cutoff:3.500A) Processing helix chain 'L' and resid 423 through 435 removed outlier: 4.026A pdb=" N THR L 427 " --> pdb=" O THR L 423 " (cutoff:3.500A) Processing helix chain 'L' and resid 494 through 509 removed outlier: 3.673A pdb=" N SER L 507 " --> pdb=" O MET L 503 " (cutoff:3.500A) Processing helix chain 'L' and resid 521 through 528 removed outlier: 5.052A pdb=" N VAL L 525 " --> pdb=" O PRO L 522 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N PHE L 526 " --> pdb=" O THR L 523 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ASN L 527 " --> pdb=" O ALA L 524 " (cutoff:3.500A) Processing helix chain 'L' and resid 548 through 556 Processing sheet with id=AA1, first strand: chain 'A' and resid 214 through 218 Processing sheet with id=AA2, first strand: chain 'A' and resid 320 through 325 removed outlier: 4.231A pdb=" N TYR A 312 " --> pdb=" O LEU A 321 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N VAL A 310 " --> pdb=" O PRO A 323 " (cutoff:3.500A) removed outlier: 4.667A pdb=" N PHE A 325 " --> pdb=" O SER A 308 " (cutoff:3.500A) removed outlier: 7.978A pdb=" N SER A 308 " --> pdb=" O PHE A 325 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N VAL A 354 " --> pdb=" O SER A 308 " (cutoff:3.500A) removed outlier: 12.954A pdb=" N SER A 378 " --> pdb=" O PHE A 420 " (cutoff:3.500A) removed outlier: 8.374A pdb=" N THR A 422 " --> pdb=" O SER A 378 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N ASP A 380 " --> pdb=" O THR A 422 " (cutoff:3.500A) removed outlier: 5.579A pdb=" N LEU A 384 " --> pdb=" O ALA A 426 " (cutoff:3.500A) removed outlier: 8.806A pdb=" N HIS A 428 " --> pdb=" O LEU A 384 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N THR A 400 " --> pdb=" O ASN A 427 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N ILE A 429 " --> pdb=" O GLU A 398 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N GLU A 398 " --> pdb=" O ILE A 429 " (cutoff:3.500A) removed outlier: 4.931A pdb=" N LYS A 431 " --> pdb=" O GLU A 396 " (cutoff:3.500A) removed outlier: 7.740A pdb=" N GLU A 396 " --> pdb=" O LYS A 431 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N THR A 362 " --> pdb=" O THR A 298 " (cutoff:3.500A) removed outlier: 4.942A pdb=" N CYS A 300 " --> pdb=" O ARG A 360 " (cutoff:3.500A) removed outlier: 7.080A pdb=" N ARG A 360 " --> pdb=" O CYS A 300 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 46 through 50 Processing sheet with id=AA4, first strand: chain 'B' and resid 110 through 111 removed outlier: 7.378A pdb=" N VAL B 111 " --> pdb=" O GLU B 128 " (cutoff:3.500A) removed outlier: 9.724A pdb=" N ILE B 130 " --> pdb=" O VAL B 111 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N SER B 200 " --> pdb=" O THR B 132 " (cutoff:3.500A) removed outlier: 4.698A pdb=" N CYS B 134 " --> pdb=" O THR B 198 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N THR B 198 " --> pdb=" O CYS B 134 " (cutoff:3.500A) removed outlier: 9.638A pdb=" N SER B 216 " --> pdb=" O THR B 258 " (cutoff:3.500A) removed outlier: 9.106A pdb=" N LEU B 260 " --> pdb=" O SER B 216 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N ASP B 218 " --> pdb=" O LEU B 260 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N ARG B 257 " --> pdb=" O LEU B 244 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 110 through 111 removed outlier: 7.378A pdb=" N VAL B 111 " --> pdb=" O GLU B 128 " (cutoff:3.500A) removed outlier: 9.724A pdb=" N ILE B 130 " --> pdb=" O VAL B 111 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLY B 129 " --> pdb=" O VAL B 235 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 153 through 158 removed outlier: 3.517A pdb=" N LYS B 153 " --> pdb=" O CYS B 148 " (cutoff:3.500A) removed outlier: 5.237A pdb=" N VAL B 141 " --> pdb=" O LYS B 194 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N LYS B 194 " --> pdb=" O VAL B 141 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ARG B 143 " --> pdb=" O THR B 192 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 251 through 252 removed outlier: 3.584A pdb=" N THR B 252 " --> pdb=" O TYR D 192 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 207 through 211 removed outlier: 6.727A pdb=" N LEU C 208 " --> pdb=" O ARG C 261 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N TYR C 263 " --> pdb=" O LEU C 208 " (cutoff:3.500A) removed outlier: 5.642A pdb=" N ILE C 210 " --> pdb=" O TYR C 263 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'C' and resid 282 through 292 removed outlier: 3.587A pdb=" N MET C 288 " --> pdb=" O GLN C 355 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N LYS C 353 " --> pdb=" O ILE C 290 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N THR C 292 " --> pdb=" O MET C 351 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N MET C 351 " --> pdb=" O THR C 292 " (cutoff:3.500A) removed outlier: 9.166A pdb=" N THR C 414 " --> pdb=" O THR C 369 " (cutoff:3.500A) removed outlier: 5.418A pdb=" N ILE C 371 " --> pdb=" O THR C 414 " (cutoff:3.500A) removed outlier: 5.919A pdb=" N HIS C 375 " --> pdb=" O VAL C 418 " (cutoff:3.500A) removed outlier: 9.147A pdb=" N HIS C 420 " --> pdb=" O HIS C 375 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N THR C 391 " --> pdb=" O ILE C 419 " (cutoff:3.500A) removed outlier: 4.878A pdb=" N TYR C 421 " --> pdb=" O ASN C 389 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N ASN C 389 " --> pdb=" O TYR C 421 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 298 through 299 Processing sheet with id=AB2, first strand: chain 'C' and resid 304 through 306 Processing sheet with id=AB3, first strand: chain 'C' and resid 408 through 409 Processing sheet with id=AB4, first strand: chain 'D' and resid 44 through 45 Processing sheet with id=AB5, first strand: chain 'D' and resid 70 through 74 Processing sheet with id=AB6, first strand: chain 'D' and resid 179 through 184 removed outlier: 6.920A pdb=" N THR D 179 " --> pdb=" O CYS D 173 " (cutoff:3.500A) removed outlier: 7.371A pdb=" N CYS D 173 " --> pdb=" O THR D 179 " (cutoff:3.500A) removed outlier: 5.046A pdb=" N GLY D 181 " --> pdb=" O ILE D 171 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N ILE D 171 " --> pdb=" O GLY D 181 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N LYS D 221 " --> pdb=" O THR D 167 " (cutoff:3.500A) removed outlier: 4.832A pdb=" N ILE D 169 " --> pdb=" O LYS D 219 " (cutoff:3.500A) removed outlier: 8.335A pdb=" N LYS D 219 " --> pdb=" O ILE D 169 " (cutoff:3.500A) removed outlier: 9.708A pdb=" N ILE D 171 " --> pdb=" O PRO D 217 " (cutoff:3.500A) removed outlier: 9.043A pdb=" N CYS D 173 " --> pdb=" O ILE D 215 " (cutoff:3.500A) removed outlier: 8.671A pdb=" N ILE D 215 " --> pdb=" O CYS D 173 " (cutoff:3.500A) removed outlier: 9.876A pdb=" N HIS D 245 " --> pdb=" O SER D 293 " (cutoff:3.500A) removed outlier: 9.459A pdb=" N ILE D 295 " --> pdb=" O HIS D 245 " (cutoff:3.500A) removed outlier: 7.207A pdb=" N GLN D 247 " --> pdb=" O ILE D 295 " (cutoff:3.500A) removed outlier: 7.391A pdb=" N VAL D 297 " --> pdb=" O GLN D 247 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N TYR D 249 " --> pdb=" O VAL D 297 " (cutoff:3.500A) removed outlier: 7.408A pdb=" N GLY D 299 " --> pdb=" O TYR D 249 " (cutoff:3.500A) removed outlier: 9.989A pdb=" N ASP D 251 " --> pdb=" O GLY D 299 " (cutoff:3.500A) removed outlier: 12.730A pdb=" N GLN D 301 " --> pdb=" O ASP D 251 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N MET D 267 " --> pdb=" O VAL D 298 " (cutoff:3.500A) removed outlier: 4.682A pdb=" N ILE D 300 " --> pdb=" O THR D 265 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N THR D 265 " --> pdb=" O ILE D 300 " (cutoff:3.500A) removed outlier: 5.002A pdb=" N VAL D 302 " --> pdb=" O ARG D 263 " (cutoff:3.500A) removed outlier: 7.402A pdb=" N ARG D 263 " --> pdb=" O VAL D 302 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N LYS D 229 " --> pdb=" O ILE D 157 " (cutoff:3.500A) removed outlier: 4.624A pdb=" N ALA D 159 " --> pdb=" O THR D 227 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N THR D 227 " --> pdb=" O ALA D 159 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 62 through 66 Processing sheet with id=AB8, first strand: chain 'E' and resid 150 through 153 removed outlier: 5.892A pdb=" N GLU E 227 " --> pdb=" O LEU E 298 " (cutoff:3.500A) removed outlier: 4.928A pdb=" N ARG E 231 " --> pdb=" O ALA E 302 " (cutoff:3.500A) removed outlier: 7.661A pdb=" N TYR E 304 " --> pdb=" O ARG E 231 " (cutoff:3.500A) removed outlier: 5.243A pdb=" N LEU E 298 " --> pdb=" O VAL E 253 " (cutoff:3.500A) removed outlier: 5.811A pdb=" N VAL E 253 " --> pdb=" O LEU E 298 " (cutoff:3.500A) removed outlier: 5.295A pdb=" N PHE E 300 " --> pdb=" O ILE E 251 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N ILE E 251 " --> pdb=" O PHE E 300 " (cutoff:3.500A) removed outlier: 5.182A pdb=" N ALA E 302 " --> pdb=" O THR E 249 " (cutoff:3.500A) removed outlier: 7.036A pdb=" N THR E 249 " --> pdb=" O ALA E 302 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N ARG E 209 " --> pdb=" O VAL E 144 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 166 through 171 removed outlier: 6.756A pdb=" N ILE E 166 " --> pdb=" O CYS E 160 " (cutoff:3.500A) removed outlier: 7.233A pdb=" N CYS E 160 " --> pdb=" O ILE E 166 " (cutoff:3.500A) removed outlier: 4.945A pdb=" N LYS E 168 " --> pdb=" O PHE E 158 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N PHE E 158 " --> pdb=" O LYS E 168 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N THR E 157 " --> pdb=" O ASP E 196 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'F' and resid 46 through 50 Processing sheet with id=AC2, first strand: chain 'F' and resid 190 through 193 removed outlier: 7.170A pdb=" N LYS F 227 " --> pdb=" O VAL F 177 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 190 through 193 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 173 through 182 current: chain 'F' and resid 294 through 303 removed outlier: 4.077A pdb=" N GLU F 294 " --> pdb=" O MET F 279 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N THR F 273 " --> pdb=" O HIS F 300 " (cutoff:3.500A) removed outlier: 4.980A pdb=" N LEU F 302 " --> pdb=" O GLY F 271 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N GLY F 271 " --> pdb=" O LEU F 302 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N LYS F 235 " --> pdb=" O THR F 167 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N VAL F 169 " --> pdb=" O GLU F 233 " (cutoff:3.500A) removed outlier: 7.020A pdb=" N GLU F 233 " --> pdb=" O VAL F 169 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'M' and resid 191 through 194 removed outlier: 4.430A pdb=" N GLU M 149 " --> pdb=" O VAL M 194 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N VAL P 23 " --> pdb=" O VAL P 50 " (cutoff:3.500A) removed outlier: 6.020A pdb=" N LEU P 20 " --> pdb=" O VAL P 73 " (cutoff:3.500A) removed outlier: 7.560A pdb=" N ILE P 75 " --> pdb=" O LEU P 20 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N LEU P 22 " --> pdb=" O ILE P 75 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N PHE P 72 " --> pdb=" O TYR P 96 " (cutoff:3.500A) removed outlier: 8.000A pdb=" N CYS P 98 " --> pdb=" O PHE P 72 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N LEU P 74 " --> pdb=" O CYS P 98 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N PHE P 95 " --> pdb=" O LYS P 116 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'M' and resid 158 through 160 Processing sheet with id=AC6, first strand: chain 'N' and resid 42 through 45 removed outlier: 3.535A pdb=" N VAL N 17 " --> pdb=" O VAL N 42 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N THR N 16 " --> pdb=" O VAL N 61 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'N' and resid 26 through 28 Processing sheet with id=AC8, first strand: chain 'N' and resid 143 through 144 Processing sheet with id=AC9, first strand: chain 'O' and resid 59 through 63 Processing sheet with id=AD1, first strand: chain 'P' and resid 271 through 277 removed outlier: 3.718A pdb=" N ALA P 272 " --> pdb=" O SER P 363 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'P' and resid 447 through 450 removed outlier: 6.592A pdb=" N LEU P 447 " --> pdb=" O VAL P 493 " (cutoff:3.500A) removed outlier: 7.924A pdb=" N ALA P 495 " --> pdb=" O LEU P 447 " (cutoff:3.500A) removed outlier: 7.100A pdb=" N CYS P 449 " --> pdb=" O ALA P 495 " (cutoff:3.500A) removed outlier: 6.122A pdb=" N VAL P 493 " --> pdb=" O ILE P 510 " (cutoff:3.500A) removed outlier: 7.795A pdb=" N ILE P 510 " --> pdb=" O VAL P 493 " (cutoff:3.500A) removed outlier: 5.363A pdb=" N ALA P 495 " --> pdb=" O VAL P 508 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N VAL P 508 " --> pdb=" O ALA P 495 " (cutoff:3.500A) removed outlier: 6.065A pdb=" N ILE P 506 " --> pdb=" O PRO P 497 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'Q' and resid 177 through 181 removed outlier: 4.876A pdb=" N ASN Q 178 " --> pdb=" O MET Q 196 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N MET Q 196 " --> pdb=" O ASN Q 178 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'R' and resid 467 through 470 removed outlier: 3.514A pdb=" N LYS R 467 " --> pdb=" O THR R 490 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N THR R 167 " --> pdb=" O GLY R 491 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ARG R 168 " --> pdb=" O TYR R 518 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N GLU R 570 " --> pdb=" O THR R 577 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'R' and resid 418 through 421 removed outlier: 3.626A pdb=" N ARG R 299 " --> pdb=" O THR R 310 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'G' and resid 191 through 194 removed outlier: 4.470A pdb=" N GLU G 149 " --> pdb=" O VAL G 194 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LEU G 177 " --> pdb=" O ILE G 148 " (cutoff:3.500A) removed outlier: 4.680A pdb=" N TYR J 47 " --> pdb=" O PHE G 176 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N VAL J 23 " --> pdb=" O VAL J 50 " (cutoff:3.500A) removed outlier: 6.024A pdb=" N LEU J 20 " --> pdb=" O VAL J 73 " (cutoff:3.500A) removed outlier: 7.558A pdb=" N ILE J 75 " --> pdb=" O LEU J 20 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N LEU J 22 " --> pdb=" O ILE J 75 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N PHE J 72 " --> pdb=" O TYR J 96 " (cutoff:3.500A) removed outlier: 7.995A pdb=" N CYS J 98 " --> pdb=" O PHE J 72 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N LEU J 74 " --> pdb=" O CYS J 98 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N PHE J 95 " --> pdb=" O LYS J 116 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'G' and resid 158 through 160 Processing sheet with id=AD8, first strand: chain 'K' and resid 218 through 219 Processing sheet with id=AD9, first strand: chain 'K' and resid 177 through 181 removed outlier: 4.857A pdb=" N ASN K 178 " --> pdb=" O MET K 196 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N MET K 196 " --> pdb=" O ASN K 178 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'H' and resid 42 through 45 removed outlier: 3.534A pdb=" N VAL H 17 " --> pdb=" O VAL H 42 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N THR H 16 " --> pdb=" O VAL H 61 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'H' and resid 26 through 28 Processing sheet with id=AE3, first strand: chain 'I' and resid 59 through 63 Processing sheet with id=AE4, first strand: chain 'J' and resid 271 through 277 removed outlier: 3.710A pdb=" N ALA J 272 " --> pdb=" O SER J 363 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'J' and resid 447 through 450 removed outlier: 6.558A pdb=" N LEU J 447 " --> pdb=" O VAL J 493 " (cutoff:3.500A) removed outlier: 7.952A pdb=" N ALA J 495 " --> pdb=" O LEU J 447 " (cutoff:3.500A) removed outlier: 7.111A pdb=" N CYS J 449 " --> pdb=" O ALA J 495 " (cutoff:3.500A) removed outlier: 6.138A pdb=" N VAL J 493 " --> pdb=" O ILE J 510 " (cutoff:3.500A) removed outlier: 7.791A pdb=" N ILE J 510 " --> pdb=" O VAL J 493 " (cutoff:3.500A) removed outlier: 5.375A pdb=" N ALA J 495 " --> pdb=" O VAL J 508 " (cutoff:3.500A) removed outlier: 7.019A pdb=" N VAL J 508 " --> pdb=" O ALA J 495 " (cutoff:3.500A) removed outlier: 6.070A pdb=" N ILE J 506 " --> pdb=" O PRO J 497 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain '2' and resid 214 through 218 Processing sheet with id=AE7, first strand: chain '2' and resid 320 through 325 removed outlier: 4.250A pdb=" N TYR 2 312 " --> pdb=" O LEU 2 321 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N VAL 2 310 " --> pdb=" O PRO 2 323 " (cutoff:3.500A) removed outlier: 4.669A pdb=" N PHE 2 325 " --> pdb=" O SER 2 308 " (cutoff:3.500A) removed outlier: 7.989A pdb=" N SER 2 308 " --> pdb=" O PHE 2 325 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N VAL 2 354 " --> pdb=" O SER 2 308 " (cutoff:3.500A) removed outlier: 12.953A pdb=" N SER 2 378 " --> pdb=" O PHE 2 420 " (cutoff:3.500A) removed outlier: 8.373A pdb=" N THR 2 422 " --> pdb=" O SER 2 378 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N ASP 2 380 " --> pdb=" O THR 2 422 " (cutoff:3.500A) removed outlier: 5.581A pdb=" N LEU 2 384 " --> pdb=" O ALA 2 426 " (cutoff:3.500A) removed outlier: 8.814A pdb=" N HIS 2 428 " --> pdb=" O LEU 2 384 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N THR 2 400 " --> pdb=" O ASN 2 427 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N ILE 2 429 " --> pdb=" O GLU 2 398 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N GLU 2 398 " --> pdb=" O ILE 2 429 " (cutoff:3.500A) removed outlier: 4.928A pdb=" N LYS 2 431 " --> pdb=" O GLU 2 396 " (cutoff:3.500A) removed outlier: 7.736A pdb=" N GLU 2 396 " --> pdb=" O LYS 2 431 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N THR 2 362 " --> pdb=" O THR 2 298 " (cutoff:3.500A) removed outlier: 4.946A pdb=" N CYS 2 300 " --> pdb=" O ARG 2 360 " (cutoff:3.500A) removed outlier: 7.075A pdb=" N ARG 2 360 " --> pdb=" O CYS 2 300 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain '3' and resid 46 through 50 Processing sheet with id=AE9, first strand: chain '3' and resid 110 through 111 removed outlier: 7.374A pdb=" N VAL 3 111 " --> pdb=" O GLU 3 128 " (cutoff:3.500A) removed outlier: 9.718A pdb=" N ILE 3 130 " --> pdb=" O VAL 3 111 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N SER 3 200 " --> pdb=" O THR 3 132 " (cutoff:3.500A) removed outlier: 4.696A pdb=" N CYS 3 134 " --> pdb=" O THR 3 198 " (cutoff:3.500A) removed outlier: 6.959A pdb=" N THR 3 198 " --> pdb=" O CYS 3 134 " (cutoff:3.500A) removed outlier: 9.641A pdb=" N SER 3 216 " --> pdb=" O THR 3 258 " (cutoff:3.500A) removed outlier: 9.110A pdb=" N LEU 3 260 " --> pdb=" O SER 3 216 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N ASP 3 218 " --> pdb=" O LEU 3 260 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N ARG 3 257 " --> pdb=" O LEU 3 244 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain '3' and resid 110 through 111 removed outlier: 7.374A pdb=" N VAL 3 111 " --> pdb=" O GLU 3 128 " (cutoff:3.500A) removed outlier: 9.718A pdb=" N ILE 3 130 " --> pdb=" O VAL 3 111 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N GLY 3 129 " --> pdb=" O VAL 3 235 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain '3' and resid 153 through 158 removed outlier: 3.517A pdb=" N LYS 3 153 " --> pdb=" O CYS 3 148 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain '3' and resid 153 through 158 removed outlier: 3.517A pdb=" N LYS 3 153 " --> pdb=" O CYS 3 148 " (cutoff:3.500A) removed outlier: 5.245A pdb=" N VAL 3 141 " --> pdb=" O LYS 3 194 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N LYS 3 194 " --> pdb=" O VAL 3 141 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ARG 3 143 " --> pdb=" O THR 3 192 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain '3' and resid 251 through 252 removed outlier: 3.592A pdb=" N THR 3 252 " --> pdb=" O TYR 5 192 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain '4' and resid 207 through 211 removed outlier: 6.726A pdb=" N LEU 4 208 " --> pdb=" O ARG 4 261 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N TYR 4 263 " --> pdb=" O LEU 4 208 " (cutoff:3.500A) removed outlier: 5.635A pdb=" N ILE 4 210 " --> pdb=" O TYR 4 263 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF5 Processing sheet with id=AF6, first strand: chain '4' and resid 282 through 292 removed outlier: 3.586A pdb=" N MET 4 288 " --> pdb=" O GLN 4 355 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N LYS 4 353 " --> pdb=" O ILE 4 290 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N THR 4 292 " --> pdb=" O MET 4 351 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N MET 4 351 " --> pdb=" O THR 4 292 " (cutoff:3.500A) removed outlier: 9.181A pdb=" N THR 4 414 " --> pdb=" O THR 4 369 " (cutoff:3.500A) removed outlier: 5.423A pdb=" N ILE 4 371 " --> pdb=" O THR 4 414 " (cutoff:3.500A) removed outlier: 5.912A pdb=" N HIS 4 375 " --> pdb=" O VAL 4 418 " (cutoff:3.500A) removed outlier: 9.134A pdb=" N HIS 4 420 " --> pdb=" O HIS 4 375 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N THR 4 391 " --> pdb=" O ILE 4 419 " (cutoff:3.500A) removed outlier: 4.875A pdb=" N TYR 4 421 " --> pdb=" O ASN 4 389 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N ASN 4 389 " --> pdb=" O TYR 4 421 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain '4' and resid 298 through 299 Processing sheet with id=AF8, first strand: chain '4' and resid 304 through 306 Processing sheet with id=AF9, first strand: chain '4' and resid 408 through 409 Processing sheet with id=AG1, first strand: chain '5' and resid 44 through 45 Processing sheet with id=AG2, first strand: chain '5' and resid 70 through 74 Processing sheet with id=AG3, first strand: chain '5' and resid 179 through 184 removed outlier: 6.919A pdb=" N THR 5 179 " --> pdb=" O CYS 5 173 " (cutoff:3.500A) removed outlier: 7.359A pdb=" N CYS 5 173 " --> pdb=" O THR 5 179 " (cutoff:3.500A) removed outlier: 5.045A pdb=" N GLY 5 181 " --> pdb=" O ILE 5 171 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N ILE 5 171 " --> pdb=" O GLY 5 181 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N LYS 5 221 " --> pdb=" O THR 5 167 " (cutoff:3.500A) removed outlier: 4.830A pdb=" N ILE 5 169 " --> pdb=" O LYS 5 219 " (cutoff:3.500A) removed outlier: 8.333A pdb=" N LYS 5 219 " --> pdb=" O ILE 5 169 " (cutoff:3.500A) removed outlier: 9.706A pdb=" N ILE 5 171 " --> pdb=" O PRO 5 217 " (cutoff:3.500A) removed outlier: 9.038A pdb=" N CYS 5 173 " --> pdb=" O ILE 5 215 " (cutoff:3.500A) removed outlier: 8.663A pdb=" N ILE 5 215 " --> pdb=" O CYS 5 173 " (cutoff:3.500A) removed outlier: 9.872A pdb=" N HIS 5 245 " --> pdb=" O SER 5 293 " (cutoff:3.500A) removed outlier: 9.452A pdb=" N ILE 5 295 " --> pdb=" O HIS 5 245 " (cutoff:3.500A) removed outlier: 7.203A pdb=" N GLN 5 247 " --> pdb=" O ILE 5 295 " (cutoff:3.500A) removed outlier: 7.389A pdb=" N VAL 5 297 " --> pdb=" O GLN 5 247 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N TYR 5 249 " --> pdb=" O VAL 5 297 " (cutoff:3.500A) removed outlier: 7.407A pdb=" N GLY 5 299 " --> pdb=" O TYR 5 249 " (cutoff:3.500A) removed outlier: 9.980A pdb=" N ASP 5 251 " --> pdb=" O GLY 5 299 " (cutoff:3.500A) removed outlier: 12.728A pdb=" N GLN 5 301 " --> pdb=" O ASP 5 251 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N MET 5 267 " --> pdb=" O VAL 5 298 " (cutoff:3.500A) removed outlier: 4.704A pdb=" N ILE 5 300 " --> pdb=" O THR 5 265 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N THR 5 265 " --> pdb=" O ILE 5 300 " (cutoff:3.500A) removed outlier: 4.996A pdb=" N VAL 5 302 " --> pdb=" O ARG 5 263 " (cutoff:3.500A) removed outlier: 7.398A pdb=" N ARG 5 263 " --> pdb=" O VAL 5 302 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N LYS 5 229 " --> pdb=" O ILE 5 157 " (cutoff:3.500A) removed outlier: 4.623A pdb=" N ALA 5 159 " --> pdb=" O THR 5 227 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N THR 5 227 " --> pdb=" O ALA 5 159 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain '6' and resid 62 through 66 Processing sheet with id=AG5, first strand: chain '6' and resid 150 through 153 removed outlier: 5.903A pdb=" N GLU 6 227 " --> pdb=" O LEU 6 298 " (cutoff:3.500A) removed outlier: 4.924A pdb=" N ARG 6 231 " --> pdb=" O ALA 6 302 " (cutoff:3.500A) removed outlier: 7.657A pdb=" N TYR 6 304 " --> pdb=" O ARG 6 231 " (cutoff:3.500A) removed outlier: 5.237A pdb=" N LEU 6 298 " --> pdb=" O VAL 6 253 " (cutoff:3.500A) removed outlier: 5.806A pdb=" N VAL 6 253 " --> pdb=" O LEU 6 298 " (cutoff:3.500A) removed outlier: 5.292A pdb=" N PHE 6 300 " --> pdb=" O ILE 6 251 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N ILE 6 251 " --> pdb=" O PHE 6 300 " (cutoff:3.500A) removed outlier: 5.179A pdb=" N ALA 6 302 " --> pdb=" O THR 6 249 " (cutoff:3.500A) removed outlier: 7.035A pdb=" N THR 6 249 " --> pdb=" O ALA 6 302 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N ARG 6 209 " --> pdb=" O VAL 6 144 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain '6' and resid 166 through 171 removed outlier: 6.767A pdb=" N ILE 6 166 " --> pdb=" O CYS 6 160 " (cutoff:3.500A) removed outlier: 7.243A pdb=" N CYS 6 160 " --> pdb=" O ILE 6 166 " (cutoff:3.500A) removed outlier: 4.949A pdb=" N LYS 6 168 " --> pdb=" O PHE 6 158 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N PHE 6 158 " --> pdb=" O LYS 6 168 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N THR 6 157 " --> pdb=" O ASP 6 196 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain '7' and resid 46 through 50 Processing sheet with id=AG8, first strand: chain '7' and resid 190 through 193 removed outlier: 7.178A pdb=" N LYS 7 227 " --> pdb=" O VAL 7 177 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain '7' and resid 190 through 193 WARNING: can't find start of bonding for strands! previous: chain '7' and resid 173 through 182 current: chain '7' and resid 294 through 303 removed outlier: 4.074A pdb=" N GLU 7 294 " --> pdb=" O MET 7 279 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N THR 7 273 " --> pdb=" O HIS 7 300 " (cutoff:3.500A) removed outlier: 4.976A pdb=" N LEU 7 302 " --> pdb=" O GLY 7 271 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N GLY 7 271 " --> pdb=" O LEU 7 302 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N LYS 7 235 " --> pdb=" O THR 7 167 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N VAL 7 169 " --> pdb=" O GLU 7 233 " (cutoff:3.500A) removed outlier: 7.022A pdb=" N GLU 7 233 " --> pdb=" O VAL 7 169 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'L' and resid 467 through 470 removed outlier: 3.511A pdb=" N LYS L 467 " --> pdb=" O THR L 490 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N THR L 167 " --> pdb=" O GLY L 491 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ARG L 168 " --> pdb=" O TYR L 518 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N GLU L 570 " --> pdb=" O THR L 577 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'L' and resid 418 through 421 removed outlier: 3.624A pdb=" N ARG L 299 " --> pdb=" O THR L 310 " (cutoff:3.500A) 2342 hydrogen bonds defined for protein. 6663 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 22.21 Time building geometry restraints manager: 22.26 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 17218 1.34 - 1.46: 10845 1.46 - 1.58: 24436 1.58 - 1.70: 0 1.70 - 1.81: 516 Bond restraints: 53015 Sorted by residual: bond pdb=" C HIS R 229 " pdb=" N PRO R 230 " ideal model delta sigma weight residual 1.333 1.356 -0.022 1.01e-02 9.80e+03 4.95e+00 bond pdb=" C HIS L 229 " pdb=" N PRO L 230 " ideal model delta sigma weight residual 1.333 1.355 -0.022 1.01e-02 9.80e+03 4.65e+00 bond pdb=" CA GLY B 107 " pdb=" C GLY B 107 " ideal model delta sigma weight residual 1.530 1.513 0.018 1.04e-02 9.25e+03 2.91e+00 bond pdb=" CA GLY 3 107 " pdb=" C GLY 3 107 " ideal model delta sigma weight residual 1.530 1.513 0.017 1.04e-02 9.25e+03 2.75e+00 bond pdb=" C ASN I 125 " pdb=" N PRO I 126 " ideal model delta sigma weight residual 1.335 1.354 -0.020 1.28e-02 6.10e+03 2.34e+00 ... (remaining 53010 not shown) Histogram of bond angle deviations from ideal: 99.52 - 106.42: 1602 106.42 - 113.31: 28694 113.31 - 120.21: 18298 120.21 - 127.11: 22479 127.11 - 134.00: 551 Bond angle restraints: 71624 Sorted by residual: angle pdb=" N SER L 11 " pdb=" CA SER L 11 " pdb=" C SER L 11 " ideal model delta sigma weight residual 114.09 108.89 5.20 1.55e+00 4.16e-01 1.13e+01 angle pdb=" N VAL L 408 " pdb=" CA VAL L 408 " pdb=" C VAL L 408 " ideal model delta sigma weight residual 106.21 109.42 -3.21 1.07e+00 8.73e-01 9.03e+00 angle pdb=" N SER R 11 " pdb=" CA SER R 11 " pdb=" C SER R 11 " ideal model delta sigma weight residual 114.09 109.46 4.63 1.55e+00 4.16e-01 8.93e+00 angle pdb=" N LYS L 409 " pdb=" CA LYS L 409 " pdb=" C LYS L 409 " ideal model delta sigma weight residual 113.18 109.45 3.73 1.33e+00 5.65e-01 7.88e+00 angle pdb=" N VAL J 115 " pdb=" CA VAL J 115 " pdb=" C VAL J 115 " ideal model delta sigma weight residual 106.55 110.52 -3.97 1.45e+00 4.76e-01 7.48e+00 ... (remaining 71619 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.56: 29628 17.56 - 35.13: 2265 35.13 - 52.69: 284 52.69 - 70.26: 328 70.26 - 87.82: 10 Dihedral angle restraints: 32515 sinusoidal: 13551 harmonic: 18964 Sorted by residual: dihedral pdb=" CA ALA K 143 " pdb=" C ALA K 143 " pdb=" N LEU K 144 " pdb=" CA LEU K 144 " ideal model delta harmonic sigma weight residual -180.00 -163.65 -16.35 0 5.00e+00 4.00e-02 1.07e+01 dihedral pdb=" CA ALA Q 143 " pdb=" C ALA Q 143 " pdb=" N LEU Q 144 " pdb=" CA LEU Q 144 " ideal model delta harmonic sigma weight residual 180.00 -163.66 -16.34 0 5.00e+00 4.00e-02 1.07e+01 dihedral pdb=" CA ASN P 484 " pdb=" CB ASN P 484 " pdb=" CG ASN P 484 " pdb=" OD1 ASN P 484 " ideal model delta sinusoidal sigma weight residual 120.00 -172.10 -67.90 2 2.00e+01 2.50e-03 1.03e+01 ... (remaining 32512 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 5255 0.031 - 0.061: 1768 0.061 - 0.092: 572 0.092 - 0.123: 352 0.123 - 0.153: 21 Chirality restraints: 7968 Sorted by residual: chirality pdb=" CA PHE K 102 " pdb=" N PHE K 102 " pdb=" C PHE K 102 " pdb=" CB PHE K 102 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.88e-01 chirality pdb=" CA PHE Q 102 " pdb=" N PHE Q 102 " pdb=" C PHE Q 102 " pdb=" CB PHE Q 102 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.85e-01 chirality pdb=" CA PRO 2 338 " pdb=" N PRO 2 338 " pdb=" C PRO 2 338 " pdb=" CB PRO 2 338 " both_signs ideal model delta sigma weight residual False 2.72 2.59 0.13 2.00e-01 2.50e+01 4.41e-01 ... (remaining 7965 not shown) Planarity restraints: 9265 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C CYS A 337 " 0.023 5.00e-02 4.00e+02 3.45e-02 1.91e+00 pdb=" N PRO A 338 " -0.060 5.00e-02 4.00e+02 pdb=" CA PRO A 338 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO A 338 " 0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C CYS 2 337 " 0.023 5.00e-02 4.00e+02 3.42e-02 1.88e+00 pdb=" N PRO 2 338 " -0.059 5.00e-02 4.00e+02 pdb=" CA PRO 2 338 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO 2 338 " 0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LYS K 140 " 0.007 2.00e-02 2.50e+03 1.36e-02 1.84e+00 pdb=" C LYS K 140 " -0.023 2.00e-02 2.50e+03 pdb=" O LYS K 140 " 0.009 2.00e-02 2.50e+03 pdb=" N SER K 141 " 0.008 2.00e-02 2.50e+03 ... (remaining 9262 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 8241 2.77 - 3.30: 48430 3.30 - 3.83: 82680 3.83 - 4.37: 97099 4.37 - 4.90: 169764 Nonbonded interactions: 406214 Sorted by model distance: nonbonded pdb=" OH TYR A 219 " pdb=" O ALA A 230 " model vdw 2.232 2.440 nonbonded pdb=" OH TYR 2 219 " pdb=" O ALA 2 230 " model vdw 2.235 2.440 nonbonded pdb=" O ASP R 395 " pdb=" OG SER R 398 " model vdw 2.248 2.440 nonbonded pdb=" O ASP L 395 " pdb=" OG SER L 398 " model vdw 2.254 2.440 nonbonded pdb=" OH TYR 6 89 " pdb=" O ILE 6 114 " model vdw 2.261 2.440 ... (remaining 406209 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 '2' selection = chain 'A' } ncs_group { reference = chain '3' selection = chain 'B' } ncs_group { reference = chain '4' selection = chain 'C' } ncs_group { reference = chain '5' selection = chain 'D' } ncs_group { reference = chain '6' selection = chain 'E' } ncs_group { reference = chain '7' selection = chain 'F' } ncs_group { reference = (chain 'G' and (resid 1 through 195 or (resid 196 and (name N or name CA or name \ C or name O or name CB or name OG )))) selection = chain 'M' } ncs_group { reference = chain 'H' selection = chain 'N' } ncs_group { reference = chain 'I' selection = chain 'O' } ncs_group { reference = chain 'J' selection = chain 'P' } ncs_group { reference = chain 'K' selection = chain 'Q' } ncs_group { reference = chain 'L' selection = chain 'R' } 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 individual isotropic 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: 9.060 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 35.260 Check model and map are aligned: 0.880 Set scattering table: 0.490 Process input model: 139.730 Find NCS groups from input model: 3.380 Set up NCS constraints: 0.520 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:3.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 192.480 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7920 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 : 0.003 0.035 53015 Z= 0.165 Angle : 0.492 7.109 71624 Z= 0.287 Chirality : 0.039 0.153 7968 Planarity : 0.003 0.035 9265 Dihedral : 13.863 87.825 20179 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 0.03 % Allowed : 7.71 % Favored : 92.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.77 (0.11), residues: 6358 helix: 2.30 (0.11), residues: 2484 sheet: -0.83 (0.15), residues: 1224 loop : -0.51 (0.12), residues: 2650 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP H 47 HIS 0.005 0.001 HIS Q 202 PHE 0.015 0.001 PHE D 225 TYR 0.011 0.001 TYR 2 181 ARG 0.004 0.000 ARG F 42 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12716 Ramachandran restraints generated. 6358 Oldfield, 0 Emsley, 6358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12716 Ramachandran restraints generated. 6358 Oldfield, 0 Emsley, 6358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1316 residues out of total 5784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 1314 time to evaluate : 6.530 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: A 177 ARG cc_start: 0.8273 (ttt90) cc_final: 0.7715 (tmt-80) REVERT: A 179 GLU cc_start: 0.8120 (tm-30) cc_final: 0.7889 (tm-30) REVERT: A 183 ARG cc_start: 0.7745 (mtp85) cc_final: 0.7266 (mtp85) REVERT: A 232 PHE cc_start: 0.8575 (m-10) cc_final: 0.8078 (m-80) REVERT: A 309 MET cc_start: 0.8113 (mtp) cc_final: 0.7583 (mtp) REVERT: A 369 LYS cc_start: 0.7831 (mttt) cc_final: 0.7580 (ttmt) REVERT: B 25 ASP cc_start: 0.8079 (m-30) cc_final: 0.7731 (m-30) REVERT: B 181 ASN cc_start: 0.8577 (m-40) cc_final: 0.8135 (t0) REVERT: B 219 ILE cc_start: 0.9021 (pt) cc_final: 0.8760 (pt) REVERT: B 222 ASP cc_start: 0.8510 (m-30) cc_final: 0.8117 (m-30) REVERT: C 251 ASP cc_start: 0.7790 (p0) cc_final: 0.7234 (t70) REVERT: C 413 LYS cc_start: 0.7951 (ptmm) cc_final: 0.7618 (ptmm) REVERT: D 244 ARG cc_start: 0.8107 (mtp180) cc_final: 0.7784 (mtt180) REVERT: D 251 ASP cc_start: 0.8583 (t70) cc_final: 0.8249 (p0) REVERT: D 263 ARG cc_start: 0.8043 (mtt90) cc_final: 0.7842 (mtp-110) REVERT: E 27 LYS cc_start: 0.9224 (tttm) cc_final: 0.8963 (mmmt) REVERT: E 103 MET cc_start: 0.8096 (tpt) cc_final: 0.7881 (tpt) REVERT: E 173 GLN cc_start: 0.8149 (mt0) cc_final: 0.7637 (mt0) REVERT: F 176 MET cc_start: 0.7768 (tpp) cc_final: 0.7108 (tpp) REVERT: F 221 LEU cc_start: 0.9042 (tp) cc_final: 0.8554 (tp) REVERT: M 47 VAL cc_start: 0.8495 (t) cc_final: 0.8286 (t) REVERT: M 96 SER cc_start: 0.8656 (m) cc_final: 0.8331 (p) REVERT: M 100 SER cc_start: 0.8221 (p) cc_final: 0.7889 (m) REVERT: M 139 ASP cc_start: 0.8518 (m-30) cc_final: 0.8132 (m-30) REVERT: M 153 LEU cc_start: 0.8796 (mt) cc_final: 0.8540 (mp) REVERT: N 39 SER cc_start: 0.8290 (m) cc_final: 0.8024 (t) REVERT: N 77 GLN cc_start: 0.9151 (tt0) cc_final: 0.8533 (tt0) REVERT: O 60 MET cc_start: 0.8876 (mtp) cc_final: 0.8667 (mtm) REVERT: O 127 GLU cc_start: 0.8248 (mm-30) cc_final: 0.7997 (mp0) REVERT: O 187 LYS cc_start: 0.8692 (mttt) cc_final: 0.8442 (mptt) REVERT: P 8 LYS cc_start: 0.8680 (mttt) cc_final: 0.8457 (mttm) REVERT: P 217 MET cc_start: 0.8469 (mtt) cc_final: 0.8148 (mtt) REVERT: P 333 MET cc_start: 0.8430 (mtp) cc_final: 0.8209 (ttm) REVERT: P 344 MET cc_start: 0.7641 (mmt) cc_final: 0.7390 (mmp) REVERT: P 551 ARG cc_start: 0.7662 (mmt90) cc_final: 0.7128 (mmt90) REVERT: Q 58 HIS cc_start: 0.7697 (m90) cc_final: 0.7286 (m170) REVERT: Q 59 MET cc_start: 0.8351 (tpp) cc_final: 0.8136 (tpp) REVERT: Q 61 GLN cc_start: 0.7775 (mm110) cc_final: 0.7483 (pm20) REVERT: Q 151 LEU cc_start: 0.8310 (mt) cc_final: 0.8035 (mp) REVERT: Q 194 ILE cc_start: 0.8699 (mm) cc_final: 0.8471 (pt) REVERT: R 459 ARG cc_start: 0.8553 (ttt180) cc_final: 0.8249 (ttt-90) REVERT: R 579 LYS cc_start: 0.8719 (tttt) cc_final: 0.8180 (tmtt) REVERT: G 96 SER cc_start: 0.8675 (m) cc_final: 0.8363 (p) REVERT: G 100 SER cc_start: 0.8266 (p) cc_final: 0.7928 (m) REVERT: G 139 ASP cc_start: 0.8552 (m-30) cc_final: 0.8157 (m-30) REVERT: G 152 CYS cc_start: 0.8697 (m) cc_final: 0.8393 (m) REVERT: G 153 LEU cc_start: 0.8764 (mt) cc_final: 0.8516 (mp) REVERT: K 59 MET cc_start: 0.8316 (tpp) cc_final: 0.8047 (tpp) REVERT: K 61 GLN cc_start: 0.7788 (mm110) cc_final: 0.7473 (pm20) REVERT: K 151 LEU cc_start: 0.8339 (mt) cc_final: 0.8057 (mp) REVERT: K 194 ILE cc_start: 0.8701 (mm) cc_final: 0.8479 (pt) REVERT: K 195 ASP cc_start: 0.8039 (m-30) cc_final: 0.7381 (m-30) REVERT: H 39 SER cc_start: 0.8269 (m) cc_final: 0.8004 (t) REVERT: I 60 MET cc_start: 0.8873 (mtp) cc_final: 0.8654 (mtm) REVERT: I 127 GLU cc_start: 0.8255 (mm-30) cc_final: 0.8000 (mp0) REVERT: I 187 LYS cc_start: 0.8680 (mttt) cc_final: 0.8454 (mptt) REVERT: J 8 LYS cc_start: 0.8705 (mttt) cc_final: 0.8417 (mttm) REVERT: J 189 TYR cc_start: 0.7270 (t80) cc_final: 0.7025 (t80) REVERT: J 217 MET cc_start: 0.8496 (mtt) cc_final: 0.8165 (mtt) REVERT: J 333 MET cc_start: 0.8462 (mtp) cc_final: 0.8229 (ttm) REVERT: J 344 MET cc_start: 0.7652 (mmt) cc_final: 0.7404 (mmp) REVERT: J 507 MET cc_start: 0.8283 (mtp) cc_final: 0.8051 (tpp) REVERT: 2 177 ARG cc_start: 0.8306 (ttt90) cc_final: 0.7724 (tmt-80) REVERT: 2 179 GLU cc_start: 0.8102 (tm-30) cc_final: 0.7886 (tm-30) REVERT: 2 183 ARG cc_start: 0.7741 (mtp85) cc_final: 0.7273 (mtp85) REVERT: 2 309 MET cc_start: 0.8217 (mtp) cc_final: 0.7761 (mtp) REVERT: 2 369 LYS cc_start: 0.7789 (mttt) cc_final: 0.7552 (ttmt) REVERT: 3 25 ASP cc_start: 0.8117 (m-30) cc_final: 0.7782 (m-30) REVERT: 3 181 ASN cc_start: 0.8624 (m-40) cc_final: 0.8152 (t0) REVERT: 3 219 ILE cc_start: 0.9053 (pt) cc_final: 0.8797 (pt) REVERT: 3 222 ASP cc_start: 0.8514 (m-30) cc_final: 0.8130 (m-30) REVERT: 4 251 ASP cc_start: 0.7715 (p0) cc_final: 0.7200 (t0) REVERT: 4 357 SER cc_start: 0.5613 (m) cc_final: 0.5327 (p) REVERT: 4 413 LYS cc_start: 0.7978 (ptmm) cc_final: 0.7647 (ptmm) REVERT: 5 244 ARG cc_start: 0.8071 (mtp180) cc_final: 0.7742 (mtt180) REVERT: 5 251 ASP cc_start: 0.8581 (t70) cc_final: 0.8250 (p0) REVERT: 6 27 LYS cc_start: 0.9215 (tttm) cc_final: 0.8992 (mmmt) REVERT: 6 103 MET cc_start: 0.8104 (tpt) cc_final: 0.7877 (tpt) REVERT: 7 176 MET cc_start: 0.7733 (tpp) cc_final: 0.7101 (tpp) REVERT: 7 221 LEU cc_start: 0.9046 (tp) cc_final: 0.8569 (tp) REVERT: L 459 ARG cc_start: 0.8565 (ttt180) cc_final: 0.8261 (ttt-90) REVERT: L 579 LYS cc_start: 0.8718 (tttt) cc_final: 0.8179 (tmtt) outliers start: 2 outliers final: 0 residues processed: 1316 average time/residue: 0.7164 time to fit residues: 1473.3122 Evaluate side-chains 768 residues out of total 5784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 768 time to evaluate : 6.782 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 634 random chunks: chunk 535 optimal weight: 1.9990 chunk 480 optimal weight: 2.9990 chunk 266 optimal weight: 0.9980 chunk 164 optimal weight: 5.9990 chunk 324 optimal weight: 0.9980 chunk 256 optimal weight: 0.7980 chunk 496 optimal weight: 2.9990 chunk 192 optimal weight: 8.9990 chunk 302 optimal weight: 5.9990 chunk 369 optimal weight: 0.9980 chunk 575 optimal weight: 0.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 211 ASN ** A 405 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 214 HIS D 31 GLN E 150 HIS F 44 GLN M 116 GLN M 172 ASN O 134 GLN P 262 ASN P 484 ASN Q 64 HIS ** Q 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 178 ASN R 208 GLN G 116 GLN G 172 ASN ** K 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 64 HIS ** K 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 178 ASN I 99 ASN I 134 GLN J 262 ASN J 484 ASN 2 191 HIS 2 211 ASN ** 2 405 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 214 HIS 5 31 GLN 5 145 GLN 6 150 HIS L 208 GLN Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7963 moved from start: 0.2162 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 53015 Z= 0.193 Angle : 0.527 8.178 71624 Z= 0.273 Chirality : 0.041 0.185 7968 Planarity : 0.004 0.071 9265 Dihedral : 3.731 58.129 7047 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 1.42 % Allowed : 11.74 % Favored : 86.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.88 (0.11), residues: 6358 helix: 2.31 (0.10), residues: 2510 sheet: -0.72 (0.15), residues: 1226 loop : -0.42 (0.12), residues: 2622 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP K 32 HIS 0.009 0.001 HIS 7 94 PHE 0.032 0.001 PHE 2 346 TYR 0.034 0.001 TYR G 156 ARG 0.007 0.000 ARG 4 400 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12716 Ramachandran restraints generated. 6358 Oldfield, 0 Emsley, 6358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12716 Ramachandran restraints generated. 6358 Oldfield, 0 Emsley, 6358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 894 residues out of total 5784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 812 time to evaluate : 6.137 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 177 ARG cc_start: 0.8214 (ttt90) cc_final: 0.7601 (tmt-80) REVERT: A 186 ASN cc_start: 0.9129 (t0) cc_final: 0.8918 (t0) REVERT: A 309 MET cc_start: 0.8094 (mtp) cc_final: 0.7576 (mtp) REVERT: A 321 LEU cc_start: 0.7445 (mp) cc_final: 0.7036 (tp) REVERT: B 138 ARG cc_start: 0.8021 (mtt180) cc_final: 0.7724 (mtm-85) REVERT: B 181 ASN cc_start: 0.8436 (m-40) cc_final: 0.8113 (t0) REVERT: B 219 ILE cc_start: 0.8840 (pt) cc_final: 0.8582 (pt) REVERT: B 222 ASP cc_start: 0.8292 (m-30) cc_final: 0.8008 (m-30) REVERT: C 251 ASP cc_start: 0.7807 (p0) cc_final: 0.7195 (t70) REVERT: C 288 MET cc_start: 0.6755 (tmm) cc_final: 0.6391 (tmm) REVERT: C 353 LYS cc_start: 0.9151 (mtpt) cc_final: 0.8884 (mmmt) REVERT: C 369 THR cc_start: 0.8610 (m) cc_final: 0.8154 (m) REVERT: D 31 GLN cc_start: 0.8029 (tt0) cc_final: 0.7808 (tt0) REVERT: D 186 ARG cc_start: 0.8246 (mtp85) cc_final: 0.8044 (mtm-85) REVERT: D 244 ARG cc_start: 0.8061 (mtp180) cc_final: 0.7807 (mtt180) REVERT: D 251 ASP cc_start: 0.8626 (t70) cc_final: 0.8372 (p0) REVERT: D 292 SER cc_start: 0.8642 (m) cc_final: 0.8372 (p) REVERT: E 28 CYS cc_start: 0.7992 (m) cc_final: 0.7587 (p) REVERT: E 42 LYS cc_start: 0.7092 (mtmm) cc_final: 0.6228 (tmmt) REVERT: E 161 MET cc_start: 0.6108 (mmm) cc_final: 0.5469 (mtt) REVERT: F 176 MET cc_start: 0.7525 (tpp) cc_final: 0.7072 (tpp) REVERT: M 42 GLN cc_start: 0.7702 (tt0) cc_final: 0.7444 (tt0) REVERT: M 46 ASP cc_start: 0.8526 (m-30) cc_final: 0.7953 (m-30) REVERT: M 96 SER cc_start: 0.8670 (m) cc_final: 0.8272 (p) REVERT: M 100 SER cc_start: 0.8238 (p) cc_final: 0.7996 (m) REVERT: M 116 GLN cc_start: 0.7804 (tp40) cc_final: 0.7566 (tp-100) REVERT: M 131 GLU cc_start: 0.8631 (mt-10) cc_final: 0.8286 (mp0) REVERT: M 152 CYS cc_start: 0.8849 (m) cc_final: 0.8614 (m) REVERT: N 39 SER cc_start: 0.8323 (m) cc_final: 0.8052 (t) REVERT: N 81 GLU cc_start: 0.7913 (mp0) cc_final: 0.7414 (mp0) REVERT: O 22 GLU cc_start: 0.8157 (mt-10) cc_final: 0.7716 (mt-10) REVERT: O 60 MET cc_start: 0.8934 (mtp) cc_final: 0.8699 (mtm) REVERT: O 127 GLU cc_start: 0.8309 (mm-30) cc_final: 0.8010 (mp0) REVERT: O 187 LYS cc_start: 0.8700 (mttt) cc_final: 0.8419 (mptt) REVERT: P 8 LYS cc_start: 0.8715 (mttt) cc_final: 0.8444 (mttm) REVERT: P 70 ARG cc_start: 0.7640 (ttm170) cc_final: 0.7336 (tpp-160) REVERT: P 192 TYR cc_start: 0.7395 (m-10) cc_final: 0.7029 (m-10) REVERT: P 344 MET cc_start: 0.7727 (mmt) cc_final: 0.7435 (mmp) REVERT: Q 27 LYS cc_start: 0.7475 (mttt) cc_final: 0.7275 (mtmt) REVERT: Q 58 HIS cc_start: 0.7800 (m90) cc_final: 0.7516 (m170) REVERT: Q 59 MET cc_start: 0.8365 (tpp) cc_final: 0.8147 (tpp) REVERT: Q 61 GLN cc_start: 0.7773 (mm110) cc_final: 0.7409 (pm20) REVERT: Q 116 GLU cc_start: 0.7694 (mt-10) cc_final: 0.6894 (mp0) REVERT: Q 209 ILE cc_start: 0.8512 (OUTLIER) cc_final: 0.8203 (pp) REVERT: R 400 LYS cc_start: 0.7745 (OUTLIER) cc_final: 0.7531 (tppt) REVERT: R 564 LEU cc_start: 0.8381 (mm) cc_final: 0.8148 (mm) REVERT: R 579 LYS cc_start: 0.8731 (tttt) cc_final: 0.8152 (tmtt) REVERT: G 46 ASP cc_start: 0.8641 (m-30) cc_final: 0.8119 (m-30) REVERT: G 51 LYS cc_start: 0.8467 (tppt) cc_final: 0.8228 (pttt) REVERT: G 96 SER cc_start: 0.8642 (m) cc_final: 0.8312 (p) REVERT: G 100 SER cc_start: 0.8236 (p) cc_final: 0.7979 (m) REVERT: G 116 GLN cc_start: 0.7784 (tp40) cc_final: 0.7554 (tp-100) REVERT: G 131 GLU cc_start: 0.8619 (mt-10) cc_final: 0.8232 (mp0) REVERT: G 152 CYS cc_start: 0.8753 (m) cc_final: 0.8503 (m) REVERT: G 156 TYR cc_start: 0.7818 (t80) cc_final: 0.7610 (t80) REVERT: K 27 LYS cc_start: 0.7499 (mttt) cc_final: 0.7297 (mtmt) REVERT: K 116 GLU cc_start: 0.7792 (mt-10) cc_final: 0.6997 (mp0) REVERT: K 178 ASN cc_start: 0.7821 (m110) cc_final: 0.7189 (m-40) REVERT: K 195 ASP cc_start: 0.7765 (m-30) cc_final: 0.7360 (m-30) REVERT: K 209 ILE cc_start: 0.8518 (OUTLIER) cc_final: 0.8209 (pp) REVERT: H 39 SER cc_start: 0.8381 (m) cc_final: 0.8113 (t) REVERT: H 81 GLU cc_start: 0.7976 (mp0) cc_final: 0.7522 (mp0) REVERT: I 22 GLU cc_start: 0.8169 (mt-10) cc_final: 0.7717 (mt-10) REVERT: I 59 LYS cc_start: 0.9035 (mtmm) cc_final: 0.8811 (mttm) REVERT: I 60 MET cc_start: 0.8923 (mtp) cc_final: 0.8673 (mtm) REVERT: I 127 GLU cc_start: 0.8314 (mm-30) cc_final: 0.8013 (mp0) REVERT: J 70 ARG cc_start: 0.7619 (ttm170) cc_final: 0.7181 (tpp80) REVERT: J 192 TYR cc_start: 0.7429 (m-10) cc_final: 0.7104 (m-10) REVERT: J 344 MET cc_start: 0.7744 (mmt) cc_final: 0.7428 (mmp) REVERT: 2 177 ARG cc_start: 0.8238 (ttt90) cc_final: 0.7617 (tmt-80) REVERT: 2 200 PHE cc_start: 0.7423 (m-80) cc_final: 0.7216 (m-80) REVERT: 2 309 MET cc_start: 0.8293 (mtp) cc_final: 0.7799 (mtp) REVERT: 2 321 LEU cc_start: 0.7458 (mp) cc_final: 0.7071 (tp) REVERT: 3 96 GLU cc_start: 0.8190 (tp30) cc_final: 0.7810 (tm-30) REVERT: 3 138 ARG cc_start: 0.8021 (mtt180) cc_final: 0.7780 (mtm-85) REVERT: 3 143 ARG cc_start: 0.7958 (ttp-170) cc_final: 0.7722 (ttp-170) REVERT: 3 181 ASN cc_start: 0.8447 (m-40) cc_final: 0.8114 (t0) REVERT: 3 219 ILE cc_start: 0.8845 (pt) cc_final: 0.8584 (pt) REVERT: 3 222 ASP cc_start: 0.8308 (m-30) cc_final: 0.8043 (m-30) REVERT: 4 197 LEU cc_start: 0.8222 (mp) cc_final: 0.8021 (mt) REVERT: 4 239 MET cc_start: 0.6035 (OUTLIER) cc_final: 0.5525 (ppp) REVERT: 4 251 ASP cc_start: 0.7709 (p0) cc_final: 0.7130 (t0) REVERT: 4 288 MET cc_start: 0.6812 (tmm) cc_final: 0.6442 (tmm) REVERT: 4 353 LYS cc_start: 0.9168 (mtpt) cc_final: 0.8908 (mmmt) REVERT: 4 357 SER cc_start: 0.6022 (m) cc_final: 0.5680 (p) REVERT: 4 369 THR cc_start: 0.8565 (m) cc_final: 0.8154 (m) REVERT: 5 142 LYS cc_start: 0.8562 (mttp) cc_final: 0.8295 (mtpp) REVERT: 5 244 ARG cc_start: 0.8070 (mtp180) cc_final: 0.7809 (mtt180) REVERT: 5 251 ASP cc_start: 0.8633 (t70) cc_final: 0.8379 (p0) REVERT: 5 292 SER cc_start: 0.8650 (m) cc_final: 0.8374 (p) REVERT: 6 28 CYS cc_start: 0.7978 (m) cc_final: 0.7553 (p) REVERT: 6 42 LYS cc_start: 0.7011 (mtmm) cc_final: 0.6121 (tmmt) REVERT: 6 161 MET cc_start: 0.6092 (mmm) cc_final: 0.5451 (mtt) REVERT: 6 199 LYS cc_start: 0.7394 (tptm) cc_final: 0.7099 (pttt) REVERT: 7 176 MET cc_start: 0.7448 (tpp) cc_final: 0.7020 (tpp) REVERT: 7 181 TYR cc_start: 0.8219 (m-80) cc_final: 0.7930 (m-80) REVERT: L 400 LYS cc_start: 0.7715 (OUTLIER) cc_final: 0.7514 (tppt) REVERT: L 564 LEU cc_start: 0.8340 (mm) cc_final: 0.8126 (mm) REVERT: L 579 LYS cc_start: 0.8730 (tttt) cc_final: 0.8152 (tmtt) outliers start: 82 outliers final: 51 residues processed: 868 average time/residue: 0.6569 time to fit residues: 926.0370 Evaluate side-chains 750 residues out of total 5784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 694 time to evaluate : 5.999 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 86 SER Chi-restraints excluded: chain C residue 202 VAL Chi-restraints excluded: chain D residue 53 THR Chi-restraints excluded: chain D residue 60 LEU Chi-restraints excluded: chain D residue 173 CYS Chi-restraints excluded: chain D residue 182 ASN Chi-restraints excluded: chain D residue 199 ASN Chi-restraints excluded: chain E residue 47 LEU Chi-restraints excluded: chain F residue 165 ILE Chi-restraints excluded: chain F residue 190 THR Chi-restraints excluded: chain F residue 236 ILE Chi-restraints excluded: chain M residue 127 SER Chi-restraints excluded: chain N residue 42 VAL Chi-restraints excluded: chain N residue 120 THR Chi-restraints excluded: chain O residue 24 LEU Chi-restraints excluded: chain O residue 192 THR Chi-restraints excluded: chain P residue 118 LEU Chi-restraints excluded: chain P residue 232 ASP Chi-restraints excluded: chain P residue 237 MET Chi-restraints excluded: chain P residue 376 ASP Chi-restraints excluded: chain P residue 480 CYS Chi-restraints excluded: chain P residue 481 SER Chi-restraints excluded: chain Q residue 178 ASN Chi-restraints excluded: chain Q residue 209 ILE Chi-restraints excluded: chain R residue 307 ASP Chi-restraints excluded: chain R residue 400 LYS Chi-restraints excluded: chain R residue 405 LYS Chi-restraints excluded: chain G residue 127 SER Chi-restraints excluded: chain K residue 173 VAL Chi-restraints excluded: chain K residue 209 ILE Chi-restraints excluded: chain H residue 42 VAL Chi-restraints excluded: chain H residue 120 THR Chi-restraints excluded: chain I residue 24 LEU Chi-restraints excluded: chain I residue 192 THR Chi-restraints excluded: chain J residue 118 LEU Chi-restraints excluded: chain J residue 232 ASP Chi-restraints excluded: chain J residue 237 MET Chi-restraints excluded: chain J residue 376 ASP Chi-restraints excluded: chain J residue 405 LEU Chi-restraints excluded: chain J residue 457 ASP Chi-restraints excluded: chain J residue 480 CYS Chi-restraints excluded: chain J residue 481 SER Chi-restraints excluded: chain 3 residue 86 SER Chi-restraints excluded: chain 4 residue 239 MET Chi-restraints excluded: chain 4 residue 270 ASN Chi-restraints excluded: chain 5 residue 53 THR Chi-restraints excluded: chain 5 residue 60 LEU Chi-restraints excluded: chain 5 residue 182 ASN Chi-restraints excluded: chain 5 residue 199 ASN Chi-restraints excluded: chain 6 residue 47 LEU Chi-restraints excluded: chain 7 residue 62 VAL Chi-restraints excluded: chain 7 residue 190 THR Chi-restraints excluded: chain 7 residue 236 ILE Chi-restraints excluded: chain L residue 296 VAL Chi-restraints excluded: chain L residue 307 ASP Chi-restraints excluded: chain L residue 400 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 634 random chunks: chunk 319 optimal weight: 7.9990 chunk 178 optimal weight: 2.9990 chunk 479 optimal weight: 2.9990 chunk 392 optimal weight: 4.9990 chunk 158 optimal weight: 9.9990 chunk 576 optimal weight: 4.9990 chunk 623 optimal weight: 0.9980 chunk 513 optimal weight: 30.0000 chunk 571 optimal weight: 5.9990 chunk 196 optimal weight: 2.9990 chunk 462 optimal weight: 10.0000 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 191 HIS C 355 GLN M 172 ASN O 134 GLN P 328 GLN ** Q 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 229 HIS R 293 GLN G 172 ASN ** K 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 54 GLN I 134 GLN J 484 ASN 4 355 GLN 7 104 HIS 7 300 HIS L 229 HIS L 293 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8052 moved from start: 0.2760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.065 53015 Z= 0.429 Angle : 0.630 10.350 71624 Z= 0.326 Chirality : 0.045 0.186 7968 Planarity : 0.005 0.059 9265 Dihedral : 4.235 58.770 7047 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 2.47 % Allowed : 13.17 % Favored : 84.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.42 (0.11), residues: 6358 helix: 1.85 (0.10), residues: 2506 sheet: -0.83 (0.15), residues: 1178 loop : -0.67 (0.12), residues: 2674 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP H 47 HIS 0.009 0.001 HIS 7 94 PHE 0.028 0.002 PHE D 225 TYR 0.036 0.002 TYR M 156 ARG 0.008 0.001 ARG G 65 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12716 Ramachandran restraints generated. 6358 Oldfield, 0 Emsley, 6358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12716 Ramachandran restraints generated. 6358 Oldfield, 0 Emsley, 6358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 835 residues out of total 5784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 143 poor density : 692 time to evaluate : 6.141 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: A 200 PHE cc_start: 0.7703 (m-80) cc_final: 0.7492 (m-80) REVERT: A 309 MET cc_start: 0.8436 (mtp) cc_final: 0.7904 (mtp) REVERT: A 312 TYR cc_start: 0.7419 (m-80) cc_final: 0.7159 (m-80) REVERT: A 321 LEU cc_start: 0.7320 (mp) cc_final: 0.6882 (tp) REVERT: A 405 ASN cc_start: 0.8133 (m-40) cc_final: 0.7760 (m110) REVERT: B 70 PHE cc_start: 0.8221 (t80) cc_final: 0.7859 (m-80) REVERT: B 222 ASP cc_start: 0.8422 (m-30) cc_final: 0.8084 (m-30) REVERT: C 251 ASP cc_start: 0.7825 (p0) cc_final: 0.7134 (t70) REVERT: C 288 MET cc_start: 0.6980 (tmm) cc_final: 0.6702 (tmm) REVERT: C 369 THR cc_start: 0.8543 (OUTLIER) cc_final: 0.8184 (m) REVERT: C 377 ASP cc_start: 0.8540 (OUTLIER) cc_final: 0.8323 (p0) REVERT: D 186 ARG cc_start: 0.8262 (mtp85) cc_final: 0.8026 (mtm-85) REVERT: D 244 ARG cc_start: 0.8073 (mtp180) cc_final: 0.7860 (mtt180) REVERT: D 292 SER cc_start: 0.8701 (m) cc_final: 0.8473 (p) REVERT: E 161 MET cc_start: 0.6129 (mmm) cc_final: 0.5496 (mtt) REVERT: F 131 ARG cc_start: 0.7898 (mtt180) cc_final: 0.7511 (mtt-85) REVERT: F 176 MET cc_start: 0.7404 (tpp) cc_final: 0.7109 (tpp) REVERT: M 51 LYS cc_start: 0.8624 (tppt) cc_final: 0.8270 (pttt) REVERT: M 96 SER cc_start: 0.8683 (m) cc_final: 0.8275 (p) REVERT: M 100 SER cc_start: 0.8277 (p) cc_final: 0.8042 (m) REVERT: M 103 ARG cc_start: 0.8230 (ttm110) cc_final: 0.7982 (ttm110) REVERT: M 111 MET cc_start: 0.8383 (mmm) cc_final: 0.7826 (tmm) REVERT: M 131 GLU cc_start: 0.8615 (mt-10) cc_final: 0.8285 (mp0) REVERT: N 39 SER cc_start: 0.8218 (m) cc_final: 0.7951 (t) REVERT: N 77 GLN cc_start: 0.8932 (tp40) cc_final: 0.8337 (tp40) REVERT: N 81 GLU cc_start: 0.7832 (mp0) cc_final: 0.7311 (mp0) REVERT: O 22 GLU cc_start: 0.8259 (mt-10) cc_final: 0.7833 (mt-10) REVERT: O 106 MET cc_start: 0.8775 (mmm) cc_final: 0.8222 (mmm) REVERT: O 127 GLU cc_start: 0.8536 (mm-30) cc_final: 0.8127 (mp0) REVERT: P 70 ARG cc_start: 0.7635 (ttm170) cc_final: 0.7009 (tpp80) REVERT: P 192 TYR cc_start: 0.7518 (m-10) cc_final: 0.7230 (m-10) REVERT: P 344 MET cc_start: 0.7762 (mmt) cc_final: 0.7432 (mmp) REVERT: Q 58 HIS cc_start: 0.7957 (m90) cc_final: 0.7633 (m170) REVERT: Q 178 ASN cc_start: 0.8241 (OUTLIER) cc_final: 0.7885 (m-40) REVERT: Q 195 ASP cc_start: 0.8544 (p0) cc_final: 0.8076 (m-30) REVERT: R 322 GLU cc_start: 0.7647 (mm-30) cc_final: 0.7433 (mm-30) REVERT: R 400 LYS cc_start: 0.7814 (OUTLIER) cc_final: 0.7518 (tppt) REVERT: R 579 LYS cc_start: 0.8755 (tttt) cc_final: 0.8144 (tmtt) REVERT: G 42 GLN cc_start: 0.7115 (tt0) cc_final: 0.6716 (tt0) REVERT: G 46 ASP cc_start: 0.8308 (m-30) cc_final: 0.7785 (m-30) REVERT: G 51 LYS cc_start: 0.8488 (tppt) cc_final: 0.8220 (pttt) REVERT: G 96 SER cc_start: 0.8673 (m) cc_final: 0.8324 (p) REVERT: G 98 LEU cc_start: 0.8783 (mt) cc_final: 0.8526 (mt) REVERT: G 100 SER cc_start: 0.8289 (p) cc_final: 0.7941 (m) REVERT: G 103 ARG cc_start: 0.8223 (ttm110) cc_final: 0.7762 (ttm110) REVERT: G 111 MET cc_start: 0.8295 (mmm) cc_final: 0.7717 (tmm) REVERT: G 131 GLU cc_start: 0.8629 (mt-10) cc_final: 0.8215 (mp0) REVERT: G 156 TYR cc_start: 0.7863 (t80) cc_final: 0.7575 (t80) REVERT: K 178 ASN cc_start: 0.8092 (m110) cc_final: 0.7532 (m-40) REVERT: K 195 ASP cc_start: 0.7978 (m-30) cc_final: 0.7578 (m-30) REVERT: H 33 LEU cc_start: 0.7407 (OUTLIER) cc_final: 0.6996 (mm) REVERT: H 39 SER cc_start: 0.8292 (m) cc_final: 0.7998 (t) REVERT: H 77 GLN cc_start: 0.8923 (tp40) cc_final: 0.8704 (tp-100) REVERT: I 22 GLU cc_start: 0.8256 (mt-10) cc_final: 0.7829 (mt-10) REVERT: I 59 LYS cc_start: 0.9018 (mtmm) cc_final: 0.8716 (mttm) REVERT: I 106 MET cc_start: 0.8779 (mmm) cc_final: 0.8221 (mmm) REVERT: I 127 GLU cc_start: 0.8542 (mm-30) cc_final: 0.8129 (mp0) REVERT: J 70 ARG cc_start: 0.7659 (ttm170) cc_final: 0.7174 (tpp80) REVERT: J 192 TYR cc_start: 0.7408 (m-80) cc_final: 0.7100 (m-10) REVERT: J 217 MET cc_start: 0.8371 (mtt) cc_final: 0.7486 (mtm) REVERT: J 344 MET cc_start: 0.7779 (mmt) cc_final: 0.7431 (mmp) REVERT: 2 309 MET cc_start: 0.8516 (mtp) cc_final: 0.7969 (mtp) REVERT: 2 321 LEU cc_start: 0.7369 (mp) cc_final: 0.6905 (tp) REVERT: 2 405 ASN cc_start: 0.8008 (m-40) cc_final: 0.7671 (m110) REVERT: 3 70 PHE cc_start: 0.8223 (t80) cc_final: 0.7871 (m-80) REVERT: 3 143 ARG cc_start: 0.7903 (ttp-170) cc_final: 0.7699 (ttp-170) REVERT: 3 222 ASP cc_start: 0.8435 (m-30) cc_final: 0.8124 (m-30) REVERT: 4 197 LEU cc_start: 0.8195 (mp) cc_final: 0.7972 (mt) REVERT: 4 251 ASP cc_start: 0.7817 (p0) cc_final: 0.7103 (t70) REVERT: 4 288 MET cc_start: 0.6999 (tmm) cc_final: 0.6395 (tmm) REVERT: 4 357 SER cc_start: 0.6184 (m) cc_final: 0.5734 (p) REVERT: 4 361 MET cc_start: 0.6693 (mmp) cc_final: 0.6470 (mmp) REVERT: 4 369 THR cc_start: 0.8513 (OUTLIER) cc_final: 0.8176 (m) REVERT: 4 377 ASP cc_start: 0.8589 (OUTLIER) cc_final: 0.8378 (p0) REVERT: 5 142 LYS cc_start: 0.8728 (mttp) cc_final: 0.8518 (mtpp) REVERT: 5 244 ARG cc_start: 0.8086 (mtp180) cc_final: 0.7850 (mtt180) REVERT: 5 292 SER cc_start: 0.8714 (m) cc_final: 0.8482 (p) REVERT: 6 161 MET cc_start: 0.6163 (mmm) cc_final: 0.5522 (mtt) REVERT: 6 219 ARG cc_start: 0.6997 (mmp-170) cc_final: 0.6398 (mmp80) REVERT: 7 107 MET cc_start: 0.7007 (ttp) cc_final: 0.6753 (tmm) REVERT: 7 176 MET cc_start: 0.7361 (tpp) cc_final: 0.7084 (tpp) REVERT: L 322 GLU cc_start: 0.7793 (mm-30) cc_final: 0.7542 (mm-30) REVERT: L 400 LYS cc_start: 0.7814 (OUTLIER) cc_final: 0.7540 (tppt) REVERT: L 579 LYS cc_start: 0.8759 (tttt) cc_final: 0.8147 (tmtt) outliers start: 143 outliers final: 86 residues processed: 799 average time/residue: 0.6436 time to fit residues: 841.3518 Evaluate side-chains 724 residues out of total 5784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 630 time to evaluate : 5.946 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 192 VAL Chi-restraints excluded: chain A residue 276 VAL Chi-restraints excluded: chain B residue 86 SER Chi-restraints excluded: chain B residue 219 ILE Chi-restraints excluded: chain C residue 270 ASN Chi-restraints excluded: chain C residue 369 THR Chi-restraints excluded: chain C residue 377 ASP Chi-restraints excluded: chain D residue 53 THR Chi-restraints excluded: chain D residue 60 LEU Chi-restraints excluded: chain D residue 121 THR Chi-restraints excluded: chain D residue 173 CYS Chi-restraints excluded: chain D residue 182 ASN Chi-restraints excluded: chain D residue 199 ASN Chi-restraints excluded: chain E residue 47 LEU Chi-restraints excluded: chain E residue 62 THR Chi-restraints excluded: chain E residue 244 CYS Chi-restraints excluded: chain E residue 308 THR Chi-restraints excluded: chain F residue 98 LEU Chi-restraints excluded: chain F residue 162 VAL Chi-restraints excluded: chain F residue 165 ILE Chi-restraints excluded: chain F residue 190 THR Chi-restraints excluded: chain F residue 236 ILE Chi-restraints excluded: chain F residue 243 VAL Chi-restraints excluded: chain M residue 108 THR Chi-restraints excluded: chain M residue 127 SER Chi-restraints excluded: chain N residue 24 ASP Chi-restraints excluded: chain N residue 26 VAL Chi-restraints excluded: chain N residue 42 VAL Chi-restraints excluded: chain N residue 44 VAL Chi-restraints excluded: chain N residue 105 ASP Chi-restraints excluded: chain N residue 120 THR Chi-restraints excluded: chain N residue 134 SER Chi-restraints excluded: chain O residue 24 LEU Chi-restraints excluded: chain O residue 78 LEU Chi-restraints excluded: chain O residue 192 THR Chi-restraints excluded: chain P residue 118 LEU Chi-restraints excluded: chain P residue 232 ASP Chi-restraints excluded: chain P residue 429 GLN Chi-restraints excluded: chain P residue 457 ASP Chi-restraints excluded: chain P residue 481 SER Chi-restraints excluded: chain P residue 510 ILE Chi-restraints excluded: chain Q residue 178 ASN Chi-restraints excluded: chain Q residue 218 VAL Chi-restraints excluded: chain R residue 307 ASP Chi-restraints excluded: chain R residue 400 LYS Chi-restraints excluded: chain G residue 108 THR Chi-restraints excluded: chain G residue 127 SER Chi-restraints excluded: chain K residue 173 VAL Chi-restraints excluded: chain K residue 218 VAL Chi-restraints excluded: chain H residue 24 ASP Chi-restraints excluded: chain H residue 26 VAL Chi-restraints excluded: chain H residue 33 LEU Chi-restraints excluded: chain H residue 42 VAL Chi-restraints excluded: chain H residue 44 VAL Chi-restraints excluded: chain H residue 105 ASP Chi-restraints excluded: chain H residue 120 THR Chi-restraints excluded: chain H residue 134 SER Chi-restraints excluded: chain I residue 24 LEU Chi-restraints excluded: chain I residue 78 LEU Chi-restraints excluded: chain I residue 192 THR Chi-restraints excluded: chain J residue 118 LEU Chi-restraints excluded: chain J residue 232 ASP Chi-restraints excluded: chain J residue 237 MET Chi-restraints excluded: chain J residue 405 LEU Chi-restraints excluded: chain J residue 429 GLN Chi-restraints excluded: chain J residue 457 ASP Chi-restraints excluded: chain J residue 481 SER Chi-restraints excluded: chain J residue 510 ILE Chi-restraints excluded: chain 2 residue 192 VAL Chi-restraints excluded: chain 2 residue 276 VAL Chi-restraints excluded: chain 3 residue 86 SER Chi-restraints excluded: chain 3 residue 219 ILE Chi-restraints excluded: chain 4 residue 202 VAL Chi-restraints excluded: chain 4 residue 270 ASN Chi-restraints excluded: chain 4 residue 369 THR Chi-restraints excluded: chain 4 residue 377 ASP Chi-restraints excluded: chain 5 residue 53 THR Chi-restraints excluded: chain 5 residue 60 LEU Chi-restraints excluded: chain 5 residue 121 THR Chi-restraints excluded: chain 5 residue 182 ASN Chi-restraints excluded: chain 5 residue 199 ASN Chi-restraints excluded: chain 6 residue 47 LEU Chi-restraints excluded: chain 6 residue 59 GLU Chi-restraints excluded: chain 6 residue 62 THR Chi-restraints excluded: chain 6 residue 244 CYS Chi-restraints excluded: chain 6 residue 308 THR Chi-restraints excluded: chain 7 residue 62 VAL Chi-restraints excluded: chain 7 residue 162 VAL Chi-restraints excluded: chain 7 residue 165 ILE Chi-restraints excluded: chain 7 residue 190 THR Chi-restraints excluded: chain 7 residue 236 ILE Chi-restraints excluded: chain 7 residue 243 VAL Chi-restraints excluded: chain L residue 307 ASP Chi-restraints excluded: chain L residue 400 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 634 random chunks: chunk 569 optimal weight: 9.9990 chunk 433 optimal weight: 4.9990 chunk 299 optimal weight: 0.0980 chunk 63 optimal weight: 5.9990 chunk 275 optimal weight: 0.7980 chunk 387 optimal weight: 0.7980 chunk 578 optimal weight: 7.9990 chunk 612 optimal weight: 0.7980 chunk 302 optimal weight: 0.9990 chunk 548 optimal weight: 2.9990 chunk 165 optimal weight: 8.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 406 ASN E 61 ASN F 104 HIS F 300 HIS N 54 GLN N 102 HIS O 134 GLN P 328 GLN P 484 ASN R 229 HIS R 293 GLN ** K 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 54 GLN H 102 HIS I 134 GLN J 484 ASN 2 406 ASN 7 300 HIS L 229 HIS L 293 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7987 moved from start: 0.2861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 53015 Z= 0.152 Angle : 0.491 8.344 71624 Z= 0.253 Chirality : 0.040 0.156 7968 Planarity : 0.004 0.042 9265 Dihedral : 3.895 54.751 7047 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 1.59 % Allowed : 14.78 % Favored : 83.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.78 (0.11), residues: 6358 helix: 2.21 (0.10), residues: 2492 sheet: -0.62 (0.15), residues: 1182 loop : -0.54 (0.12), residues: 2684 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP K 32 HIS 0.004 0.001 HIS 7 94 PHE 0.022 0.001 PHE 2 346 TYR 0.026 0.001 TYR M 156 ARG 0.006 0.000 ARG 5 186 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12716 Ramachandran restraints generated. 6358 Oldfield, 0 Emsley, 6358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12716 Ramachandran restraints generated. 6358 Oldfield, 0 Emsley, 6358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 767 residues out of total 5784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 675 time to evaluate : 5.864 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: A 309 MET cc_start: 0.8416 (mtp) cc_final: 0.7895 (mtp) REVERT: A 321 LEU cc_start: 0.7126 (mp) cc_final: 0.6700 (tp) REVERT: B 65 MET cc_start: 0.9190 (tpt) cc_final: 0.8862 (tpt) REVERT: B 138 ARG cc_start: 0.8009 (mtt180) cc_final: 0.7744 (mtm-85) REVERT: B 219 ILE cc_start: 0.8879 (OUTLIER) cc_final: 0.8575 (pt) REVERT: B 222 ASP cc_start: 0.8280 (m-30) cc_final: 0.7978 (m-30) REVERT: C 251 ASP cc_start: 0.7740 (p0) cc_final: 0.7058 (t70) REVERT: C 288 MET cc_start: 0.7015 (tmm) cc_final: 0.6727 (tmm) REVERT: C 361 MET cc_start: 0.7040 (tpp) cc_final: 0.6797 (tpp) REVERT: D 186 ARG cc_start: 0.8266 (mtp85) cc_final: 0.8041 (mtm-85) REVERT: D 244 ARG cc_start: 0.8112 (mtp180) cc_final: 0.7828 (mtt180) REVERT: E 161 MET cc_start: 0.6078 (mmm) cc_final: 0.5506 (mtt) REVERT: F 108 MET cc_start: 0.7036 (mmm) cc_final: 0.6797 (mmt) REVERT: F 176 MET cc_start: 0.7294 (tpp) cc_final: 0.7074 (tpp) REVERT: M 43 ASN cc_start: 0.8168 (t0) cc_final: 0.7831 (m-40) REVERT: M 51 LYS cc_start: 0.8581 (tppt) cc_final: 0.8246 (pttm) REVERT: M 96 SER cc_start: 0.8604 (m) cc_final: 0.8233 (p) REVERT: M 103 ARG cc_start: 0.8128 (ttm110) cc_final: 0.7610 (ttm110) REVERT: M 111 MET cc_start: 0.8342 (mmm) cc_final: 0.7770 (tmm) REVERT: M 116 GLN cc_start: 0.8109 (tp-100) cc_final: 0.7849 (tp40) REVERT: M 131 GLU cc_start: 0.8648 (mt-10) cc_final: 0.8274 (mp0) REVERT: N 33 LEU cc_start: 0.7419 (OUTLIER) cc_final: 0.7042 (mm) REVERT: N 39 SER cc_start: 0.8335 (m) cc_final: 0.8075 (t) REVERT: N 77 GLN cc_start: 0.8904 (tp40) cc_final: 0.8588 (tp-100) REVERT: N 81 GLU cc_start: 0.7800 (mp0) cc_final: 0.7470 (mp0) REVERT: O 22 GLU cc_start: 0.8211 (mt-10) cc_final: 0.7818 (mp0) REVERT: O 127 GLU cc_start: 0.8298 (mm-30) cc_final: 0.8018 (mp0) REVERT: P 70 ARG cc_start: 0.7686 (ttm170) cc_final: 0.7482 (tpp-160) REVERT: P 192 TYR cc_start: 0.7473 (m-80) cc_final: 0.7181 (m-10) REVERT: P 344 MET cc_start: 0.7668 (mmt) cc_final: 0.7358 (mmp) REVERT: Q 58 HIS cc_start: 0.7880 (m90) cc_final: 0.7517 (m170) REVERT: Q 61 GLN cc_start: 0.7797 (mm110) cc_final: 0.7455 (pm20) REVERT: Q 195 ASP cc_start: 0.8545 (p0) cc_final: 0.8075 (m-30) REVERT: Q 209 ILE cc_start: 0.8481 (OUTLIER) cc_final: 0.8077 (pp) REVERT: R 400 LYS cc_start: 0.7847 (OUTLIER) cc_final: 0.7575 (tppt) REVERT: R 579 LYS cc_start: 0.8733 (tttt) cc_final: 0.8119 (tmtt) REVERT: G 42 GLN cc_start: 0.7184 (tt0) cc_final: 0.6969 (tt0) REVERT: G 51 LYS cc_start: 0.8533 (tppt) cc_final: 0.8233 (pttm) REVERT: G 96 SER cc_start: 0.8647 (m) cc_final: 0.8288 (p) REVERT: G 103 ARG cc_start: 0.8099 (ttm110) cc_final: 0.7843 (ttm110) REVERT: G 111 MET cc_start: 0.8350 (mmm) cc_final: 0.7814 (tmm) REVERT: G 116 GLN cc_start: 0.7936 (tp-100) cc_final: 0.7732 (tp40) REVERT: G 131 GLU cc_start: 0.8662 (mt-10) cc_final: 0.8106 (mp0) REVERT: K 178 ASN cc_start: 0.8152 (m110) cc_final: 0.7582 (m-40) REVERT: K 195 ASP cc_start: 0.8014 (m-30) cc_final: 0.7631 (m-30) REVERT: K 209 ILE cc_start: 0.8488 (OUTLIER) cc_final: 0.8083 (pp) REVERT: H 33 LEU cc_start: 0.7448 (OUTLIER) cc_final: 0.7146 (mm) REVERT: H 39 SER cc_start: 0.8256 (m) cc_final: 0.8024 (t) REVERT: H 77 GLN cc_start: 0.9011 (tp40) cc_final: 0.8686 (tp-100) REVERT: H 81 GLU cc_start: 0.7969 (mp0) cc_final: 0.7638 (mp0) REVERT: I 22 GLU cc_start: 0.8208 (mt-10) cc_final: 0.7816 (mp0) REVERT: I 59 LYS cc_start: 0.9031 (mtmm) cc_final: 0.8775 (mttm) REVERT: I 127 GLU cc_start: 0.8302 (mm-30) cc_final: 0.8023 (mp0) REVERT: J 9 GLU cc_start: 0.8104 (tp30) cc_final: 0.7755 (tp30) REVERT: J 70 ARG cc_start: 0.7757 (ttm170) cc_final: 0.7541 (tpp80) REVERT: J 192 TYR cc_start: 0.7382 (m-80) cc_final: 0.7093 (m-10) REVERT: J 344 MET cc_start: 0.7688 (mmt) cc_final: 0.7364 (mmp) REVERT: 2 309 MET cc_start: 0.8497 (mtp) cc_final: 0.7982 (mtp) REVERT: 2 321 LEU cc_start: 0.7138 (mp) cc_final: 0.6768 (tp) REVERT: 3 65 MET cc_start: 0.9186 (tpt) cc_final: 0.8881 (tpt) REVERT: 3 138 ARG cc_start: 0.8002 (mtt180) cc_final: 0.7745 (mtm-85) REVERT: 3 219 ILE cc_start: 0.8859 (OUTLIER) cc_final: 0.8557 (pt) REVERT: 3 222 ASP cc_start: 0.8302 (m-30) cc_final: 0.8004 (m-30) REVERT: 4 197 LEU cc_start: 0.8250 (mp) cc_final: 0.7983 (mt) REVERT: 4 251 ASP cc_start: 0.7768 (p0) cc_final: 0.7092 (t70) REVERT: 4 288 MET cc_start: 0.7039 (tmm) cc_final: 0.6718 (tmm) REVERT: 4 357 SER cc_start: 0.6264 (m) cc_final: 0.5860 (p) REVERT: 5 142 LYS cc_start: 0.8622 (mttp) cc_final: 0.8308 (mtpp) REVERT: 5 244 ARG cc_start: 0.8096 (mtp180) cc_final: 0.7815 (mtt180) REVERT: 5 292 SER cc_start: 0.8742 (m) cc_final: 0.8539 (p) REVERT: 6 161 MET cc_start: 0.6081 (mmm) cc_final: 0.5501 (mtt) REVERT: L 400 LYS cc_start: 0.7816 (OUTLIER) cc_final: 0.7539 (tppt) REVERT: L 579 LYS cc_start: 0.8704 (tttt) cc_final: 0.8075 (tmtt) outliers start: 92 outliers final: 51 residues processed: 745 average time/residue: 0.6486 time to fit residues: 793.0879 Evaluate side-chains 678 residues out of total 5784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 619 time to evaluate : 5.999 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 207 MET Chi-restraints excluded: chain A residue 228 VAL Chi-restraints excluded: chain A residue 417 PHE Chi-restraints excluded: chain B residue 219 ILE Chi-restraints excluded: chain C residue 215 LEU Chi-restraints excluded: chain C residue 270 ASN Chi-restraints excluded: chain C residue 399 ILE Chi-restraints excluded: chain D residue 121 THR Chi-restraints excluded: chain D residue 199 ASN Chi-restraints excluded: chain D residue 225 PHE Chi-restraints excluded: chain E residue 47 LEU Chi-restraints excluded: chain F residue 53 ASP Chi-restraints excluded: chain F residue 98 LEU Chi-restraints excluded: chain F residue 165 ILE Chi-restraints excluded: chain F residue 190 THR Chi-restraints excluded: chain F residue 236 ILE Chi-restraints excluded: chain N residue 24 ASP Chi-restraints excluded: chain N residue 33 LEU Chi-restraints excluded: chain N residue 42 VAL Chi-restraints excluded: chain O residue 24 LEU Chi-restraints excluded: chain P residue 232 ASP Chi-restraints excluded: chain P residue 237 MET Chi-restraints excluded: chain P residue 376 ASP Chi-restraints excluded: chain P residue 411 ASP Chi-restraints excluded: chain P residue 510 ILE Chi-restraints excluded: chain Q residue 209 ILE Chi-restraints excluded: chain R residue 296 VAL Chi-restraints excluded: chain R residue 307 ASP Chi-restraints excluded: chain R residue 400 LYS Chi-restraints excluded: chain R residue 541 ASP Chi-restraints excluded: chain R residue 573 ASP Chi-restraints excluded: chain K residue 209 ILE Chi-restraints excluded: chain H residue 24 ASP Chi-restraints excluded: chain H residue 33 LEU Chi-restraints excluded: chain H residue 42 VAL Chi-restraints excluded: chain I residue 24 LEU Chi-restraints excluded: chain J residue 232 ASP Chi-restraints excluded: chain J residue 237 MET Chi-restraints excluded: chain J residue 376 ASP Chi-restraints excluded: chain J residue 405 LEU Chi-restraints excluded: chain J residue 411 ASP Chi-restraints excluded: chain 2 residue 207 MET Chi-restraints excluded: chain 2 residue 228 VAL Chi-restraints excluded: chain 2 residue 285 LEU Chi-restraints excluded: chain 3 residue 219 ILE Chi-restraints excluded: chain 4 residue 270 ASN Chi-restraints excluded: chain 4 residue 399 ILE Chi-restraints excluded: chain 5 residue 121 THR Chi-restraints excluded: chain 5 residue 199 ASN Chi-restraints excluded: chain 5 residue 225 PHE Chi-restraints excluded: chain 6 residue 47 LEU Chi-restraints excluded: chain 6 residue 62 THR Chi-restraints excluded: chain 7 residue 53 ASP Chi-restraints excluded: chain 7 residue 62 VAL Chi-restraints excluded: chain 7 residue 98 LEU Chi-restraints excluded: chain 7 residue 165 ILE Chi-restraints excluded: chain 7 residue 190 THR Chi-restraints excluded: chain L residue 307 ASP Chi-restraints excluded: chain L residue 400 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 634 random chunks: chunk 510 optimal weight: 9.9990 chunk 347 optimal weight: 5.9990 chunk 8 optimal weight: 2.9990 chunk 456 optimal weight: 6.9990 chunk 252 optimal weight: 6.9990 chunk 522 optimal weight: 1.9990 chunk 423 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 312 optimal weight: 4.9990 chunk 550 optimal weight: 2.9990 chunk 154 optimal weight: 7.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 300 HIS P 484 ASN R 229 HIS R 293 GLN R 543 GLN J 328 GLN J 484 ASN 4 214 HIS 7 300 HIS L 229 HIS L 293 GLN L 543 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8072 moved from start: 0.3149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.064 53015 Z= 0.454 Angle : 0.633 10.676 71624 Z= 0.327 Chirality : 0.046 0.189 7968 Planarity : 0.005 0.054 9265 Dihedral : 4.310 55.739 7047 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 3.06 % Allowed : 14.54 % Favored : 82.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.32 (0.11), residues: 6358 helix: 1.76 (0.10), residues: 2516 sheet: -0.85 (0.15), residues: 1180 loop : -0.74 (0.12), residues: 2662 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP H 47 HIS 0.011 0.001 HIS F 94 PHE 0.024 0.002 PHE 5 225 TYR 0.035 0.002 TYR G 156 ARG 0.013 0.001 ARG 2 183 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12716 Ramachandran restraints generated. 6358 Oldfield, 0 Emsley, 6358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12716 Ramachandran restraints generated. 6358 Oldfield, 0 Emsley, 6358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 796 residues out of total 5784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 177 poor density : 619 time to evaluate : 6.004 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: A 309 MET cc_start: 0.8611 (mtp) cc_final: 0.8056 (mtp) REVERT: B 29 GLN cc_start: 0.8419 (OUTLIER) cc_final: 0.8026 (mt0) REVERT: B 65 MET cc_start: 0.9239 (tpt) cc_final: 0.9025 (tpt) REVERT: B 70 PHE cc_start: 0.8254 (t80) cc_final: 0.7834 (m-80) REVERT: B 222 ASP cc_start: 0.8352 (m-30) cc_final: 0.8120 (m-30) REVERT: C 251 ASP cc_start: 0.7784 (p0) cc_final: 0.7100 (t70) REVERT: D 186 ARG cc_start: 0.8310 (mtp85) cc_final: 0.8038 (mtm-85) REVERT: D 244 ARG cc_start: 0.8081 (mtp180) cc_final: 0.7870 (mtt180) REVERT: F 176 MET cc_start: 0.7430 (tpp) cc_final: 0.7190 (tpp) REVERT: M 43 ASN cc_start: 0.8111 (t0) cc_final: 0.7823 (m-40) REVERT: M 51 LYS cc_start: 0.8605 (tppt) cc_final: 0.8278 (pttm) REVERT: M 96 SER cc_start: 0.8681 (m) cc_final: 0.8266 (p) REVERT: M 103 ARG cc_start: 0.8049 (ttm110) cc_final: 0.7797 (ttm110) REVERT: M 111 MET cc_start: 0.8423 (mmm) cc_final: 0.7795 (tmm) REVERT: M 131 GLU cc_start: 0.8646 (mt-10) cc_final: 0.8229 (mp0) REVERT: N 39 SER cc_start: 0.8291 (m) cc_final: 0.8002 (t) REVERT: N 77 GLN cc_start: 0.8902 (tp40) cc_final: 0.8518 (tp-100) REVERT: N 81 GLU cc_start: 0.7828 (mp0) cc_final: 0.7447 (mp0) REVERT: O 106 MET cc_start: 0.8815 (mmm) cc_final: 0.8245 (mmm) REVERT: O 127 GLU cc_start: 0.8584 (mm-30) cc_final: 0.8110 (mp0) REVERT: P 70 ARG cc_start: 0.7716 (ttm170) cc_final: 0.7451 (tpp-160) REVERT: P 192 TYR cc_start: 0.7592 (m-80) cc_final: 0.7326 (m-10) REVERT: P 344 MET cc_start: 0.7843 (mmt) cc_final: 0.7465 (mmp) REVERT: Q 58 HIS cc_start: 0.7939 (m90) cc_final: 0.7641 (m170) REVERT: Q 195 ASP cc_start: 0.8631 (p0) cc_final: 0.8031 (m-30) REVERT: Q 218 VAL cc_start: 0.8346 (OUTLIER) cc_final: 0.8044 (m) REVERT: R 400 LYS cc_start: 0.7807 (OUTLIER) cc_final: 0.7497 (tppt) REVERT: R 579 LYS cc_start: 0.8772 (tttt) cc_final: 0.8161 (tmtt) REVERT: G 51 LYS cc_start: 0.8580 (tppt) cc_final: 0.8256 (pttm) REVERT: G 96 SER cc_start: 0.8683 (m) cc_final: 0.8272 (p) REVERT: G 111 MET cc_start: 0.8403 (mmm) cc_final: 0.7809 (tmm) REVERT: G 131 GLU cc_start: 0.8649 (mt-10) cc_final: 0.8223 (mp0) REVERT: K 178 ASN cc_start: 0.8146 (m110) cc_final: 0.7637 (m-40) REVERT: K 195 ASP cc_start: 0.8064 (m-30) cc_final: 0.7715 (m-30) REVERT: K 218 VAL cc_start: 0.8426 (OUTLIER) cc_final: 0.8120 (m) REVERT: H 33 LEU cc_start: 0.7620 (OUTLIER) cc_final: 0.7296 (mm) REVERT: H 39 SER cc_start: 0.8256 (m) cc_final: 0.7972 (t) REVERT: H 77 GLN cc_start: 0.9018 (tp40) cc_final: 0.8688 (tp-100) REVERT: I 22 GLU cc_start: 0.8284 (mt-10) cc_final: 0.7842 (mp0) REVERT: I 106 MET cc_start: 0.8819 (mmm) cc_final: 0.8239 (mmm) REVERT: I 127 GLU cc_start: 0.8601 (mm-30) cc_final: 0.8132 (mp0) REVERT: J 70 ARG cc_start: 0.7743 (ttm170) cc_final: 0.7070 (tpp80) REVERT: J 102 ARG cc_start: 0.7372 (mmp80) cc_final: 0.7067 (mmp80) REVERT: J 183 ARG cc_start: 0.6436 (mmm-85) cc_final: 0.5913 (mtm180) REVERT: J 192 TYR cc_start: 0.7366 (m-80) cc_final: 0.7082 (m-10) REVERT: J 344 MET cc_start: 0.7820 (mmt) cc_final: 0.7449 (mmp) REVERT: 2 309 MET cc_start: 0.8633 (mtp) cc_final: 0.8106 (mtp) REVERT: 2 321 LEU cc_start: 0.7216 (mp) cc_final: 0.7002 (tp) REVERT: 2 351 GLU cc_start: 0.8127 (OUTLIER) cc_final: 0.7869 (mp0) REVERT: 3 25 ASP cc_start: 0.8304 (t0) cc_final: 0.8088 (t0) REVERT: 3 65 MET cc_start: 0.9227 (tpt) cc_final: 0.8991 (tpt) REVERT: 3 70 PHE cc_start: 0.8259 (t80) cc_final: 0.7849 (m-80) REVERT: 3 141 VAL cc_start: 0.8665 (t) cc_final: 0.8442 (p) REVERT: 3 222 ASP cc_start: 0.8341 (m-30) cc_final: 0.8105 (m-30) REVERT: 4 197 LEU cc_start: 0.8180 (mp) cc_final: 0.7899 (mt) REVERT: 4 251 ASP cc_start: 0.7755 (p0) cc_final: 0.7136 (t70) REVERT: 4 288 MET cc_start: 0.7030 (tmm) cc_final: 0.6807 (tmm) REVERT: 4 381 LYS cc_start: 0.8212 (mmmt) cc_final: 0.7865 (mmtm) REVERT: 5 142 LYS cc_start: 0.8758 (mttp) cc_final: 0.8522 (mtpp) REVERT: 5 244 ARG cc_start: 0.8065 (mtp180) cc_final: 0.7858 (mtt180) REVERT: L 400 LYS cc_start: 0.7787 (OUTLIER) cc_final: 0.7477 (tppt) REVERT: L 579 LYS cc_start: 0.8772 (tttt) cc_final: 0.8159 (tmtt) outliers start: 177 outliers final: 119 residues processed: 753 average time/residue: 0.6205 time to fit residues: 771.4124 Evaluate side-chains 708 residues out of total 5784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 126 poor density : 582 time to evaluate : 5.940 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 192 VAL Chi-restraints excluded: chain A residue 207 MET Chi-restraints excluded: chain A residue 228 VAL Chi-restraints excluded: chain A residue 276 VAL Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain B residue 29 GLN Chi-restraints excluded: chain B residue 86 SER Chi-restraints excluded: chain B residue 219 ILE Chi-restraints excluded: chain C residue 202 VAL Chi-restraints excluded: chain C residue 215 LEU Chi-restraints excluded: chain C residue 270 ASN Chi-restraints excluded: chain C residue 399 ILE Chi-restraints excluded: chain D residue 53 THR Chi-restraints excluded: chain D residue 60 LEU Chi-restraints excluded: chain D residue 121 THR Chi-restraints excluded: chain D residue 155 ILE Chi-restraints excluded: chain D residue 173 CYS Chi-restraints excluded: chain D residue 182 ASN Chi-restraints excluded: chain D residue 199 ASN Chi-restraints excluded: chain D residue 225 PHE Chi-restraints excluded: chain E residue 47 LEU Chi-restraints excluded: chain E residue 62 THR Chi-restraints excluded: chain E residue 237 SER Chi-restraints excluded: chain E residue 308 THR Chi-restraints excluded: chain F residue 53 ASP Chi-restraints excluded: chain F residue 98 LEU Chi-restraints excluded: chain F residue 162 VAL Chi-restraints excluded: chain F residue 165 ILE Chi-restraints excluded: chain F residue 184 ASP Chi-restraints excluded: chain F residue 190 THR Chi-restraints excluded: chain F residue 236 ILE Chi-restraints excluded: chain F residue 243 VAL Chi-restraints excluded: chain M residue 108 THR Chi-restraints excluded: chain M residue 128 LEU Chi-restraints excluded: chain M residue 136 ILE Chi-restraints excluded: chain N residue 24 ASP Chi-restraints excluded: chain N residue 26 VAL Chi-restraints excluded: chain N residue 42 VAL Chi-restraints excluded: chain N residue 44 VAL Chi-restraints excluded: chain N residue 105 ASP Chi-restraints excluded: chain N residue 120 THR Chi-restraints excluded: chain O residue 24 LEU Chi-restraints excluded: chain O residue 78 LEU Chi-restraints excluded: chain O residue 131 THR Chi-restraints excluded: chain O residue 192 THR Chi-restraints excluded: chain P residue 118 LEU Chi-restraints excluded: chain P residue 232 ASP Chi-restraints excluded: chain P residue 237 MET Chi-restraints excluded: chain P residue 388 THR Chi-restraints excluded: chain P residue 411 ASP Chi-restraints excluded: chain P residue 429 GLN Chi-restraints excluded: chain P residue 457 ASP Chi-restraints excluded: chain P residue 481 SER Chi-restraints excluded: chain P residue 510 ILE Chi-restraints excluded: chain Q residue 46 SER Chi-restraints excluded: chain Q residue 186 THR Chi-restraints excluded: chain Q residue 218 VAL Chi-restraints excluded: chain R residue 307 ASP Chi-restraints excluded: chain R residue 400 LYS Chi-restraints excluded: chain R residue 573 ASP Chi-restraints excluded: chain G residue 108 THR Chi-restraints excluded: chain G residue 128 LEU Chi-restraints excluded: chain G residue 136 ILE Chi-restraints excluded: chain K residue 46 SER Chi-restraints excluded: chain K residue 173 VAL Chi-restraints excluded: chain K residue 186 THR Chi-restraints excluded: chain K residue 218 VAL Chi-restraints excluded: chain H residue 24 ASP Chi-restraints excluded: chain H residue 26 VAL Chi-restraints excluded: chain H residue 33 LEU Chi-restraints excluded: chain H residue 42 VAL Chi-restraints excluded: chain H residue 44 VAL Chi-restraints excluded: chain H residue 105 ASP Chi-restraints excluded: chain H residue 120 THR Chi-restraints excluded: chain I residue 24 LEU Chi-restraints excluded: chain I residue 78 LEU Chi-restraints excluded: chain I residue 131 THR Chi-restraints excluded: chain I residue 192 THR Chi-restraints excluded: chain J residue 118 LEU Chi-restraints excluded: chain J residue 232 ASP Chi-restraints excluded: chain J residue 237 MET Chi-restraints excluded: chain J residue 388 THR Chi-restraints excluded: chain J residue 405 LEU Chi-restraints excluded: chain J residue 411 ASP Chi-restraints excluded: chain J residue 429 GLN Chi-restraints excluded: chain J residue 457 ASP Chi-restraints excluded: chain J residue 481 SER Chi-restraints excluded: chain J residue 510 ILE Chi-restraints excluded: chain 2 residue 192 VAL Chi-restraints excluded: chain 2 residue 207 MET Chi-restraints excluded: chain 2 residue 228 VAL Chi-restraints excluded: chain 2 residue 276 VAL Chi-restraints excluded: chain 2 residue 287 LEU Chi-restraints excluded: chain 2 residue 351 GLU Chi-restraints excluded: chain 3 residue 86 SER Chi-restraints excluded: chain 3 residue 181 ASN Chi-restraints excluded: chain 3 residue 219 ILE Chi-restraints excluded: chain 4 residue 270 ASN Chi-restraints excluded: chain 4 residue 399 ILE Chi-restraints excluded: chain 4 residue 424 THR Chi-restraints excluded: chain 5 residue 53 THR Chi-restraints excluded: chain 5 residue 60 LEU Chi-restraints excluded: chain 5 residue 121 THR Chi-restraints excluded: chain 5 residue 155 ILE Chi-restraints excluded: chain 5 residue 173 CYS Chi-restraints excluded: chain 5 residue 182 ASN Chi-restraints excluded: chain 5 residue 199 ASN Chi-restraints excluded: chain 5 residue 225 PHE Chi-restraints excluded: chain 6 residue 47 LEU Chi-restraints excluded: chain 6 residue 62 THR Chi-restraints excluded: chain 6 residue 109 ASN Chi-restraints excluded: chain 6 residue 308 THR Chi-restraints excluded: chain 7 residue 53 ASP Chi-restraints excluded: chain 7 residue 62 VAL Chi-restraints excluded: chain 7 residue 66 CYS Chi-restraints excluded: chain 7 residue 98 LEU Chi-restraints excluded: chain 7 residue 162 VAL Chi-restraints excluded: chain 7 residue 165 ILE Chi-restraints excluded: chain 7 residue 184 ASP Chi-restraints excluded: chain 7 residue 190 THR Chi-restraints excluded: chain 7 residue 221 LEU Chi-restraints excluded: chain 7 residue 236 ILE Chi-restraints excluded: chain 7 residue 243 VAL Chi-restraints excluded: chain L residue 307 ASP Chi-restraints excluded: chain L residue 400 LYS Chi-restraints excluded: chain L residue 573 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 634 random chunks: chunk 206 optimal weight: 0.8980 chunk 551 optimal weight: 9.9990 chunk 121 optimal weight: 9.9990 chunk 359 optimal weight: 0.9990 chunk 151 optimal weight: 0.9980 chunk 613 optimal weight: 0.7980 chunk 509 optimal weight: 5.9990 chunk 284 optimal weight: 2.9990 chunk 51 optimal weight: 0.7980 chunk 202 optimal weight: 0.6980 chunk 322 optimal weight: 0.6980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 29 GLN D 145 GLN D 231 GLN F 300 HIS M 172 ASN R 229 HIS J 484 ASN 7 300 HIS L 229 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8007 moved from start: 0.3173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 53015 Z= 0.161 Angle : 0.499 9.613 71624 Z= 0.257 Chirality : 0.040 0.177 7968 Planarity : 0.004 0.050 9265 Dihedral : 3.970 51.929 7047 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 1.80 % Allowed : 15.96 % Favored : 82.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.70 (0.11), residues: 6358 helix: 2.20 (0.10), residues: 2488 sheet: -0.68 (0.15), residues: 1202 loop : -0.63 (0.12), residues: 2668 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP K 32 HIS 0.005 0.001 HIS L 229 PHE 0.019 0.001 PHE 2 346 TYR 0.031 0.001 TYR G 156 ARG 0.007 0.000 ARG 5 186 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12716 Ramachandran restraints generated. 6358 Oldfield, 0 Emsley, 6358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12716 Ramachandran restraints generated. 6358 Oldfield, 0 Emsley, 6358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 725 residues out of total 5784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 621 time to evaluate : 6.036 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 309 MET cc_start: 0.8526 (mtp) cc_final: 0.7998 (mtp) REVERT: A 321 LEU cc_start: 0.6913 (mp) cc_final: 0.6696 (tp) REVERT: B 65 MET cc_start: 0.9229 (tpt) cc_final: 0.8961 (tpt) REVERT: B 219 ILE cc_start: 0.8856 (OUTLIER) cc_final: 0.8546 (pt) REVERT: B 222 ASP cc_start: 0.8322 (m-30) cc_final: 0.8017 (m-30) REVERT: C 251 ASP cc_start: 0.7783 (p0) cc_final: 0.7083 (t70) REVERT: D 186 ARG cc_start: 0.8296 (mtp85) cc_final: 0.8053 (mtm-85) REVERT: D 244 ARG cc_start: 0.8085 (mtp180) cc_final: 0.7872 (mtt180) REVERT: E 161 MET cc_start: 0.6044 (mmm) cc_final: 0.5256 (mtt) REVERT: F 302 LEU cc_start: 0.8578 (OUTLIER) cc_final: 0.8273 (tt) REVERT: M 43 ASN cc_start: 0.8107 (t0) cc_final: 0.7832 (m110) REVERT: M 51 LYS cc_start: 0.8569 (tppt) cc_final: 0.8267 (pttm) REVERT: M 96 SER cc_start: 0.8683 (m) cc_final: 0.8257 (p) REVERT: M 111 MET cc_start: 0.8420 (mmm) cc_final: 0.8131 (tmm) REVERT: M 131 GLU cc_start: 0.8659 (mt-10) cc_final: 0.8217 (mp0) REVERT: N 39 SER cc_start: 0.8310 (m) cc_final: 0.8055 (t) REVERT: N 77 GLN cc_start: 0.8897 (tp40) cc_final: 0.8618 (tp-100) REVERT: N 81 GLU cc_start: 0.7771 (mp0) cc_final: 0.7510 (mp0) REVERT: O 22 GLU cc_start: 0.8219 (mt-10) cc_final: 0.7839 (mp0) REVERT: O 127 GLU cc_start: 0.8334 (mm-30) cc_final: 0.8040 (mp0) REVERT: P 192 TYR cc_start: 0.7514 (m-80) cc_final: 0.7269 (m-10) REVERT: P 201 MET cc_start: 0.7517 (mmm) cc_final: 0.7257 (mtp) REVERT: P 344 MET cc_start: 0.7738 (mmt) cc_final: 0.7408 (mmp) REVERT: Q 58 HIS cc_start: 0.7888 (m90) cc_final: 0.7583 (m170) REVERT: Q 187 ASP cc_start: 0.8437 (t70) cc_final: 0.8171 (t0) REVERT: Q 195 ASP cc_start: 0.8631 (p0) cc_final: 0.8134 (m-30) REVERT: Q 218 VAL cc_start: 0.8411 (OUTLIER) cc_final: 0.8171 (m) REVERT: R 400 LYS cc_start: 0.7837 (OUTLIER) cc_final: 0.7533 (tppt) REVERT: R 579 LYS cc_start: 0.8705 (tttt) cc_final: 0.8030 (tmtt) REVERT: G 51 LYS cc_start: 0.8531 (tppt) cc_final: 0.8228 (pttm) REVERT: G 96 SER cc_start: 0.8695 (m) cc_final: 0.8275 (p) REVERT: G 111 MET cc_start: 0.8398 (mmm) cc_final: 0.8096 (tmm) REVERT: G 131 GLU cc_start: 0.8652 (mt-10) cc_final: 0.8211 (mp0) REVERT: K 178 ASN cc_start: 0.8144 (m110) cc_final: 0.7571 (m-40) REVERT: K 187 ASP cc_start: 0.8452 (t70) cc_final: 0.8190 (t0) REVERT: K 195 ASP cc_start: 0.8096 (m-30) cc_final: 0.7730 (m-30) REVERT: K 218 VAL cc_start: 0.8404 (OUTLIER) cc_final: 0.8174 (m) REVERT: H 33 LEU cc_start: 0.7510 (OUTLIER) cc_final: 0.7231 (mm) REVERT: H 39 SER cc_start: 0.8263 (m) cc_final: 0.8011 (t) REVERT: H 77 GLN cc_start: 0.8979 (tp40) cc_final: 0.8633 (tp-100) REVERT: I 22 GLU cc_start: 0.8223 (mt-10) cc_final: 0.7819 (mp0) REVERT: I 59 LYS cc_start: 0.9069 (mtmm) cc_final: 0.8792 (mttm) REVERT: I 127 GLU cc_start: 0.8337 (mm-30) cc_final: 0.8041 (mp0) REVERT: J 70 ARG cc_start: 0.7746 (ttm170) cc_final: 0.7515 (tpp-160) REVERT: J 183 ARG cc_start: 0.6434 (mmm-85) cc_final: 0.5905 (mtm180) REVERT: J 192 TYR cc_start: 0.7363 (m-80) cc_final: 0.7096 (m-10) REVERT: J 201 MET cc_start: 0.7496 (mmm) cc_final: 0.7224 (mtp) REVERT: J 344 MET cc_start: 0.7727 (mmt) cc_final: 0.7395 (mmp) REVERT: 2 309 MET cc_start: 0.8551 (mtp) cc_final: 0.8028 (mtp) REVERT: 2 321 LEU cc_start: 0.6986 (mp) cc_final: 0.6786 (tp) REVERT: 3 143 ARG cc_start: 0.7977 (ttp-170) cc_final: 0.7595 (ttm-80) REVERT: 3 219 ILE cc_start: 0.8849 (OUTLIER) cc_final: 0.8535 (pt) REVERT: 3 222 ASP cc_start: 0.8352 (m-30) cc_final: 0.8032 (m-30) REVERT: 4 197 LEU cc_start: 0.8214 (mp) cc_final: 0.7928 (mt) REVERT: 4 251 ASP cc_start: 0.7770 (p0) cc_final: 0.7130 (t70) REVERT: 5 142 LYS cc_start: 0.8694 (mttp) cc_final: 0.8445 (mtpp) REVERT: 5 244 ARG cc_start: 0.8075 (mtp180) cc_final: 0.7866 (mtt180) REVERT: 6 161 MET cc_start: 0.6150 (mmm) cc_final: 0.5383 (mtt) REVERT: 7 108 MET cc_start: 0.7117 (mmm) cc_final: 0.6747 (mmm) REVERT: 7 302 LEU cc_start: 0.8634 (OUTLIER) cc_final: 0.8335 (tt) REVERT: L 322 GLU cc_start: 0.7661 (mm-30) cc_final: 0.7457 (mm-30) REVERT: L 400 LYS cc_start: 0.7822 (OUTLIER) cc_final: 0.7528 (tppt) REVERT: L 579 LYS cc_start: 0.8696 (tttt) cc_final: 0.8032 (tmtt) outliers start: 104 outliers final: 69 residues processed: 702 average time/residue: 0.6338 time to fit residues: 732.4317 Evaluate side-chains 677 residues out of total 5784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 599 time to evaluate : 6.103 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 207 MET Chi-restraints excluded: chain A residue 228 VAL Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain B residue 86 SER Chi-restraints excluded: chain B residue 165 LEU Chi-restraints excluded: chain B residue 219 ILE Chi-restraints excluded: chain C residue 215 LEU Chi-restraints excluded: chain C residue 270 ASN Chi-restraints excluded: chain C residue 399 ILE Chi-restraints excluded: chain D residue 53 THR Chi-restraints excluded: chain D residue 121 THR Chi-restraints excluded: chain D residue 173 CYS Chi-restraints excluded: chain D residue 199 ASN Chi-restraints excluded: chain D residue 225 PHE Chi-restraints excluded: chain E residue 47 LEU Chi-restraints excluded: chain E residue 62 THR Chi-restraints excluded: chain E residue 109 ASN Chi-restraints excluded: chain F residue 53 ASP Chi-restraints excluded: chain F residue 98 LEU Chi-restraints excluded: chain F residue 165 ILE Chi-restraints excluded: chain F residue 236 ILE Chi-restraints excluded: chain F residue 302 LEU Chi-restraints excluded: chain M residue 128 LEU Chi-restraints excluded: chain N residue 24 ASP Chi-restraints excluded: chain N residue 42 VAL Chi-restraints excluded: chain N residue 44 VAL Chi-restraints excluded: chain O residue 24 LEU Chi-restraints excluded: chain P residue 232 ASP Chi-restraints excluded: chain P residue 237 MET Chi-restraints excluded: chain P residue 376 ASP Chi-restraints excluded: chain P residue 405 LEU Chi-restraints excluded: chain P residue 411 ASP Chi-restraints excluded: chain P residue 481 SER Chi-restraints excluded: chain P residue 510 ILE Chi-restraints excluded: chain Q residue 218 VAL Chi-restraints excluded: chain R residue 307 ASP Chi-restraints excluded: chain R residue 313 MET Chi-restraints excluded: chain R residue 400 LYS Chi-restraints excluded: chain R residue 577 THR Chi-restraints excluded: chain G residue 108 THR Chi-restraints excluded: chain G residue 128 LEU Chi-restraints excluded: chain K residue 56 LEU Chi-restraints excluded: chain K residue 218 VAL Chi-restraints excluded: chain H residue 24 ASP Chi-restraints excluded: chain H residue 33 LEU Chi-restraints excluded: chain H residue 42 VAL Chi-restraints excluded: chain I residue 24 LEU Chi-restraints excluded: chain J residue 232 ASP Chi-restraints excluded: chain J residue 237 MET Chi-restraints excluded: chain J residue 376 ASP Chi-restraints excluded: chain J residue 405 LEU Chi-restraints excluded: chain J residue 411 ASP Chi-restraints excluded: chain J residue 481 SER Chi-restraints excluded: chain 2 residue 207 MET Chi-restraints excluded: chain 2 residue 228 VAL Chi-restraints excluded: chain 2 residue 285 LEU Chi-restraints excluded: chain 3 residue 86 SER Chi-restraints excluded: chain 3 residue 165 LEU Chi-restraints excluded: chain 3 residue 219 ILE Chi-restraints excluded: chain 4 residue 270 ASN Chi-restraints excluded: chain 4 residue 399 ILE Chi-restraints excluded: chain 5 residue 53 THR Chi-restraints excluded: chain 5 residue 121 THR Chi-restraints excluded: chain 5 residue 199 ASN Chi-restraints excluded: chain 5 residue 225 PHE Chi-restraints excluded: chain 6 residue 47 LEU Chi-restraints excluded: chain 6 residue 62 THR Chi-restraints excluded: chain 6 residue 109 ASN Chi-restraints excluded: chain 7 residue 53 ASP Chi-restraints excluded: chain 7 residue 62 VAL Chi-restraints excluded: chain 7 residue 165 ILE Chi-restraints excluded: chain 7 residue 236 ILE Chi-restraints excluded: chain 7 residue 302 LEU Chi-restraints excluded: chain L residue 307 ASP Chi-restraints excluded: chain L residue 313 MET Chi-restraints excluded: chain L residue 400 LYS Chi-restraints excluded: chain L residue 573 ASP Chi-restraints excluded: chain L residue 577 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 634 random chunks: chunk 591 optimal weight: 7.9990 chunk 69 optimal weight: 0.1980 chunk 349 optimal weight: 6.9990 chunk 447 optimal weight: 0.7980 chunk 347 optimal weight: 4.9990 chunk 516 optimal weight: 8.9990 chunk 342 optimal weight: 3.9990 chunk 611 optimal weight: 0.9990 chunk 382 optimal weight: 1.9990 chunk 372 optimal weight: 3.9990 chunk 282 optimal weight: 0.0070 overall best weight: 0.8002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 300 HIS N 54 GLN P 328 GLN R 293 GLN G 116 GLN G 172 ASN H 54 GLN 5 231 GLN 7 300 HIS L 293 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8004 moved from start: 0.3249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 53015 Z= 0.163 Angle : 0.487 10.184 71624 Z= 0.249 Chirality : 0.040 0.161 7968 Planarity : 0.004 0.044 9265 Dihedral : 3.802 47.791 7047 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 1.82 % Allowed : 16.08 % Favored : 82.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.85 (0.11), residues: 6358 helix: 2.32 (0.10), residues: 2490 sheet: -0.54 (0.15), residues: 1196 loop : -0.57 (0.12), residues: 2672 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP K 32 HIS 0.006 0.001 HIS 2 182 PHE 0.017 0.001 PHE 2 346 TYR 0.028 0.001 TYR G 156 ARG 0.007 0.000 ARG 5 186 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12716 Ramachandran restraints generated. 6358 Oldfield, 0 Emsley, 6358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12716 Ramachandran restraints generated. 6358 Oldfield, 0 Emsley, 6358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 724 residues out of total 5784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 619 time to evaluate : 4.898 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: A 179 GLU cc_start: 0.8019 (OUTLIER) cc_final: 0.7637 (tp30) REVERT: A 309 MET cc_start: 0.8537 (mtp) cc_final: 0.8000 (mtp) REVERT: A 321 LEU cc_start: 0.6896 (mp) cc_final: 0.6679 (tp) REVERT: B 219 ILE cc_start: 0.8868 (OUTLIER) cc_final: 0.8580 (pt) REVERT: B 222 ASP cc_start: 0.8281 (m-30) cc_final: 0.7968 (m-30) REVERT: C 251 ASP cc_start: 0.7764 (p0) cc_final: 0.7093 (t70) REVERT: D 186 ARG cc_start: 0.8293 (mtp85) cc_final: 0.8032 (mtm-85) REVERT: D 244 ARG cc_start: 0.8087 (mtp180) cc_final: 0.7876 (mtt180) REVERT: E 161 MET cc_start: 0.5920 (mmm) cc_final: 0.5252 (mtt) REVERT: F 108 MET cc_start: 0.6267 (mmt) cc_final: 0.5886 (mmm) REVERT: F 181 TYR cc_start: 0.8248 (m-80) cc_final: 0.7849 (m-80) REVERT: F 302 LEU cc_start: 0.8588 (OUTLIER) cc_final: 0.8279 (tt) REVERT: M 42 GLN cc_start: 0.7237 (tt0) cc_final: 0.6910 (tt0) REVERT: M 46 ASP cc_start: 0.8311 (m-30) cc_final: 0.7739 (m-30) REVERT: M 51 LYS cc_start: 0.8514 (tppt) cc_final: 0.8234 (pttm) REVERT: M 96 SER cc_start: 0.8701 (m) cc_final: 0.8259 (p) REVERT: M 111 MET cc_start: 0.8390 (mmm) cc_final: 0.8093 (tmm) REVERT: M 131 GLU cc_start: 0.8676 (mt-10) cc_final: 0.8226 (mp0) REVERT: N 39 SER cc_start: 0.8268 (m) cc_final: 0.8025 (t) REVERT: N 77 GLN cc_start: 0.8875 (tp40) cc_final: 0.8589 (tp-100) REVERT: N 81 GLU cc_start: 0.7822 (mp0) cc_final: 0.7498 (mp0) REVERT: O 22 GLU cc_start: 0.8202 (mt-10) cc_final: 0.7828 (mp0) REVERT: O 127 GLU cc_start: 0.8307 (mm-30) cc_final: 0.7989 (mp0) REVERT: P 192 TYR cc_start: 0.7527 (m-80) cc_final: 0.7314 (m-10) REVERT: P 201 MET cc_start: 0.7536 (mmm) cc_final: 0.7296 (mtp) REVERT: P 344 MET cc_start: 0.7757 (mmt) cc_final: 0.7435 (mmp) REVERT: Q 58 HIS cc_start: 0.7846 (m90) cc_final: 0.7595 (m170) REVERT: Q 187 ASP cc_start: 0.8363 (t70) cc_final: 0.8134 (t0) REVERT: Q 195 ASP cc_start: 0.8627 (p0) cc_final: 0.8130 (m-30) REVERT: Q 209 ILE cc_start: 0.8453 (OUTLIER) cc_final: 0.8035 (pp) REVERT: Q 218 VAL cc_start: 0.8399 (OUTLIER) cc_final: 0.8169 (m) REVERT: R 181 ASP cc_start: 0.8704 (t0) cc_final: 0.8496 (m-30) REVERT: R 400 LYS cc_start: 0.7841 (OUTLIER) cc_final: 0.7532 (tppt) REVERT: R 579 LYS cc_start: 0.8725 (tttt) cc_final: 0.8115 (tmtt) REVERT: G 42 GLN cc_start: 0.7272 (tt0) cc_final: 0.6971 (tt0) REVERT: G 51 LYS cc_start: 0.8500 (tppt) cc_final: 0.8188 (pttm) REVERT: G 96 SER cc_start: 0.8715 (m) cc_final: 0.8274 (p) REVERT: G 111 MET cc_start: 0.8367 (mmm) cc_final: 0.8059 (tmm) REVERT: G 131 GLU cc_start: 0.8656 (mt-10) cc_final: 0.8213 (mp0) REVERT: K 178 ASN cc_start: 0.8156 (m110) cc_final: 0.7565 (m-40) REVERT: K 187 ASP cc_start: 0.8357 (t70) cc_final: 0.8136 (t0) REVERT: K 195 ASP cc_start: 0.8116 (m-30) cc_final: 0.7766 (m-30) REVERT: K 209 ILE cc_start: 0.8454 (OUTLIER) cc_final: 0.8036 (pp) REVERT: K 218 VAL cc_start: 0.8395 (OUTLIER) cc_final: 0.8182 (m) REVERT: H 33 LEU cc_start: 0.7432 (OUTLIER) cc_final: 0.7119 (mm) REVERT: H 39 SER cc_start: 0.8246 (m) cc_final: 0.7985 (t) REVERT: H 77 GLN cc_start: 0.8983 (tp40) cc_final: 0.8491 (tp-100) REVERT: H 81 GLU cc_start: 0.7973 (mp0) cc_final: 0.7503 (mp0) REVERT: I 22 GLU cc_start: 0.8200 (mt-10) cc_final: 0.7826 (mp0) REVERT: I 59 LYS cc_start: 0.9102 (mtmm) cc_final: 0.8770 (mttm) REVERT: I 127 GLU cc_start: 0.8325 (mm-30) cc_final: 0.8012 (mp0) REVERT: J 9 GLU cc_start: 0.8088 (tp30) cc_final: 0.7797 (tp30) REVERT: J 70 ARG cc_start: 0.7761 (ttm170) cc_final: 0.7540 (tpp-160) REVERT: J 183 ARG cc_start: 0.6453 (mmm-85) cc_final: 0.5865 (mtm180) REVERT: J 192 TYR cc_start: 0.7336 (m-80) cc_final: 0.7087 (m-10) REVERT: J 201 MET cc_start: 0.7559 (mmm) cc_final: 0.7298 (mtp) REVERT: J 344 MET cc_start: 0.7731 (mmt) cc_final: 0.7405 (mmp) REVERT: 2 309 MET cc_start: 0.8565 (mtp) cc_final: 0.8032 (mtp) REVERT: 3 143 ARG cc_start: 0.7954 (ttp-170) cc_final: 0.7651 (ttp-170) REVERT: 3 219 ILE cc_start: 0.8870 (OUTLIER) cc_final: 0.8578 (pt) REVERT: 3 222 ASP cc_start: 0.8318 (m-30) cc_final: 0.8023 (m-30) REVERT: 4 197 LEU cc_start: 0.8208 (mp) cc_final: 0.7915 (mt) REVERT: 4 251 ASP cc_start: 0.7786 (p0) cc_final: 0.7149 (t70) REVERT: 5 142 LYS cc_start: 0.8690 (mttp) cc_final: 0.8440 (mtpp) REVERT: 5 244 ARG cc_start: 0.8099 (mtp180) cc_final: 0.7865 (mtt180) REVERT: 6 161 MET cc_start: 0.6095 (mmm) cc_final: 0.5331 (mtt) REVERT: 7 181 TYR cc_start: 0.8115 (m-80) cc_final: 0.7802 (m-80) REVERT: 7 302 LEU cc_start: 0.8635 (OUTLIER) cc_final: 0.8340 (tt) REVERT: L 181 ASP cc_start: 0.8699 (t0) cc_final: 0.8494 (m-30) REVERT: L 322 GLU cc_start: 0.7733 (mm-30) cc_final: 0.7483 (mm-30) REVERT: L 400 LYS cc_start: 0.7847 (OUTLIER) cc_final: 0.7550 (tppt) REVERT: L 579 LYS cc_start: 0.8721 (tttt) cc_final: 0.8113 (tmtt) outliers start: 105 outliers final: 76 residues processed: 697 average time/residue: 0.6495 time to fit residues: 745.7666 Evaluate side-chains 696 residues out of total 5784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 608 time to evaluate : 4.936 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 179 GLU Chi-restraints excluded: chain A residue 207 MET Chi-restraints excluded: chain A residue 228 VAL Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain B residue 86 SER Chi-restraints excluded: chain B residue 165 LEU Chi-restraints excluded: chain B residue 219 ILE Chi-restraints excluded: chain C residue 215 LEU Chi-restraints excluded: chain C residue 270 ASN Chi-restraints excluded: chain C residue 399 ILE Chi-restraints excluded: chain D residue 53 THR Chi-restraints excluded: chain D residue 121 THR Chi-restraints excluded: chain D residue 173 CYS Chi-restraints excluded: chain D residue 199 ASN Chi-restraints excluded: chain D residue 225 PHE Chi-restraints excluded: chain E residue 47 LEU Chi-restraints excluded: chain E residue 62 THR Chi-restraints excluded: chain F residue 53 ASP Chi-restraints excluded: chain F residue 54 LEU Chi-restraints excluded: chain F residue 98 LEU Chi-restraints excluded: chain F residue 165 ILE Chi-restraints excluded: chain F residue 236 ILE Chi-restraints excluded: chain F residue 302 LEU Chi-restraints excluded: chain M residue 44 GLN Chi-restraints excluded: chain M residue 108 THR Chi-restraints excluded: chain M residue 128 LEU Chi-restraints excluded: chain N residue 24 ASP Chi-restraints excluded: chain N residue 42 VAL Chi-restraints excluded: chain N residue 44 VAL Chi-restraints excluded: chain N residue 120 THR Chi-restraints excluded: chain O residue 24 LEU Chi-restraints excluded: chain P residue 232 ASP Chi-restraints excluded: chain P residue 237 MET Chi-restraints excluded: chain P residue 405 LEU Chi-restraints excluded: chain P residue 411 ASP Chi-restraints excluded: chain P residue 481 SER Chi-restraints excluded: chain P residue 510 ILE Chi-restraints excluded: chain Q residue 209 ILE Chi-restraints excluded: chain Q residue 218 VAL Chi-restraints excluded: chain R residue 307 ASP Chi-restraints excluded: chain R residue 313 MET Chi-restraints excluded: chain R residue 400 LYS Chi-restraints excluded: chain R residue 573 ASP Chi-restraints excluded: chain R residue 577 THR Chi-restraints excluded: chain G residue 108 THR Chi-restraints excluded: chain G residue 128 LEU Chi-restraints excluded: chain K residue 56 LEU Chi-restraints excluded: chain K residue 209 ILE Chi-restraints excluded: chain K residue 218 VAL Chi-restraints excluded: chain H residue 24 ASP Chi-restraints excluded: chain H residue 33 LEU Chi-restraints excluded: chain H residue 42 VAL Chi-restraints excluded: chain H residue 105 ASP Chi-restraints excluded: chain I residue 24 LEU Chi-restraints excluded: chain I residue 78 LEU Chi-restraints excluded: chain J residue 104 ILE Chi-restraints excluded: chain J residue 232 ASP Chi-restraints excluded: chain J residue 405 LEU Chi-restraints excluded: chain J residue 411 ASP Chi-restraints excluded: chain J residue 481 SER Chi-restraints excluded: chain 2 residue 207 MET Chi-restraints excluded: chain 2 residue 228 VAL Chi-restraints excluded: chain 2 residue 285 LEU Chi-restraints excluded: chain 3 residue 86 SER Chi-restraints excluded: chain 3 residue 165 LEU Chi-restraints excluded: chain 3 residue 219 ILE Chi-restraints excluded: chain 4 residue 215 LEU Chi-restraints excluded: chain 4 residue 270 ASN Chi-restraints excluded: chain 4 residue 399 ILE Chi-restraints excluded: chain 5 residue 53 THR Chi-restraints excluded: chain 5 residue 121 THR Chi-restraints excluded: chain 5 residue 199 ASN Chi-restraints excluded: chain 5 residue 225 PHE Chi-restraints excluded: chain 6 residue 47 LEU Chi-restraints excluded: chain 6 residue 62 THR Chi-restraints excluded: chain 6 residue 109 ASN Chi-restraints excluded: chain 7 residue 53 ASP Chi-restraints excluded: chain 7 residue 62 VAL Chi-restraints excluded: chain 7 residue 98 LEU Chi-restraints excluded: chain 7 residue 107 MET Chi-restraints excluded: chain 7 residue 165 ILE Chi-restraints excluded: chain 7 residue 236 ILE Chi-restraints excluded: chain 7 residue 302 LEU Chi-restraints excluded: chain L residue 307 ASP Chi-restraints excluded: chain L residue 313 MET Chi-restraints excluded: chain L residue 400 LYS Chi-restraints excluded: chain L residue 573 ASP Chi-restraints excluded: chain L residue 577 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 634 random chunks: chunk 378 optimal weight: 9.9990 chunk 244 optimal weight: 6.9990 chunk 364 optimal weight: 6.9990 chunk 184 optimal weight: 0.6980 chunk 120 optimal weight: 5.9990 chunk 118 optimal weight: 0.6980 chunk 388 optimal weight: 0.0270 chunk 416 optimal weight: 0.0970 chunk 302 optimal weight: 0.0770 chunk 56 optimal weight: 10.0000 chunk 480 optimal weight: 0.0040 overall best weight: 0.1806 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 61 ASN F 247 ASN F 300 HIS M 172 ASN G 43 ASN 6 61 ASN 7 300 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7956 moved from start: 0.3379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.055 53015 Z= 0.127 Angle : 0.472 10.199 71624 Z= 0.240 Chirality : 0.039 0.175 7968 Planarity : 0.003 0.045 9265 Dihedral : 3.586 40.945 7047 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 1.40 % Allowed : 16.41 % Favored : 82.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.04 (0.11), residues: 6358 helix: 2.50 (0.10), residues: 2482 sheet: -0.40 (0.15), residues: 1198 loop : -0.51 (0.12), residues: 2678 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP M 180 HIS 0.006 0.001 HIS H 142 PHE 0.018 0.001 PHE M 64 TYR 0.023 0.001 TYR G 156 ARG 0.007 0.000 ARG 5 186 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12716 Ramachandran restraints generated. 6358 Oldfield, 0 Emsley, 6358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12716 Ramachandran restraints generated. 6358 Oldfield, 0 Emsley, 6358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 749 residues out of total 5784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 668 time to evaluate : 5.540 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 179 GLU cc_start: 0.8018 (OUTLIER) cc_final: 0.7693 (tp30) REVERT: A 186 ASN cc_start: 0.9153 (t0) cc_final: 0.8917 (t0) REVERT: A 309 MET cc_start: 0.8504 (mtp) cc_final: 0.8000 (mtp) REVERT: C 251 ASP cc_start: 0.7732 (p0) cc_final: 0.7013 (t70) REVERT: D 144 GLU cc_start: 0.7403 (tm-30) cc_final: 0.6945 (tm-30) REVERT: D 186 ARG cc_start: 0.8314 (mtp85) cc_final: 0.8057 (mtm-85) REVERT: D 244 ARG cc_start: 0.8107 (mtp180) cc_final: 0.7822 (mtt180) REVERT: E 161 MET cc_start: 0.5946 (mmm) cc_final: 0.5400 (mtt) REVERT: F 108 MET cc_start: 0.6230 (mmt) cc_final: 0.5847 (mmm) REVERT: F 181 TYR cc_start: 0.8260 (m-80) cc_final: 0.7896 (m-80) REVERT: F 200 MET cc_start: 0.8479 (tpt) cc_final: 0.8223 (tpp) REVERT: F 302 LEU cc_start: 0.8584 (OUTLIER) cc_final: 0.8293 (tt) REVERT: M 51 LYS cc_start: 0.8476 (tppt) cc_final: 0.8201 (pttm) REVERT: M 96 SER cc_start: 0.8646 (m) cc_final: 0.8222 (p) REVERT: M 103 ARG cc_start: 0.8283 (ttm-80) cc_final: 0.7902 (ttm110) REVERT: M 111 MET cc_start: 0.8409 (mmm) cc_final: 0.8115 (tmm) REVERT: M 131 GLU cc_start: 0.8732 (mt-10) cc_final: 0.8282 (mp0) REVERT: M 181 LYS cc_start: 0.8252 (mtpp) cc_final: 0.8045 (mtmm) REVERT: N 39 SER cc_start: 0.8343 (m) cc_final: 0.8059 (t) REVERT: N 77 GLN cc_start: 0.8893 (tp40) cc_final: 0.7567 (tp40) REVERT: N 81 GLU cc_start: 0.7824 (mp0) cc_final: 0.7134 (mp0) REVERT: N 151 MET cc_start: 0.8696 (tpp) cc_final: 0.8295 (tpt) REVERT: O 22 GLU cc_start: 0.8139 (mt-10) cc_final: 0.7742 (mp0) REVERT: O 127 GLU cc_start: 0.8208 (mm-30) cc_final: 0.7983 (mp0) REVERT: P 192 TYR cc_start: 0.7551 (m-80) cc_final: 0.7351 (m-10) REVERT: P 201 MET cc_start: 0.7538 (mmm) cc_final: 0.7297 (mtp) REVERT: P 344 MET cc_start: 0.7660 (mmt) cc_final: 0.7359 (mmp) REVERT: Q 58 HIS cc_start: 0.7852 (m90) cc_final: 0.7646 (m170) REVERT: Q 195 ASP cc_start: 0.8603 (p0) cc_final: 0.8156 (m-30) REVERT: Q 209 ILE cc_start: 0.8414 (OUTLIER) cc_final: 0.8020 (pp) REVERT: R 400 LYS cc_start: 0.7859 (OUTLIER) cc_final: 0.7534 (tppt) REVERT: R 567 ARG cc_start: 0.8057 (tpt170) cc_final: 0.7783 (tpt90) REVERT: R 579 LYS cc_start: 0.8754 (tttt) cc_final: 0.8114 (tmtt) REVERT: G 43 ASN cc_start: 0.8020 (m110) cc_final: 0.7462 (m-40) REVERT: G 51 LYS cc_start: 0.8510 (tppt) cc_final: 0.8222 (pttt) REVERT: G 96 SER cc_start: 0.8665 (m) cc_final: 0.8242 (p) REVERT: G 111 MET cc_start: 0.8349 (mmm) cc_final: 0.7988 (tmm) REVERT: G 131 GLU cc_start: 0.8688 (mt-10) cc_final: 0.8253 (mp0) REVERT: G 156 TYR cc_start: 0.8041 (t80) cc_final: 0.7542 (t80) REVERT: K 178 ASN cc_start: 0.8102 (m110) cc_final: 0.7604 (m-40) REVERT: K 195 ASP cc_start: 0.7984 (m-30) cc_final: 0.7663 (m-30) REVERT: K 209 ILE cc_start: 0.8417 (OUTLIER) cc_final: 0.8024 (pp) REVERT: H 39 SER cc_start: 0.8320 (m) cc_final: 0.8042 (t) REVERT: H 77 GLN cc_start: 0.9003 (tp40) cc_final: 0.8499 (tp-100) REVERT: H 81 GLU cc_start: 0.7947 (mp0) cc_final: 0.7445 (mp0) REVERT: H 151 MET cc_start: 0.8696 (tpp) cc_final: 0.8304 (tpt) REVERT: I 22 GLU cc_start: 0.8139 (mt-10) cc_final: 0.7742 (mp0) REVERT: I 59 LYS cc_start: 0.9078 (mtmm) cc_final: 0.8753 (mttm) REVERT: I 60 MET cc_start: 0.8764 (mtp) cc_final: 0.8496 (mtm) REVERT: I 127 GLU cc_start: 0.8199 (mm-30) cc_final: 0.7975 (mp0) REVERT: J 9 GLU cc_start: 0.8068 (tp30) cc_final: 0.7772 (tp30) REVERT: J 183 ARG cc_start: 0.6427 (mmm-85) cc_final: 0.5830 (mtm180) REVERT: J 192 TYR cc_start: 0.7347 (m-80) cc_final: 0.7112 (m-10) REVERT: J 201 MET cc_start: 0.7500 (mmm) cc_final: 0.7276 (mtp) REVERT: J 344 MET cc_start: 0.7695 (mmt) cc_final: 0.7396 (mmp) REVERT: 2 186 ASN cc_start: 0.9196 (t0) cc_final: 0.8970 (t0) REVERT: 2 309 MET cc_start: 0.8378 (mtp) cc_final: 0.7860 (mtp) REVERT: 3 143 ARG cc_start: 0.7933 (ttp-170) cc_final: 0.7533 (ttm-80) REVERT: 4 197 LEU cc_start: 0.8184 (mp) cc_final: 0.7886 (mt) REVERT: 4 251 ASP cc_start: 0.7715 (p0) cc_final: 0.7103 (t70) REVERT: 5 142 LYS cc_start: 0.8649 (mttp) cc_final: 0.8379 (mtpp) REVERT: 5 244 ARG cc_start: 0.8091 (mtp180) cc_final: 0.7863 (mtt180) REVERT: 6 161 MET cc_start: 0.5848 (mmm) cc_final: 0.5216 (mtt) REVERT: 7 108 MET cc_start: 0.6806 (mmm) cc_final: 0.6589 (mmt) REVERT: 7 181 TYR cc_start: 0.8077 (m-80) cc_final: 0.7806 (m-80) REVERT: 7 200 MET cc_start: 0.8489 (tpt) cc_final: 0.8236 (tpp) REVERT: 7 302 LEU cc_start: 0.8616 (OUTLIER) cc_final: 0.8347 (tt) REVERT: L 322 GLU cc_start: 0.7649 (mm-30) cc_final: 0.7374 (mm-30) REVERT: L 400 LYS cc_start: 0.7844 (OUTLIER) cc_final: 0.7548 (tppt) REVERT: L 567 ARG cc_start: 0.8052 (tpt170) cc_final: 0.7777 (tpt90) REVERT: L 579 LYS cc_start: 0.8751 (tttt) cc_final: 0.8114 (tmtt) outliers start: 81 outliers final: 47 residues processed: 724 average time/residue: 0.6026 time to fit residues: 713.6857 Evaluate side-chains 669 residues out of total 5784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 615 time to evaluate : 5.612 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 179 GLU Chi-restraints excluded: chain A residue 228 VAL Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain B residue 86 SER Chi-restraints excluded: chain C residue 215 LEU Chi-restraints excluded: chain C residue 270 ASN Chi-restraints excluded: chain C residue 399 ILE Chi-restraints excluded: chain D residue 53 THR Chi-restraints excluded: chain D residue 121 THR Chi-restraints excluded: chain E residue 47 LEU Chi-restraints excluded: chain E residue 62 THR Chi-restraints excluded: chain F residue 53 ASP Chi-restraints excluded: chain F residue 98 LEU Chi-restraints excluded: chain F residue 302 LEU Chi-restraints excluded: chain M residue 108 THR Chi-restraints excluded: chain N residue 24 ASP Chi-restraints excluded: chain N residue 42 VAL Chi-restraints excluded: chain P residue 232 ASP Chi-restraints excluded: chain P residue 376 ASP Chi-restraints excluded: chain P residue 481 SER Chi-restraints excluded: chain Q residue 209 ILE Chi-restraints excluded: chain R residue 307 ASP Chi-restraints excluded: chain R residue 400 LYS Chi-restraints excluded: chain R residue 541 ASP Chi-restraints excluded: chain R residue 573 ASP Chi-restraints excluded: chain R residue 577 THR Chi-restraints excluded: chain G residue 108 THR Chi-restraints excluded: chain K residue 209 ILE Chi-restraints excluded: chain H residue 24 ASP Chi-restraints excluded: chain H residue 42 VAL Chi-restraints excluded: chain H residue 120 THR Chi-restraints excluded: chain J residue 104 ILE Chi-restraints excluded: chain J residue 232 ASP Chi-restraints excluded: chain J residue 411 ASP Chi-restraints excluded: chain J residue 481 SER Chi-restraints excluded: chain 2 residue 228 VAL Chi-restraints excluded: chain 2 residue 285 LEU Chi-restraints excluded: chain 3 residue 86 SER Chi-restraints excluded: chain 4 residue 270 ASN Chi-restraints excluded: chain 4 residue 399 ILE Chi-restraints excluded: chain 5 residue 53 THR Chi-restraints excluded: chain 5 residue 121 THR Chi-restraints excluded: chain 5 residue 182 ASN Chi-restraints excluded: chain 5 residue 199 ASN Chi-restraints excluded: chain 6 residue 47 LEU Chi-restraints excluded: chain 7 residue 62 VAL Chi-restraints excluded: chain 7 residue 98 LEU Chi-restraints excluded: chain 7 residue 107 MET Chi-restraints excluded: chain 7 residue 165 ILE Chi-restraints excluded: chain 7 residue 302 LEU Chi-restraints excluded: chain L residue 307 ASP Chi-restraints excluded: chain L residue 400 LYS Chi-restraints excluded: chain L residue 573 ASP Chi-restraints excluded: chain L residue 577 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 634 random chunks: chunk 555 optimal weight: 0.9980 chunk 585 optimal weight: 0.0270 chunk 534 optimal weight: 0.6980 chunk 569 optimal weight: 5.9990 chunk 342 optimal weight: 0.9990 chunk 248 optimal weight: 5.9990 chunk 447 optimal weight: 0.8980 chunk 174 optimal weight: 3.9990 chunk 514 optimal weight: 9.9990 chunk 538 optimal weight: 2.9990 chunk 567 optimal weight: 0.0970 overall best weight: 0.5436 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 406 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 61 ASN F 300 HIS M 43 ASN ** M 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 99 ASN G 172 ASN 2 415 ASN 6 61 ASN 7 300 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7970 moved from start: 0.3446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 53015 Z= 0.144 Angle : 0.491 11.081 71624 Z= 0.246 Chirality : 0.040 0.169 7968 Planarity : 0.003 0.043 9265 Dihedral : 3.535 37.135 7047 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 1.31 % Allowed : 16.60 % Favored : 82.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.11 (0.11), residues: 6358 helix: 2.54 (0.10), residues: 2488 sheet: -0.31 (0.16), residues: 1188 loop : -0.49 (0.12), residues: 2682 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP M 180 HIS 0.008 0.001 HIS 2 182 PHE 0.020 0.001 PHE P 315 TYR 0.027 0.001 TYR A 181 ARG 0.011 0.000 ARG J 537 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12716 Ramachandran restraints generated. 6358 Oldfield, 0 Emsley, 6358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12716 Ramachandran restraints generated. 6358 Oldfield, 0 Emsley, 6358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 707 residues out of total 5784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 631 time to evaluate : 5.773 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: A 179 GLU cc_start: 0.8024 (OUTLIER) cc_final: 0.7688 (tp30) REVERT: A 186 ASN cc_start: 0.9144 (t0) cc_final: 0.8910 (t0) REVERT: A 309 MET cc_start: 0.8520 (mtp) cc_final: 0.8006 (mtp) REVERT: A 324 PHE cc_start: 0.7051 (m-80) cc_final: 0.6697 (m-80) REVERT: C 251 ASP cc_start: 0.7753 (p0) cc_final: 0.7029 (t70) REVERT: D 144 GLU cc_start: 0.7435 (tm-30) cc_final: 0.6980 (tm-30) REVERT: D 186 ARG cc_start: 0.8315 (mtp85) cc_final: 0.8050 (mtm-85) REVERT: D 244 ARG cc_start: 0.8111 (mtp180) cc_final: 0.7891 (mtt180) REVERT: E 161 MET cc_start: 0.5962 (mmm) cc_final: 0.5431 (mtt) REVERT: F 108 MET cc_start: 0.6290 (mmt) cc_final: 0.5904 (mmm) REVERT: F 181 TYR cc_start: 0.8267 (m-80) cc_final: 0.7924 (m-80) REVERT: F 200 MET cc_start: 0.8480 (tpt) cc_final: 0.8225 (tpp) REVERT: F 204 MET cc_start: 0.7357 (tmm) cc_final: 0.7000 (tmm) REVERT: F 302 LEU cc_start: 0.8589 (OUTLIER) cc_final: 0.8299 (tt) REVERT: M 43 ASN cc_start: 0.8076 (m110) cc_final: 0.7570 (m-40) REVERT: M 51 LYS cc_start: 0.8483 (tppt) cc_final: 0.8229 (pttm) REVERT: M 96 SER cc_start: 0.8643 (m) cc_final: 0.8210 (p) REVERT: M 111 MET cc_start: 0.8420 (mmm) cc_final: 0.8116 (tmm) REVERT: M 131 GLU cc_start: 0.8740 (mt-10) cc_final: 0.8304 (mp0) REVERT: N 39 SER cc_start: 0.8312 (m) cc_final: 0.8046 (t) REVERT: N 77 GLN cc_start: 0.8895 (tp40) cc_final: 0.7601 (tp40) REVERT: N 81 GLU cc_start: 0.7842 (mp0) cc_final: 0.7146 (mp0) REVERT: N 151 MET cc_start: 0.8719 (tpp) cc_final: 0.8271 (tpt) REVERT: O 22 GLU cc_start: 0.8155 (mt-10) cc_final: 0.7777 (mp0) REVERT: O 127 GLU cc_start: 0.8225 (mm-30) cc_final: 0.7949 (mp0) REVERT: P 70 ARG cc_start: 0.8168 (tpp-160) cc_final: 0.7816 (tpp-160) REVERT: P 201 MET cc_start: 0.7495 (mmm) cc_final: 0.7254 (mtp) REVERT: P 344 MET cc_start: 0.7714 (mmt) cc_final: 0.7384 (mmp) REVERT: Q 58 HIS cc_start: 0.7876 (m90) cc_final: 0.7461 (m170) REVERT: Q 61 GLN cc_start: 0.7740 (mm110) cc_final: 0.7367 (pm20) REVERT: Q 195 ASP cc_start: 0.8608 (p0) cc_final: 0.8165 (m-30) REVERT: Q 209 ILE cc_start: 0.8455 (OUTLIER) cc_final: 0.8055 (pp) REVERT: R 400 LYS cc_start: 0.7864 (OUTLIER) cc_final: 0.7534 (tppt) REVERT: R 517 LEU cc_start: 0.9053 (OUTLIER) cc_final: 0.8785 (mt) REVERT: R 567 ARG cc_start: 0.8090 (tpt170) cc_final: 0.7834 (tpt90) REVERT: R 579 LYS cc_start: 0.8748 (tttt) cc_final: 0.8118 (tmtt) REVERT: G 43 ASN cc_start: 0.8119 (m110) cc_final: 0.7481 (m-40) REVERT: G 51 LYS cc_start: 0.8489 (tppt) cc_final: 0.8202 (pttt) REVERT: G 96 SER cc_start: 0.8647 (m) cc_final: 0.8225 (p) REVERT: G 111 MET cc_start: 0.8369 (mmm) cc_final: 0.7994 (tmm) REVERT: G 131 GLU cc_start: 0.8686 (mt-10) cc_final: 0.8253 (mp0) REVERT: G 156 TYR cc_start: 0.8046 (t80) cc_final: 0.7646 (t80) REVERT: K 178 ASN cc_start: 0.8256 (m110) cc_final: 0.7822 (m-40) REVERT: K 195 ASP cc_start: 0.7876 (m-30) cc_final: 0.7549 (m-30) REVERT: K 209 ILE cc_start: 0.8458 (OUTLIER) cc_final: 0.8058 (pp) REVERT: H 39 SER cc_start: 0.8337 (m) cc_final: 0.8046 (t) REVERT: H 77 GLN cc_start: 0.8992 (tp40) cc_final: 0.7517 (tp40) REVERT: H 81 GLU cc_start: 0.7943 (mp0) cc_final: 0.7092 (mp0) REVERT: H 151 MET cc_start: 0.8714 (tpp) cc_final: 0.8304 (tpt) REVERT: I 22 GLU cc_start: 0.8164 (mt-10) cc_final: 0.7755 (mp0) REVERT: I 59 LYS cc_start: 0.9086 (mtmm) cc_final: 0.8750 (mttm) REVERT: I 60 MET cc_start: 0.8805 (mtp) cc_final: 0.8500 (mtm) REVERT: I 127 GLU cc_start: 0.8234 (mm-30) cc_final: 0.7954 (mp0) REVERT: J 9 GLU cc_start: 0.8034 (tp30) cc_final: 0.7722 (tp30) REVERT: J 70 ARG cc_start: 0.7932 (tpp-160) cc_final: 0.7714 (tpp-160) REVERT: J 183 ARG cc_start: 0.6434 (mmm-85) cc_final: 0.5832 (mtm180) REVERT: J 192 TYR cc_start: 0.7338 (m-80) cc_final: 0.7104 (m-10) REVERT: J 201 MET cc_start: 0.7470 (mmm) cc_final: 0.7232 (mtp) REVERT: J 344 MET cc_start: 0.7741 (mmt) cc_final: 0.7425 (mmp) REVERT: 2 186 ASN cc_start: 0.9191 (t0) cc_final: 0.8967 (t0) REVERT: 2 309 MET cc_start: 0.8376 (mtp) cc_final: 0.7866 (mtp) REVERT: 3 143 ARG cc_start: 0.7954 (ttp-170) cc_final: 0.7554 (ttm-80) REVERT: 3 219 ILE cc_start: 0.8815 (OUTLIER) cc_final: 0.8505 (pt) REVERT: 4 197 LEU cc_start: 0.8139 (mp) cc_final: 0.7835 (mt) REVERT: 4 251 ASP cc_start: 0.7715 (p0) cc_final: 0.7105 (t70) REVERT: 5 142 LYS cc_start: 0.8646 (mttp) cc_final: 0.8381 (mtpp) REVERT: 5 244 ARG cc_start: 0.8093 (mtp180) cc_final: 0.7870 (mtt180) REVERT: 6 161 MET cc_start: 0.5825 (mmm) cc_final: 0.5127 (mtt) REVERT: 7 108 MET cc_start: 0.6872 (mmm) cc_final: 0.6382 (mmm) REVERT: 7 181 TYR cc_start: 0.8156 (m-80) cc_final: 0.7907 (m-80) REVERT: 7 200 MET cc_start: 0.8489 (tpt) cc_final: 0.8236 (tpp) REVERT: 7 302 LEU cc_start: 0.8627 (OUTLIER) cc_final: 0.8364 (tt) REVERT: L 322 GLU cc_start: 0.7664 (mm-30) cc_final: 0.7376 (mm-30) REVERT: L 400 LYS cc_start: 0.7879 (OUTLIER) cc_final: 0.7612 (tppt) REVERT: L 517 LEU cc_start: 0.9035 (OUTLIER) cc_final: 0.8775 (mt) REVERT: L 567 ARG cc_start: 0.8100 (tpt170) cc_final: 0.7842 (tpt90) REVERT: L 579 LYS cc_start: 0.8745 (tttt) cc_final: 0.8118 (tmtt) outliers start: 76 outliers final: 52 residues processed: 685 average time/residue: 0.5580 time to fit residues: 630.2100 Evaluate side-chains 678 residues out of total 5784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 616 time to evaluate : 5.759 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 179 GLU Chi-restraints excluded: chain A residue 210 GLU Chi-restraints excluded: chain A residue 228 VAL Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain B residue 86 SER Chi-restraints excluded: chain C residue 215 LEU Chi-restraints excluded: chain C residue 270 ASN Chi-restraints excluded: chain C residue 399 ILE Chi-restraints excluded: chain D residue 53 THR Chi-restraints excluded: chain D residue 199 ASN Chi-restraints excluded: chain E residue 47 LEU Chi-restraints excluded: chain E residue 62 THR Chi-restraints excluded: chain F residue 53 ASP Chi-restraints excluded: chain F residue 98 LEU Chi-restraints excluded: chain F residue 302 LEU Chi-restraints excluded: chain M residue 108 THR Chi-restraints excluded: chain N residue 24 ASP Chi-restraints excluded: chain N residue 42 VAL Chi-restraints excluded: chain P residue 232 ASP Chi-restraints excluded: chain P residue 481 SER Chi-restraints excluded: chain Q residue 209 ILE Chi-restraints excluded: chain R residue 307 ASP Chi-restraints excluded: chain R residue 400 LYS Chi-restraints excluded: chain R residue 429 LEU Chi-restraints excluded: chain R residue 517 LEU Chi-restraints excluded: chain R residue 573 ASP Chi-restraints excluded: chain R residue 577 THR Chi-restraints excluded: chain G residue 108 THR Chi-restraints excluded: chain K residue 209 ILE Chi-restraints excluded: chain H residue 24 ASP Chi-restraints excluded: chain H residue 42 VAL Chi-restraints excluded: chain H residue 120 THR Chi-restraints excluded: chain J residue 104 ILE Chi-restraints excluded: chain J residue 232 ASP Chi-restraints excluded: chain J residue 303 LEU Chi-restraints excluded: chain J residue 376 ASP Chi-restraints excluded: chain J residue 411 ASP Chi-restraints excluded: chain J residue 481 SER Chi-restraints excluded: chain 2 residue 210 GLU Chi-restraints excluded: chain 2 residue 228 VAL Chi-restraints excluded: chain 2 residue 285 LEU Chi-restraints excluded: chain 3 residue 86 SER Chi-restraints excluded: chain 3 residue 219 ILE Chi-restraints excluded: chain 4 residue 270 ASN Chi-restraints excluded: chain 4 residue 399 ILE Chi-restraints excluded: chain 5 residue 53 THR Chi-restraints excluded: chain 5 residue 182 ASN Chi-restraints excluded: chain 5 residue 199 ASN Chi-restraints excluded: chain 6 residue 47 LEU Chi-restraints excluded: chain 6 residue 109 ASN Chi-restraints excluded: chain 6 residue 308 THR Chi-restraints excluded: chain 7 residue 53 ASP Chi-restraints excluded: chain 7 residue 62 VAL Chi-restraints excluded: chain 7 residue 98 LEU Chi-restraints excluded: chain 7 residue 165 ILE Chi-restraints excluded: chain 7 residue 302 LEU Chi-restraints excluded: chain L residue 307 ASP Chi-restraints excluded: chain L residue 400 LYS Chi-restraints excluded: chain L residue 429 LEU Chi-restraints excluded: chain L residue 517 LEU Chi-restraints excluded: chain L residue 573 ASP Chi-restraints excluded: chain L residue 577 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 634 random chunks: chunk 373 optimal weight: 0.3980 chunk 602 optimal weight: 0.7980 chunk 367 optimal weight: 0.9980 chunk 285 optimal weight: 6.9990 chunk 418 optimal weight: 0.0270 chunk 631 optimal weight: 2.9990 chunk 581 optimal weight: 8.9990 chunk 502 optimal weight: 2.9990 chunk 52 optimal weight: 10.0000 chunk 388 optimal weight: 0.0670 chunk 308 optimal weight: 1.9990 overall best weight: 0.4576 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 406 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 61 ASN F 300 HIS ** P 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 61 ASN 7 300 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7961 moved from start: 0.3520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 53015 Z= 0.137 Angle : 0.489 11.432 71624 Z= 0.246 Chirality : 0.039 0.154 7968 Planarity : 0.003 0.043 9265 Dihedral : 3.481 32.323 7047 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 1.26 % Allowed : 16.82 % Favored : 81.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.16 (0.11), residues: 6358 helix: 2.58 (0.10), residues: 2490 sheet: -0.29 (0.16), residues: 1182 loop : -0.46 (0.12), residues: 2686 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP M 180 HIS 0.008 0.001 HIS 2 182 PHE 0.027 0.001 PHE J 558 TYR 0.021 0.001 TYR M 156 ARG 0.007 0.000 ARG 5 186 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12716 Ramachandran restraints generated. 6358 Oldfield, 0 Emsley, 6358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12716 Ramachandran restraints generated. 6358 Oldfield, 0 Emsley, 6358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 712 residues out of total 5784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 639 time to evaluate : 4.859 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: A 179 GLU cc_start: 0.7988 (OUTLIER) cc_final: 0.7684 (tp30) REVERT: A 186 ASN cc_start: 0.9135 (t0) cc_final: 0.8894 (t0) REVERT: A 309 MET cc_start: 0.8362 (mtp) cc_final: 0.7867 (mtp) REVERT: B 219 ILE cc_start: 0.8827 (OUTLIER) cc_final: 0.8519 (pt) REVERT: C 251 ASP cc_start: 0.7717 (p0) cc_final: 0.6980 (t70) REVERT: D 144 GLU cc_start: 0.7488 (tm-30) cc_final: 0.7041 (tm-30) REVERT: D 186 ARG cc_start: 0.8316 (mtp85) cc_final: 0.8050 (mtm-85) REVERT: D 244 ARG cc_start: 0.8102 (mtp180) cc_final: 0.7830 (mtt180) REVERT: E 61 ASN cc_start: 0.8019 (OUTLIER) cc_final: 0.7737 (t0) REVERT: E 161 MET cc_start: 0.5942 (mmm) cc_final: 0.5405 (mtt) REVERT: F 108 MET cc_start: 0.6338 (mmt) cc_final: 0.5967 (mmm) REVERT: F 181 TYR cc_start: 0.8257 (m-80) cc_final: 0.7958 (m-80) REVERT: F 200 MET cc_start: 0.8508 (tpt) cc_final: 0.8252 (tpp) REVERT: F 204 MET cc_start: 0.7377 (tmm) cc_final: 0.7033 (tmm) REVERT: F 302 LEU cc_start: 0.8603 (OUTLIER) cc_final: 0.8318 (tt) REVERT: M 51 LYS cc_start: 0.8467 (tppt) cc_final: 0.8216 (pttt) REVERT: M 96 SER cc_start: 0.8629 (m) cc_final: 0.8204 (p) REVERT: M 111 MET cc_start: 0.8441 (mmm) cc_final: 0.8122 (tmm) REVERT: M 131 GLU cc_start: 0.8740 (mt-10) cc_final: 0.8306 (mp0) REVERT: N 39 SER cc_start: 0.8319 (m) cc_final: 0.8046 (t) REVERT: N 77 GLN cc_start: 0.8867 (tp40) cc_final: 0.7534 (tp40) REVERT: N 81 GLU cc_start: 0.7853 (mp0) cc_final: 0.7154 (mp0) REVERT: N 151 MET cc_start: 0.8724 (tpp) cc_final: 0.8309 (tpt) REVERT: O 22 GLU cc_start: 0.8114 (mt-10) cc_final: 0.7737 (mp0) REVERT: O 52 ASP cc_start: 0.8406 (t70) cc_final: 0.8164 (t0) REVERT: O 127 GLU cc_start: 0.8191 (mm-30) cc_final: 0.7935 (mp0) REVERT: P 70 ARG cc_start: 0.8218 (tpp-160) cc_final: 0.7838 (tpp-160) REVERT: P 201 MET cc_start: 0.7502 (mmm) cc_final: 0.7264 (mtp) REVERT: P 344 MET cc_start: 0.7684 (mmt) cc_final: 0.7360 (mmp) REVERT: Q 58 HIS cc_start: 0.7855 (m90) cc_final: 0.7433 (m170) REVERT: Q 61 GLN cc_start: 0.7671 (mm110) cc_final: 0.7382 (pm20) REVERT: Q 194 ILE cc_start: 0.8784 (mm) cc_final: 0.8368 (tt) REVERT: Q 195 ASP cc_start: 0.8601 (p0) cc_final: 0.8184 (m-30) REVERT: Q 209 ILE cc_start: 0.8437 (OUTLIER) cc_final: 0.8041 (pp) REVERT: R 400 LYS cc_start: 0.7865 (OUTLIER) cc_final: 0.7534 (tppt) REVERT: R 517 LEU cc_start: 0.9041 (OUTLIER) cc_final: 0.8783 (mt) REVERT: R 567 ARG cc_start: 0.8092 (tpt170) cc_final: 0.7837 (tpt90) REVERT: R 579 LYS cc_start: 0.8656 (tttt) cc_final: 0.7995 (tmtt) REVERT: G 43 ASN cc_start: 0.8105 (m110) cc_final: 0.7464 (m-40) REVERT: G 51 LYS cc_start: 0.8486 (tppt) cc_final: 0.8200 (pttt) REVERT: G 96 SER cc_start: 0.8632 (m) cc_final: 0.8205 (p) REVERT: G 111 MET cc_start: 0.8429 (mmm) cc_final: 0.8064 (tmm) REVERT: G 131 GLU cc_start: 0.8712 (mt-10) cc_final: 0.8291 (mp0) REVERT: G 156 TYR cc_start: 0.8062 (t80) cc_final: 0.7842 (t80) REVERT: K 178 ASN cc_start: 0.8282 (m110) cc_final: 0.7807 (m-40) REVERT: K 195 ASP cc_start: 0.7723 (m-30) cc_final: 0.7365 (m-30) REVERT: K 209 ILE cc_start: 0.8439 (OUTLIER) cc_final: 0.8046 (pp) REVERT: H 39 SER cc_start: 0.8365 (m) cc_final: 0.8068 (t) REVERT: H 77 GLN cc_start: 0.9010 (tp40) cc_final: 0.7567 (tp40) REVERT: H 81 GLU cc_start: 0.7928 (mp0) cc_final: 0.7080 (mp0) REVERT: H 151 MET cc_start: 0.8723 (tpp) cc_final: 0.8313 (tpt) REVERT: I 22 GLU cc_start: 0.8115 (mt-10) cc_final: 0.7742 (mp0) REVERT: I 52 ASP cc_start: 0.8358 (t70) cc_final: 0.8125 (t0) REVERT: I 60 MET cc_start: 0.8776 (mtp) cc_final: 0.8465 (mtm) REVERT: I 127 GLU cc_start: 0.8198 (mm-30) cc_final: 0.7936 (mp0) REVERT: J 9 GLU cc_start: 0.8065 (tp30) cc_final: 0.7740 (tp30) REVERT: J 70 ARG cc_start: 0.8023 (tpp-160) cc_final: 0.7808 (tpp-160) REVERT: J 192 TYR cc_start: 0.7335 (m-80) cc_final: 0.7096 (m-10) REVERT: J 201 MET cc_start: 0.7461 (mmm) cc_final: 0.7215 (mtp) REVERT: J 344 MET cc_start: 0.7709 (mmt) cc_final: 0.7407 (mmp) REVERT: J 528 GLU cc_start: 0.8166 (pt0) cc_final: 0.7555 (tp30) REVERT: 2 309 MET cc_start: 0.8359 (mtp) cc_final: 0.7845 (mtp) REVERT: 3 143 ARG cc_start: 0.7938 (ttp-170) cc_final: 0.7548 (ttm-80) REVERT: 3 219 ILE cc_start: 0.8817 (OUTLIER) cc_final: 0.8507 (pt) REVERT: 4 197 LEU cc_start: 0.8141 (mp) cc_final: 0.7837 (mt) REVERT: 4 251 ASP cc_start: 0.7721 (p0) cc_final: 0.7104 (t70) REVERT: 5 142 LYS cc_start: 0.8612 (mttp) cc_final: 0.8373 (mtpp) REVERT: 5 244 ARG cc_start: 0.8091 (mtp180) cc_final: 0.7883 (mtt180) REVERT: 6 161 MET cc_start: 0.5812 (mmm) cc_final: 0.5164 (mtt) REVERT: 7 200 MET cc_start: 0.8510 (tpt) cc_final: 0.8262 (tpp) REVERT: 7 204 MET cc_start: 0.7443 (tmm) cc_final: 0.7096 (tmm) REVERT: 7 302 LEU cc_start: 0.8614 (OUTLIER) cc_final: 0.8352 (tt) REVERT: L 322 GLU cc_start: 0.7670 (mm-30) cc_final: 0.7376 (mm-30) REVERT: L 400 LYS cc_start: 0.7902 (OUTLIER) cc_final: 0.7619 (tppt) REVERT: L 517 LEU cc_start: 0.9020 (OUTLIER) cc_final: 0.8769 (mt) REVERT: L 567 ARG cc_start: 0.8086 (tpt170) cc_final: 0.7831 (tpt90) REVERT: L 579 LYS cc_start: 0.8648 (tttt) cc_final: 0.7986 (tmtt) outliers start: 73 outliers final: 52 residues processed: 690 average time/residue: 0.5589 time to fit residues: 634.9658 Evaluate side-chains 689 residues out of total 5784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 625 time to evaluate : 5.713 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 179 GLU Chi-restraints excluded: chain A residue 210 GLU Chi-restraints excluded: chain A residue 228 VAL Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain B residue 86 SER Chi-restraints excluded: chain B residue 219 ILE Chi-restraints excluded: chain C residue 215 LEU Chi-restraints excluded: chain C residue 270 ASN Chi-restraints excluded: chain C residue 399 ILE Chi-restraints excluded: chain D residue 53 THR Chi-restraints excluded: chain D residue 199 ASN Chi-restraints excluded: chain E residue 47 LEU Chi-restraints excluded: chain E residue 61 ASN Chi-restraints excluded: chain E residue 62 THR Chi-restraints excluded: chain F residue 53 ASP Chi-restraints excluded: chain F residue 98 LEU Chi-restraints excluded: chain F residue 302 LEU Chi-restraints excluded: chain M residue 108 THR Chi-restraints excluded: chain N residue 24 ASP Chi-restraints excluded: chain N residue 42 VAL Chi-restraints excluded: chain P residue 232 ASP Chi-restraints excluded: chain P residue 303 LEU Chi-restraints excluded: chain P residue 376 ASP Chi-restraints excluded: chain P residue 481 SER Chi-restraints excluded: chain Q residue 209 ILE Chi-restraints excluded: chain R residue 307 ASP Chi-restraints excluded: chain R residue 400 LYS Chi-restraints excluded: chain R residue 429 LEU Chi-restraints excluded: chain R residue 517 LEU Chi-restraints excluded: chain R residue 573 ASP Chi-restraints excluded: chain R residue 577 THR Chi-restraints excluded: chain G residue 108 THR Chi-restraints excluded: chain K residue 209 ILE Chi-restraints excluded: chain H residue 24 ASP Chi-restraints excluded: chain H residue 42 VAL Chi-restraints excluded: chain H residue 120 THR Chi-restraints excluded: chain J residue 104 ILE Chi-restraints excluded: chain J residue 232 ASP Chi-restraints excluded: chain J residue 303 LEU Chi-restraints excluded: chain J residue 376 ASP Chi-restraints excluded: chain J residue 481 SER Chi-restraints excluded: chain 2 residue 210 GLU Chi-restraints excluded: chain 2 residue 228 VAL Chi-restraints excluded: chain 2 residue 285 LEU Chi-restraints excluded: chain 3 residue 86 SER Chi-restraints excluded: chain 3 residue 219 ILE Chi-restraints excluded: chain 4 residue 270 ASN Chi-restraints excluded: chain 4 residue 397 VAL Chi-restraints excluded: chain 4 residue 399 ILE Chi-restraints excluded: chain 5 residue 53 THR Chi-restraints excluded: chain 5 residue 182 ASN Chi-restraints excluded: chain 5 residue 199 ASN Chi-restraints excluded: chain 6 residue 47 LEU Chi-restraints excluded: chain 6 residue 308 THR Chi-restraints excluded: chain 7 residue 53 ASP Chi-restraints excluded: chain 7 residue 62 VAL Chi-restraints excluded: chain 7 residue 98 LEU Chi-restraints excluded: chain 7 residue 165 ILE Chi-restraints excluded: chain 7 residue 302 LEU Chi-restraints excluded: chain L residue 307 ASP Chi-restraints excluded: chain L residue 400 LYS Chi-restraints excluded: chain L residue 517 LEU Chi-restraints excluded: chain L residue 573 ASP Chi-restraints excluded: chain L residue 577 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 634 random chunks: chunk 399 optimal weight: 10.0000 chunk 535 optimal weight: 0.9980 chunk 154 optimal weight: 6.9990 chunk 463 optimal weight: 7.9990 chunk 74 optimal weight: 0.9980 chunk 139 optimal weight: 0.1980 chunk 503 optimal weight: 3.9990 chunk 210 optimal weight: 0.4980 chunk 517 optimal weight: 4.9990 chunk 63 optimal weight: 6.9990 chunk 92 optimal weight: 6.9990 overall best weight: 1.3382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 406 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 300 HIS ** M 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 406 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 247 ASN 7 300 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4055 r_free = 0.4055 target = 0.148496 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.102490 restraints weight = 79237.090| |-----------------------------------------------------------------------------| r_work (start): 0.3443 rms_B_bonded: 2.62 r_work: 0.3245 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3110 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.3110 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8297 moved from start: 0.3507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 53015 Z= 0.219 Angle : 0.522 11.279 71624 Z= 0.264 Chirality : 0.041 0.167 7968 Planarity : 0.004 0.054 9265 Dihedral : 3.597 30.465 7047 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 1.28 % Allowed : 16.94 % Favored : 81.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.07 (0.11), residues: 6358 helix: 2.47 (0.10), residues: 2500 sheet: -0.35 (0.15), residues: 1180 loop : -0.47 (0.12), residues: 2678 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP R 234 HIS 0.009 0.001 HIS 2 182 PHE 0.036 0.001 PHE A 324 TYR 0.028 0.001 TYR 7 181 ARG 0.019 0.000 ARG E 60 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14866.55 seconds wall clock time: 264 minutes 56.29 seconds (15896.29 seconds total)