Starting phenix.real_space_refine on Thu Sep 18 23:10:21 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9nez_49340/09_2025/9nez_49340.cif Found real_map, /net/cci-nas-00/data/ceres_data/9nez_49340/09_2025/9nez_49340.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.47 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9nez_49340/09_2025/9nez_49340.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9nez_49340/09_2025/9nez_49340.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9nez_49340/09_2025/9nez_49340.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9nez_49340/09_2025/9nez_49340.map" } resolution = 3.47 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= -0.043 sd= 0.442 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Fe 62 7.16 5 Ni 2 6.56 5 P 4 5.49 5 S 202 5.16 5 C 13500 2.51 5 N 3528 2.21 5 O 3822 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 21120 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 2006 Number of conformers: 1 Conformer: "" Number of residues, atoms: 255, 2006 Classifications: {'peptide': 255} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 242} Chain: "B" Number of atoms: 2873 Number of conformers: 1 Conformer: "" Number of residues, atoms: 343, 2873 Classifications: {'peptide': 343} Link IDs: {'PTRANS': 15, 'TRANS': 327} Chain: "C" Number of atoms: 2236 Number of conformers: 1 Conformer: "" Number of residues, atoms: 281, 2236 Classifications: {'peptide': 281} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 261} Chain: "D" Number of atoms: 3324 Number of conformers: 1 Conformer: "" Number of residues, atoms: 419, 3324 Classifications: {'peptide': 419} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 399} Chain: "E" Number of atoms: 2006 Number of conformers: 1 Conformer: "" Number of residues, atoms: 255, 2006 Classifications: {'peptide': 255} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 242} Chain: "F" Number of atoms: 2873 Number of conformers: 1 Conformer: "" Number of residues, atoms: 343, 2873 Classifications: {'peptide': 343} Link IDs: {'PTRANS': 15, 'TRANS': 327} Chain: "G" Number of atoms: 2236 Number of conformers: 1 Conformer: "" Number of residues, atoms: 281, 2236 Classifications: {'peptide': 281} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 261} Chain: "H" Number of atoms: 3324 Number of conformers: 1 Conformer: "" Number of residues, atoms: 419, 3324 Classifications: {'peptide': 419} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 399} Chain: "A" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 24 Unusual residues: {'SF4': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 32 Unusual residues: {'SF4': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "C" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 57 Unusual residues: {'FAD': 1, 'FES': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 8 Unusual residues: {'NFU': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 24 Unusual residues: {'SF4': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "F" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 32 Unusual residues: {'SF4': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "G" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 57 Unusual residues: {'FAD': 1, 'FES': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "H" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 8 Unusual residues: {'NFU': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 657 SG CYS A 86 52.754 163.989 48.626 1.00 34.10 S ATOM 1062 SG CYS A 136 56.175 159.649 49.833 1.00 35.78 S ATOM 94 SG CYS A 14 58.946 165.031 47.282 1.00 49.49 S ATOM 116 SG CYS A 17 55.540 161.790 43.388 1.00 44.79 S ATOM 1585 SG CYS A 206 57.306 154.574 50.357 1.00 39.87 S ATOM 1493 SG CYS A 192 57.936 148.631 48.592 1.00 33.75 S ATOM 1567 SG CYS A 203 55.760 149.554 54.579 1.00 43.04 S ATOM 1523 SG CYS A 196 61.318 151.394 53.846 1.00 39.65 S ATOM 1312 SG CYS A 167 60.199 141.083 53.861 1.00 35.39 S ATOM 1289 SG CYS A 164 53.954 141.380 54.800 1.00 34.44 S ATOM 1434 SG CYS A 183 57.207 145.749 57.727 1.00 45.71 S ATOM 1366 SG CYS A 174 58.082 139.133 59.064 1.00 41.12 S ATOM 4012 SG CYS B 233 44.862 135.056 57.510 1.00 40.03 S ATOM 4049 SG CYS B 239 49.205 131.275 54.788 1.00 29.85 S ATOM 4716 SG CYS B 322 50.087 133.234 60.980 1.00 33.49 S ATOM 4031 SG CYS B 236 50.714 137.396 56.451 1.00 33.58 S ATOM 4077 SG CYS B 243 53.111 124.963 51.408 1.00 27.44 S ATOM 4649 SG CYS B 312 51.331 120.118 55.704 1.00 34.68 S ATOM 4687 SG CYS B 318 51.799 125.738 58.043 1.00 30.82 S ATOM 4666 SG CYS B 315 56.972 123.178 55.542 1.00 32.29 S ATOM 2851 SG CYS B 96 60.652 119.506 55.447 1.00 38.66 S ATOM 3192 SG CYS B 137 59.903 118.605 61.179 1.00 51.88 S ATOM 3209 SG CYS B 139 59.814 115.257 59.987 1.00 49.44 S ATOM 3192 SG CYS B 137 59.903 118.605 61.179 1.00 51.88 S ATOM 3142 SG CYS B 131 64.465 116.451 59.887 1.00 52.80 S ATOM 4114 SG CYS B 248 47.874 128.059 43.565 1.00 31.92 S ATOM 4545 SG CYS B 299 45.463 123.478 47.248 1.00 36.42 S ATOM 4308 SG CYS B 271 44.999 129.500 47.986 1.00 27.72 S ATOM 4097 SG CYS B 246 51.177 126.706 48.844 1.00 29.95 S ATOM 6831 SG CYS C 253 47.943 126.508 34.325 1.00 48.97 S ATOM 6862 SG CYS C 258 45.708 127.934 36.860 1.00 37.53 S ATOM 6882 SG CYS C 261 42.436 125.873 36.599 1.00 41.38 S ATOM 6976 SG CYS C 273 44.147 123.078 34.575 1.00 52.13 S ATOM 10416 SG CYS D 421 64.228 172.114 50.649 1.00 30.00 S ATOM 10396 SG CYS D 418 64.699 172.377 46.717 1.00 65.13 S ATOM 10416 SG CYS D 421 64.228 172.114 50.649 1.00 30.00 S ATOM 11096 SG CYS E 86 51.557 49.616 48.486 1.00 33.49 S ATOM 11501 SG CYS E 136 48.194 53.987 49.858 1.00 35.70 S ATOM 10533 SG CYS E 14 45.409 48.440 47.474 1.00 48.07 S ATOM 10555 SG CYS E 17 48.568 51.913 43.459 1.00 45.36 S ATOM 12024 SG CYS E 206 47.246 58.958 50.322 1.00 34.08 S ATOM 11932 SG CYS E 192 46.413 64.863 48.588 1.00 30.40 S ATOM 12006 SG CYS E 203 48.546 64.277 54.478 1.00 35.16 S ATOM 11962 SG CYS E 196 43.043 62.048 53.748 1.00 36.65 S ATOM 11751 SG CYS E 167 44.097 72.440 53.804 1.00 35.31 S ATOM 11728 SG CYS E 164 50.418 72.212 54.769 1.00 38.53 S ATOM 11873 SG CYS E 183 47.159 67.913 57.793 1.00 42.70 S ATOM 11805 SG CYS E 174 46.392 74.503 58.985 1.00 40.94 S ATOM 14451 SG CYS F 233 59.452 78.557 57.497 1.00 39.59 S ATOM 14488 SG CYS F 239 55.082 82.348 54.808 1.00 29.64 S ATOM 15155 SG CYS F 322 54.209 80.366 60.965 1.00 33.84 S ATOM 14470 SG CYS F 236 53.599 76.203 56.444 1.00 34.12 S ATOM 14516 SG CYS F 243 51.250 88.673 51.465 1.00 27.15 S ATOM 15088 SG CYS F 312 52.999 93.516 55.729 1.00 35.90 S ATOM 15126 SG CYS F 318 52.674 87.867 57.985 1.00 30.98 S ATOM 15105 SG CYS F 315 47.295 90.476 55.530 1.00 32.50 S ATOM 13290 SG CYS F 96 43.511 94.141 55.629 1.00 39.57 S ATOM 13648 SG CYS F 139 44.953 99.083 59.921 1.00 49.62 S ATOM 13631 SG CYS F 137 43.599 93.136 61.907 1.00 52.30 S ATOM 13581 SG CYS F 131 39.032 96.392 59.224 1.00 54.54 S ATOM 14553 SG CYS F 248 56.571 85.659 43.547 1.00 30.16 S ATOM 14984 SG CYS F 299 58.845 90.152 47.220 1.00 35.82 S ATOM 14747 SG CYS F 271 59.399 84.129 48.139 1.00 26.47 S ATOM 14536 SG CYS F 246 53.212 86.931 48.919 1.00 29.32 S ATOM 17270 SG CYS G 253 56.402 87.087 34.338 1.00 50.86 S ATOM 17301 SG CYS G 258 58.629 85.673 36.851 1.00 37.99 S ATOM 17321 SG CYS G 261 61.931 87.769 36.579 1.00 41.64 S ATOM 17415 SG CYS G 273 60.080 90.507 34.487 1.00 52.75 S ATOM 18016 SG CYS H 65 41.295 42.488 48.618 1.00 30.00 S Time building chain proxies: 4.53, per 1000 atoms: 0.21 Number of scatterers: 21120 At special positions: 0 Unit cell: (105.156, 215.28, 85.284, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Ni 2 28.00 Fe 62 26.01 S 202 16.00 P 4 15.00 O 3822 8.00 N 3528 7.00 C 13500 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS B 191 " - pdb=" SG CYS F 343 " distance=2.03 Simple disulfide: pdb=" SG CYS B 343 " - pdb=" SG CYS F 191 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=3, symmetry=0 Number of additional bonds: simple=3, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.59 Conformation dependent library (CDL) restraints added in 891.4 milliseconds Enol-peptide restraints added in 715.3 nanoseconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" FES C 301 " pdb="FE1 FES C 301 " - pdb=" SG CYS C 258 " pdb="FE2 FES C 301 " - pdb=" SG CYS C 261 " pdb="FE2 FES C 301 " - pdb=" SG CYS C 273 " pdb="FE1 FES C 301 " - pdb=" SG CYS C 253 " pdb=" FES G 301 " pdb="FE1 FES G 301 " - pdb=" SG CYS G 258 " pdb="FE2 FES G 301 " - pdb=" SG CYS G 261 " pdb="FE2 FES G 301 " - pdb=" SG CYS G 273 " pdb="FE1 FES G 301 " - pdb=" SG CYS G 253 " pdb=" SF4 A 301 " pdb="FE3 SF4 A 301 " - pdb=" NE2 HIS D 160 " pdb="FE3 SF4 A 301 " - pdb=" SG CYS A 14 " pdb="FE2 SF4 A 301 " - pdb=" SG CYS A 136 " pdb="FE1 SF4 A 301 " - pdb=" SG CYS A 86 " pdb="FE4 SF4 A 301 " - pdb=" SG CYS A 17 " pdb=" SF4 A 302 " pdb="FE4 SF4 A 302 " - pdb=" SG CYS A 196 " pdb="FE2 SF4 A 302 " - pdb=" SG CYS A 192 " pdb="FE3 SF4 A 302 " - pdb=" SG CYS A 203 " pdb="FE1 SF4 A 302 " - pdb=" SG CYS A 206 " pdb=" SF4 A 303 " pdb="FE2 SF4 A 303 " - pdb=" SG CYS A 164 " pdb="FE1 SF4 A 303 " - pdb=" SG CYS A 167 " pdb="FE4 SF4 A 303 " - pdb=" SG CYS A 174 " pdb="FE3 SF4 A 303 " - pdb=" SG CYS A 183 " pdb=" SF4 B 401 " pdb="FE2 SF4 B 401 " - pdb=" SG CYS B 239 " pdb="FE3 SF4 B 401 " - pdb=" SG CYS B 322 " pdb="FE4 SF4 B 401 " - pdb=" SG CYS B 236 " pdb="FE1 SF4 B 401 " - pdb=" SG CYS B 233 " pdb=" SF4 B 402 " pdb="FE4 SF4 B 402 " - pdb=" SG CYS B 315 " pdb="FE2 SF4 B 402 " - pdb=" SG CYS B 312 " pdb="FE3 SF4 B 402 " - pdb=" SG CYS B 318 " pdb="FE1 SF4 B 402 " - pdb=" SG CYS B 243 " pdb=" SF4 B 403 " pdb="FE4 SF4 B 403 " - pdb=" ND1 HIS B 94 " pdb="FE1 SF4 B 403 " - pdb=" SG CYS B 96 " pdb="FE3 SF4 B 403 " - pdb=" SG CYS B 137 " pdb="FE4 SF4 B 403 " - pdb=" SG CYS B 131 " pdb="FE2 SF4 B 403 " - pdb=" SG CYS B 139 " pdb=" SF4 B 404 " pdb="FE3 SF4 B 404 " - pdb=" SG CYS B 271 " pdb="FE1 SF4 B 404 " - pdb=" SG CYS B 248 " pdb="FE4 SF4 B 404 " - pdb=" SG CYS B 246 " pdb="FE2 SF4 B 404 " - pdb=" SG CYS B 299 " pdb=" SF4 E 301 " pdb="FE3 SF4 E 301 " - pdb=" NE2 HIS H 160 " pdb="FE2 SF4 E 301 " - pdb=" SG CYS E 136 " pdb="FE3 SF4 E 301 " - pdb=" SG CYS E 14 " pdb="FE1 SF4 E 301 " - pdb=" SG CYS E 86 " pdb="FE4 SF4 E 301 " - pdb=" SG CYS E 17 " pdb=" SF4 E 302 " pdb="FE4 SF4 E 302 " - pdb=" SG CYS E 196 " pdb="FE2 SF4 E 302 " - pdb=" SG CYS E 192 " pdb="FE3 SF4 E 302 " - pdb=" SG CYS E 203 " pdb="FE1 SF4 E 302 " - pdb=" SG CYS E 206 " pdb=" SF4 E 303 " pdb="FE2 SF4 E 303 " - pdb=" SG CYS E 164 " pdb="FE1 SF4 E 303 " - pdb=" SG CYS E 167 " pdb="FE3 SF4 E 303 " - pdb=" SG CYS E 183 " pdb="FE4 SF4 E 303 " - pdb=" SG CYS E 174 " pdb=" SF4 F 401 " pdb="FE3 SF4 F 401 " - pdb=" SG CYS F 322 " pdb="FE4 SF4 F 401 " - pdb=" SG CYS F 236 " pdb="FE2 SF4 F 401 " - pdb=" SG CYS F 239 " pdb="FE1 SF4 F 401 " - pdb=" SG CYS F 233 " pdb=" SF4 F 402 " pdb="FE3 SF4 F 402 " - pdb=" SG CYS F 318 " pdb="FE2 SF4 F 402 " - pdb=" SG CYS F 312 " pdb="FE4 SF4 F 402 " - pdb=" SG CYS F 315 " pdb="FE1 SF4 F 402 " - pdb=" SG CYS F 243 " pdb=" SF4 F 403 " pdb="FE4 SF4 F 403 " - pdb=" SG CYS F 131 " pdb="FE3 SF4 F 403 " - pdb=" SG CYS F 137 " pdb="FE1 SF4 F 403 " - pdb=" SG CYS F 96 " pdb="FE2 SF4 F 403 " - pdb=" SG CYS F 139 " pdb=" SF4 F 404 " pdb="FE3 SF4 F 404 " - pdb=" SG CYS F 271 " pdb="FE1 SF4 F 404 " - pdb=" SG CYS F 248 " pdb="FE4 SF4 F 404 " - pdb=" SG CYS F 246 " pdb="FE2 SF4 F 404 " - pdb=" SG CYS F 299 " Number of angles added : 180 5160 Ramachandran restraints generated. 2580 Oldfield, 0 Emsley, 2580 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4816 Finding SS restraints... Secondary structure from input PDB file: 119 helices and 24 sheets defined 45.2% alpha, 15.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.79 Creating SS restraints... Processing helix chain 'A' and resid 15 through 24 removed outlier: 3.501A pdb=" N MET A 24 " --> pdb=" O GLN A 20 " (cutoff:3.500A) Processing helix chain 'A' and resid 26 through 33 removed outlier: 3.571A pdb=" N ILE A 31 " --> pdb=" O LEU A 27 " (cutoff:3.500A) Proline residue: A 32 - end of helix Processing helix chain 'A' and resid 64 through 76 Processing helix chain 'A' and resid 84 through 90 Processing helix chain 'A' and resid 91 through 95 Processing helix chain 'A' and resid 99 through 108 Processing helix chain 'A' and resid 122 through 126 Processing helix chain 'A' and resid 139 through 153 Processing helix chain 'A' and resid 162 through 171 removed outlier: 4.348A pdb=" N GLU A 166 " --> pdb=" O PRO A 162 " (cutoff:3.500A) Processing helix chain 'A' and resid 174 through 179 Processing helix chain 'A' and resid 184 through 188 Processing helix chain 'A' and resid 194 through 199 Processing helix chain 'A' and resid 216 through 227 removed outlier: 3.691A pdb=" N LEU A 220 " --> pdb=" O TRP A 216 " (cutoff:3.500A) Processing helix chain 'A' and resid 230 through 238 Processing helix chain 'A' and resid 246 through 256 removed outlier: 4.144A pdb=" N LYS A 250 " --> pdb=" O GLU A 246 " (cutoff:3.500A) Processing helix chain 'B' and resid 10 through 19 Processing helix chain 'B' and resid 42 through 46 Processing helix chain 'B' and resid 56 through 60 removed outlier: 3.624A pdb=" N PHE B 60 " --> pdb=" O PRO B 57 " (cutoff:3.500A) Processing helix chain 'B' and resid 94 through 109 Processing helix chain 'B' and resid 114 through 122 removed outlier: 3.663A pdb=" N ARG B 120 " --> pdb=" O TYR B 116 " (cutoff:3.500A) Processing helix chain 'B' and resid 170 through 178 Processing helix chain 'B' and resid 179 through 182 Processing helix chain 'B' and resid 186 through 203 removed outlier: 3.759A pdb=" N ALA B 192 " --> pdb=" O LYS B 188 " (cutoff:3.500A) Processing helix chain 'B' and resid 212 through 220 removed outlier: 4.222A pdb=" N GLU B 218 " --> pdb=" O ARG B 214 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N LEU B 219 " --> pdb=" O TYR B 215 " (cutoff:3.500A) Processing helix chain 'B' and resid 223 through 233 removed outlier: 3.814A pdb=" N ASP B 227 " --> pdb=" O HIS B 223 " (cutoff:3.500A) Processing helix chain 'B' and resid 237 through 242 Processing helix chain 'B' and resid 273 through 277 removed outlier: 3.853A pdb=" N GLY B 277 " --> pdb=" O ARG B 274 " (cutoff:3.500A) Processing helix chain 'B' and resid 279 through 283 removed outlier: 3.705A pdb=" N GLY B 282 " --> pdb=" O VAL B 279 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N HIS B 283 " --> pdb=" O ALA B 280 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 279 through 283' Processing helix chain 'B' and resid 288 through 301 Processing helix chain 'B' and resid 316 through 321 Processing helix chain 'B' and resid 327 through 337 Processing helix chain 'C' and resid 41 through 48 removed outlier: 3.564A pdb=" N LYS C 47 " --> pdb=" O GLU C 43 " (cutoff:3.500A) Processing helix chain 'C' and resid 88 through 96 removed outlier: 3.625A pdb=" N ARG C 96 " --> pdb=" O THR C 92 " (cutoff:3.500A) Processing helix chain 'C' and resid 131 through 145 removed outlier: 3.971A pdb=" N LEU C 135 " --> pdb=" O GLY C 131 " (cutoff:3.500A) Processing helix chain 'C' and resid 146 through 149 Processing helix chain 'C' and resid 166 through 173 Processing helix chain 'C' and resid 173 through 180 Processing helix chain 'C' and resid 200 through 206 removed outlier: 3.765A pdb=" N VAL C 206 " --> pdb=" O GLN C 202 " (cutoff:3.500A) Processing helix chain 'C' and resid 211 through 213 No H-bonds generated for 'chain 'C' and resid 211 through 213' Processing helix chain 'C' and resid 225 through 236 Processing helix chain 'C' and resid 239 through 241 No H-bonds generated for 'chain 'C' and resid 239 through 241' Processing helix chain 'C' and resid 272 through 276 Processing helix chain 'C' and resid 280 through 287 Processing helix chain 'D' and resid 53 through 61 removed outlier: 3.703A pdb=" N ILE D 60 " --> pdb=" O GLU D 56 " (cutoff:3.500A) Processing helix chain 'D' and resid 62 through 65 removed outlier: 3.715A pdb=" N CYS D 65 " --> pdb=" O PRO D 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 62 through 65' Processing helix chain 'D' and resid 68 through 84 removed outlier: 3.729A pdb=" N HIS D 72 " --> pdb=" O CYS D 68 " (cutoff:3.500A) Processing helix chain 'D' and resid 89 through 115 Processing helix chain 'D' and resid 116 through 121 Processing helix chain 'D' and resid 127 through 131 removed outlier: 3.713A pdb=" N VAL D 130 " --> pdb=" O LEU D 127 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N ASN D 131 " --> pdb=" O LYS D 128 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 127 through 131' Processing helix chain 'D' and resid 133 through 155 Processing helix chain 'D' and resid 174 through 201 Proline residue: D 190 - end of helix Processing helix chain 'D' and resid 240 through 242 No H-bonds generated for 'chain 'D' and resid 240 through 242' Processing helix chain 'D' and resid 243 through 247 removed outlier: 3.949A pdb=" N TYR D 247 " --> pdb=" O LYS D 243 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 243 through 247' Processing helix chain 'D' and resid 271 through 280 removed outlier: 4.165A pdb=" N ASN D 278 " --> pdb=" O SER D 274 " (cutoff:3.500A) Processing helix chain 'D' and resid 281 through 283 No H-bonds generated for 'chain 'D' and resid 281 through 283' Processing helix chain 'D' and resid 285 through 294 removed outlier: 3.588A pdb=" N GLU D 289 " --> pdb=" O GLY D 285 " (cutoff:3.500A) Processing helix chain 'D' and resid 304 through 329 removed outlier: 4.496A pdb=" N LEU D 308 " --> pdb=" O PHE D 304 " (cutoff:3.500A) Processing helix chain 'D' and resid 376 through 395 removed outlier: 4.406A pdb=" N ALA D 383 " --> pdb=" O ALA D 379 " (cutoff:3.500A) removed outlier: 5.096A pdb=" N MET D 384 " --> pdb=" O PHE D 380 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLU D 387 " --> pdb=" O ALA D 383 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N LYS D 395 " --> pdb=" O MET D 391 " (cutoff:3.500A) Processing helix chain 'D' and resid 400 through 415 Processing helix chain 'D' and resid 418 through 423 Processing helix chain 'E' and resid 15 through 24 removed outlier: 3.502A pdb=" N MET E 24 " --> pdb=" O GLN E 20 " (cutoff:3.500A) Processing helix chain 'E' and resid 26 through 33 removed outlier: 3.602A pdb=" N ILE E 31 " --> pdb=" O LEU E 27 " (cutoff:3.500A) Proline residue: E 32 - end of helix Processing helix chain 'E' and resid 64 through 77 Processing helix chain 'E' and resid 84 through 90 Processing helix chain 'E' and resid 91 through 95 removed outlier: 3.510A pdb=" N SER E 94 " --> pdb=" O GLY E 91 " (cutoff:3.500A) Processing helix chain 'E' and resid 99 through 108 Processing helix chain 'E' and resid 122 through 126 Processing helix chain 'E' and resid 139 through 153 Processing helix chain 'E' and resid 162 through 171 removed outlier: 4.313A pdb=" N GLU E 166 " --> pdb=" O PRO E 162 " (cutoff:3.500A) Processing helix chain 'E' and resid 174 through 179 Processing helix chain 'E' and resid 184 through 188 Processing helix chain 'E' and resid 194 through 200 Processing helix chain 'E' and resid 216 through 227 removed outlier: 3.573A pdb=" N LEU E 220 " --> pdb=" O TRP E 216 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LYS E 227 " --> pdb=" O VAL E 223 " (cutoff:3.500A) Processing helix chain 'E' and resid 230 through 238 Processing helix chain 'E' and resid 246 through 256 removed outlier: 4.002A pdb=" N LYS E 250 " --> pdb=" O GLU E 246 " (cutoff:3.500A) Processing helix chain 'F' and resid 10 through 19 Processing helix chain 'F' and resid 42 through 46 Processing helix chain 'F' and resid 56 through 60 removed outlier: 3.612A pdb=" N PHE F 60 " --> pdb=" O PRO F 57 " (cutoff:3.500A) Processing helix chain 'F' and resid 94 through 109 Processing helix chain 'F' and resid 114 through 123 removed outlier: 3.655A pdb=" N ARG F 120 " --> pdb=" O TYR F 116 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N LYS F 123 " --> pdb=" O VAL F 119 " (cutoff:3.500A) Processing helix chain 'F' and resid 168 through 178 removed outlier: 3.718A pdb=" N ASN F 178 " --> pdb=" O LEU F 174 " (cutoff:3.500A) Processing helix chain 'F' and resid 179 through 182 Processing helix chain 'F' and resid 186 through 203 removed outlier: 3.824A pdb=" N ALA F 192 " --> pdb=" O LYS F 188 " (cutoff:3.500A) Processing helix chain 'F' and resid 212 through 220 removed outlier: 3.837A pdb=" N GLU F 218 " --> pdb=" O ARG F 214 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N LEU F 219 " --> pdb=" O TYR F 215 " (cutoff:3.500A) Processing helix chain 'F' and resid 223 through 233 removed outlier: 3.911A pdb=" N ASP F 227 " --> pdb=" O HIS F 223 " (cutoff:3.500A) Processing helix chain 'F' and resid 237 through 242 Processing helix chain 'F' and resid 273 through 277 removed outlier: 3.899A pdb=" N GLY F 277 " --> pdb=" O ARG F 274 " (cutoff:3.500A) Processing helix chain 'F' and resid 279 through 283 removed outlier: 3.642A pdb=" N GLY F 282 " --> pdb=" O VAL F 279 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N HIS F 283 " --> pdb=" O ALA F 280 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 279 through 283' Processing helix chain 'F' and resid 288 through 301 Processing helix chain 'F' and resid 316 through 321 Processing helix chain 'F' and resid 327 through 337 removed outlier: 3.609A pdb=" N ASN F 331 " --> pdb=" O SER F 327 " (cutoff:3.500A) Processing helix chain 'G' and resid 41 through 48 Processing helix chain 'G' and resid 88 through 96 removed outlier: 3.731A pdb=" N ARG G 96 " --> pdb=" O THR G 92 " (cutoff:3.500A) Processing helix chain 'G' and resid 131 through 145 removed outlier: 3.877A pdb=" N LEU G 135 " --> pdb=" O GLY G 131 " (cutoff:3.500A) Processing helix chain 'G' and resid 146 through 149 Processing helix chain 'G' and resid 166 through 179 removed outlier: 4.475A pdb=" N ASP G 175 " --> pdb=" O GLU G 171 " (cutoff:3.500A) removed outlier: 4.879A pdb=" N LEU G 176 " --> pdb=" O ALA G 172 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ALA G 179 " --> pdb=" O ASP G 175 " (cutoff:3.500A) Processing helix chain 'G' and resid 200 through 205 Processing helix chain 'G' and resid 211 through 213 No H-bonds generated for 'chain 'G' and resid 211 through 213' Processing helix chain 'G' and resid 225 through 236 Processing helix chain 'G' and resid 239 through 241 No H-bonds generated for 'chain 'G' and resid 239 through 241' Processing helix chain 'G' and resid 272 through 276 Processing helix chain 'G' and resid 280 through 287 Processing helix chain 'H' and resid 53 through 59 removed outlier: 3.857A pdb=" N ALA H 59 " --> pdb=" O GLU H 55 " (cutoff:3.500A) Processing helix chain 'H' and resid 60 through 64 Processing helix chain 'H' and resid 68 through 85 Processing helix chain 'H' and resid 89 through 115 Processing helix chain 'H' and resid 117 through 122 removed outlier: 3.848A pdb=" N GLY H 122 " --> pdb=" O ASP H 119 " (cutoff:3.500A) Processing helix chain 'H' and resid 125 through 129 Processing helix chain 'H' and resid 133 through 156 Processing helix chain 'H' and resid 174 through 201 Proline residue: H 190 - end of helix Processing helix chain 'H' and resid 240 through 242 No H-bonds generated for 'chain 'H' and resid 240 through 242' Processing helix chain 'H' and resid 243 through 247 Processing helix chain 'H' and resid 271 through 280 removed outlier: 4.217A pdb=" N ASN H 278 " --> pdb=" O SER H 274 " (cutoff:3.500A) Processing helix chain 'H' and resid 281 through 283 No H-bonds generated for 'chain 'H' and resid 281 through 283' Processing helix chain 'H' and resid 285 through 294 Processing helix chain 'H' and resid 304 through 331 removed outlier: 4.538A pdb=" N LEU H 308 " --> pdb=" O PHE H 304 " (cutoff:3.500A) Processing helix chain 'H' and resid 376 through 395 removed outlier: 4.293A pdb=" N ALA H 383 " --> pdb=" O ALA H 379 " (cutoff:3.500A) removed outlier: 4.884A pdb=" N MET H 384 " --> pdb=" O PHE H 380 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N GLU H 386 " --> pdb=" O LEU H 382 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N GLU H 387 " --> pdb=" O ALA H 383 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N LYS H 395 " --> pdb=" O MET H 391 " (cutoff:3.500A) Processing helix chain 'H' and resid 400 through 416 Processing helix chain 'H' and resid 418 through 424 Processing sheet with id=AA1, first strand: chain 'A' and resid 34 through 39 removed outlier: 6.092A pdb=" N VAL A 4 " --> pdb=" O ALA A 34 " (cutoff:3.500A) removed outlier: 5.208A pdb=" N ILE A 36 " --> pdb=" O VAL A 4 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N ILE A 6 " --> pdb=" O ILE A 36 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N CYS A 38 " --> pdb=" O ILE A 6 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N ARG A 5 " --> pdb=" O ILE A 54 " (cutoff:3.500A) removed outlier: 7.473A pdb=" N PHE A 56 " --> pdb=" O ARG A 5 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N GLY A 7 " --> pdb=" O PHE A 56 " (cutoff:3.500A) removed outlier: 7.162A pdb=" N GLU A 58 " --> pdb=" O GLY A 7 " (cutoff:3.500A) removed outlier: 6.106A pdb=" N TYR A 9 " --> pdb=" O GLU A 58 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N ASP A 53 " --> pdb=" O ILE A 79 " (cutoff:3.500A) removed outlier: 7.358A pdb=" N VAL A 81 " --> pdb=" O ASP A 53 " (cutoff:3.500A) removed outlier: 6.013A pdb=" N ALA A 55 " --> pdb=" O VAL A 81 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N VAL A 83 " --> pdb=" O ALA A 55 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N ILE A 57 " --> pdb=" O VAL A 83 " (cutoff:3.500A) removed outlier: 8.676A pdb=" N TYR A 131 " --> pdb=" O LYS A 78 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N VAL A 80 " --> pdb=" O TYR A 131 " (cutoff:3.500A) removed outlier: 8.269A pdb=" N ILE A 133 " --> pdb=" O VAL A 80 " (cutoff:3.500A) removed outlier: 7.084A pdb=" N ALA A 82 " --> pdb=" O ILE A 133 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 61 through 63 removed outlier: 5.777A pdb=" N THR A 63 " --> pdb=" O LYS A 119 " (cutoff:3.500A) removed outlier: 7.473A pdb=" N LYS A 119 " --> pdb=" O THR A 63 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 35 through 39 removed outlier: 9.642A pdb=" N VAL B 93 " --> pdb=" O PRO B 27 " (cutoff:3.500A) removed outlier: 16.193A pdb=" N LYS B 29 " --> pdb=" O VAL B 93 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N ILE B 125 " --> pdb=" O ILE B 89 " (cutoff:3.500A) removed outlier: 5.073A pdb=" N PHE B 91 " --> pdb=" O ILE B 125 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N ILE B 127 " --> pdb=" O PHE B 91 " (cutoff:3.500A) removed outlier: 8.798A pdb=" N LEU B 153 " --> pdb=" O GLY B 124 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N ILE B 126 " --> pdb=" O LEU B 153 " (cutoff:3.500A) removed outlier: 7.615A pdb=" N PHE B 155 " --> pdb=" O ILE B 126 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N GLY B 128 " --> pdb=" O PHE B 155 " (cutoff:3.500A) removed outlier: 7.290A pdb=" N GLU B 157 " --> pdb=" O GLY B 128 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 77 through 80 removed outlier: 3.538A pdb=" N GLU B 77 " --> pdb=" O ASP B 72 " (cutoff:3.500A) removed outlier: 5.504A pdb=" N LYS B 67 " --> pdb=" O ARG B 266 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N ARG B 266 " --> pdb=" O LYS B 67 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N PHE B 69 " --> pdb=" O ARG B 264 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 64 through 69 removed outlier: 3.506A pdb=" N GLY C 64 " --> pdb=" O ILE C 60 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N PHE C 55 " --> pdb=" O PRO C 108 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N GLN C 57 " --> pdb=" O ARG C 106 " (cutoff:3.500A) removed outlier: 5.592A pdb=" N VAL C 22 " --> pdb=" O ARG C 38 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N ARG C 38 " --> pdb=" O VAL C 22 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N LYS C 24 " --> pdb=" O LEU C 36 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 197 through 198 removed outlier: 4.376A pdb=" N LEU C 197 " --> pdb=" O GLN C 186 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N ILE C 152 " --> pdb=" O LYS C 183 " (cutoff:3.500A) removed outlier: 7.714A pdb=" N ILE C 185 " --> pdb=" O ILE C 152 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N PHE C 154 " --> pdb=" O ILE C 185 " (cutoff:3.500A) removed outlier: 7.781A pdb=" N SER C 187 " --> pdb=" O PHE C 154 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N ASN C 156 " --> pdb=" O SER C 187 " (cutoff:3.500A) removed outlier: 6.209A pdb=" N ASP C 122 " --> pdb=" O ALA C 216 " (cutoff:3.500A) removed outlier: 7.736A pdb=" N ALA C 218 " --> pdb=" O ASP C 122 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N LEU C 124 " --> pdb=" O ALA C 218 " (cutoff:3.500A) removed outlier: 7.802A pdb=" N CYS C 220 " --> pdb=" O LEU C 124 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N ILE C 126 " --> pdb=" O CYS C 220 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 262 through 264 Processing sheet with id=AA8, first strand: chain 'D' and resid 8 through 9 removed outlier: 3.894A pdb=" N GLU D 33 " --> pdb=" O ILE D 25 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N GLY D 27 " --> pdb=" O VAL D 31 " (cutoff:3.500A) removed outlier: 5.651A pdb=" N VAL D 31 " --> pdb=" O GLY D 27 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 164 through 165 removed outlier: 3.611A pdb=" N VAL D 165 " --> pdb=" O GLY D 168 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 215 through 219 removed outlier: 4.508A pdb=" N TYR D 230 " --> pdb=" O LYS D 218 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N PHE D 239 " --> pdb=" O ILE D 231 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 248 through 252 Processing sheet with id=AB3, first strand: chain 'D' and resid 345 through 349 removed outlier: 7.067A pdb=" N VAL D 359 " --> pdb=" O ILE D 374 " (cutoff:3.500A) removed outlier: 4.743A pdb=" N ILE D 374 " --> pdb=" O VAL D 359 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N ALA D 361 " --> pdb=" O ALA D 372 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N ALA D 372 " --> pdb=" O ALA D 361 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N LYS D 363 " --> pdb=" O SER D 370 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 34 through 39 removed outlier: 6.224A pdb=" N VAL E 4 " --> pdb=" O ALA E 34 " (cutoff:3.500A) removed outlier: 5.252A pdb=" N ILE E 36 " --> pdb=" O VAL E 4 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N ILE E 6 " --> pdb=" O ILE E 36 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N CYS E 38 " --> pdb=" O ILE E 6 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N ARG E 5 " --> pdb=" O ILE E 54 " (cutoff:3.500A) removed outlier: 7.481A pdb=" N PHE E 56 " --> pdb=" O ARG E 5 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N GLY E 7 " --> pdb=" O PHE E 56 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N GLU E 58 " --> pdb=" O GLY E 7 " (cutoff:3.500A) removed outlier: 6.022A pdb=" N TYR E 9 " --> pdb=" O GLU E 58 " (cutoff:3.500A) removed outlier: 5.971A pdb=" N ALA E 55 " --> pdb=" O VAL E 81 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N VAL E 83 " --> pdb=" O ALA E 55 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N ILE E 57 " --> pdb=" O VAL E 83 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N VAL E 80 " --> pdb=" O TYR E 131 " (cutoff:3.500A) removed outlier: 8.198A pdb=" N ILE E 133 " --> pdb=" O VAL E 80 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N ALA E 82 " --> pdb=" O ILE E 133 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 61 through 63 removed outlier: 5.727A pdb=" N THR E 63 " --> pdb=" O LYS E 119 " (cutoff:3.500A) removed outlier: 7.404A pdb=" N LYS E 119 " --> pdb=" O THR E 63 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'F' and resid 35 through 39 removed outlier: 6.079A pdb=" N TYR F 25 " --> pdb=" O PHE F 91 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N VAL F 93 " --> pdb=" O TYR F 25 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N ILE F 125 " --> pdb=" O ILE F 89 " (cutoff:3.500A) removed outlier: 5.154A pdb=" N PHE F 91 " --> pdb=" O ILE F 125 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N ILE F 127 " --> pdb=" O PHE F 91 " (cutoff:3.500A) removed outlier: 9.069A pdb=" N LEU F 153 " --> pdb=" O GLY F 124 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N ILE F 126 " --> pdb=" O LEU F 153 " (cutoff:3.500A) removed outlier: 7.647A pdb=" N PHE F 155 " --> pdb=" O ILE F 126 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N GLY F 128 " --> pdb=" O PHE F 155 " (cutoff:3.500A) removed outlier: 7.321A pdb=" N GLU F 157 " --> pdb=" O GLY F 128 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 77 through 80 removed outlier: 6.501A pdb=" N ARG F 264 " --> pdb=" O LEU F 68 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N GLU F 70 " --> pdb=" O GLY F 262 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N GLY F 262 " --> pdb=" O GLU F 70 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'G' and resid 64 through 69 removed outlier: 5.447A pdb=" N VAL G 22 " --> pdb=" O ARG G 38 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N ARG G 38 " --> pdb=" O VAL G 22 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N LYS G 24 " --> pdb=" O LEU G 36 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'G' and resid 185 through 188 removed outlier: 7.668A pdb=" N ILE G 185 " --> pdb=" O ILE G 152 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N PHE G 154 " --> pdb=" O ILE G 185 " (cutoff:3.500A) removed outlier: 7.887A pdb=" N SER G 187 " --> pdb=" O PHE G 154 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N ASN G 156 " --> pdb=" O SER G 187 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N ASP G 122 " --> pdb=" O ALA G 216 " (cutoff:3.500A) removed outlier: 7.842A pdb=" N ALA G 218 " --> pdb=" O ASP G 122 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N LEU G 124 " --> pdb=" O ALA G 218 " (cutoff:3.500A) removed outlier: 7.894A pdb=" N CYS G 220 " --> pdb=" O LEU G 124 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N ILE G 126 " --> pdb=" O CYS G 220 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'G' and resid 262 through 264 Processing sheet with id=AC2, first strand: chain 'H' and resid 8 through 9 removed outlier: 3.692A pdb=" N ILE H 25 " --> pdb=" O GLU H 33 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N GLU H 33 " --> pdb=" O ILE H 25 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'H' and resid 164 through 165 Processing sheet with id=AC4, first strand: chain 'H' and resid 238 through 239 removed outlier: 4.306A pdb=" N TYR H 230 " --> pdb=" O LYS H 218 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'H' and resid 248 through 252 Processing sheet with id=AC6, first strand: chain 'H' and resid 345 through 352 removed outlier: 3.641A pdb=" N GLY H 345 " --> pdb=" O VAL H 364 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N VAL H 364 " --> pdb=" O GLY H 345 " (cutoff:3.500A) removed outlier: 7.458A pdb=" N VAL H 359 " --> pdb=" O ILE H 374 " (cutoff:3.500A) removed outlier: 4.920A pdb=" N ILE H 374 " --> pdb=" O VAL H 359 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N ALA H 361 " --> pdb=" O ALA H 372 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N ALA H 372 " --> pdb=" O ALA H 361 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N LYS H 363 " --> pdb=" O SER H 370 " (cutoff:3.500A) 835 hydrogen bonds defined for protein. 2343 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: 3.23 Time building geometry restraints manager: 2.13 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.13 - 1.43: 9106 1.43 - 1.73: 12190 1.73 - 2.04: 206 2.04 - 2.34: 176 2.34 - 2.64: 2 Bond restraints: 21680 Sorted by residual: bond pdb=" O3P FAD G 302 " pdb=" P FAD G 302 " ideal model delta sigma weight residual 1.660 1.582 0.078 2.00e-02 2.50e+03 1.52e+01 bond pdb=" O3P FAD C 302 " pdb=" P FAD C 302 " ideal model delta sigma weight residual 1.660 1.583 0.077 2.00e-02 2.50e+03 1.48e+01 bond pdb=" O5' FAD G 302 " pdb=" P FAD G 302 " ideal model delta sigma weight residual 1.637 1.574 0.063 2.00e-02 2.50e+03 9.99e+00 bond pdb=" O5' FAD C 302 " pdb=" P FAD C 302 " ideal model delta sigma weight residual 1.637 1.575 0.062 2.00e-02 2.50e+03 9.73e+00 bond pdb=" O5B FAD C 302 " pdb=" PA FAD C 302 " ideal model delta sigma weight residual 1.634 1.577 0.057 2.00e-02 2.50e+03 8.01e+00 ... (remaining 21675 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.74: 29048 1.74 - 3.48: 289 3.48 - 5.23: 35 5.23 - 6.97: 20 6.97 - 8.71: 6 Bond angle restraints: 29398 Sorted by residual: angle pdb=" C PRO B 169 " pdb=" N THR B 170 " pdb=" CA THR B 170 " ideal model delta sigma weight residual 121.54 129.12 -7.58 1.91e+00 2.74e-01 1.58e+01 angle pdb=" C GLY H 155 " pdb=" N SER H 156 " pdb=" CA SER H 156 " ideal model delta sigma weight residual 121.54 127.69 -6.15 1.91e+00 2.74e-01 1.04e+01 angle pdb=" O1P FAD G 302 " pdb=" P FAD G 302 " pdb=" O2P FAD G 302 " ideal model delta sigma weight residual 122.50 113.79 8.71 3.00e+00 1.11e-01 8.43e+00 angle pdb=" O1P FAD C 302 " pdb=" P FAD C 302 " pdb=" O2P FAD C 302 " ideal model delta sigma weight residual 122.50 114.62 7.88 3.00e+00 1.11e-01 6.91e+00 angle pdb=" N GLY B 171 " pdb=" CA GLY B 171 " pdb=" C GLY B 171 " ideal model delta sigma weight residual 113.18 107.06 6.12 2.37e+00 1.78e-01 6.68e+00 ... (remaining 29393 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.77: 12036 16.77 - 33.54: 738 33.54 - 50.31: 155 50.31 - 67.08: 38 67.08 - 83.85: 19 Dihedral angle restraints: 12986 sinusoidal: 5462 harmonic: 7524 Sorted by residual: dihedral pdb=" CA VAL F 260 " pdb=" C VAL F 260 " pdb=" N THR F 261 " pdb=" CA THR F 261 " ideal model delta harmonic sigma weight residual 180.00 156.97 23.03 0 5.00e+00 4.00e-02 2.12e+01 dihedral pdb=" CA ASP F 258 " pdb=" C ASP F 258 " pdb=" N GLY F 259 " pdb=" CA GLY F 259 " ideal model delta harmonic sigma weight residual 180.00 161.70 18.30 0 5.00e+00 4.00e-02 1.34e+01 dihedral pdb=" CA PHE F 69 " pdb=" C PHE F 69 " pdb=" N GLU F 70 " pdb=" CA GLU F 70 " ideal model delta harmonic sigma weight residual 180.00 163.67 16.33 0 5.00e+00 4.00e-02 1.07e+01 ... (remaining 12983 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 1731 0.027 - 0.054: 837 0.054 - 0.081: 323 0.081 - 0.107: 200 0.107 - 0.134: 63 Chirality restraints: 3154 Sorted by residual: chirality pdb=" C2B FAD C 302 " pdb=" C1B FAD C 302 " pdb=" C3B FAD C 302 " pdb=" O2B FAD C 302 " both_signs ideal model delta sigma weight residual False -2.53 -2.67 0.13 2.00e-01 2.50e+01 4.50e-01 chirality pdb=" CA CYS A 196 " pdb=" N CYS A 196 " pdb=" C CYS A 196 " pdb=" CB CYS A 196 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.50e-01 chirality pdb=" C2B FAD G 302 " pdb=" C1B FAD G 302 " pdb=" C3B FAD G 302 " pdb=" O2B FAD G 302 " both_signs ideal model delta sigma weight residual False -2.53 -2.67 0.13 2.00e-01 2.50e+01 4.46e-01 ... (remaining 3151 not shown) Planarity restraints: 3720 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR B 170 " -0.015 2.00e-02 2.50e+03 3.05e-02 9.32e+00 pdb=" C THR B 170 " 0.053 2.00e-02 2.50e+03 pdb=" O THR B 170 " -0.020 2.00e-02 2.50e+03 pdb=" N GLY B 171 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL G 66 " -0.026 5.00e-02 4.00e+02 3.99e-02 2.55e+00 pdb=" N PRO G 67 " 0.069 5.00e-02 4.00e+02 pdb=" CA PRO G 67 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO G 67 " -0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA HIS H 111 " 0.008 2.00e-02 2.50e+03 1.58e-02 2.51e+00 pdb=" C HIS H 111 " -0.027 2.00e-02 2.50e+03 pdb=" O HIS H 111 " 0.010 2.00e-02 2.50e+03 pdb=" N LEU H 112 " 0.009 2.00e-02 2.50e+03 ... (remaining 3717 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 2244 2.75 - 3.29: 20940 3.29 - 3.82: 35868 3.82 - 4.36: 42739 4.36 - 4.90: 73973 Nonbonded interactions: 175764 Sorted by model distance: nonbonded pdb=" OE1 GLU D 78 " pdb=" OG1 THR D 351 " model vdw 2.210 3.040 nonbonded pdb=" OH TYR F 249 " pdb=" OH TYR G 15 " model vdw 2.223 3.040 nonbonded pdb=" OH TYR B 249 " pdb=" OH TYR C 15 " model vdw 2.225 3.040 nonbonded pdb=" OG1 THR C 29 " pdb=" OE1 GLU C 32 " model vdw 2.225 3.040 nonbonded pdb=" O PHE B 151 " pdb=" OG1 THR B 168 " model vdw 2.240 3.040 ... (remaining 175759 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'E' } ncs_group { reference = chain 'B' selection = chain 'F' } ncs_group { reference = chain 'C' selection = chain 'G' } ncs_group { reference = chain 'D' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 3.670 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.320 Check model and map are aligned: 0.070 Set scattering table: 0.050 Process input model: 20.590 Find NCS groups from input model: 0.320 Set up NCS constraints: 0.050 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: 0.000 Load rotamer database and sin/cos tables:1.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.280 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7566 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.421 21752 Z= 0.392 Angle : 1.031 65.378 29582 Z= 0.265 Chirality : 0.042 0.134 3154 Planarity : 0.004 0.040 3720 Dihedral : 11.895 83.853 8164 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 3.48 % Allowed : 7.23 % Favored : 89.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.62 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.35 (0.16), residues: 2580 helix: 0.09 (0.16), residues: 1006 sheet: 0.10 (0.27), residues: 380 loop : -0.50 (0.18), residues: 1194 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 142 TYR 0.012 0.001 TYR H 113 PHE 0.017 0.001 PHE F 138 TRP 0.007 0.001 TRP C 48 HIS 0.004 0.001 HIS B 94 Details of bonding type rmsd covalent geometry : bond 0.00316 (21680) covalent geometry : angle 0.50300 (29398) SS BOND : bond 0.00073 ( 2) SS BOND : angle 0.32738 ( 4) hydrogen bonds : bond 0.18030 ( 835) hydrogen bonds : angle 7.06927 ( 2343) metal coordination : bond 0.02090 ( 67) metal coordination : angle 11.54243 ( 180) Misc. bond : bond 0.30815 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5160 Ramachandran restraints generated. 2580 Oldfield, 0 Emsley, 2580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5160 Ramachandran restraints generated. 2580 Oldfield, 0 Emsley, 2580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 713 residues out of total 2240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 635 time to evaluate : 0.834 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 161 TYR cc_start: 0.8992 (OUTLIER) cc_final: 0.7562 (p90) REVERT: A 227 LYS cc_start: 0.8472 (mmtt) cc_final: 0.8234 (mmtp) REVERT: B 72 ASP cc_start: 0.7470 (t0) cc_final: 0.7209 (t0) REVERT: C 80 PHE cc_start: 0.6799 (p90) cc_final: 0.6354 (p90) REVERT: C 97 LEU cc_start: 0.8024 (OUTLIER) cc_final: 0.7816 (tp) REVERT: C 101 ASP cc_start: 0.8041 (m-30) cc_final: 0.7595 (m-30) REVERT: C 136 ARG cc_start: 0.7965 (ttt-90) cc_final: 0.7480 (ttp-170) REVERT: C 148 LYS cc_start: 0.8448 (ptmt) cc_final: 0.6707 (ptmt) REVERT: C 193 ASN cc_start: 0.8687 (p0) cc_final: 0.8125 (t0) REVERT: D 181 MET cc_start: 0.8222 (tpt) cc_final: 0.7713 (tpt) REVERT: D 239 PHE cc_start: 0.7361 (p90) cc_final: 0.7066 (p90) REVERT: D 373 ASP cc_start: 0.6122 (m-30) cc_final: 0.5819 (m-30) REVERT: D 384 MET cc_start: 0.6376 (mmm) cc_final: 0.6044 (mmm) REVERT: D 391 MET cc_start: 0.8176 (mtt) cc_final: 0.7803 (mtt) REVERT: E 29 GLN cc_start: 0.8508 (mt0) cc_final: 0.8269 (mt0) REVERT: E 47 ILE cc_start: 0.8782 (mt) cc_final: 0.8499 (mt) REVERT: E 161 TYR cc_start: 0.8876 (OUTLIER) cc_final: 0.7593 (p90) REVERT: E 235 ILE cc_start: 0.8909 (OUTLIER) cc_final: 0.8684 (tp) REVERT: F 227 ASP cc_start: 0.7632 (m-30) cc_final: 0.6715 (m-30) REVERT: G 32 GLU cc_start: 0.8105 (mp0) cc_final: 0.7676 (mp0) REVERT: G 152 ILE cc_start: 0.8918 (pt) cc_final: 0.8689 (mp) REVERT: H 61 TYR cc_start: 0.6872 (m-10) cc_final: 0.6625 (m-80) REVERT: H 148 THR cc_start: 0.8424 (m) cc_final: 0.8145 (t) REVERT: H 312 LEU cc_start: 0.8651 (tp) cc_final: 0.8420 (tt) REVERT: H 421 CYS cc_start: 0.5424 (OUTLIER) cc_final: 0.5050 (m) outliers start: 78 outliers final: 26 residues processed: 693 average time/residue: 0.1833 time to fit residues: 182.6408 Evaluate side-chains 527 residues out of total 2240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 496 time to evaluate : 0.871 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 THR Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 161 TYR Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 244 HIS Chi-restraints excluded: chain B residue 260 VAL Chi-restraints excluded: chain C residue 95 HIS Chi-restraints excluded: chain C residue 97 LEU Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain D residue 154 LEU Chi-restraints excluded: chain D residue 360 TYR Chi-restraints excluded: chain D residue 392 MET Chi-restraints excluded: chain D residue 423 VAL Chi-restraints excluded: chain E residue 12 THR Chi-restraints excluded: chain E residue 40 PHE Chi-restraints excluded: chain E residue 161 TYR Chi-restraints excluded: chain E residue 235 ILE Chi-restraints excluded: chain E residue 244 HIS Chi-restraints excluded: chain F residue 51 ASN Chi-restraints excluded: chain F residue 85 VAL Chi-restraints excluded: chain F residue 257 LEU Chi-restraints excluded: chain F residue 261 THR Chi-restraints excluded: chain G residue 22 VAL Chi-restraints excluded: chain G residue 95 HIS Chi-restraints excluded: chain G residue 190 ARG Chi-restraints excluded: chain H residue 260 HIS Chi-restraints excluded: chain H residue 359 VAL Chi-restraints excluded: chain H residue 360 TYR Chi-restraints excluded: chain H residue 364 VAL Chi-restraints excluded: chain H residue 421 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 197 optimal weight: 4.9990 chunk 215 optimal weight: 0.4980 chunk 20 optimal weight: 6.9990 chunk 132 optimal weight: 5.9990 chunk 248 optimal weight: 0.7980 chunk 207 optimal weight: 5.9990 chunk 155 optimal weight: 0.0970 chunk 244 optimal weight: 7.9990 chunk 183 optimal weight: 1.9990 chunk 111 optimal weight: 9.9990 chunk 71 optimal weight: 0.5980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 178 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 272 GLN D 294 ASN ** D 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 207 HIS G 151 ASN H 204 GLN H 260 HIS ** H 396 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.102547 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.084565 restraints weight = 52088.204| |-----------------------------------------------------------------------------| r_work (start): 0.3365 rms_B_bonded: 2.76 r_work: 0.3226 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3226 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8025 moved from start: 0.2315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.097 21752 Z= 0.161 Angle : 1.106 65.725 29582 Z= 0.335 Chirality : 0.045 0.234 3154 Planarity : 0.005 0.075 3720 Dihedral : 7.934 71.756 3013 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 11.73 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.15 % Favored : 95.81 % Rotamer: Outliers : 4.02 % Allowed : 15.62 % Favored : 80.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.62 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.29 (0.17), residues: 2580 helix: 0.25 (0.16), residues: 1020 sheet: -0.12 (0.27), residues: 378 loop : -0.49 (0.19), residues: 1182 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG H 186 TYR 0.018 0.002 TYR H 371 PHE 0.017 0.002 PHE G 80 TRP 0.019 0.001 TRP G 194 HIS 0.007 0.001 HIS F 49 Details of bonding type rmsd covalent geometry : bond 0.00356 (21680) covalent geometry : angle 0.62533 (29398) SS BOND : bond 0.00098 ( 2) SS BOND : angle 0.21149 ( 4) hydrogen bonds : bond 0.04554 ( 835) hydrogen bonds : angle 5.75160 ( 2343) metal coordination : bond 0.02011 ( 67) metal coordination : angle 11.70551 ( 180) Misc. bond : bond 0.00145 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5160 Ramachandran restraints generated. 2580 Oldfield, 0 Emsley, 2580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5160 Ramachandran restraints generated. 2580 Oldfield, 0 Emsley, 2580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 606 residues out of total 2240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 516 time to evaluate : 0.577 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 227 LYS cc_start: 0.8713 (mmtt) cc_final: 0.8481 (mmtp) REVERT: B 55 MET cc_start: 0.7606 (OUTLIER) cc_final: 0.7246 (ttm) REVERT: B 72 ASP cc_start: 0.7711 (t0) cc_final: 0.7444 (t0) REVERT: B 228 GLU cc_start: 0.8299 (tp30) cc_final: 0.8086 (tp30) REVERT: C 70 ILE cc_start: 0.7269 (mm) cc_final: 0.7030 (mm) REVERT: C 101 ASP cc_start: 0.8138 (m-30) cc_final: 0.7777 (m-30) REVERT: C 148 LYS cc_start: 0.8482 (ptmt) cc_final: 0.8091 (ptmm) REVERT: C 193 ASN cc_start: 0.9006 (p0) cc_final: 0.8465 (t0) REVERT: D 93 GLN cc_start: 0.8664 (mm-40) cc_final: 0.8402 (mm-40) REVERT: D 129 MET cc_start: 0.5948 (ptp) cc_final: 0.5517 (ptp) REVERT: D 279 ASN cc_start: 0.8397 (p0) cc_final: 0.8157 (p0) REVERT: D 390 ARG cc_start: 0.9128 (ptm-80) cc_final: 0.8912 (ttp80) REVERT: E 64 GLU cc_start: 0.7651 (mp0) cc_final: 0.7344 (mp0) REVERT: E 161 TYR cc_start: 0.9041 (OUTLIER) cc_final: 0.7700 (p90) REVERT: F 9 GLU cc_start: 0.7729 (pm20) cc_final: 0.7304 (pm20) REVERT: F 10 ASN cc_start: 0.8077 (m-40) cc_final: 0.7124 (m-40) REVERT: G 32 GLU cc_start: 0.8385 (mp0) cc_final: 0.8067 (mp0) REVERT: G 169 GLU cc_start: 0.8854 (tm-30) cc_final: 0.8592 (tm-30) REVERT: G 214 ASN cc_start: 0.8364 (t0) cc_final: 0.7956 (t0) REVERT: H 61 TYR cc_start: 0.6937 (m-10) cc_final: 0.6656 (m-80) REVERT: H 148 THR cc_start: 0.8549 (m) cc_final: 0.7877 (t) REVERT: H 152 ASP cc_start: 0.8231 (OUTLIER) cc_final: 0.6645 (m-30) REVERT: H 260 HIS cc_start: 0.5576 (OUTLIER) cc_final: 0.4528 (m170) REVERT: H 302 ASN cc_start: 0.6063 (t0) cc_final: 0.5780 (t0) REVERT: H 365 GLU cc_start: 0.6761 (pp20) cc_final: 0.6537 (pp20) REVERT: H 371 TYR cc_start: 0.7587 (t80) cc_final: 0.6802 (t80) REVERT: H 384 MET cc_start: 0.7221 (mmm) cc_final: 0.6715 (mmm) REVERT: H 388 HIS cc_start: 0.8283 (m90) cc_final: 0.8017 (m90) outliers start: 90 outliers final: 46 residues processed: 579 average time/residue: 0.1796 time to fit residues: 149.7028 Evaluate side-chains 521 residues out of total 2240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 471 time to evaluate : 0.811 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 161 TYR Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 244 HIS Chi-restraints excluded: chain B residue 28 VAL Chi-restraints excluded: chain B residue 55 MET Chi-restraints excluded: chain B residue 221 MET Chi-restraints excluded: chain C residue 31 THR Chi-restraints excluded: chain C residue 44 LEU Chi-restraints excluded: chain C residue 95 HIS Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 126 ILE Chi-restraints excluded: chain C residue 211 ASN Chi-restraints excluded: chain D residue 16 VAL Chi-restraints excluded: chain D residue 154 LEU Chi-restraints excluded: chain D residue 253 VAL Chi-restraints excluded: chain D residue 260 HIS Chi-restraints excluded: chain D residue 306 ASN Chi-restraints excluded: chain D residue 360 TYR Chi-restraints excluded: chain E residue 12 THR Chi-restraints excluded: chain E residue 40 PHE Chi-restraints excluded: chain E residue 152 ILE Chi-restraints excluded: chain E residue 161 TYR Chi-restraints excluded: chain E residue 218 ASP Chi-restraints excluded: chain E residue 235 ILE Chi-restraints excluded: chain E residue 244 HIS Chi-restraints excluded: chain F residue 15 LEU Chi-restraints excluded: chain F residue 85 VAL Chi-restraints excluded: chain F residue 174 LEU Chi-restraints excluded: chain F residue 207 HIS Chi-restraints excluded: chain F residue 221 MET Chi-restraints excluded: chain F residue 257 LEU Chi-restraints excluded: chain F residue 261 THR Chi-restraints excluded: chain G residue 22 VAL Chi-restraints excluded: chain G residue 73 SER Chi-restraints excluded: chain G residue 95 HIS Chi-restraints excluded: chain G residue 126 ILE Chi-restraints excluded: chain G residue 190 ARG Chi-restraints excluded: chain G residue 227 LYS Chi-restraints excluded: chain G residue 285 VAL Chi-restraints excluded: chain H residue 125 SER Chi-restraints excluded: chain H residue 131 ASN Chi-restraints excluded: chain H residue 139 ILE Chi-restraints excluded: chain H residue 152 ASP Chi-restraints excluded: chain H residue 256 SER Chi-restraints excluded: chain H residue 260 HIS Chi-restraints excluded: chain H residue 350 THR Chi-restraints excluded: chain H residue 359 VAL Chi-restraints excluded: chain H residue 360 TYR Chi-restraints excluded: chain H residue 364 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 188 optimal weight: 0.9980 chunk 224 optimal weight: 1.9990 chunk 62 optimal weight: 2.9990 chunk 77 optimal weight: 0.1980 chunk 203 optimal weight: 6.9990 chunk 55 optimal weight: 0.9980 chunk 116 optimal weight: 1.9990 chunk 204 optimal weight: 0.9980 chunk 133 optimal weight: 0.5980 chunk 237 optimal weight: 9.9990 chunk 160 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 49 HIS ** B 178 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 203 GLN ** D 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 240 ASN G 145 ASN H 255 HIS H 294 ASN ** H 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.102518 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.084749 restraints weight = 52312.298| |-----------------------------------------------------------------------------| r_work (start): 0.3368 rms_B_bonded: 2.68 r_work: 0.3228 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3228 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8015 moved from start: 0.2762 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.090 21752 Z= 0.143 Angle : 1.098 65.103 29582 Z= 0.328 Chirality : 0.045 0.251 3154 Planarity : 0.005 0.047 3720 Dihedral : 6.965 67.005 3000 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 12.06 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.41 % Favored : 96.55 % Rotamer: Outliers : 4.15 % Allowed : 17.01 % Favored : 78.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.62 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.34 (0.16), residues: 2580 helix: 0.26 (0.16), residues: 998 sheet: -0.03 (0.27), residues: 366 loop : -0.59 (0.18), residues: 1216 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG G 159 TYR 0.019 0.002 TYR H 371 PHE 0.037 0.002 PHE G 166 TRP 0.031 0.001 TRP G 194 HIS 0.008 0.001 HIS F 207 Details of bonding type rmsd covalent geometry : bond 0.00322 (21680) covalent geometry : angle 0.61644 (29398) SS BOND : bond 0.00065 ( 2) SS BOND : angle 0.13835 ( 4) hydrogen bonds : bond 0.04174 ( 835) hydrogen bonds : angle 5.54172 ( 2343) metal coordination : bond 0.01951 ( 67) metal coordination : angle 11.66309 ( 180) Misc. bond : bond 0.00123 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5160 Ramachandran restraints generated. 2580 Oldfield, 0 Emsley, 2580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5160 Ramachandran restraints generated. 2580 Oldfield, 0 Emsley, 2580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 583 residues out of total 2240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 490 time to evaluate : 0.768 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 GLU cc_start: 0.7360 (mp0) cc_final: 0.7046 (mp0) REVERT: A 112 LYS cc_start: 0.8077 (tppt) cc_final: 0.7848 (tptt) REVERT: A 251 MET cc_start: 0.8589 (OUTLIER) cc_final: 0.8239 (mtt) REVERT: B 9 GLU cc_start: 0.7649 (pm20) cc_final: 0.7233 (pm20) REVERT: B 29 LYS cc_start: 0.8509 (mmtm) cc_final: 0.8281 (mmtt) REVERT: B 55 MET cc_start: 0.7612 (OUTLIER) cc_final: 0.7278 (ttm) REVERT: B 72 ASP cc_start: 0.7713 (t0) cc_final: 0.7465 (t0) REVERT: C 70 ILE cc_start: 0.7278 (mm) cc_final: 0.6860 (mm) REVERT: C 148 LYS cc_start: 0.8415 (ptmt) cc_final: 0.8092 (ptmm) REVERT: C 173 MET cc_start: 0.8351 (mtm) cc_final: 0.8114 (ptp) REVERT: C 193 ASN cc_start: 0.8964 (p0) cc_final: 0.8381 (t0) REVERT: D 15 ARG cc_start: 0.7971 (mpp80) cc_final: 0.6810 (mpp80) REVERT: D 93 GLN cc_start: 0.8638 (mm-40) cc_final: 0.8393 (mm-40) REVERT: D 129 MET cc_start: 0.5754 (ptp) cc_final: 0.5518 (ptp) REVERT: D 279 ASN cc_start: 0.8285 (p0) cc_final: 0.8027 (p0) REVERT: D 390 ARG cc_start: 0.9217 (ptm-80) cc_final: 0.8894 (ttp-110) REVERT: E 64 GLU cc_start: 0.7569 (mp0) cc_final: 0.7210 (mp0) REVERT: E 161 TYR cc_start: 0.9020 (OUTLIER) cc_final: 0.7665 (p90) REVERT: F 9 GLU cc_start: 0.7569 (pm20) cc_final: 0.7318 (pm20) REVERT: F 10 ASN cc_start: 0.7753 (m-40) cc_final: 0.7509 (m-40) REVERT: G 214 ASN cc_start: 0.8416 (t0) cc_final: 0.8095 (t0) REVERT: H 61 TYR cc_start: 0.6603 (m-10) cc_final: 0.6331 (m-80) REVERT: H 93 GLN cc_start: 0.8535 (tp40) cc_final: 0.8275 (tp40) REVERT: H 148 THR cc_start: 0.8481 (m) cc_final: 0.7869 (t) REVERT: H 152 ASP cc_start: 0.8160 (OUTLIER) cc_final: 0.6536 (m-30) REVERT: H 260 HIS cc_start: 0.5670 (OUTLIER) cc_final: 0.4486 (m170) REVERT: H 269 MET cc_start: 0.6708 (tmm) cc_final: 0.6492 (tmm) REVERT: H 298 LEU cc_start: 0.8865 (OUTLIER) cc_final: 0.8590 (tt) REVERT: H 371 TYR cc_start: 0.7550 (t80) cc_final: 0.7346 (t80) REVERT: H 384 MET cc_start: 0.7226 (mmm) cc_final: 0.6843 (mmm) REVERT: H 395 LYS cc_start: 0.8969 (mmtm) cc_final: 0.8583 (mptt) outliers start: 93 outliers final: 49 residues processed: 560 average time/residue: 0.1859 time to fit residues: 151.1400 Evaluate side-chains 495 residues out of total 2240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 440 time to evaluate : 0.838 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 THR Chi-restraints excluded: chain A residue 96 SER Chi-restraints excluded: chain A residue 161 TYR Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 244 HIS Chi-restraints excluded: chain A residue 251 MET Chi-restraints excluded: chain B residue 28 VAL Chi-restraints excluded: chain B residue 55 MET Chi-restraints excluded: chain B residue 335 ILE Chi-restraints excluded: chain C residue 44 LEU Chi-restraints excluded: chain C residue 95 HIS Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 126 ILE Chi-restraints excluded: chain C residue 211 ASN Chi-restraints excluded: chain D residue 16 VAL Chi-restraints excluded: chain D residue 54 LEU Chi-restraints excluded: chain D residue 154 LEU Chi-restraints excluded: chain D residue 253 VAL Chi-restraints excluded: chain D residue 260 HIS Chi-restraints excluded: chain D residue 306 ASN Chi-restraints excluded: chain D residue 360 TYR Chi-restraints excluded: chain D residue 380 PHE Chi-restraints excluded: chain E residue 12 THR Chi-restraints excluded: chain E residue 47 ILE Chi-restraints excluded: chain E residue 152 ILE Chi-restraints excluded: chain E residue 161 TYR Chi-restraints excluded: chain E residue 184 LEU Chi-restraints excluded: chain E residue 218 ASP Chi-restraints excluded: chain E residue 235 ILE Chi-restraints excluded: chain E residue 244 HIS Chi-restraints excluded: chain F residue 15 LEU Chi-restraints excluded: chain F residue 51 ASN Chi-restraints excluded: chain F residue 174 LEU Chi-restraints excluded: chain F residue 181 LEU Chi-restraints excluded: chain F residue 257 LEU Chi-restraints excluded: chain G residue 22 VAL Chi-restraints excluded: chain G residue 27 SER Chi-restraints excluded: chain G residue 44 LEU Chi-restraints excluded: chain G residue 95 HIS Chi-restraints excluded: chain G residue 126 ILE Chi-restraints excluded: chain G residue 190 ARG Chi-restraints excluded: chain G residue 285 VAL Chi-restraints excluded: chain H residue 125 SER Chi-restraints excluded: chain H residue 131 ASN Chi-restraints excluded: chain H residue 139 ILE Chi-restraints excluded: chain H residue 152 ASP Chi-restraints excluded: chain H residue 256 SER Chi-restraints excluded: chain H residue 260 HIS Chi-restraints excluded: chain H residue 294 ASN Chi-restraints excluded: chain H residue 298 LEU Chi-restraints excluded: chain H residue 306 ASN Chi-restraints excluded: chain H residue 350 THR Chi-restraints excluded: chain H residue 359 VAL Chi-restraints excluded: chain H residue 360 TYR Chi-restraints excluded: chain H residue 364 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 118 optimal weight: 3.9990 chunk 55 optimal weight: 4.9990 chunk 172 optimal weight: 0.7980 chunk 168 optimal weight: 1.9990 chunk 169 optimal weight: 2.9990 chunk 210 optimal weight: 5.9990 chunk 243 optimal weight: 6.9990 chunk 162 optimal weight: 0.6980 chunk 148 optimal weight: 7.9990 chunk 110 optimal weight: 0.9990 chunk 117 optimal weight: 2.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 178 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 49 HIS ** F 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 240 ASN F 331 ASN G 145 ASN G 193 ASN H 255 HIS ** H 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 381 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.100529 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.082434 restraints weight = 51963.376| |-----------------------------------------------------------------------------| r_work (start): 0.3316 rms_B_bonded: 2.71 r_work: 0.3172 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3172 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8076 moved from start: 0.3087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.109 21752 Z= 0.204 Angle : 1.155 66.226 29582 Z= 0.354 Chirality : 0.047 0.224 3154 Planarity : 0.005 0.057 3720 Dihedral : 6.804 66.333 2995 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 13.61 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.15 % Favored : 95.81 % Rotamer: Outliers : 4.46 % Allowed : 17.01 % Favored : 78.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.62 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.50 (0.16), residues: 2580 helix: 0.14 (0.16), residues: 996 sheet: -0.07 (0.27), residues: 360 loop : -0.71 (0.18), residues: 1224 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG F 199 TYR 0.020 0.002 TYR H 316 PHE 0.023 0.002 PHE G 166 TRP 0.032 0.002 TRP G 194 HIS 0.004 0.001 HIS B 94 Details of bonding type rmsd covalent geometry : bond 0.00469 (21680) covalent geometry : angle 0.66171 (29398) SS BOND : bond 0.00058 ( 2) SS BOND : angle 0.18714 ( 4) hydrogen bonds : bond 0.04502 ( 835) hydrogen bonds : angle 5.60926 ( 2343) metal coordination : bond 0.02456 ( 67) metal coordination : angle 12.15246 ( 180) Misc. bond : bond 0.00355 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5160 Ramachandran restraints generated. 2580 Oldfield, 0 Emsley, 2580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5160 Ramachandran restraints generated. 2580 Oldfield, 0 Emsley, 2580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 588 residues out of total 2240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 488 time to evaluate : 0.808 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 76 ASN cc_start: 0.8338 (t0) cc_final: 0.7955 (t0) REVERT: A 238 MET cc_start: 0.8403 (OUTLIER) cc_final: 0.7077 (mtp) REVERT: A 251 MET cc_start: 0.8588 (mtt) cc_final: 0.8344 (mtt) REVERT: B 55 MET cc_start: 0.7755 (OUTLIER) cc_final: 0.7419 (ttm) REVERT: B 72 ASP cc_start: 0.7739 (t0) cc_final: 0.7532 (t0) REVERT: C 148 LYS cc_start: 0.8483 (ptmt) cc_final: 0.8226 (ptmm) REVERT: C 173 MET cc_start: 0.8520 (mtm) cc_final: 0.8272 (ptp) REVERT: C 193 ASN cc_start: 0.8974 (p0) cc_final: 0.8408 (t0) REVERT: C 227 LYS cc_start: 0.8617 (tptt) cc_final: 0.8391 (tptt) REVERT: D 15 ARG cc_start: 0.7900 (mpp80) cc_final: 0.7335 (mpp80) REVERT: D 93 GLN cc_start: 0.8660 (mm-40) cc_final: 0.8402 (mm-40) REVERT: D 120 TYR cc_start: 0.8929 (OUTLIER) cc_final: 0.8109 (t80) REVERT: D 269 MET cc_start: 0.6654 (tmm) cc_final: 0.6372 (tmm) REVERT: D 279 ASN cc_start: 0.8278 (p0) cc_final: 0.7859 (p0) REVERT: D 317 PHE cc_start: 0.8063 (m-80) cc_final: 0.7759 (t80) REVERT: D 385 MET cc_start: 0.8408 (ttp) cc_final: 0.8173 (ttt) REVERT: D 390 ARG cc_start: 0.9195 (ptm-80) cc_final: 0.8945 (ttp80) REVERT: E 237 ARG cc_start: 0.8459 (tpp-160) cc_final: 0.8256 (tpt170) REVERT: E 238 MET cc_start: 0.8366 (OUTLIER) cc_final: 0.7201 (mtp) REVERT: F 172 HIS cc_start: 0.7659 (OUTLIER) cc_final: 0.7427 (t-90) REVERT: F 229 GLU cc_start: 0.7760 (mm-30) cc_final: 0.7556 (mm-30) REVERT: G 51 LYS cc_start: 0.9139 (mmtm) cc_final: 0.8894 (mmmt) REVERT: G 214 ASN cc_start: 0.8430 (t0) cc_final: 0.7930 (t0) REVERT: H 93 GLN cc_start: 0.8560 (tp40) cc_final: 0.8300 (tp40) REVERT: H 113 TYR cc_start: 0.8467 (m-80) cc_final: 0.8227 (m-80) REVERT: H 148 THR cc_start: 0.8516 (m) cc_final: 0.7993 (t) REVERT: H 152 ASP cc_start: 0.8238 (OUTLIER) cc_final: 0.7345 (m-30) REVERT: H 171 LYS cc_start: 0.8173 (mttt) cc_final: 0.7949 (mttp) REVERT: H 260 HIS cc_start: 0.5821 (OUTLIER) cc_final: 0.4959 (m170) REVERT: H 317 PHE cc_start: 0.7948 (m-80) cc_final: 0.7744 (t80) REVERT: H 327 GLU cc_start: 0.7953 (tm-30) cc_final: 0.7716 (tm-30) REVERT: H 385 MET cc_start: 0.8725 (ttp) cc_final: 0.8367 (ttp) REVERT: H 395 LYS cc_start: 0.9016 (mmtm) cc_final: 0.8816 (mptt) outliers start: 100 outliers final: 65 residues processed: 556 average time/residue: 0.1736 time to fit residues: 140.0934 Evaluate side-chains 517 residues out of total 2240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 445 time to evaluate : 0.813 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 PHE Chi-restraints excluded: chain A residue 47 ILE Chi-restraints excluded: chain A residue 96 SER Chi-restraints excluded: chain A residue 161 TYR Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 238 MET Chi-restraints excluded: chain A residue 244 HIS Chi-restraints excluded: chain B residue 28 VAL Chi-restraints excluded: chain B residue 51 ASN Chi-restraints excluded: chain B residue 55 MET Chi-restraints excluded: chain B residue 168 THR Chi-restraints excluded: chain B residue 225 MET Chi-restraints excluded: chain B residue 327 SER Chi-restraints excluded: chain B residue 335 ILE Chi-restraints excluded: chain C residue 44 LEU Chi-restraints excluded: chain C residue 95 HIS Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 126 ILE Chi-restraints excluded: chain C residue 211 ASN Chi-restraints excluded: chain D residue 16 VAL Chi-restraints excluded: chain D residue 24 ILE Chi-restraints excluded: chain D residue 74 LEU Chi-restraints excluded: chain D residue 120 TYR Chi-restraints excluded: chain D residue 154 LEU Chi-restraints excluded: chain D residue 248 ILE Chi-restraints excluded: chain D residue 253 VAL Chi-restraints excluded: chain D residue 260 HIS Chi-restraints excluded: chain D residue 306 ASN Chi-restraints excluded: chain D residue 360 TYR Chi-restraints excluded: chain D residue 380 PHE Chi-restraints excluded: chain D residue 418 CYS Chi-restraints excluded: chain E residue 40 PHE Chi-restraints excluded: chain E residue 47 ILE Chi-restraints excluded: chain E residue 152 ILE Chi-restraints excluded: chain E residue 158 ASP Chi-restraints excluded: chain E residue 161 TYR Chi-restraints excluded: chain E residue 184 LEU Chi-restraints excluded: chain E residue 235 ILE Chi-restraints excluded: chain E residue 238 MET Chi-restraints excluded: chain E residue 244 HIS Chi-restraints excluded: chain F residue 15 LEU Chi-restraints excluded: chain F residue 51 ASN Chi-restraints excluded: chain F residue 132 MET Chi-restraints excluded: chain F residue 160 ASP Chi-restraints excluded: chain F residue 172 HIS Chi-restraints excluded: chain F residue 180 LYS Chi-restraints excluded: chain F residue 181 LEU Chi-restraints excluded: chain F residue 257 LEU Chi-restraints excluded: chain F residue 260 VAL Chi-restraints excluded: chain F residue 261 THR Chi-restraints excluded: chain F residue 332 LEU Chi-restraints excluded: chain G residue 22 VAL Chi-restraints excluded: chain G residue 27 SER Chi-restraints excluded: chain G residue 73 SER Chi-restraints excluded: chain G residue 95 HIS Chi-restraints excluded: chain G residue 126 ILE Chi-restraints excluded: chain G residue 190 ARG Chi-restraints excluded: chain G residue 285 VAL Chi-restraints excluded: chain H residue 114 LEU Chi-restraints excluded: chain H residue 125 SER Chi-restraints excluded: chain H residue 131 ASN Chi-restraints excluded: chain H residue 139 ILE Chi-restraints excluded: chain H residue 152 ASP Chi-restraints excluded: chain H residue 256 SER Chi-restraints excluded: chain H residue 260 HIS Chi-restraints excluded: chain H residue 294 ASN Chi-restraints excluded: chain H residue 306 ASN Chi-restraints excluded: chain H residue 350 THR Chi-restraints excluded: chain H residue 359 VAL Chi-restraints excluded: chain H residue 360 TYR Chi-restraints excluded: chain H residue 364 VAL Chi-restraints excluded: chain H residue 381 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 147 optimal weight: 0.6980 chunk 178 optimal weight: 0.9980 chunk 60 optimal weight: 4.9990 chunk 169 optimal weight: 0.9980 chunk 230 optimal weight: 0.0020 chunk 61 optimal weight: 0.6980 chunk 28 optimal weight: 0.7980 chunk 65 optimal weight: 5.9990 chunk 76 optimal weight: 5.9990 chunk 33 optimal weight: 2.9990 chunk 172 optimal weight: 0.8980 overall best weight: 0.6188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 178 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 260 HIS ** D 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 172 HIS ** F 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 145 ASN G 193 ASN ** G 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 294 ASN ** H 381 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.102102 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.084248 restraints weight = 51894.287| |-----------------------------------------------------------------------------| r_work (start): 0.3362 rms_B_bonded: 2.63 r_work: 0.3227 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3227 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8023 moved from start: 0.3296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.105 21752 Z= 0.140 Angle : 1.126 65.886 29582 Z= 0.336 Chirality : 0.045 0.199 3154 Planarity : 0.004 0.058 3720 Dihedral : 6.659 65.298 2994 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 12.40 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.84 % Favored : 96.12 % Rotamer: Outliers : 3.84 % Allowed : 19.11 % Favored : 77.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.62 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.47 (0.16), residues: 2580 helix: 0.21 (0.16), residues: 990 sheet: -0.19 (0.27), residues: 362 loop : -0.70 (0.18), residues: 1228 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 44 TYR 0.018 0.001 TYR H 415 PHE 0.024 0.001 PHE C 166 TRP 0.032 0.001 TRP G 194 HIS 0.003 0.001 HIS D 160 Details of bonding type rmsd covalent geometry : bond 0.00314 (21680) covalent geometry : angle 0.62944 (29398) SS BOND : bond 0.00062 ( 2) SS BOND : angle 0.18344 ( 4) hydrogen bonds : bond 0.04030 ( 835) hydrogen bonds : angle 5.46410 ( 2343) metal coordination : bond 0.02045 ( 67) metal coordination : angle 11.98138 ( 180) Misc. bond : bond 0.00963 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5160 Ramachandran restraints generated. 2580 Oldfield, 0 Emsley, 2580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5160 Ramachandran restraints generated. 2580 Oldfield, 0 Emsley, 2580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 555 residues out of total 2240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 469 time to evaluate : 0.841 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 GLU cc_start: 0.7314 (mp0) cc_final: 0.6689 (mp0) REVERT: A 76 ASN cc_start: 0.8399 (t0) cc_final: 0.8022 (t0) REVERT: A 238 MET cc_start: 0.8318 (OUTLIER) cc_final: 0.6984 (mtp) REVERT: B 72 ASP cc_start: 0.7743 (t0) cc_final: 0.7451 (t0) REVERT: C 146 ARG cc_start: 0.7809 (tpt170) cc_final: 0.7500 (tpm170) REVERT: C 148 LYS cc_start: 0.8455 (ptmt) cc_final: 0.8202 (ptmm) REVERT: C 149 TYR cc_start: 0.7975 (m-80) cc_final: 0.7633 (m-80) REVERT: C 173 MET cc_start: 0.8487 (mtm) cc_final: 0.8246 (ptp) REVERT: C 193 ASN cc_start: 0.8953 (p0) cc_final: 0.8431 (t0) REVERT: C 206 VAL cc_start: 0.8827 (p) cc_final: 0.8602 (m) REVERT: D 93 GLN cc_start: 0.8685 (mm-40) cc_final: 0.8425 (mm-40) REVERT: D 120 TYR cc_start: 0.8918 (OUTLIER) cc_final: 0.8141 (t80) REVERT: D 171 LYS cc_start: 0.8073 (mttt) cc_final: 0.7729 (mttp) REVERT: D 181 MET cc_start: 0.8797 (tpp) cc_final: 0.7940 (tpp) REVERT: D 269 MET cc_start: 0.6551 (tmm) cc_final: 0.6211 (tmm) REVERT: D 279 ASN cc_start: 0.8199 (p0) cc_final: 0.7933 (p0) REVERT: D 363 LYS cc_start: 0.6845 (tptt) cc_final: 0.6618 (tptp) REVERT: D 385 MET cc_start: 0.8202 (ttp) cc_final: 0.7988 (ttt) REVERT: D 410 MET cc_start: 0.8911 (mmm) cc_final: 0.8673 (mmm) REVERT: E 66 GLU cc_start: 0.7465 (mt-10) cc_final: 0.7196 (mt-10) REVERT: E 161 TYR cc_start: 0.9042 (OUTLIER) cc_final: 0.7668 (p90) REVERT: E 238 MET cc_start: 0.8338 (OUTLIER) cc_final: 0.7234 (mtp) REVERT: E 254 LYS cc_start: 0.8289 (pttm) cc_final: 0.7948 (ptpp) REVERT: F 9 GLU cc_start: 0.7779 (pm20) cc_final: 0.7327 (pm20) REVERT: F 10 ASN cc_start: 0.8108 (m-40) cc_final: 0.7684 (m-40) REVERT: F 72 ASP cc_start: 0.7466 (t0) cc_final: 0.7237 (t0) REVERT: G 47 LYS cc_start: 0.8960 (ptpt) cc_final: 0.8746 (pttm) REVERT: G 214 ASN cc_start: 0.8405 (t0) cc_final: 0.7918 (t0) REVERT: H 93 GLN cc_start: 0.8543 (OUTLIER) cc_final: 0.8323 (tp40) REVERT: H 148 THR cc_start: 0.8467 (m) cc_final: 0.8163 (t) REVERT: H 152 ASP cc_start: 0.8132 (OUTLIER) cc_final: 0.7051 (m-30) REVERT: H 171 LYS cc_start: 0.8090 (mttt) cc_final: 0.7876 (mttp) REVERT: H 247 TYR cc_start: 0.8249 (m-80) cc_final: 0.7915 (m-80) REVERT: H 260 HIS cc_start: 0.5975 (OUTLIER) cc_final: 0.5114 (m170) REVERT: H 269 MET cc_start: 0.6799 (tmm) cc_final: 0.6337 (tmm) REVERT: H 298 LEU cc_start: 0.8897 (OUTLIER) cc_final: 0.8583 (tt) REVERT: H 327 GLU cc_start: 0.7871 (tm-30) cc_final: 0.7620 (tm-30) REVERT: H 331 LYS cc_start: 0.8696 (mmtt) cc_final: 0.8378 (mmtt) REVERT: H 360 TYR cc_start: 0.7911 (OUTLIER) cc_final: 0.6636 (m-80) REVERT: H 384 MET cc_start: 0.7019 (mmm) cc_final: 0.6545 (mmm) REVERT: H 385 MET cc_start: 0.8749 (ttp) cc_final: 0.8532 (ttm) REVERT: H 386 GLU cc_start: 0.8644 (mm-30) cc_final: 0.8331 (mm-30) REVERT: H 395 LYS cc_start: 0.8900 (mmtm) cc_final: 0.8624 (mmtt) outliers start: 86 outliers final: 56 residues processed: 529 average time/residue: 0.2007 time to fit residues: 152.3885 Evaluate side-chains 506 residues out of total 2240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 441 time to evaluate : 0.846 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 THR Chi-restraints excluded: chain A residue 47 ILE Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 96 SER Chi-restraints excluded: chain A residue 161 TYR Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 238 MET Chi-restraints excluded: chain A residue 244 HIS Chi-restraints excluded: chain B residue 15 LEU Chi-restraints excluded: chain B residue 28 VAL Chi-restraints excluded: chain B residue 168 THR Chi-restraints excluded: chain B residue 225 MET Chi-restraints excluded: chain B residue 327 SER Chi-restraints excluded: chain B residue 335 ILE Chi-restraints excluded: chain C residue 44 LEU Chi-restraints excluded: chain C residue 95 HIS Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 126 ILE Chi-restraints excluded: chain D residue 16 VAL Chi-restraints excluded: chain D residue 74 LEU Chi-restraints excluded: chain D residue 120 TYR Chi-restraints excluded: chain D residue 154 LEU Chi-restraints excluded: chain D residue 248 ILE Chi-restraints excluded: chain D residue 253 VAL Chi-restraints excluded: chain D residue 260 HIS Chi-restraints excluded: chain D residue 360 TYR Chi-restraints excluded: chain D residue 380 PHE Chi-restraints excluded: chain D residue 415 TYR Chi-restraints excluded: chain D residue 418 CYS Chi-restraints excluded: chain E residue 12 THR Chi-restraints excluded: chain E residue 40 PHE Chi-restraints excluded: chain E residue 47 ILE Chi-restraints excluded: chain E residue 152 ILE Chi-restraints excluded: chain E residue 158 ASP Chi-restraints excluded: chain E residue 161 TYR Chi-restraints excluded: chain E residue 184 LEU Chi-restraints excluded: chain E residue 235 ILE Chi-restraints excluded: chain E residue 238 MET Chi-restraints excluded: chain E residue 244 HIS Chi-restraints excluded: chain F residue 132 MET Chi-restraints excluded: chain F residue 257 LEU Chi-restraints excluded: chain F residue 260 VAL Chi-restraints excluded: chain F residue 261 THR Chi-restraints excluded: chain F residue 327 SER Chi-restraints excluded: chain F residue 332 LEU Chi-restraints excluded: chain G residue 22 VAL Chi-restraints excluded: chain G residue 95 HIS Chi-restraints excluded: chain G residue 126 ILE Chi-restraints excluded: chain G residue 190 ARG Chi-restraints excluded: chain G residue 285 VAL Chi-restraints excluded: chain H residue 93 GLN Chi-restraints excluded: chain H residue 112 LEU Chi-restraints excluded: chain H residue 125 SER Chi-restraints excluded: chain H residue 131 ASN Chi-restraints excluded: chain H residue 139 ILE Chi-restraints excluded: chain H residue 152 ASP Chi-restraints excluded: chain H residue 256 SER Chi-restraints excluded: chain H residue 260 HIS Chi-restraints excluded: chain H residue 298 LEU Chi-restraints excluded: chain H residue 306 ASN Chi-restraints excluded: chain H residue 350 THR Chi-restraints excluded: chain H residue 359 VAL Chi-restraints excluded: chain H residue 360 TYR Chi-restraints excluded: chain H residue 364 VAL Chi-restraints excluded: chain H residue 381 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 239 optimal weight: 7.9990 chunk 67 optimal weight: 0.8980 chunk 249 optimal weight: 9.9990 chunk 179 optimal weight: 0.6980 chunk 177 optimal weight: 1.9990 chunk 188 optimal weight: 0.9990 chunk 207 optimal weight: 1.9990 chunk 105 optimal weight: 0.9990 chunk 68 optimal weight: 2.9990 chunk 126 optimal weight: 6.9990 chunk 121 optimal weight: 5.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 178 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 111 ASN ** D 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 207 HIS F 240 ASN F 331 ASN G 193 ASN ** G 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 255 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.101084 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.083164 restraints weight = 51942.194| |-----------------------------------------------------------------------------| r_work (start): 0.3336 rms_B_bonded: 2.71 r_work: 0.3196 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3196 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8057 moved from start: 0.3447 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.101 21752 Z= 0.174 Angle : 1.149 66.382 29582 Z= 0.353 Chirality : 0.046 0.211 3154 Planarity : 0.005 0.066 3720 Dihedral : 6.715 67.411 2992 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 13.47 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.19 % Favored : 95.74 % Rotamer: Outliers : 4.20 % Allowed : 19.69 % Favored : 76.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.62 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.58 (0.16), residues: 2580 helix: 0.15 (0.16), residues: 992 sheet: -0.28 (0.27), residues: 364 loop : -0.77 (0.18), residues: 1224 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 168 TYR 0.020 0.002 TYR G 109 PHE 0.026 0.002 PHE G 166 TRP 0.035 0.002 TRP G 194 HIS 0.009 0.001 HIS D 260 Details of bonding type rmsd covalent geometry : bond 0.00397 (21680) covalent geometry : angle 0.65880 (29398) SS BOND : bond 0.00113 ( 2) SS BOND : angle 0.61829 ( 4) hydrogen bonds : bond 0.04302 ( 835) hydrogen bonds : angle 5.50668 ( 2343) metal coordination : bond 0.02208 ( 67) metal coordination : angle 12.08637 ( 180) Misc. bond : bond 0.00399 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5160 Ramachandran restraints generated. 2580 Oldfield, 0 Emsley, 2580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5160 Ramachandran restraints generated. 2580 Oldfield, 0 Emsley, 2580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 542 residues out of total 2240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 448 time to evaluate : 0.830 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 76 ASN cc_start: 0.8388 (t0) cc_final: 0.8033 (t0) REVERT: A 238 MET cc_start: 0.8370 (OUTLIER) cc_final: 0.7062 (mtp) REVERT: A 251 MET cc_start: 0.8429 (mtt) cc_final: 0.8172 (mtt) REVERT: B 72 ASP cc_start: 0.7783 (t0) cc_final: 0.7559 (t0) REVERT: B 146 PHE cc_start: 0.8433 (OUTLIER) cc_final: 0.8008 (t80) REVERT: C 148 LYS cc_start: 0.8491 (ptmt) cc_final: 0.8191 (ptmm) REVERT: C 168 LYS cc_start: 0.9050 (tppt) cc_final: 0.8575 (mmmm) REVERT: C 173 MET cc_start: 0.8456 (mtm) cc_final: 0.8224 (ptp) REVERT: C 193 ASN cc_start: 0.8963 (p0) cc_final: 0.8451 (t0) REVERT: C 203 GLN cc_start: 0.8203 (OUTLIER) cc_final: 0.7926 (pt0) REVERT: D 120 TYR cc_start: 0.8911 (OUTLIER) cc_final: 0.8217 (t80) REVERT: D 181 MET cc_start: 0.8852 (tpp) cc_final: 0.8280 (tpp) REVERT: D 269 MET cc_start: 0.6686 (tmm) cc_final: 0.5979 (tmm) REVERT: D 279 ASN cc_start: 0.8216 (p0) cc_final: 0.7833 (p0) REVERT: D 317 PHE cc_start: 0.8043 (m-80) cc_final: 0.7822 (t80) REVERT: D 384 MET cc_start: 0.7161 (mmm) cc_final: 0.6714 (mmm) REVERT: D 394 GLU cc_start: 0.8753 (mt-10) cc_final: 0.8335 (mt-10) REVERT: E 63 THR cc_start: 0.8629 (OUTLIER) cc_final: 0.8382 (m) REVERT: E 161 TYR cc_start: 0.9097 (OUTLIER) cc_final: 0.7549 (p90) REVERT: E 238 MET cc_start: 0.8370 (OUTLIER) cc_final: 0.7153 (mtp) REVERT: F 9 GLU cc_start: 0.7795 (pm20) cc_final: 0.7342 (pm20) REVERT: F 10 ASN cc_start: 0.8070 (m-40) cc_final: 0.7642 (m-40) REVERT: F 72 ASP cc_start: 0.7517 (t0) cc_final: 0.7289 (t0) REVERT: F 229 GLU cc_start: 0.7599 (mp0) cc_final: 0.7309 (mt-10) REVERT: G 32 GLU cc_start: 0.8464 (mp0) cc_final: 0.7979 (mp0) REVERT: G 43 GLU cc_start: 0.9063 (pm20) cc_final: 0.8808 (pm20) REVERT: G 47 LYS cc_start: 0.9001 (ptpt) cc_final: 0.8747 (pttm) REVERT: G 214 ASN cc_start: 0.8425 (t0) cc_final: 0.7928 (t0) REVERT: H 152 ASP cc_start: 0.8218 (OUTLIER) cc_final: 0.7010 (t0) REVERT: H 247 TYR cc_start: 0.8304 (m-80) cc_final: 0.7940 (m-80) REVERT: H 260 HIS cc_start: 0.5904 (OUTLIER) cc_final: 0.5017 (m170) REVERT: H 298 LEU cc_start: 0.8944 (OUTLIER) cc_final: 0.8655 (tt) REVERT: H 360 TYR cc_start: 0.8054 (OUTLIER) cc_final: 0.6726 (m-80) REVERT: H 384 MET cc_start: 0.7314 (mmm) cc_final: 0.7063 (mmm) outliers start: 94 outliers final: 65 residues processed: 511 average time/residue: 0.1904 time to fit residues: 140.6097 Evaluate side-chains 504 residues out of total 2240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 428 time to evaluate : 0.887 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 CYS Chi-restraints excluded: chain A residue 47 ILE Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 96 SER Chi-restraints excluded: chain A residue 161 TYR Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 238 MET Chi-restraints excluded: chain A residue 244 HIS Chi-restraints excluded: chain B residue 55 MET Chi-restraints excluded: chain B residue 146 PHE Chi-restraints excluded: chain B residue 168 THR Chi-restraints excluded: chain B residue 327 SER Chi-restraints excluded: chain B residue 335 ILE Chi-restraints excluded: chain C residue 44 LEU Chi-restraints excluded: chain C residue 95 HIS Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 126 ILE Chi-restraints excluded: chain C residue 203 GLN Chi-restraints excluded: chain C residue 219 ILE Chi-restraints excluded: chain D residue 16 VAL Chi-restraints excluded: chain D residue 58 LEU Chi-restraints excluded: chain D residue 74 LEU Chi-restraints excluded: chain D residue 120 TYR Chi-restraints excluded: chain D residue 154 LEU Chi-restraints excluded: chain D residue 248 ILE Chi-restraints excluded: chain D residue 253 VAL Chi-restraints excluded: chain D residue 260 HIS Chi-restraints excluded: chain D residue 306 ASN Chi-restraints excluded: chain D residue 351 THR Chi-restraints excluded: chain D residue 360 TYR Chi-restraints excluded: chain D residue 380 PHE Chi-restraints excluded: chain D residue 418 CYS Chi-restraints excluded: chain E residue 12 THR Chi-restraints excluded: chain E residue 40 PHE Chi-restraints excluded: chain E residue 47 ILE Chi-restraints excluded: chain E residue 63 THR Chi-restraints excluded: chain E residue 152 ILE Chi-restraints excluded: chain E residue 158 ASP Chi-restraints excluded: chain E residue 161 TYR Chi-restraints excluded: chain E residue 184 LEU Chi-restraints excluded: chain E residue 235 ILE Chi-restraints excluded: chain E residue 238 MET Chi-restraints excluded: chain E residue 244 HIS Chi-restraints excluded: chain F residue 51 ASN Chi-restraints excluded: chain F residue 55 MET Chi-restraints excluded: chain F residue 132 MET Chi-restraints excluded: chain F residue 202 GLN Chi-restraints excluded: chain F residue 207 HIS Chi-restraints excluded: chain F residue 257 LEU Chi-restraints excluded: chain F residue 260 VAL Chi-restraints excluded: chain F residue 327 SER Chi-restraints excluded: chain F residue 332 LEU Chi-restraints excluded: chain G residue 22 VAL Chi-restraints excluded: chain G residue 44 LEU Chi-restraints excluded: chain G residue 73 SER Chi-restraints excluded: chain G residue 95 HIS Chi-restraints excluded: chain G residue 126 ILE Chi-restraints excluded: chain G residue 190 ARG Chi-restraints excluded: chain G residue 285 VAL Chi-restraints excluded: chain H residue 93 GLN Chi-restraints excluded: chain H residue 112 LEU Chi-restraints excluded: chain H residue 125 SER Chi-restraints excluded: chain H residue 131 ASN Chi-restraints excluded: chain H residue 139 ILE Chi-restraints excluded: chain H residue 152 ASP Chi-restraints excluded: chain H residue 256 SER Chi-restraints excluded: chain H residue 260 HIS Chi-restraints excluded: chain H residue 298 LEU Chi-restraints excluded: chain H residue 306 ASN Chi-restraints excluded: chain H residue 350 THR Chi-restraints excluded: chain H residue 359 VAL Chi-restraints excluded: chain H residue 360 TYR Chi-restraints excluded: chain H residue 380 PHE Chi-restraints excluded: chain H residue 392 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 199 optimal weight: 0.2980 chunk 171 optimal weight: 0.7980 chunk 162 optimal weight: 0.9980 chunk 213 optimal weight: 1.9990 chunk 201 optimal weight: 3.9990 chunk 33 optimal weight: 0.9980 chunk 95 optimal weight: 2.9990 chunk 81 optimal weight: 2.9990 chunk 55 optimal weight: 0.9980 chunk 54 optimal weight: 0.6980 chunk 66 optimal weight: 4.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 49 HIS ** B 178 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 93 GLN ** D 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 255 HIS ** H 381 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.101826 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.084029 restraints weight = 51938.496| |-----------------------------------------------------------------------------| r_work (start): 0.3359 rms_B_bonded: 2.66 r_work: 0.3222 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3222 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8032 moved from start: 0.3569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.093 21752 Z= 0.150 Angle : 1.144 65.947 29582 Z= 0.355 Chirality : 0.046 0.248 3154 Planarity : 0.005 0.064 3720 Dihedral : 6.672 70.410 2991 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 12.76 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.15 % Favored : 95.78 % Rotamer: Outliers : 3.97 % Allowed : 20.49 % Favored : 75.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.62 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.67 (0.16), residues: 2580 helix: 0.01 (0.16), residues: 1008 sheet: -0.30 (0.26), residues: 380 loop : -0.79 (0.18), residues: 1192 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG H 186 TYR 0.017 0.001 TYR G 109 PHE 0.026 0.002 PHE G 166 TRP 0.038 0.001 TRP G 194 HIS 0.016 0.001 HIS F 207 Details of bonding type rmsd covalent geometry : bond 0.00340 (21680) covalent geometry : angle 0.66585 (29398) SS BOND : bond 0.00124 ( 2) SS BOND : angle 0.37862 ( 4) hydrogen bonds : bond 0.04131 ( 835) hydrogen bonds : angle 5.49382 ( 2343) metal coordination : bond 0.01981 ( 67) metal coordination : angle 11.94189 ( 180) Misc. bond : bond 0.00472 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5160 Ramachandran restraints generated. 2580 Oldfield, 0 Emsley, 2580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5160 Ramachandran restraints generated. 2580 Oldfield, 0 Emsley, 2580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 533 residues out of total 2240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 444 time to evaluate : 0.830 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 76 ASN cc_start: 0.8391 (t0) cc_final: 0.8037 (t0) REVERT: A 218 ASP cc_start: 0.8118 (m-30) cc_final: 0.7021 (m-30) REVERT: A 238 MET cc_start: 0.8339 (OUTLIER) cc_final: 0.7035 (mtp) REVERT: A 251 MET cc_start: 0.8396 (mtt) cc_final: 0.7952 (mtt) REVERT: B 146 PHE cc_start: 0.8421 (OUTLIER) cc_final: 0.8044 (t80) REVERT: C 146 ARG cc_start: 0.7836 (tpt170) cc_final: 0.7357 (tpm170) REVERT: C 148 LYS cc_start: 0.8475 (ptmt) cc_final: 0.8194 (ptmm) REVERT: C 149 TYR cc_start: 0.7991 (m-80) cc_final: 0.7601 (m-80) REVERT: C 168 LYS cc_start: 0.9059 (tppt) cc_final: 0.8692 (mmmm) REVERT: C 173 MET cc_start: 0.8466 (mtm) cc_final: 0.8213 (ptp) REVERT: C 193 ASN cc_start: 0.8945 (p0) cc_final: 0.8372 (t0) REVERT: D 15 ARG cc_start: 0.8489 (mpp80) cc_final: 0.8259 (mpp80) REVERT: D 120 TYR cc_start: 0.8897 (OUTLIER) cc_final: 0.8244 (t80) REVERT: D 171 LYS cc_start: 0.8039 (mttt) cc_final: 0.7684 (mttp) REVERT: D 181 MET cc_start: 0.8789 (tpp) cc_final: 0.8061 (tpp) REVERT: D 279 ASN cc_start: 0.8120 (p0) cc_final: 0.7818 (p0) REVERT: D 299 LYS cc_start: 0.8387 (mmtt) cc_final: 0.8097 (mmtt) REVERT: D 384 MET cc_start: 0.7262 (mmm) cc_final: 0.6708 (mmm) REVERT: D 394 GLU cc_start: 0.8770 (mt-10) cc_final: 0.8332 (mt-10) REVERT: E 43 ASP cc_start: 0.7898 (t0) cc_final: 0.7579 (t70) REVERT: E 161 TYR cc_start: 0.9046 (OUTLIER) cc_final: 0.7636 (p90) REVERT: E 238 MET cc_start: 0.8368 (OUTLIER) cc_final: 0.7152 (mtp) REVERT: F 9 GLU cc_start: 0.7745 (pm20) cc_final: 0.7370 (pm20) REVERT: F 10 ASN cc_start: 0.8153 (m-40) cc_final: 0.7676 (m-40) REVERT: F 72 ASP cc_start: 0.7474 (t0) cc_final: 0.7237 (t0) REVERT: F 110 ASP cc_start: 0.8418 (p0) cc_final: 0.6916 (p0) REVERT: G 47 LYS cc_start: 0.9010 (ptpt) cc_final: 0.8756 (pttm) REVERT: G 145 ASN cc_start: 0.8389 (m-40) cc_final: 0.8155 (m110) REVERT: G 214 ASN cc_start: 0.8389 (t0) cc_final: 0.7898 (t0) REVERT: H 93 GLN cc_start: 0.8567 (OUTLIER) cc_final: 0.8355 (tp40) REVERT: H 152 ASP cc_start: 0.8082 (OUTLIER) cc_final: 0.7074 (m-30) REVERT: H 171 LYS cc_start: 0.8147 (mttt) cc_final: 0.7938 (mttp) REVERT: H 247 TYR cc_start: 0.8285 (m-80) cc_final: 0.7901 (m-80) REVERT: H 260 HIS cc_start: 0.5891 (OUTLIER) cc_final: 0.5032 (m170) REVERT: H 298 LEU cc_start: 0.8923 (OUTLIER) cc_final: 0.8535 (tt) REVERT: H 360 TYR cc_start: 0.7977 (OUTLIER) cc_final: 0.6736 (m-80) REVERT: H 384 MET cc_start: 0.7225 (mmm) cc_final: 0.6767 (mmm) outliers start: 89 outliers final: 62 residues processed: 502 average time/residue: 0.1998 time to fit residues: 144.4018 Evaluate side-chains 500 residues out of total 2240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 428 time to evaluate : 0.848 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 THR Chi-restraints excluded: chain A residue 17 CYS Chi-restraints excluded: chain A residue 47 ILE Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 96 SER Chi-restraints excluded: chain A residue 161 TYR Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 238 MET Chi-restraints excluded: chain A residue 244 HIS Chi-restraints excluded: chain B residue 146 PHE Chi-restraints excluded: chain B residue 168 THR Chi-restraints excluded: chain B residue 202 GLN Chi-restraints excluded: chain B residue 327 SER Chi-restraints excluded: chain B residue 335 ILE Chi-restraints excluded: chain C residue 44 LEU Chi-restraints excluded: chain C residue 95 HIS Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 104 LEU Chi-restraints excluded: chain C residue 126 ILE Chi-restraints excluded: chain C residue 219 ILE Chi-restraints excluded: chain D residue 16 VAL Chi-restraints excluded: chain D residue 58 LEU Chi-restraints excluded: chain D residue 74 LEU Chi-restraints excluded: chain D residue 120 TYR Chi-restraints excluded: chain D residue 154 LEU Chi-restraints excluded: chain D residue 248 ILE Chi-restraints excluded: chain D residue 253 VAL Chi-restraints excluded: chain D residue 260 HIS Chi-restraints excluded: chain D residue 306 ASN Chi-restraints excluded: chain D residue 351 THR Chi-restraints excluded: chain D residue 360 TYR Chi-restraints excluded: chain E residue 12 THR Chi-restraints excluded: chain E residue 40 PHE Chi-restraints excluded: chain E residue 47 ILE Chi-restraints excluded: chain E residue 152 ILE Chi-restraints excluded: chain E residue 158 ASP Chi-restraints excluded: chain E residue 161 TYR Chi-restraints excluded: chain E residue 184 LEU Chi-restraints excluded: chain E residue 235 ILE Chi-restraints excluded: chain E residue 238 MET Chi-restraints excluded: chain E residue 244 HIS Chi-restraints excluded: chain F residue 55 MET Chi-restraints excluded: chain F residue 132 MET Chi-restraints excluded: chain F residue 202 GLN Chi-restraints excluded: chain F residue 207 HIS Chi-restraints excluded: chain F residue 257 LEU Chi-restraints excluded: chain F residue 260 VAL Chi-restraints excluded: chain F residue 327 SER Chi-restraints excluded: chain F residue 332 LEU Chi-restraints excluded: chain G residue 22 VAL Chi-restraints excluded: chain G residue 44 LEU Chi-restraints excluded: chain G residue 73 SER Chi-restraints excluded: chain G residue 95 HIS Chi-restraints excluded: chain G residue 126 ILE Chi-restraints excluded: chain G residue 190 ARG Chi-restraints excluded: chain G residue 285 VAL Chi-restraints excluded: chain H residue 93 GLN Chi-restraints excluded: chain H residue 112 LEU Chi-restraints excluded: chain H residue 114 LEU Chi-restraints excluded: chain H residue 125 SER Chi-restraints excluded: chain H residue 131 ASN Chi-restraints excluded: chain H residue 152 ASP Chi-restraints excluded: chain H residue 256 SER Chi-restraints excluded: chain H residue 260 HIS Chi-restraints excluded: chain H residue 298 LEU Chi-restraints excluded: chain H residue 306 ASN Chi-restraints excluded: chain H residue 350 THR Chi-restraints excluded: chain H residue 359 VAL Chi-restraints excluded: chain H residue 360 TYR Chi-restraints excluded: chain H residue 392 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 37 optimal weight: 2.9990 chunk 151 optimal weight: 3.9990 chunk 204 optimal weight: 3.9990 chunk 222 optimal weight: 1.9990 chunk 218 optimal weight: 3.9990 chunk 162 optimal weight: 1.9990 chunk 113 optimal weight: 0.7980 chunk 105 optimal weight: 0.7980 chunk 84 optimal weight: 0.4980 chunk 14 optimal weight: 0.7980 chunk 200 optimal weight: 3.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 178 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 93 GLN ** D 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 381 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 388 HIS G 193 ASN ** G 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 255 HIS ** H 381 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.101475 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.083812 restraints weight = 51832.108| |-----------------------------------------------------------------------------| r_work (start): 0.3339 rms_B_bonded: 2.62 r_work: 0.3204 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3204 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8036 moved from start: 0.3672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.097 21752 Z= 0.166 Angle : 1.155 65.935 29582 Z= 0.365 Chirality : 0.046 0.244 3154 Planarity : 0.005 0.067 3720 Dihedral : 6.705 71.426 2991 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 13.57 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.34 % Favored : 95.58 % Rotamer: Outliers : 3.84 % Allowed : 21.16 % Favored : 75.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.62 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.68 (0.16), residues: 2580 helix: 0.02 (0.16), residues: 1006 sheet: -0.27 (0.26), residues: 376 loop : -0.83 (0.18), residues: 1198 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.025 0.001 ARG H 186 TYR 0.057 0.002 TYR B 50 PHE 0.041 0.002 PHE H 317 TRP 0.039 0.001 TRP G 194 HIS 0.015 0.001 HIS B 94 Details of bonding type rmsd covalent geometry : bond 0.00380 (21680) covalent geometry : angle 0.68500 (29398) SS BOND : bond 0.00137 ( 2) SS BOND : angle 0.41166 ( 4) hydrogen bonds : bond 0.04232 ( 835) hydrogen bonds : angle 5.48353 ( 2343) metal coordination : bond 0.01974 ( 67) metal coordination : angle 11.94228 ( 180) Misc. bond : bond 0.00908 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5160 Ramachandran restraints generated. 2580 Oldfield, 0 Emsley, 2580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5160 Ramachandran restraints generated. 2580 Oldfield, 0 Emsley, 2580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 535 residues out of total 2240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 449 time to evaluate : 0.912 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 76 ASN cc_start: 0.8406 (t0) cc_final: 0.8064 (t0) REVERT: A 238 MET cc_start: 0.8338 (OUTLIER) cc_final: 0.7011 (mtp) REVERT: A 251 MET cc_start: 0.8365 (mtt) cc_final: 0.8068 (mtt) REVERT: A 254 LYS cc_start: 0.8498 (ttpp) cc_final: 0.8276 (ttpp) REVERT: B 146 PHE cc_start: 0.8448 (OUTLIER) cc_final: 0.8114 (t80) REVERT: C 146 ARG cc_start: 0.7841 (tpt170) cc_final: 0.7278 (tpm170) REVERT: C 148 LYS cc_start: 0.8461 (ptmt) cc_final: 0.8174 (ptmm) REVERT: C 149 TYR cc_start: 0.7971 (m-80) cc_final: 0.7569 (m-80) REVERT: C 168 LYS cc_start: 0.9045 (tppt) cc_final: 0.8685 (mmmm) REVERT: C 173 MET cc_start: 0.8411 (mtm) cc_final: 0.8195 (ptp) REVERT: C 193 ASN cc_start: 0.8899 (p0) cc_final: 0.8286 (t0) REVERT: C 198 LYS cc_start: 0.8368 (mptt) cc_final: 0.8068 (mmtm) REVERT: C 214 ASN cc_start: 0.8549 (t0) cc_final: 0.8229 (t0) REVERT: D 15 ARG cc_start: 0.8530 (mpp80) cc_final: 0.8326 (mpp80) REVERT: D 120 TYR cc_start: 0.8893 (OUTLIER) cc_final: 0.8235 (t80) REVERT: D 279 ASN cc_start: 0.8159 (p0) cc_final: 0.7927 (p0) REVERT: D 299 LYS cc_start: 0.8393 (mmtt) cc_final: 0.8093 (mmtt) REVERT: D 394 GLU cc_start: 0.8731 (mt-10) cc_final: 0.8320 (mt-10) REVERT: E 161 TYR cc_start: 0.9061 (OUTLIER) cc_final: 0.7607 (p90) REVERT: E 238 MET cc_start: 0.8358 (OUTLIER) cc_final: 0.7211 (mtp) REVERT: F 9 GLU cc_start: 0.7723 (pm20) cc_final: 0.7394 (pm20) REVERT: F 10 ASN cc_start: 0.8155 (m-40) cc_final: 0.7676 (m-40) REVERT: F 110 ASP cc_start: 0.8076 (p0) cc_final: 0.7541 (p0) REVERT: F 111 GLU cc_start: 0.7731 (mp0) cc_final: 0.7192 (mp0) REVERT: G 32 GLU cc_start: 0.8417 (mp0) cc_final: 0.8181 (mp0) REVERT: G 47 LYS cc_start: 0.9029 (ptpt) cc_final: 0.8815 (pttt) REVERT: G 145 ASN cc_start: 0.8403 (m-40) cc_final: 0.8171 (m110) REVERT: G 214 ASN cc_start: 0.8394 (t0) cc_final: 0.7920 (t0) REVERT: H 152 ASP cc_start: 0.8166 (OUTLIER) cc_final: 0.7134 (m-30) REVERT: H 171 LYS cc_start: 0.8187 (mttt) cc_final: 0.7957 (mttp) REVERT: H 247 TYR cc_start: 0.8238 (m-80) cc_final: 0.7865 (m-80) REVERT: H 298 LEU cc_start: 0.8923 (OUTLIER) cc_final: 0.8506 (tt) REVERT: H 360 TYR cc_start: 0.8001 (OUTLIER) cc_final: 0.6845 (m-80) REVERT: H 384 MET cc_start: 0.7246 (mmm) cc_final: 0.6979 (mmm) REVERT: H 395 LYS cc_start: 0.8976 (mmtm) cc_final: 0.8589 (mptt) outliers start: 86 outliers final: 67 residues processed: 505 average time/residue: 0.2003 time to fit residues: 146.0087 Evaluate side-chains 510 residues out of total 2240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 435 time to evaluate : 1.053 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 THR Chi-restraints excluded: chain A residue 17 CYS Chi-restraints excluded: chain A residue 47 ILE Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 96 SER Chi-restraints excluded: chain A residue 161 TYR Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 238 MET Chi-restraints excluded: chain A residue 244 HIS Chi-restraints excluded: chain B residue 55 MET Chi-restraints excluded: chain B residue 146 PHE Chi-restraints excluded: chain B residue 168 THR Chi-restraints excluded: chain B residue 202 GLN Chi-restraints excluded: chain B residue 327 SER Chi-restraints excluded: chain B residue 335 ILE Chi-restraints excluded: chain C residue 95 HIS Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 104 LEU Chi-restraints excluded: chain C residue 126 ILE Chi-restraints excluded: chain C residue 160 TYR Chi-restraints excluded: chain C residue 165 LEU Chi-restraints excluded: chain C residue 219 ILE Chi-restraints excluded: chain D residue 16 VAL Chi-restraints excluded: chain D residue 58 LEU Chi-restraints excluded: chain D residue 74 LEU Chi-restraints excluded: chain D residue 93 GLN Chi-restraints excluded: chain D residue 120 TYR Chi-restraints excluded: chain D residue 154 LEU Chi-restraints excluded: chain D residue 248 ILE Chi-restraints excluded: chain D residue 253 VAL Chi-restraints excluded: chain D residue 260 HIS Chi-restraints excluded: chain D residue 306 ASN Chi-restraints excluded: chain D residue 351 THR Chi-restraints excluded: chain D residue 360 TYR Chi-restraints excluded: chain E residue 12 THR Chi-restraints excluded: chain E residue 40 PHE Chi-restraints excluded: chain E residue 47 ILE Chi-restraints excluded: chain E residue 152 ILE Chi-restraints excluded: chain E residue 158 ASP Chi-restraints excluded: chain E residue 161 TYR Chi-restraints excluded: chain E residue 235 ILE Chi-restraints excluded: chain E residue 238 MET Chi-restraints excluded: chain E residue 244 HIS Chi-restraints excluded: chain F residue 51 ASN Chi-restraints excluded: chain F residue 55 MET Chi-restraints excluded: chain F residue 132 MET Chi-restraints excluded: chain F residue 202 GLN Chi-restraints excluded: chain F residue 257 LEU Chi-restraints excluded: chain F residue 260 VAL Chi-restraints excluded: chain F residue 327 SER Chi-restraints excluded: chain F residue 332 LEU Chi-restraints excluded: chain G residue 22 VAL Chi-restraints excluded: chain G residue 44 LEU Chi-restraints excluded: chain G residue 73 SER Chi-restraints excluded: chain G residue 95 HIS Chi-restraints excluded: chain G residue 126 ILE Chi-restraints excluded: chain G residue 190 ARG Chi-restraints excluded: chain G residue 285 VAL Chi-restraints excluded: chain H residue 93 GLN Chi-restraints excluded: chain H residue 112 LEU Chi-restraints excluded: chain H residue 114 LEU Chi-restraints excluded: chain H residue 125 SER Chi-restraints excluded: chain H residue 131 ASN Chi-restraints excluded: chain H residue 152 ASP Chi-restraints excluded: chain H residue 256 SER Chi-restraints excluded: chain H residue 260 HIS Chi-restraints excluded: chain H residue 298 LEU Chi-restraints excluded: chain H residue 306 ASN Chi-restraints excluded: chain H residue 350 THR Chi-restraints excluded: chain H residue 359 VAL Chi-restraints excluded: chain H residue 360 TYR Chi-restraints excluded: chain H residue 385 MET Chi-restraints excluded: chain H residue 392 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 14 optimal weight: 0.6980 chunk 142 optimal weight: 1.9990 chunk 44 optimal weight: 0.8980 chunk 119 optimal weight: 3.9990 chunk 19 optimal weight: 0.4980 chunk 235 optimal weight: 5.9990 chunk 185 optimal weight: 0.0050 chunk 46 optimal weight: 0.9980 chunk 104 optimal weight: 1.9990 chunk 67 optimal weight: 0.3980 chunk 253 optimal weight: 0.7980 overall best weight: 0.4794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 172 HIS ** B 178 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 93 GLN ** D 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 381 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 388 HIS ** F 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 193 ASN ** G 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 381 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.102766 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.085064 restraints weight = 52041.645| |-----------------------------------------------------------------------------| r_work (start): 0.3382 rms_B_bonded: 2.62 r_work: 0.3247 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3247 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8004 moved from start: 0.3773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.091 21752 Z= 0.141 Angle : 1.142 64.965 29582 Z= 0.366 Chirality : 0.045 0.220 3154 Planarity : 0.005 0.067 3720 Dihedral : 6.618 72.544 2991 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 12.87 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.19 % Favored : 95.74 % Rotamer: Outliers : 3.66 % Allowed : 21.38 % Favored : 74.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.62 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.66 (0.16), residues: 2580 helix: 0.03 (0.16), residues: 1004 sheet: -0.33 (0.26), residues: 378 loop : -0.76 (0.18), residues: 1198 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.027 0.001 ARG H 186 TYR 0.059 0.001 TYR B 50 PHE 0.042 0.002 PHE H 317 TRP 0.042 0.001 TRP G 194 HIS 0.020 0.001 HIS B 94 Details of bonding type rmsd covalent geometry : bond 0.00319 (21680) covalent geometry : angle 0.68922 (29398) SS BOND : bond 0.00106 ( 2) SS BOND : angle 0.33285 ( 4) hydrogen bonds : bond 0.04016 ( 835) hydrogen bonds : angle 5.44805 ( 2343) metal coordination : bond 0.01742 ( 67) metal coordination : angle 11.68948 ( 180) Misc. bond : bond 0.00754 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5160 Ramachandran restraints generated. 2580 Oldfield, 0 Emsley, 2580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5160 Ramachandran restraints generated. 2580 Oldfield, 0 Emsley, 2580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 534 residues out of total 2240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 452 time to evaluate : 0.873 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 76 ASN cc_start: 0.8395 (t0) cc_final: 0.8050 (t0) REVERT: A 238 MET cc_start: 0.8340 (OUTLIER) cc_final: 0.7031 (mtp) REVERT: A 251 MET cc_start: 0.8337 (mtt) cc_final: 0.7770 (mtt) REVERT: B 50 TYR cc_start: 0.7690 (p90) cc_final: 0.7327 (p90) REVERT: B 146 PHE cc_start: 0.8398 (OUTLIER) cc_final: 0.8048 (t80) REVERT: B 172 HIS cc_start: 0.7534 (OUTLIER) cc_final: 0.7056 (t-170) REVERT: C 146 ARG cc_start: 0.7754 (tpt170) cc_final: 0.7195 (tpm170) REVERT: C 148 LYS cc_start: 0.8428 (ptmt) cc_final: 0.8165 (ptmm) REVERT: C 149 TYR cc_start: 0.7945 (m-80) cc_final: 0.7496 (m-80) REVERT: C 168 LYS cc_start: 0.9057 (tppt) cc_final: 0.8745 (mmmm) REVERT: C 173 MET cc_start: 0.8419 (mtm) cc_final: 0.8162 (ptp) REVERT: C 193 ASN cc_start: 0.8882 (p0) cc_final: 0.8292 (t0) REVERT: C 198 LYS cc_start: 0.8367 (mptt) cc_final: 0.8096 (mptt) REVERT: D 120 TYR cc_start: 0.8857 (OUTLIER) cc_final: 0.8169 (t80) REVERT: D 247 TYR cc_start: 0.8155 (m-80) cc_final: 0.7806 (m-80) REVERT: D 279 ASN cc_start: 0.8159 (p0) cc_final: 0.7941 (p0) REVERT: D 299 LYS cc_start: 0.8383 (mmtt) cc_final: 0.8084 (mmtt) REVERT: D 394 GLU cc_start: 0.8751 (mt-10) cc_final: 0.8351 (mt-10) REVERT: E 238 MET cc_start: 0.8333 (OUTLIER) cc_final: 0.7136 (mtp) REVERT: F 9 GLU cc_start: 0.7694 (pm20) cc_final: 0.7393 (pm20) REVERT: F 10 ASN cc_start: 0.8152 (m-40) cc_final: 0.7678 (m-40) REVERT: F 110 ASP cc_start: 0.8113 (p0) cc_final: 0.7065 (p0) REVERT: F 111 GLU cc_start: 0.7745 (mp0) cc_final: 0.7252 (mp0) REVERT: G 32 GLU cc_start: 0.8356 (mp0) cc_final: 0.8135 (mp0) REVERT: G 47 LYS cc_start: 0.9027 (ptpt) cc_final: 0.8801 (pttm) REVERT: G 145 ASN cc_start: 0.8390 (m-40) cc_final: 0.8150 (m110) REVERT: G 207 GLU cc_start: 0.8046 (mp0) cc_final: 0.7829 (pp20) REVERT: G 214 ASN cc_start: 0.8394 (t0) cc_final: 0.7901 (t0) REVERT: H 152 ASP cc_start: 0.8136 (OUTLIER) cc_final: 0.6127 (m-30) REVERT: H 171 LYS cc_start: 0.8169 (mttt) cc_final: 0.7949 (mttp) REVERT: H 186 ARG cc_start: 0.8123 (ptp90) cc_final: 0.7666 (ptp90) REVERT: H 247 TYR cc_start: 0.8233 (m-80) cc_final: 0.7867 (m-80) REVERT: H 278 ASN cc_start: 0.7665 (t0) cc_final: 0.7352 (t0) REVERT: H 360 TYR cc_start: 0.7841 (OUTLIER) cc_final: 0.6842 (m-80) REVERT: H 384 MET cc_start: 0.7272 (mmm) cc_final: 0.6876 (mmm) REVERT: H 395 LYS cc_start: 0.9000 (mmtm) cc_final: 0.8707 (mmtm) outliers start: 82 outliers final: 60 residues processed: 504 average time/residue: 0.1986 time to fit residues: 144.3269 Evaluate side-chains 506 residues out of total 2240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 439 time to evaluate : 0.876 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 THR Chi-restraints excluded: chain A residue 17 CYS Chi-restraints excluded: chain A residue 47 ILE Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 161 TYR Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 238 MET Chi-restraints excluded: chain A residue 244 HIS Chi-restraints excluded: chain B residue 146 PHE Chi-restraints excluded: chain B residue 168 THR Chi-restraints excluded: chain B residue 172 HIS Chi-restraints excluded: chain B residue 202 GLN Chi-restraints excluded: chain B residue 335 ILE Chi-restraints excluded: chain C residue 44 LEU Chi-restraints excluded: chain C residue 95 HIS Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 126 ILE Chi-restraints excluded: chain C residue 219 ILE Chi-restraints excluded: chain D residue 16 VAL Chi-restraints excluded: chain D residue 58 LEU Chi-restraints excluded: chain D residue 74 LEU Chi-restraints excluded: chain D residue 120 TYR Chi-restraints excluded: chain D residue 154 LEU Chi-restraints excluded: chain D residue 248 ILE Chi-restraints excluded: chain D residue 253 VAL Chi-restraints excluded: chain D residue 260 HIS Chi-restraints excluded: chain D residue 351 THR Chi-restraints excluded: chain D residue 360 TYR Chi-restraints excluded: chain D residue 380 PHE Chi-restraints excluded: chain D residue 396 HIS Chi-restraints excluded: chain D residue 424 HIS Chi-restraints excluded: chain E residue 12 THR Chi-restraints excluded: chain E residue 40 PHE Chi-restraints excluded: chain E residue 47 ILE Chi-restraints excluded: chain E residue 152 ILE Chi-restraints excluded: chain E residue 158 ASP Chi-restraints excluded: chain E residue 161 TYR Chi-restraints excluded: chain E residue 235 ILE Chi-restraints excluded: chain E residue 238 MET Chi-restraints excluded: chain E residue 244 HIS Chi-restraints excluded: chain F residue 55 MET Chi-restraints excluded: chain F residue 132 MET Chi-restraints excluded: chain F residue 202 GLN Chi-restraints excluded: chain F residue 257 LEU Chi-restraints excluded: chain F residue 260 VAL Chi-restraints excluded: chain F residue 327 SER Chi-restraints excluded: chain F residue 332 LEU Chi-restraints excluded: chain G residue 22 VAL Chi-restraints excluded: chain G residue 73 SER Chi-restraints excluded: chain G residue 95 HIS Chi-restraints excluded: chain G residue 126 ILE Chi-restraints excluded: chain G residue 190 ARG Chi-restraints excluded: chain G residue 285 VAL Chi-restraints excluded: chain H residue 93 GLN Chi-restraints excluded: chain H residue 112 LEU Chi-restraints excluded: chain H residue 114 LEU Chi-restraints excluded: chain H residue 131 ASN Chi-restraints excluded: chain H residue 152 ASP Chi-restraints excluded: chain H residue 256 SER Chi-restraints excluded: chain H residue 260 HIS Chi-restraints excluded: chain H residue 306 ASN Chi-restraints excluded: chain H residue 350 THR Chi-restraints excluded: chain H residue 359 VAL Chi-restraints excluded: chain H residue 360 TYR Chi-restraints excluded: chain H residue 385 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 225 optimal weight: 0.7980 chunk 118 optimal weight: 0.9990 chunk 177 optimal weight: 0.9980 chunk 230 optimal weight: 0.0980 chunk 176 optimal weight: 0.8980 chunk 219 optimal weight: 0.9980 chunk 100 optimal weight: 4.9990 chunk 218 optimal weight: 1.9990 chunk 56 optimal weight: 0.9990 chunk 86 optimal weight: 2.9990 chunk 84 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 172 HIS ** B 178 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 381 ASN ** F 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 193 ASN ** G 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 381 ASN ** H 396 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.102476 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.084753 restraints weight = 52221.075| |-----------------------------------------------------------------------------| r_work (start): 0.3376 rms_B_bonded: 2.65 r_work: 0.3241 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3241 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8012 moved from start: 0.3849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.093 21752 Z= 0.155 Angle : 1.158 64.561 29582 Z= 0.379 Chirality : 0.046 0.214 3154 Planarity : 0.005 0.061 3720 Dihedral : 6.656 74.121 2991 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 13.49 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.07 % Favored : 95.85 % Rotamer: Outliers : 3.30 % Allowed : 21.88 % Favored : 74.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.62 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.67 (0.16), residues: 2580 helix: -0.01 (0.16), residues: 1006 sheet: -0.27 (0.26), residues: 372 loop : -0.77 (0.18), residues: 1202 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.026 0.001 ARG H 186 TYR 0.052 0.002 TYR B 50 PHE 0.046 0.002 PHE H 317 TRP 0.045 0.001 TRP G 194 HIS 0.016 0.001 HIS B 94 Details of bonding type rmsd covalent geometry : bond 0.00355 (21680) covalent geometry : angle 0.71796 (29398) SS BOND : bond 0.00107 ( 2) SS BOND : angle 0.32431 ( 4) hydrogen bonds : bond 0.04151 ( 835) hydrogen bonds : angle 5.48986 ( 2343) metal coordination : bond 0.01863 ( 67) metal coordination : angle 11.66495 ( 180) Misc. bond : bond 0.00753 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5160 Ramachandran restraints generated. 2580 Oldfield, 0 Emsley, 2580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5160 Ramachandran restraints generated. 2580 Oldfield, 0 Emsley, 2580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 519 residues out of total 2240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 445 time to evaluate : 0.849 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 76 ASN cc_start: 0.8427 (t0) cc_final: 0.8078 (t0) REVERT: A 106 LYS cc_start: 0.8951 (tppp) cc_final: 0.8608 (tppt) REVERT: A 238 MET cc_start: 0.8384 (OUTLIER) cc_final: 0.7074 (mtp) REVERT: A 251 MET cc_start: 0.8386 (mtt) cc_final: 0.8077 (mtt) REVERT: B 146 PHE cc_start: 0.8418 (OUTLIER) cc_final: 0.8073 (t80) REVERT: C 146 ARG cc_start: 0.7777 (tpt170) cc_final: 0.7136 (tpm170) REVERT: C 148 LYS cc_start: 0.8460 (ptmt) cc_final: 0.8169 (ptmm) REVERT: C 149 TYR cc_start: 0.7953 (m-80) cc_final: 0.7526 (m-80) REVERT: C 173 MET cc_start: 0.8456 (mtm) cc_final: 0.8172 (ptp) REVERT: C 193 ASN cc_start: 0.8924 (p0) cc_final: 0.8279 (t0) REVERT: C 198 LYS cc_start: 0.8366 (mptt) cc_final: 0.8151 (mmtm) REVERT: D 120 TYR cc_start: 0.8870 (OUTLIER) cc_final: 0.8175 (t80) REVERT: D 247 TYR cc_start: 0.8217 (m-80) cc_final: 0.7820 (m-80) REVERT: D 279 ASN cc_start: 0.8179 (p0) cc_final: 0.7959 (p0) REVERT: D 299 LYS cc_start: 0.8456 (mmtt) cc_final: 0.8163 (mmtt) REVERT: D 394 GLU cc_start: 0.8748 (mt-10) cc_final: 0.8344 (mt-10) REVERT: E 238 MET cc_start: 0.8305 (OUTLIER) cc_final: 0.7212 (mtp) REVERT: F 9 GLU cc_start: 0.7708 (pm20) cc_final: 0.7415 (pm20) REVERT: F 10 ASN cc_start: 0.8148 (m-40) cc_final: 0.7637 (m-40) REVERT: F 110 ASP cc_start: 0.8193 (p0) cc_final: 0.7130 (p0) REVERT: F 111 GLU cc_start: 0.7856 (mp0) cc_final: 0.7453 (mp0) REVERT: G 32 GLU cc_start: 0.8383 (mp0) cc_final: 0.8122 (mp0) REVERT: G 47 LYS cc_start: 0.9044 (ptpt) cc_final: 0.8808 (pttm) REVERT: G 145 ASN cc_start: 0.8429 (m-40) cc_final: 0.8186 (m110) REVERT: G 214 ASN cc_start: 0.8405 (t0) cc_final: 0.7936 (t0) REVERT: H 152 ASP cc_start: 0.8223 (OUTLIER) cc_final: 0.6215 (m-30) REVERT: H 171 LYS cc_start: 0.8182 (mttt) cc_final: 0.7959 (mttp) REVERT: H 266 ARG cc_start: 0.7973 (tpp-160) cc_final: 0.7724 (tpm170) REVERT: H 278 ASN cc_start: 0.7660 (t0) cc_final: 0.7364 (t0) REVERT: H 331 LYS cc_start: 0.8538 (mmtm) cc_final: 0.8305 (mmtm) REVERT: H 360 TYR cc_start: 0.7917 (OUTLIER) cc_final: 0.7025 (m-80) REVERT: H 384 MET cc_start: 0.7337 (mmm) cc_final: 0.6939 (mmm) REVERT: H 395 LYS cc_start: 0.9015 (mmtm) cc_final: 0.8717 (mmtm) outliers start: 74 outliers final: 61 residues processed: 493 average time/residue: 0.1970 time to fit residues: 140.6274 Evaluate side-chains 488 residues out of total 2240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 421 time to evaluate : 0.780 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 THR Chi-restraints excluded: chain A residue 17 CYS Chi-restraints excluded: chain A residue 47 ILE Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 161 TYR Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 238 MET Chi-restraints excluded: chain A residue 244 HIS Chi-restraints excluded: chain B residue 55 MET Chi-restraints excluded: chain B residue 75 LYS Chi-restraints excluded: chain B residue 146 PHE Chi-restraints excluded: chain B residue 168 THR Chi-restraints excluded: chain B residue 202 GLN Chi-restraints excluded: chain B residue 335 ILE Chi-restraints excluded: chain C residue 95 HIS Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 126 ILE Chi-restraints excluded: chain C residue 219 ILE Chi-restraints excluded: chain D residue 16 VAL Chi-restraints excluded: chain D residue 58 LEU Chi-restraints excluded: chain D residue 74 LEU Chi-restraints excluded: chain D residue 120 TYR Chi-restraints excluded: chain D residue 154 LEU Chi-restraints excluded: chain D residue 248 ILE Chi-restraints excluded: chain D residue 253 VAL Chi-restraints excluded: chain D residue 260 HIS Chi-restraints excluded: chain D residue 306 ASN Chi-restraints excluded: chain D residue 351 THR Chi-restraints excluded: chain D residue 360 TYR Chi-restraints excluded: chain D residue 380 PHE Chi-restraints excluded: chain D residue 381 ASN Chi-restraints excluded: chain D residue 396 HIS Chi-restraints excluded: chain D residue 424 HIS Chi-restraints excluded: chain E residue 12 THR Chi-restraints excluded: chain E residue 40 PHE Chi-restraints excluded: chain E residue 47 ILE Chi-restraints excluded: chain E residue 152 ILE Chi-restraints excluded: chain E residue 158 ASP Chi-restraints excluded: chain E residue 161 TYR Chi-restraints excluded: chain E residue 235 ILE Chi-restraints excluded: chain E residue 238 MET Chi-restraints excluded: chain E residue 244 HIS Chi-restraints excluded: chain F residue 55 MET Chi-restraints excluded: chain F residue 132 MET Chi-restraints excluded: chain F residue 202 GLN Chi-restraints excluded: chain F residue 257 LEU Chi-restraints excluded: chain F residue 260 VAL Chi-restraints excluded: chain F residue 327 SER Chi-restraints excluded: chain G residue 22 VAL Chi-restraints excluded: chain G residue 73 SER Chi-restraints excluded: chain G residue 95 HIS Chi-restraints excluded: chain G residue 126 ILE Chi-restraints excluded: chain G residue 190 ARG Chi-restraints excluded: chain G residue 285 VAL Chi-restraints excluded: chain H residue 93 GLN Chi-restraints excluded: chain H residue 112 LEU Chi-restraints excluded: chain H residue 114 LEU Chi-restraints excluded: chain H residue 131 ASN Chi-restraints excluded: chain H residue 152 ASP Chi-restraints excluded: chain H residue 256 SER Chi-restraints excluded: chain H residue 260 HIS Chi-restraints excluded: chain H residue 306 ASN Chi-restraints excluded: chain H residue 350 THR Chi-restraints excluded: chain H residue 359 VAL Chi-restraints excluded: chain H residue 360 TYR Chi-restraints excluded: chain H residue 381 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 32 optimal weight: 1.9990 chunk 254 optimal weight: 6.9990 chunk 221 optimal weight: 0.6980 chunk 76 optimal weight: 2.9990 chunk 83 optimal weight: 2.9990 chunk 55 optimal weight: 2.9990 chunk 66 optimal weight: 0.9980 chunk 241 optimal weight: 5.9990 chunk 14 optimal weight: 0.5980 chunk 144 optimal weight: 0.9980 chunk 79 optimal weight: 7.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 172 HIS ** B 178 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 93 GLN ** D 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 388 HIS F 331 ASN G 193 ASN ** G 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 381 ASN H 388 HIS ** H 396 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.101773 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.083978 restraints weight = 51987.332| |-----------------------------------------------------------------------------| r_work (start): 0.3344 rms_B_bonded: 2.61 r_work: 0.3211 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3211 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8031 moved from start: 0.3889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.099 21752 Z= 0.178 Angle : 1.186 65.010 29582 Z= 0.395 Chirality : 0.047 0.233 3154 Planarity : 0.005 0.060 3720 Dihedral : 6.714 73.920 2991 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 14.21 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.26 % Favored : 95.66 % Rotamer: Outliers : 3.44 % Allowed : 22.72 % Favored : 73.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.62 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.74 (0.16), residues: 2580 helix: -0.09 (0.16), residues: 1006 sheet: -0.28 (0.26), residues: 372 loop : -0.79 (0.18), residues: 1202 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.025 0.001 ARG H 186 TYR 0.048 0.002 TYR B 50 PHE 0.051 0.002 PHE D 317 TRP 0.046 0.002 TRP G 194 HIS 0.013 0.001 HIS B 94 Details of bonding type rmsd covalent geometry : bond 0.00412 (21680) covalent geometry : angle 0.74832 (29398) SS BOND : bond 0.00105 ( 2) SS BOND : angle 0.32932 ( 4) hydrogen bonds : bond 0.04315 ( 835) hydrogen bonds : angle 5.53489 ( 2343) metal coordination : bond 0.02056 ( 67) metal coordination : angle 11.81168 ( 180) Misc. bond : bond 0.00281 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5018.33 seconds wall clock time: 87 minutes 9.80 seconds (5229.80 seconds total)