Starting phenix.real_space_refine on Thu Sep 18 23:40:48 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9nf0_49341/09_2025/9nf0_49341.cif Found real_map, /net/cci-nas-00/data/ceres_data/9nf0_49341/09_2025/9nf0_49341.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.06 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9nf0_49341/09_2025/9nf0_49341.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9nf0_49341/09_2025/9nf0_49341.map" model { file = "/net/cci-nas-00/data/ceres_data/9nf0_49341/09_2025/9nf0_49341.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9nf0_49341/09_2025/9nf0_49341.cif" } resolution = 3.06 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= 0.044 sd= 0.581 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: 8 Type Number sf(0) Gaussians Fe 62 7.16 5 Ni 2 6.56 5 P 10 5.49 5 Mg 2 5.21 5 S 208 5.16 5 C 13629 2.51 5 N 3555 2.21 5 O 3876 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 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: 21344 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: 2841 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2841 Classifications: {'peptide': 339} Link IDs: {'PTRANS': 15, 'TRANS': 323} Chain: "C" Number of atoms: 2325 Number of conformers: 1 Conformer: "" Number of residues, atoms: 292, 2325 Classifications: {'peptide': 292} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 19, 'TRANS': 270} 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: 2841 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2841 Classifications: {'peptide': 339} Link IDs: {'PTRANS': 15, 'TRANS': 323} Chain: "G" Number of atoms: 2325 Number of conformers: 1 Conformer: "" Number of residues, atoms: 292, 2325 Classifications: {'peptide': 292} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 19, 'TRANS': 270} Chain: "H" Number of atoms: 3336 Number of conformers: 1 Conformer: "" Number of residues, atoms: 420, 3336 Classifications: {'peptide': 420} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 400} 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: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 105 Unusual residues: {'FAD': 1, 'FES': 1, 'NAP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 9 Unusual residues: {' MG': 1, 'NFU': 1} Classifications: {'undetermined': 2} Link IDs: {None: 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: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 105 Unusual residues: {'FAD': 1, 'FES': 1, 'NAP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "H" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 9 Unusual residues: {' MG': 1, 'NFU': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 657 SG CYS A 86 49.731 160.423 36.651 1.00 31.58 S ATOM 1062 SG CYS A 136 47.054 155.441 35.281 1.00 22.80 S ATOM 94 SG CYS A 14 43.368 160.395 37.836 1.00 25.00 S ATOM 116 SG CYS A 17 47.554 157.919 41.479 1.00 33.79 S ATOM 1585 SG CYS A 206 47.998 149.985 35.203 1.00 28.61 S ATOM 1493 SG CYS A 192 47.446 144.019 36.604 1.00 9.58 S ATOM 1567 SG CYS A 203 49.534 145.401 30.903 1.00 10.99 S ATOM 1523 SG CYS A 196 43.591 146.376 31.641 1.00 14.63 S ATOM 1312 SG CYS A 167 46.644 136.617 31.666 1.00 20.54 S ATOM 1289 SG CYS A 164 52.738 137.625 30.689 1.00 0.00 S ATOM 1434 SG CYS A 183 48.918 141.433 27.502 1.00 12.78 S ATOM 1366 SG CYS A 174 48.912 134.864 26.302 1.00 23.03 S ATOM 4012 SG CYS B 233 62.557 133.277 28.503 1.00 15.99 S ATOM 4049 SG CYS B 239 58.844 128.803 30.839 1.00 16.17 S ATOM 4716 SG CYS B 322 57.828 130.313 24.606 1.00 25.31 S ATOM 4031 SG CYS B 236 56.252 134.221 29.169 1.00 19.91 S ATOM 4077 SG CYS B 243 56.084 121.744 34.285 1.00 14.50 S ATOM 4649 SG CYS B 312 58.730 117.427 29.931 1.00 29.99 S ATOM 4687 SG CYS B 318 57.369 122.813 27.799 1.00 1.73 S ATOM 4666 SG CYS B 315 52.467 119.280 29.984 1.00 6.76 S ATOM 2851 SG CYS B 96 49.550 114.745 29.809 1.00 24.35 S ATOM 3209 SG CYS B 139 51.838 110.850 25.861 1.00 35.92 S ATOM 3192 SG CYS B 137 49.819 116.221 23.453 1.00 44.04 S ATOM 3142 SG CYS B 131 45.517 111.659 25.750 1.00 34.54 S ATOM 4114 SG CYS B 248 60.509 126.311 42.170 1.00 9.57 S ATOM 4545 SG CYS B 299 63.274 121.709 38.382 1.00 17.24 S ATOM 4308 SG CYS B 271 62.786 127.985 36.469 1.00 8.03 S ATOM 4097 SG CYS B 246 57.625 124.158 36.994 1.00 13.24 S ATOM 6879 SG CYS C 253 60.304 124.803 51.502 1.00 17.87 S ATOM 6910 SG CYS C 258 61.420 127.149 48.852 1.00 30.75 S ATOM 6930 SG CYS C 261 66.307 124.030 49.016 1.00 22.12 S ATOM 7024 SG CYS C 273 64.689 121.974 51.308 1.00 21.04 S ATOM 7657 SG CYS D 68 35.274 163.795 35.252 1.00 35.47 S ATOM 7657 SG CYS D 68 35.274 163.795 35.252 1.00 35.47 S ATOM 11989 SG CYS E 192 73.457 64.690 36.587 1.00 9.52 S ATOM 12081 SG CYS E 206 72.892 58.665 35.226 1.00 27.69 S ATOM 12019 SG CYS E 196 77.253 62.244 31.644 1.00 14.29 S ATOM 12063 SG CYS E 203 71.334 63.241 30.878 1.00 10.57 S ATOM 10612 SG CYS E 17 73.193 50.951 42.018 1.00 31.83 S ATOM 10590 SG CYS E 14 77.186 48.282 37.890 1.00 26.25 S ATOM 11558 SG CYS E 136 73.830 52.849 35.482 1.00 20.37 S ATOM 11153 SG CYS E 86 70.884 48.026 36.398 1.00 31.50 S ATOM 11808 SG CYS E 167 74.318 72.039 31.691 1.00 19.59 S ATOM 11930 SG CYS E 183 71.997 67.236 27.504 1.00 10.16 S ATOM 11862 SG CYS E 174 71.994 73.789 26.328 1.00 23.70 S ATOM 11785 SG CYS E 164 68.165 71.035 30.640 1.00 0.00 S ATOM 14545 SG CYS F 239 62.057 79.887 30.823 1.00 16.06 S ATOM 14527 SG CYS F 236 64.638 74.405 29.217 1.00 14.38 S ATOM 15212 SG CYS F 322 63.049 78.302 24.591 1.00 25.83 S ATOM 14508 SG CYS F 233 58.336 75.440 28.494 1.00 12.52 S ATOM 15162 SG CYS F 315 68.472 89.398 30.029 1.00 6.67 S ATOM 14573 SG CYS F 243 64.710 87.045 34.253 1.00 13.10 S ATOM 15183 SG CYS F 318 63.518 85.868 27.784 1.00 2.41 S ATOM 15145 SG CYS F 312 62.151 91.286 29.962 1.00 30.89 S ATOM 15041 SG CYS F 299 57.648 86.967 38.358 1.00 16.67 S ATOM 14610 SG CYS F 248 60.352 82.404 42.215 1.00 10.31 S ATOM 14593 SG CYS F 246 63.279 84.500 36.931 1.00 14.48 S ATOM 14804 SG CYS F 271 58.091 80.724 36.503 1.00 7.63 S ATOM 13347 SG CYS F 96 71.415 93.994 29.691 1.00 25.05 S ATOM 13688 SG CYS F 137 71.099 92.387 23.243 1.00 43.71 S ATOM 13638 SG CYS F 131 75.301 97.006 25.685 1.00 36.50 S ATOM 13705 SG CYS F 139 69.053 97.828 25.882 1.00 35.32 S ATOM 17426 SG CYS G 261 54.581 84.112 49.369 1.00 27.56 S ATOM 17520 SG CYS G 273 56.243 86.683 51.377 1.00 17.20 S ATOM 17375 SG CYS G 253 60.591 83.821 51.489 1.00 19.47 S ATOM 17406 SG CYS G 258 59.516 81.479 48.850 1.00 30.37 S ATOM 18165 SG CYS H 68 85.740 44.880 35.243 1.00 40.76 S ATOM 18165 SG CYS H 68 85.740 44.880 35.243 1.00 40.76 S Time building chain proxies: 4.33, per 1000 atoms: 0.20 Number of scatterers: 21344 At special positions: 0 Unit cell: (122.544, 208.656, 87.768, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) Ni 2 28.00 Fe 62 26.01 S 208 16.00 P 10 15.00 Mg 2 11.99 O 3876 8.00 N 3555 7.00 C 13629 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=4, symmetry=0 Number of additional bonds: simple=4, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.82 Conformation dependent library (CDL) restraints added in 789.6 milliseconds Enol-peptide restraints added in 953.7 nanoseconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" FES C 301 " pdb="FE2 FES C 301 " - pdb=" SG CYS C 261 " pdb="FE1 FES C 301 " - pdb=" SG CYS C 258 " 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 261 " pdb="FE2 FES G 301 " - pdb=" SG CYS G 258 " pdb="FE1 FES G 301 " - pdb=" SG CYS G 273 " pdb="FE2 FES G 301 " - pdb=" SG CYS G 253 " pdb=" SF4 A 301 " pdb="FE3 SF4 A 301 " - pdb=" NE2 HIS D 160 " pdb="FE2 SF4 A 301 " - pdb=" SG CYS A 136 " pdb="FE3 SF4 A 301 " - pdb=" SG CYS A 14 " 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="FE2 SF4 A 302 " - pdb=" SG CYS A 192 " pdb="FE1 SF4 A 302 " - pdb=" SG CYS A 206 " pdb="FE3 SF4 A 302 " - pdb=" SG CYS A 203 " pdb="FE4 SF4 A 302 " - pdb=" SG CYS A 196 " 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="FE4 SF4 B 401 " - pdb=" SG CYS B 236 " pdb="FE2 SF4 B 401 " - pdb=" SG CYS B 239 " pdb="FE1 SF4 B 401 " - pdb=" SG CYS B 233 " pdb="FE3 SF4 B 401 " - pdb=" SG CYS B 322 " pdb=" SF4 B 402 " pdb="FE3 SF4 B 402 " - pdb=" SG CYS B 318 " pdb="FE4 SF4 B 402 " - pdb=" SG CYS B 315 " pdb="FE2 SF4 B 402 " - pdb=" SG CYS B 312 " pdb="FE1 SF4 B 402 " - pdb=" SG CYS B 243 " pdb=" SF4 B 403 " pdb="FE4 SF4 B 403 " - pdb=" SG CYS B 131 " pdb="FE2 SF4 B 403 " - pdb=" SG CYS B 139 " pdb="FE3 SF4 B 403 " - pdb=" SG CYS B 137 " pdb="FE1 SF4 B 403 " - pdb=" SG CYS B 96 " pdb=" SF4 B 404 " 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="FE3 SF4 B 404 " - pdb=" SG CYS B 271 " pdb=" SF4 E 301 " pdb="FE2 SF4 E 301 " - pdb=" SG CYS E 206 " pdb="FE1 SF4 E 301 " - pdb=" SG CYS E 192 " pdb="FE4 SF4 E 301 " - pdb=" SG CYS E 203 " pdb="FE3 SF4 E 301 " - pdb=" SG CYS E 196 " pdb=" SF4 E 302 " pdb="FE2 SF4 E 302 " - pdb=" SG CYS E 14 " pdb="FE3 SF4 E 302 " - pdb=" SG CYS E 136 " pdb="FE4 SF4 E 302 " - pdb=" SG CYS E 86 " pdb="FE1 SF4 E 302 " - pdb=" SG CYS E 17 " pdb=" SF4 E 303 " pdb="FE4 SF4 E 303 " - pdb=" SG CYS E 164 " pdb="FE3 SF4 E 303 " - pdb=" SG CYS E 174 " pdb="FE1 SF4 E 303 " - pdb=" SG CYS E 167 " pdb="FE2 SF4 E 303 " - pdb=" SG CYS E 183 " pdb=" SF4 F 401 " pdb="FE2 SF4 F 401 " - pdb=" SG CYS F 236 " pdb="FE1 SF4 F 401 " - pdb=" SG CYS F 239 " pdb="FE3 SF4 F 401 " - pdb=" SG CYS F 322 " pdb="FE4 SF4 F 401 " - pdb=" SG CYS F 233 " pdb=" SF4 F 402 " pdb="FE1 SF4 F 402 " - pdb=" SG CYS F 315 " pdb="FE4 SF4 F 402 " - pdb=" SG CYS F 312 " pdb="FE3 SF4 F 402 " - pdb=" SG CYS F 318 " pdb="FE2 SF4 F 402 " - pdb=" SG CYS F 243 " pdb=" SF4 F 403 " pdb="FE2 SF4 F 403 " - pdb=" SG CYS F 248 " pdb="FE3 SF4 F 403 " - pdb=" SG CYS F 246 " pdb="FE1 SF4 F 403 " - pdb=" SG CYS F 299 " pdb="FE4 SF4 F 403 " - pdb=" SG CYS F 271 " pdb=" SF4 F 404 " pdb="FE3 SF4 F 404 " - pdb=" SG CYS F 131 " pdb="FE4 SF4 F 404 " - pdb=" SG CYS F 139 " pdb="FE2 SF4 F 404 " - pdb=" SG CYS F 137 " pdb="FE1 SF4 F 404 " - pdb=" SG CYS F 96 " Number of angles added : 180 5190 Ramachandran restraints generated. 2595 Oldfield, 0 Emsley, 2595 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4846 Finding SS restraints... Secondary structure from input PDB file: 121 helices and 22 sheets defined 45.0% alpha, 15.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.73 Creating SS restraints... Processing helix chain 'A' and resid 15 through 23 removed outlier: 3.838A pdb=" N LEU A 21 " --> pdb=" O CYS A 17 " (cutoff:3.500A) Processing helix chain 'A' and resid 24 through 28 removed outlier: 3.665A pdb=" N LEU A 28 " --> pdb=" O ASP A 25 " (cutoff:3.500A) Processing helix chain 'A' and resid 29 through 33 removed outlier: 3.993A pdb=" N ASN A 33 " --> pdb=" O GLN A 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 29 through 33' Processing helix chain 'A' and resid 63 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 109 Processing helix chain 'A' and resid 122 through 126 Processing helix chain 'A' and resid 139 through 153 Processing helix chain 'A' and resid 163 through 170 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: 3.569A pdb=" N LYS A 227 " --> pdb=" O VAL A 223 " (cutoff:3.500A) Processing helix chain 'A' and resid 230 through 238 Processing helix chain 'A' and resid 246 through 257 removed outlier: 4.081A pdb=" N LYS A 250 " --> pdb=" O GLU A 246 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ILE A 255 " --> pdb=" O MET A 251 " (cutoff:3.500A) Processing helix chain 'B' and resid 10 through 19 removed outlier: 3.595A pdb=" N LYS B 19 " --> pdb=" O LEU B 15 " (cutoff:3.500A) Processing helix chain 'B' and resid 20 through 22 No H-bonds generated for 'chain 'B' and resid 20 through 22' Processing helix chain 'B' and resid 42 through 46 Processing helix chain 'B' and resid 56 through 61 removed outlier: 3.531A 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: 3.837A pdb=" N ARG B 120 " --> pdb=" O TYR B 116 " (cutoff:3.500A) Processing helix chain 'B' and resid 168 through 178 removed outlier: 3.581A pdb=" N ASN B 178 " --> pdb=" O LEU B 174 " (cutoff:3.500A) Processing helix chain 'B' and resid 179 through 182 Processing helix chain 'B' and resid 186 through 203 Processing helix chain 'B' and resid 212 through 220 Processing helix chain 'B' and resid 223 through 231 removed outlier: 4.116A 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: 3.510A pdb=" N HIS B 276 " --> pdb=" O PHE B 273 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N GLY B 277 " --> pdb=" O ARG B 274 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 273 through 277' Processing helix chain 'B' and resid 288 through 301 removed outlier: 3.686A pdb=" N TYR B 297 " --> pdb=" O PHE B 293 " (cutoff:3.500A) Processing helix chain 'B' and resid 316 through 321 Processing helix chain 'B' and resid 327 through 337 Processing helix chain 'C' and resid 3 through 8 Processing helix chain 'C' and resid 41 through 48 Processing helix chain 'C' and resid 88 through 95 Processing helix chain 'C' and resid 131 through 145 removed outlier: 3.701A pdb=" N LEU C 135 " --> pdb=" O GLY C 131 " (cutoff:3.500A) Processing helix chain 'C' and resid 160 through 164 removed outlier: 3.828A pdb=" N LEU C 164 " --> pdb=" O GLY C 161 " (cutoff:3.500A) Processing helix chain 'C' and resid 166 through 173 Processing helix chain 'C' and resid 200 through 204 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 281 through 287 Processing helix chain 'D' and resid 44 through 49 Processing helix chain 'D' and resid 53 through 59 removed outlier: 3.737A pdb=" N ALA D 59 " --> pdb=" O GLU D 55 " (cutoff:3.500A) Processing helix chain 'D' and resid 60 through 65 removed outlier: 3.899A pdb=" N CYS D 65 " --> pdb=" O PRO D 62 " (cutoff:3.500A) Processing helix chain 'D' and resid 68 through 85 Processing helix chain 'D' and resid 89 through 115 Processing helix chain 'D' and resid 116 through 121 removed outlier: 3.551A pdb=" N TYR D 120 " --> pdb=" O VAL D 116 " (cutoff:3.500A) Processing helix chain 'D' and resid 125 through 129 Processing helix chain 'D' and resid 134 through 155 Processing helix chain 'D' and resid 174 through 201 Proline residue: D 190 - end of helix Processing helix chain 'D' and resid 205 through 209 removed outlier: 3.820A pdb=" N VAL D 208 " --> pdb=" O TYR D 205 " (cutoff:3.500A) Processing helix chain 'D' and resid 243 through 247 removed outlier: 3.953A 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 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 Processing helix chain 'D' and resid 304 through 330 removed outlier: 4.642A pdb=" N LEU D 308 " --> pdb=" O PHE D 304 " (cutoff:3.500A) Processing helix chain 'D' and resid 376 through 396 removed outlier: 4.961A pdb=" N ALA D 383 " --> pdb=" O ALA D 379 " (cutoff:3.500A) removed outlier: 5.102A pdb=" N MET D 384 " --> pdb=" O PHE D 380 " (cutoff:3.500A) Processing helix chain 'D' and resid 400 through 414 Processing helix chain 'D' and resid 418 through 424 Processing helix chain 'E' and resid 15 through 23 Processing helix chain 'E' and resid 26 through 33 removed outlier: 3.618A pdb=" N LEU E 30 " --> pdb=" O GLU E 26 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ILE E 31 " --> pdb=" O LEU E 27 " (cutoff:3.500A) Proline residue: E 32 - end of helix No H-bonds generated for 'chain 'E' and resid 26 through 33' Processing helix chain 'E' and resid 63 through 76 Processing helix chain 'E' and resid 84 through 90 Processing helix chain 'E' and resid 91 through 95 Processing helix chain 'E' and resid 99 through 109 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 170 removed outlier: 4.415A 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 199 Processing helix chain 'E' and resid 216 through 227 removed outlier: 3.568A pdb=" N LYS E 227 " --> pdb=" O VAL E 223 " (cutoff:3.500A) Processing helix chain 'E' and resid 230 through 239 Processing helix chain 'E' and resid 246 through 256 removed outlier: 4.077A pdb=" N LYS E 250 " --> pdb=" O GLU E 246 " (cutoff:3.500A) Processing helix chain 'F' and resid 10 through 19 removed outlier: 3.648A pdb=" N LYS F 19 " --> pdb=" O LEU F 15 " (cutoff:3.500A) Processing helix chain 'F' and resid 42 through 46 Processing helix chain 'F' and resid 56 through 61 Processing helix chain 'F' and resid 94 through 109 Processing helix chain 'F' and resid 114 through 123 removed outlier: 3.760A pdb=" N ARG F 120 " --> pdb=" O TYR F 116 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N LYS F 123 " --> pdb=" O VAL F 119 " (cutoff:3.500A) Processing helix chain 'F' and resid 168 through 178 removed outlier: 3.575A 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 Processing helix chain 'F' and resid 212 through 220 Processing helix chain 'F' and resid 223 through 233 removed outlier: 4.160A pdb=" N ASP F 227 " --> pdb=" O HIS F 223 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N LYS F 232 " --> pdb=" O GLU F 228 " (cutoff:3.500A) Processing helix chain 'F' and resid 237 through 242 Processing helix chain 'F' and resid 273 through 277 removed outlier: 3.503A pdb=" N HIS F 276 " --> pdb=" O PHE F 273 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N GLY F 277 " --> pdb=" O ARG F 274 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 273 through 277' Processing helix chain 'F' and resid 288 through 301 removed outlier: 3.669A pdb=" N TYR F 297 " --> pdb=" O PHE F 293 " (cutoff:3.500A) Processing helix chain 'F' and resid 316 through 321 Processing helix chain 'F' and resid 327 through 337 Processing helix chain 'G' and resid 41 through 48 Processing helix chain 'G' and resid 88 through 95 Processing helix chain 'G' and resid 131 through 145 removed outlier: 3.637A pdb=" N LEU G 135 " --> pdb=" O GLY G 131 " (cutoff:3.500A) Processing helix chain 'G' and resid 160 through 164 removed outlier: 3.862A pdb=" N LEU G 164 " --> pdb=" O GLY G 161 " (cutoff:3.500A) Processing helix chain 'G' and resid 166 through 178 removed outlier: 4.586A pdb=" N ASP G 175 " --> pdb=" O GLU G 171 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N LEU G 176 " --> pdb=" O ALA G 172 " (cutoff:3.500A) Processing helix chain 'G' and resid 200 through 205 removed outlier: 3.709A pdb=" N PHE G 204 " --> pdb=" O ARG G 200 " (cutoff:3.500A) 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 237 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 281 through 287 removed outlier: 3.570A pdb=" N THR G 287 " --> pdb=" O ASP G 283 " (cutoff:3.500A) Processing helix chain 'H' and resid 44 through 49 removed outlier: 3.643A pdb=" N THR H 49 " --> pdb=" O PHE H 45 " (cutoff:3.500A) Processing helix chain 'H' and resid 53 through 59 removed outlier: 3.620A pdb=" N ALA H 59 " --> pdb=" O GLU H 55 " (cutoff:3.500A) Processing helix chain 'H' and resid 60 through 65 removed outlier: 3.814A pdb=" N CYS H 65 " --> pdb=" O PRO H 62 " (cutoff:3.500A) Processing helix chain 'H' and resid 68 through 85 Processing helix chain 'H' and resid 89 through 115 Processing helix chain 'H' and resid 125 through 129 Processing helix chain 'H' and resid 133 through 155 Processing helix chain 'H' and resid 174 through 201 Proline residue: H 190 - end of helix Processing helix chain 'H' and resid 205 through 209 removed outlier: 3.775A pdb=" N VAL H 208 " --> pdb=" O TYR H 205 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLU H 209 " --> pdb=" O SER H 206 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 205 through 209' Processing helix chain 'H' and resid 243 through 247 removed outlier: 3.959A pdb=" N TYR H 247 " --> pdb=" O LYS H 243 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 243 through 247' Processing helix chain 'H' and resid 271 through 280 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 302 through 304 No H-bonds generated for 'chain 'H' and resid 302 through 304' Processing helix chain 'H' and resid 305 through 330 removed outlier: 3.819A pdb=" N GLU H 319 " --> pdb=" O VAL H 315 " (cutoff:3.500A) Processing helix chain 'H' and resid 376 through 396 removed outlier: 4.901A pdb=" N ALA H 383 " --> pdb=" O ALA H 379 " (cutoff:3.500A) removed outlier: 4.874A pdb=" N MET H 384 " --> pdb=" O PHE H 380 " (cutoff:3.500A) Processing helix chain 'H' and resid 400 through 415 removed outlier: 3.837A pdb=" N TYR H 415 " --> pdb=" O VAL H 411 " (cutoff:3.500A) Processing helix chain 'H' and resid 418 through 424 Processing sheet with id=AA1, first strand: chain 'A' and resid 34 through 36 removed outlier: 6.029A pdb=" N VAL A 4 " --> pdb=" O GLU A 35 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N ARG A 5 " --> pdb=" O ILE A 54 " (cutoff:3.500A) removed outlier: 7.614A pdb=" N PHE A 56 " --> pdb=" O ARG A 5 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N GLY A 7 " --> pdb=" O PHE A 56 " (cutoff:3.500A) removed outlier: 7.675A pdb=" N GLU A 58 " --> pdb=" O GLY A 7 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N TYR A 9 " --> pdb=" O GLU A 58 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N ASP A 53 " --> pdb=" O ILE A 79 " (cutoff:3.500A) removed outlier: 7.847A pdb=" N VAL A 81 " --> pdb=" O ASP A 53 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N ALA A 55 " --> pdb=" O VAL A 81 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N VAL A 83 " --> pdb=" O ALA A 55 " (cutoff:3.500A) removed outlier: 5.983A pdb=" N ILE A 57 " --> pdb=" O VAL A 83 " (cutoff:3.500A) removed outlier: 8.439A pdb=" N TYR A 131 " --> pdb=" O LYS A 78 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N VAL A 80 " --> pdb=" O TYR A 131 " (cutoff:3.500A) removed outlier: 7.990A pdb=" N ILE A 133 " --> pdb=" O VAL A 80 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N ALA A 82 " --> pdb=" O ILE A 133 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'B' and resid 5 through 7 removed outlier: 3.520A pdb=" N GLY B 161 " --> pdb=" O LEU B 158 " (cutoff:3.500A) removed outlier: 9.251A pdb=" N LEU B 153 " --> pdb=" O GLY B 124 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N ILE B 126 " --> pdb=" O LEU B 153 " (cutoff:3.500A) removed outlier: 7.890A pdb=" N PHE B 155 " --> pdb=" O ILE B 126 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N GLY B 128 " --> pdb=" O PHE B 155 " (cutoff:3.500A) removed outlier: 8.153A pdb=" N GLU B 157 " --> pdb=" O GLY B 128 " (cutoff:3.500A) removed outlier: 5.018A pdb=" N ILE B 129 " --> pdb=" O GLY B 92 " (cutoff:3.500A) removed outlier: 9.353A pdb=" N VAL B 93 " --> pdb=" O PRO B 27 " (cutoff:3.500A) removed outlier: 15.800A pdb=" N LYS B 29 " --> pdb=" O VAL B 93 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 77 through 80 removed outlier: 6.525A pdb=" N ARG B 264 " --> pdb=" O LEU B 68 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N GLU B 70 " --> pdb=" O GLY B 262 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N GLY B 262 " --> pdb=" O GLU B 70 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 64 through 69 removed outlier: 6.340A pdb=" N PHE C 55 " --> pdb=" O PRO C 108 " (cutoff:3.500A) removed outlier: 5.394A pdb=" N VAL C 22 " --> pdb=" O ARG C 38 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N ARG C 38 " --> pdb=" O VAL C 22 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N LYS C 24 " --> pdb=" O LEU C 36 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 197 through 198 removed outlier: 4.097A pdb=" N LEU C 197 " --> pdb=" O GLN C 186 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N ASP C 122 " --> pdb=" O ALA C 216 " (cutoff:3.500A) removed outlier: 7.615A pdb=" N ALA C 218 " --> pdb=" O ASP C 122 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N LEU C 124 " --> pdb=" O ALA C 218 " (cutoff:3.500A) removed outlier: 7.906A pdb=" N CYS C 220 " --> pdb=" O LEU C 124 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N ILE C 126 " --> pdb=" O CYS C 220 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 262 through 264 Processing sheet with id=AA7, first strand: chain 'D' and resid 8 through 10 Processing sheet with id=AA8, first strand: chain 'D' and resid 164 through 165 Processing sheet with id=AA9, first strand: chain 'D' and resid 215 through 219 removed outlier: 4.138A pdb=" N TYR D 230 " --> pdb=" O LYS D 218 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 248 through 252 Processing sheet with id=AB2, first strand: chain 'D' and resid 345 through 353 removed outlier: 6.894A pdb=" N VAL D 359 " --> pdb=" O ILE D 374 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N ILE D 374 " --> pdb=" O VAL D 359 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N ALA D 361 " --> pdb=" O ALA D 372 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N ALA D 372 " --> pdb=" O ALA D 361 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N LYS D 363 " --> pdb=" O SER D 370 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 34 through 36 removed outlier: 6.067A pdb=" N VAL E 4 " --> pdb=" O GLU E 35 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N ARG E 5 " --> pdb=" O ILE E 54 " (cutoff:3.500A) removed outlier: 7.660A pdb=" N PHE E 56 " --> pdb=" O ARG E 5 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N GLY E 7 " --> pdb=" O PHE E 56 " (cutoff:3.500A) removed outlier: 7.579A pdb=" N GLU E 58 " --> pdb=" O GLY E 7 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N TYR E 9 " --> pdb=" O GLU E 58 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N ASP E 53 " --> pdb=" O ILE E 79 " (cutoff:3.500A) removed outlier: 7.784A pdb=" N VAL E 81 " --> pdb=" O ASP E 53 " (cutoff:3.500A) removed outlier: 6.206A pdb=" N ALA E 55 " --> pdb=" O VAL E 81 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N VAL E 83 " --> pdb=" O ALA E 55 " (cutoff:3.500A) removed outlier: 6.032A pdb=" N ILE E 57 " --> pdb=" O VAL E 83 " (cutoff:3.500A) removed outlier: 8.495A pdb=" N TYR E 131 " --> pdb=" O LYS E 78 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N VAL E 80 " --> pdb=" O TYR E 131 " (cutoff:3.500A) removed outlier: 8.018A pdb=" N ILE E 133 " --> pdb=" O VAL E 80 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N ALA E 82 " --> pdb=" O ILE E 133 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'F' and resid 2 through 6 removed outlier: 4.006A pdb=" N ARG F 2 " --> pdb=" O VAL F 166 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N GLY F 161 " --> pdb=" O LEU F 158 " (cutoff:3.500A) removed outlier: 9.286A pdb=" N LEU F 153 " --> pdb=" O GLY F 124 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N ILE F 126 " --> pdb=" O LEU F 153 " (cutoff:3.500A) removed outlier: 7.990A pdb=" N PHE F 155 " --> pdb=" O ILE F 126 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N GLY F 128 " --> pdb=" O PHE F 155 " (cutoff:3.500A) removed outlier: 8.161A pdb=" N GLU F 157 " --> pdb=" O GLY F 128 " (cutoff:3.500A) removed outlier: 4.969A pdb=" N ILE F 129 " --> pdb=" O GLY F 92 " (cutoff:3.500A) removed outlier: 9.259A pdb=" N VAL F 93 " --> pdb=" O PRO F 27 " (cutoff:3.500A) removed outlier: 15.733A pdb=" N LYS F 29 " --> pdb=" O VAL F 93 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'F' and resid 77 through 80 removed outlier: 6.537A pdb=" N ARG F 264 " --> pdb=" O LEU F 68 " (cutoff:3.500A) removed outlier: 4.607A pdb=" N GLU F 70 " --> pdb=" O GLY F 262 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N GLY F 262 " --> pdb=" O GLU F 70 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'G' and resid 64 through 69 removed outlier: 6.372A pdb=" N PHE G 55 " --> pdb=" O PRO G 108 " (cutoff:3.500A) removed outlier: 5.512A pdb=" N VAL G 22 " --> pdb=" O ARG G 38 " (cutoff:3.500A) removed outlier: 6.992A pdb=" N ARG G 38 " --> pdb=" O VAL G 22 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N LYS G 24 " --> pdb=" O LEU G 36 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'G' and resid 197 through 198 removed outlier: 4.010A pdb=" N LEU G 197 " --> pdb=" O GLN G 186 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N ASP G 122 " --> pdb=" O ALA G 216 " (cutoff:3.500A) removed outlier: 7.831A pdb=" N ALA G 218 " --> pdb=" O ASP G 122 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N LEU G 124 " --> pdb=" O ALA G 218 " (cutoff:3.500A) removed outlier: 7.965A pdb=" N CYS G 220 " --> pdb=" O LEU G 124 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N ILE G 126 " --> pdb=" O CYS G 220 " (cutoff:3.500A) removed outlier: 7.996A pdb=" N PHE G 244 " --> pdb=" O THR G 215 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N VAL G 217 " --> pdb=" O PHE G 244 " (cutoff:3.500A) removed outlier: 8.083A pdb=" N THR G 246 " --> pdb=" O VAL G 217 " (cutoff:3.500A) removed outlier: 7.554A pdb=" N ILE G 219 " --> pdb=" O THR G 246 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'G' and resid 262 through 264 Processing sheet with id=AB9, first strand: chain 'H' and resid 8 through 10 Processing sheet with id=AC1, first strand: chain 'H' and resid 164 through 165 Processing sheet with id=AC2, first strand: chain 'H' and resid 215 through 219 removed outlier: 4.188A pdb=" N TYR H 230 " --> pdb=" O LYS H 218 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'H' and resid 248 through 252 Processing sheet with id=AC4, first strand: chain 'H' and resid 345 through 353 removed outlier: 6.863A pdb=" N VAL H 359 " --> pdb=" O ILE H 374 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N ILE H 374 " --> pdb=" O VAL H 359 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N ALA H 361 " --> pdb=" O ALA H 372 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N ALA H 372 " --> pdb=" O ALA H 361 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N LYS H 363 " --> pdb=" O SER H 370 " (cutoff:3.500A) 876 hydrogen bonds defined for protein. 2460 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: 3.56 Time building geometry restraints manager: 2.36 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: 9116 1.43 - 1.73: 12401 1.73 - 2.03: 220 2.03 - 2.34: 176 2.34 - 2.64: 2 Bond restraints: 21915 Sorted by residual: bond pdb=" O2B NAP G 303 " pdb=" P2B NAP G 303 " ideal model delta sigma weight residual 1.736 1.615 0.121 2.00e-02 2.50e+03 3.64e+01 bond pdb=" O2B NAP C 303 " pdb=" P2B NAP C 303 " ideal model delta sigma weight residual 1.736 1.616 0.120 2.00e-02 2.50e+03 3.59e+01 bond pdb=" O3P FAD C 302 " pdb=" P FAD C 302 " ideal model delta sigma weight residual 1.660 1.579 0.081 2.00e-02 2.50e+03 1.63e+01 bond pdb=" O3P FAD G 302 " pdb=" P FAD G 302 " ideal model delta sigma weight residual 1.660 1.583 0.077 2.00e-02 2.50e+03 1.48e+01 bond pdb=" O5B FAD C 302 " pdb=" PA FAD C 302 " ideal model delta sigma weight residual 1.634 1.569 0.065 2.00e-02 2.50e+03 1.05e+01 ... (remaining 21910 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.92: 29353 1.92 - 3.85: 310 3.85 - 5.77: 61 5.77 - 7.69: 8 7.69 - 9.61: 4 Bond angle restraints: 29736 Sorted by residual: angle pdb=" C3B NAP G 303 " pdb=" C2B NAP G 303 " pdb=" O2B NAP G 303 " ideal model delta sigma weight residual 106.96 116.57 -9.61 3.00e+00 1.11e-01 1.03e+01 angle pdb=" C VAL E 113 " pdb=" N LYS E 114 " pdb=" CA LYS E 114 " ideal model delta sigma weight residual 121.54 127.61 -6.07 1.91e+00 2.74e-01 1.01e+01 angle pdb=" CA GLY E 135 " pdb=" C GLY E 135 " pdb=" N CYS E 136 " ideal model delta sigma weight residual 114.23 116.92 -2.69 8.80e-01 1.29e+00 9.38e+00 angle pdb=" C LEU E 184 " pdb=" N GLY E 185 " pdb=" CA GLY E 185 " ideal model delta sigma weight residual 121.13 123.31 -2.18 7.30e-01 1.88e+00 8.93e+00 angle pdb=" C ASP G 175 " pdb=" N LEU G 176 " pdb=" CA LEU G 176 " ideal model delta sigma weight residual 121.54 127.16 -5.62 1.91e+00 2.74e-01 8.65e+00 ... (remaining 29731 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.15: 12907 32.15 - 64.30: 255 64.30 - 96.45: 42 96.45 - 128.60: 0 128.60 - 160.75: 2 Dihedral angle restraints: 13206 sinusoidal: 5636 harmonic: 7570 Sorted by residual: dihedral pdb=" O5' FAD C 302 " pdb=" O3P FAD C 302 " pdb=" P FAD C 302 " pdb=" PA FAD C 302 " ideal model delta sinusoidal sigma weight residual 298.23 137.48 160.75 1 3.00e+01 1.11e-03 2.07e+01 dihedral pdb=" O5' FAD G 302 " pdb=" O3P FAD G 302 " pdb=" P FAD G 302 " pdb=" PA FAD G 302 " ideal model delta sinusoidal sigma weight residual 298.23 144.70 153.53 1 3.00e+01 1.11e-03 2.02e+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 180.00 162.16 17.84 0 5.00e+00 4.00e-02 1.27e+01 ... (remaining 13203 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 2568 0.053 - 0.106: 523 0.106 - 0.159: 91 0.159 - 0.212: 3 0.212 - 0.265: 4 Chirality restraints: 3189 Sorted by residual: chirality pdb=" C2B NAP G 303 " pdb=" C1B NAP G 303 " pdb=" C3B NAP G 303 " pdb=" O2B NAP G 303 " both_signs ideal model delta sigma weight residual False -2.75 -2.49 -0.27 2.00e-01 2.50e+01 1.76e+00 chirality pdb=" C3B NAP C 303 " pdb=" C2B NAP C 303 " pdb=" C4B NAP C 303 " pdb=" O3B NAP C 303 " both_signs ideal model delta sigma weight residual False -2.52 -2.78 0.26 2.00e-01 2.50e+01 1.67e+00 chirality pdb=" C3B NAP G 303 " pdb=" C2B NAP G 303 " pdb=" C4B NAP G 303 " pdb=" O3B NAP G 303 " both_signs ideal model delta sigma weight residual False -2.52 -2.77 0.25 2.00e-01 2.50e+01 1.60e+00 ... (remaining 3186 not shown) Planarity restraints: 3748 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1D NAP C 303 " -0.105 2.00e-02 2.50e+03 7.00e-02 9.80e+01 pdb=" C2N NAP C 303 " 0.145 2.00e-02 2.50e+03 pdb=" C3N NAP C 303 " 0.004 2.00e-02 2.50e+03 pdb=" C4N NAP C 303 " -0.050 2.00e-02 2.50e+03 pdb=" C5N NAP C 303 " 0.002 2.00e-02 2.50e+03 pdb=" C6N NAP C 303 " 0.031 2.00e-02 2.50e+03 pdb=" C7N NAP C 303 " -0.054 2.00e-02 2.50e+03 pdb=" N1N NAP C 303 " 0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1D NAP G 303 " -0.015 2.00e-02 2.50e+03 2.93e-02 1.72e+01 pdb=" C2N NAP G 303 " -0.021 2.00e-02 2.50e+03 pdb=" C3N NAP G 303 " -0.018 2.00e-02 2.50e+03 pdb=" C4N NAP G 303 " -0.047 2.00e-02 2.50e+03 pdb=" C5N NAP G 303 " 0.007 2.00e-02 2.50e+03 pdb=" C6N NAP G 303 " 0.044 2.00e-02 2.50e+03 pdb=" C7N NAP G 303 " 0.041 2.00e-02 2.50e+03 pdb=" N1N NAP G 303 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS C 174 " -0.014 2.00e-02 2.50e+03 2.80e-02 7.85e+00 pdb=" C LYS C 174 " 0.048 2.00e-02 2.50e+03 pdb=" O LYS C 174 " -0.018 2.00e-02 2.50e+03 pdb=" N ASP C 175 " -0.016 2.00e-02 2.50e+03 ... (remaining 3745 not shown) Histogram of nonbonded interaction distances: 2.05 - 2.62: 195 2.62 - 3.19: 17667 3.19 - 3.76: 33282 3.76 - 4.33: 49080 4.33 - 4.90: 81704 Nonbonded interactions: 181928 Sorted by model distance: nonbonded pdb=" OE2 GLU H 46 " pdb="MG MG H 502 " model vdw 2.054 2.170 nonbonded pdb=" OE2 GLU D 46 " pdb="MG MG D 502 " model vdw 2.101 2.170 nonbonded pdb=" O ILE D 374 " pdb="MG MG D 502 " model vdw 2.121 2.170 nonbonded pdb=" O ILE H 374 " pdb="MG MG H 502 " model vdw 2.136 2.170 nonbonded pdb=" NE2 HIS H 424 " pdb="MG MG H 502 " model vdw 2.154 2.250 ... (remaining 181923 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'E' } ncs_group { reference = chain 'B' selection = chain 'F' } ncs_group { reference = chain 'C' selection = chain 'G' } ncs_group { reference = chain 'D' selection = (chain 'H' and resid 6 through 502) } 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: 3.390 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.300 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 20.300 Find NCS groups from input model: 0.390 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:1.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.910 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8552 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 0.329 21984 Z= 0.361 Angle : 0.771 33.221 29916 Z= 0.284 Chirality : 0.044 0.265 3189 Planarity : 0.005 0.070 3748 Dihedral : 13.398 160.751 8360 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 2.97 % Allowed : 6.43 % Favored : 90.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.97 % 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: -0.33 (0.16), residues: 2595 helix: 0.05 (0.16), residues: 1022 sheet: 0.29 (0.25), residues: 436 loop : -0.53 (0.18), residues: 1137 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 249 TYR 0.021 0.001 TYR H 224 PHE 0.016 0.002 PHE H 199 TRP 0.009 0.001 TRP E 216 HIS 0.003 0.001 HIS D 424 Details of bonding type rmsd covalent geometry : bond 0.00373 (21915) covalent geometry : angle 0.55252 (29736) hydrogen bonds : bond 0.17130 ( 876) hydrogen bonds : angle 6.91988 ( 2460) metal coordination : bond 0.01813 ( 65) metal coordination : angle 6.95207 ( 180) Misc. bond : bond 0.23229 ( 4) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5190 Ramachandran restraints generated. 2595 Oldfield, 0 Emsley, 2595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5190 Ramachandran restraints generated. 2595 Oldfield, 0 Emsley, 2595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 450 residues out of total 2255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 383 time to evaluate : 0.748 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 216 LEU cc_start: 0.9034 (OUTLIER) cc_final: 0.8717 (mt) REVERT: C 32 GLU cc_start: 0.7793 (mp0) cc_final: 0.7417 (mp0) REVERT: C 41 ASP cc_start: 0.8825 (t0) cc_final: 0.8622 (t70) REVERT: C 75 MET cc_start: 0.9122 (mmt) cc_final: 0.8870 (mmt) REVERT: E 238 MET cc_start: 0.8877 (mtt) cc_final: 0.8561 (mtt) REVERT: H 9 THR cc_start: 0.8787 (m) cc_final: 0.7678 (p) REVERT: H 133 TYR cc_start: 0.7984 (m-80) cc_final: 0.7592 (m-80) outliers start: 67 outliers final: 25 residues processed: 436 average time/residue: 0.1823 time to fit residues: 116.3330 Evaluate side-chains 318 residues out of total 2255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 292 time to evaluate : 0.841 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 LYS Chi-restraints excluded: chain A residue 218 ASP Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 261 THR Chi-restraints excluded: chain B residue 309 LEU Chi-restraints excluded: chain C residue 22 VAL Chi-restraints excluded: chain C residue 287 THR Chi-restraints excluded: chain D residue 16 VAL Chi-restraints excluded: chain D residue 26 ILE Chi-restraints excluded: chain D residue 55 GLU Chi-restraints excluded: chain D residue 297 LEU Chi-restraints excluded: chain D residue 416 ASP Chi-restraints excluded: chain E residue 218 ASP Chi-restraints excluded: chain F residue 4 VAL Chi-restraints excluded: chain F residue 195 ASP Chi-restraints excluded: chain F residue 261 THR Chi-restraints excluded: chain F residue 288 THR Chi-restraints excluded: chain G residue 29 THR Chi-restraints excluded: chain G residue 123 LEU Chi-restraints excluded: chain G residue 287 THR Chi-restraints excluded: chain H residue 139 ILE Chi-restraints excluded: chain H residue 226 ILE Chi-restraints excluded: chain H residue 340 VAL Chi-restraints excluded: chain H residue 344 ASP Chi-restraints excluded: chain H residue 396 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 257 random chunks: chunk 197 optimal weight: 0.4980 chunk 215 optimal weight: 5.9990 chunk 20 optimal weight: 1.9990 chunk 132 optimal weight: 2.9990 chunk 248 optimal weight: 0.4980 chunk 207 optimal weight: 0.0060 chunk 155 optimal weight: 2.9990 chunk 244 optimal weight: 0.9990 chunk 183 optimal weight: 2.9990 chunk 111 optimal weight: 0.0980 chunk 71 optimal weight: 0.8980 overall best weight: 0.3996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 132 ASN E 132 ASN G 151 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2658 r_free = 0.2658 target = 0.055198 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2479 r_free = 0.2479 target = 0.047951 restraints weight = 44311.424| |-----------------------------------------------------------------------------| r_work (start): 0.2477 rms_B_bonded: 1.26 r_work: 0.2387 rms_B_bonded: 1.72 restraints_weight: 0.5000 r_work: 0.2268 rms_B_bonded: 3.00 restraints_weight: 0.2500 r_work (final): 0.2268 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8839 moved from start: 0.1169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.113 21984 Z= 0.124 Angle : 0.750 30.562 29916 Z= 0.282 Chirality : 0.043 0.171 3189 Planarity : 0.004 0.044 3748 Dihedral : 11.613 152.276 3157 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 2.35 % Allowed : 9.45 % Favored : 88.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.97 % 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: 0.02 (0.16), residues: 2595 helix: 0.34 (0.16), residues: 1037 sheet: 0.25 (0.25), residues: 448 loop : -0.24 (0.18), residues: 1110 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 224 TYR 0.019 0.001 TYR B 215 PHE 0.016 0.001 PHE F 71 TRP 0.008 0.001 TRP A 216 HIS 0.008 0.001 HIS G 18 Details of bonding type rmsd covalent geometry : bond 0.00263 (21915) covalent geometry : angle 0.52727 (29736) hydrogen bonds : bond 0.04833 ( 876) hydrogen bonds : angle 5.71247 ( 2460) metal coordination : bond 0.01569 ( 65) metal coordination : angle 6.89512 ( 180) Misc. bond : bond 0.00202 ( 4) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5190 Ramachandran restraints generated. 2595 Oldfield, 0 Emsley, 2595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5190 Ramachandran restraints generated. 2595 Oldfield, 0 Emsley, 2595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 367 residues out of total 2255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 314 time to evaluate : 0.963 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 106 LYS cc_start: 0.9252 (OUTLIER) cc_final: 0.8877 (ttpp) REVERT: A 226 GLU cc_start: 0.8472 (OUTLIER) cc_final: 0.7968 (mp0) REVERT: C 32 GLU cc_start: 0.8122 (OUTLIER) cc_final: 0.7921 (mp0) REVERT: C 75 MET cc_start: 0.9182 (mmt) cc_final: 0.8957 (mmt) REVERT: C 148 LYS cc_start: 0.9147 (ttpt) cc_final: 0.8941 (tttt) REVERT: D 141 LEU cc_start: 0.8535 (mm) cc_final: 0.8083 (tp) REVERT: E 238 MET cc_start: 0.9049 (mtt) cc_final: 0.8802 (mtt) REVERT: G 2 MET cc_start: 0.8047 (mpp) cc_final: 0.7612 (mpp) REVERT: H 141 LEU cc_start: 0.8490 (mp) cc_final: 0.8270 (tt) outliers start: 53 outliers final: 30 residues processed: 350 average time/residue: 0.1921 time to fit residues: 98.4268 Evaluate side-chains 326 residues out of total 2255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 293 time to evaluate : 0.894 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 106 LYS Chi-restraints excluded: chain A residue 152 ILE Chi-restraints excluded: chain A residue 154 SER Chi-restraints excluded: chain A residue 226 GLU Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 261 THR Chi-restraints excluded: chain B residue 309 LEU Chi-restraints excluded: chain C residue 22 VAL Chi-restraints excluded: chain C residue 32 GLU Chi-restraints excluded: chain C residue 51 LYS Chi-restraints excluded: chain D residue 16 VAL Chi-restraints excluded: chain D residue 26 ILE Chi-restraints excluded: chain D residue 181 MET Chi-restraints excluded: chain D residue 281 ASP Chi-restraints excluded: chain D residue 297 LEU Chi-restraints excluded: chain D residue 416 ASP Chi-restraints excluded: chain E residue 67 VAL Chi-restraints excluded: chain E residue 152 ILE Chi-restraints excluded: chain E residue 154 SER Chi-restraints excluded: chain E residue 226 GLU Chi-restraints excluded: chain E residue 257 SER Chi-restraints excluded: chain F residue 4 VAL Chi-restraints excluded: chain F residue 195 ASP Chi-restraints excluded: chain F residue 261 THR Chi-restraints excluded: chain F residue 288 THR Chi-restraints excluded: chain G residue 29 THR Chi-restraints excluded: chain G residue 287 THR Chi-restraints excluded: chain H residue 16 VAL Chi-restraints excluded: chain H residue 139 ILE Chi-restraints excluded: chain H residue 226 ILE Chi-restraints excluded: chain H residue 299 LYS Chi-restraints excluded: chain H residue 340 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 257 random chunks: chunk 159 optimal weight: 2.9990 chunk 134 optimal weight: 0.1980 chunk 176 optimal weight: 1.9990 chunk 109 optimal weight: 5.9990 chunk 161 optimal weight: 4.9990 chunk 12 optimal weight: 1.9990 chunk 250 optimal weight: 0.9990 chunk 239 optimal weight: 0.6980 chunk 179 optimal weight: 0.6980 chunk 106 optimal weight: 1.9990 chunk 80 optimal weight: 1.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 132 ASN ** D 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 132 ASN H 111 HIS H 160 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2626 r_free = 0.2626 target = 0.053952 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2442 r_free = 0.2442 target = 0.046645 restraints weight = 44713.117| |-----------------------------------------------------------------------------| r_work (start): 0.2437 rms_B_bonded: 1.27 r_work: 0.2346 rms_B_bonded: 1.73 restraints_weight: 0.5000 r_work: 0.2225 rms_B_bonded: 3.01 restraints_weight: 0.2500 r_work (final): 0.2225 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8866 moved from start: 0.1333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.133 21984 Z= 0.158 Angle : 0.760 31.268 29916 Z= 0.287 Chirality : 0.044 0.175 3189 Planarity : 0.004 0.044 3748 Dihedral : 10.932 154.160 3141 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 2.75 % Allowed : 9.98 % Favored : 87.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.97 % 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: 0.02 (0.16), residues: 2595 helix: 0.36 (0.16), residues: 1038 sheet: 0.27 (0.25), residues: 432 loop : -0.27 (0.18), residues: 1125 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG G 190 TYR 0.022 0.001 TYR H 224 PHE 0.018 0.002 PHE F 71 TRP 0.011 0.001 TRP A 216 HIS 0.007 0.001 HIS F 49 Details of bonding type rmsd covalent geometry : bond 0.00366 (21915) covalent geometry : angle 0.53932 (29736) hydrogen bonds : bond 0.05053 ( 876) hydrogen bonds : angle 5.52368 ( 2460) metal coordination : bond 0.01916 ( 65) metal coordination : angle 6.92452 ( 180) Misc. bond : bond 0.00203 ( 4) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5190 Ramachandran restraints generated. 2595 Oldfield, 0 Emsley, 2595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5190 Ramachandran restraints generated. 2595 Oldfield, 0 Emsley, 2595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 362 residues out of total 2255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 300 time to evaluate : 0.886 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 106 LYS cc_start: 0.9246 (OUTLIER) cc_final: 0.8914 (ttpp) REVERT: C 32 GLU cc_start: 0.8174 (OUTLIER) cc_final: 0.7867 (mp0) REVERT: C 75 MET cc_start: 0.9237 (mmt) cc_final: 0.8995 (mmt) REVERT: D 384 MET cc_start: 0.8986 (tpp) cc_final: 0.8641 (tpp) REVERT: G 2 MET cc_start: 0.7929 (mpp) cc_final: 0.7622 (mpp) REVERT: H 141 LEU cc_start: 0.8542 (mp) cc_final: 0.8284 (tt) outliers start: 62 outliers final: 41 residues processed: 344 average time/residue: 0.1861 time to fit residues: 95.0837 Evaluate side-chains 330 residues out of total 2255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 287 time to evaluate : 0.898 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 106 LYS Chi-restraints excluded: chain A residue 154 SER Chi-restraints excluded: chain A residue 226 GLU Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 246 CYS Chi-restraints excluded: chain B residue 261 THR Chi-restraints excluded: chain B residue 309 LEU Chi-restraints excluded: chain C residue 22 VAL Chi-restraints excluded: chain C residue 32 GLU Chi-restraints excluded: chain C residue 51 LYS Chi-restraints excluded: chain D residue 16 VAL Chi-restraints excluded: chain D residue 26 ILE Chi-restraints excluded: chain D residue 139 ILE Chi-restraints excluded: chain D residue 181 MET Chi-restraints excluded: chain D residue 281 ASP Chi-restraints excluded: chain D residue 297 LEU Chi-restraints excluded: chain D residue 416 ASP Chi-restraints excluded: chain E residue 45 ASP Chi-restraints excluded: chain E residue 67 VAL Chi-restraints excluded: chain E residue 92 VAL Chi-restraints excluded: chain E residue 152 ILE Chi-restraints excluded: chain E residue 154 SER Chi-restraints excluded: chain E residue 226 GLU Chi-restraints excluded: chain E residue 257 SER Chi-restraints excluded: chain F residue 4 VAL Chi-restraints excluded: chain F residue 82 ILE Chi-restraints excluded: chain F residue 83 GLU Chi-restraints excluded: chain F residue 195 ASP Chi-restraints excluded: chain F residue 261 THR Chi-restraints excluded: chain F residue 275 SER Chi-restraints excluded: chain F residue 288 THR Chi-restraints excluded: chain G residue 29 THR Chi-restraints excluded: chain G residue 266 SER Chi-restraints excluded: chain H residue 16 VAL Chi-restraints excluded: chain H residue 124 SER Chi-restraints excluded: chain H residue 139 ILE Chi-restraints excluded: chain H residue 226 ILE Chi-restraints excluded: chain H residue 282 LEU Chi-restraints excluded: chain H residue 299 LYS Chi-restraints excluded: chain H residue 340 VAL Chi-restraints excluded: chain H residue 396 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 257 random chunks: chunk 177 optimal weight: 5.9990 chunk 208 optimal weight: 0.8980 chunk 91 optimal weight: 0.2980 chunk 110 optimal weight: 4.9990 chunk 230 optimal weight: 3.9990 chunk 64 optimal weight: 3.9990 chunk 126 optimal weight: 2.9990 chunk 235 optimal weight: 4.9990 chunk 170 optimal weight: 0.7980 chunk 202 optimal weight: 0.7980 chunk 89 optimal weight: 6.9990 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 132 ASN D 111 HIS D 310 GLN E 132 ASN H 160 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2603 r_free = 0.2603 target = 0.053091 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2418 r_free = 0.2418 target = 0.045833 restraints weight = 44484.731| |-----------------------------------------------------------------------------| r_work (start): 0.2416 rms_B_bonded: 1.26 r_work: 0.2326 rms_B_bonded: 1.71 restraints_weight: 0.5000 r_work: 0.2205 rms_B_bonded: 2.98 restraints_weight: 0.2500 r_work (final): 0.2205 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8879 moved from start: 0.1435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.145 21984 Z= 0.181 Angle : 0.781 32.149 29916 Z= 0.297 Chirality : 0.045 0.180 3189 Planarity : 0.005 0.069 3748 Dihedral : 10.649 157.921 3140 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 3.10 % Allowed : 10.86 % Favored : 86.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.97 % 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: -0.02 (0.16), residues: 2595 helix: 0.33 (0.16), residues: 1038 sheet: 0.28 (0.25), residues: 429 loop : -0.31 (0.18), residues: 1128 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D 266 TYR 0.025 0.002 TYR H 224 PHE 0.020 0.002 PHE D 239 TRP 0.010 0.001 TRP C 194 HIS 0.005 0.001 HIS G 95 Details of bonding type rmsd covalent geometry : bond 0.00430 (21915) covalent geometry : angle 0.55861 (29736) hydrogen bonds : bond 0.05212 ( 876) hydrogen bonds : angle 5.53917 ( 2460) metal coordination : bond 0.02110 ( 65) metal coordination : angle 7.05694 ( 180) Misc. bond : bond 0.00238 ( 4) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5190 Ramachandran restraints generated. 2595 Oldfield, 0 Emsley, 2595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5190 Ramachandran restraints generated. 2595 Oldfield, 0 Emsley, 2595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 356 residues out of total 2255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 286 time to evaluate : 0.879 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 32 GLU cc_start: 0.8216 (OUTLIER) cc_final: 0.7912 (mp0) REVERT: D 384 MET cc_start: 0.9034 (tpp) cc_final: 0.8781 (tpp) REVERT: H 141 LEU cc_start: 0.8567 (mp) cc_final: 0.8334 (tp) REVERT: H 352 GLU cc_start: 0.7497 (tp30) cc_final: 0.7227 (tp30) outliers start: 70 outliers final: 52 residues processed: 339 average time/residue: 0.1807 time to fit residues: 91.4911 Evaluate side-chains 340 residues out of total 2255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 287 time to evaluate : 0.880 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 ASP Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 106 LYS Chi-restraints excluded: chain A residue 154 SER Chi-restraints excluded: chain A residue 226 GLU Chi-restraints excluded: chain A residue 257 SER Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 246 CYS Chi-restraints excluded: chain B residue 261 THR Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 309 LEU Chi-restraints excluded: chain C residue 22 VAL Chi-restraints excluded: chain C residue 32 GLU Chi-restraints excluded: chain C residue 51 LYS Chi-restraints excluded: chain C residue 187 SER Chi-restraints excluded: chain D residue 16 VAL Chi-restraints excluded: chain D residue 26 ILE Chi-restraints excluded: chain D residue 60 ILE Chi-restraints excluded: chain D residue 139 ILE Chi-restraints excluded: chain D residue 181 MET Chi-restraints excluded: chain D residue 281 ASP Chi-restraints excluded: chain D residue 297 LEU Chi-restraints excluded: chain D residue 416 ASP Chi-restraints excluded: chain E residue 67 VAL Chi-restraints excluded: chain E residue 92 VAL Chi-restraints excluded: chain E residue 152 ILE Chi-restraints excluded: chain E residue 154 SER Chi-restraints excluded: chain E residue 226 GLU Chi-restraints excluded: chain E residue 257 SER Chi-restraints excluded: chain F residue 4 VAL Chi-restraints excluded: chain F residue 82 ILE Chi-restraints excluded: chain F residue 83 GLU Chi-restraints excluded: chain F residue 104 LEU Chi-restraints excluded: chain F residue 195 ASP Chi-restraints excluded: chain F residue 261 THR Chi-restraints excluded: chain F residue 275 SER Chi-restraints excluded: chain F residue 288 THR Chi-restraints excluded: chain G residue 29 THR Chi-restraints excluded: chain G residue 105 VAL Chi-restraints excluded: chain G residue 123 LEU Chi-restraints excluded: chain G residue 152 ILE Chi-restraints excluded: chain G residue 266 SER Chi-restraints excluded: chain H residue 16 VAL Chi-restraints excluded: chain H residue 124 SER Chi-restraints excluded: chain H residue 139 ILE Chi-restraints excluded: chain H residue 226 ILE Chi-restraints excluded: chain H residue 253 VAL Chi-restraints excluded: chain H residue 282 LEU Chi-restraints excluded: chain H residue 299 LYS Chi-restraints excluded: chain H residue 340 VAL Chi-restraints excluded: chain H residue 396 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 257 random chunks: chunk 166 optimal weight: 2.9990 chunk 65 optimal weight: 2.9990 chunk 54 optimal weight: 0.7980 chunk 211 optimal weight: 0.0470 chunk 0 optimal weight: 3.9990 chunk 96 optimal weight: 3.9990 chunk 132 optimal weight: 0.9980 chunk 89 optimal weight: 5.9990 chunk 136 optimal weight: 0.0770 chunk 244 optimal weight: 3.9990 chunk 119 optimal weight: 0.0980 overall best weight: 0.4036 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 132 ASN C 260 HIS E 132 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2657 r_free = 0.2657 target = 0.055212 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2476 r_free = 0.2476 target = 0.047947 restraints weight = 44252.655| |-----------------------------------------------------------------------------| r_work (start): 0.2476 rms_B_bonded: 1.26 r_work: 0.2387 rms_B_bonded: 1.72 restraints_weight: 0.5000 r_work: 0.2268 rms_B_bonded: 3.01 restraints_weight: 0.2500 r_work (final): 0.2268 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8837 moved from start: 0.1591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.108 21984 Z= 0.112 Angle : 0.718 29.605 29916 Z= 0.264 Chirality : 0.042 0.166 3189 Planarity : 0.004 0.046 3748 Dihedral : 10.095 155.387 3140 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 2.57 % Allowed : 11.84 % Favored : 85.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.97 % 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: 0.20 (0.16), residues: 2595 helix: 0.50 (0.16), residues: 1038 sheet: 0.34 (0.25), residues: 421 loop : -0.14 (0.18), residues: 1136 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG D 266 TYR 0.018 0.001 TYR B 215 PHE 0.014 0.001 PHE F 71 TRP 0.009 0.001 TRP A 216 HIS 0.006 0.001 HIS H 424 Details of bonding type rmsd covalent geometry : bond 0.00244 (21915) covalent geometry : angle 0.49671 (29736) hydrogen bonds : bond 0.04157 ( 876) hydrogen bonds : angle 5.31771 ( 2460) metal coordination : bond 0.01497 ( 65) metal coordination : angle 6.71097 ( 180) Misc. bond : bond 0.00192 ( 4) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5190 Ramachandran restraints generated. 2595 Oldfield, 0 Emsley, 2595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5190 Ramachandran restraints generated. 2595 Oldfield, 0 Emsley, 2595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 367 residues out of total 2255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 309 time to evaluate : 0.987 Fit side-chains revert: symmetry clash REVERT: A 106 LYS cc_start: 0.9196 (OUTLIER) cc_final: 0.8932 (ttpp) REVERT: A 226 GLU cc_start: 0.8444 (OUTLIER) cc_final: 0.7979 (mp0) REVERT: C 32 GLU cc_start: 0.8166 (OUTLIER) cc_final: 0.7936 (mp0) REVERT: E 44 ARG cc_start: 0.8846 (ttt-90) cc_final: 0.8634 (ttt-90) REVERT: E 226 GLU cc_start: 0.8365 (OUTLIER) cc_final: 0.7884 (mp0) REVERT: E 251 MET cc_start: 0.8686 (mtt) cc_final: 0.8476 (mtp) REVERT: H 141 LEU cc_start: 0.8505 (mp) cc_final: 0.8249 (tt) REVERT: H 352 GLU cc_start: 0.7464 (tp30) cc_final: 0.7219 (tp30) REVERT: H 410 MET cc_start: 0.8700 (mtp) cc_final: 0.8458 (mtp) outliers start: 58 outliers final: 38 residues processed: 351 average time/residue: 0.1850 time to fit residues: 96.9000 Evaluate side-chains 327 residues out of total 2255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 285 time to evaluate : 0.881 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 106 LYS Chi-restraints excluded: chain A residue 154 SER Chi-restraints excluded: chain A residue 226 GLU Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 246 CYS Chi-restraints excluded: chain B residue 261 THR Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 309 LEU Chi-restraints excluded: chain C residue 22 VAL Chi-restraints excluded: chain C residue 32 GLU Chi-restraints excluded: chain C residue 51 LYS Chi-restraints excluded: chain C residue 71 CYS Chi-restraints excluded: chain D residue 16 VAL Chi-restraints excluded: chain D residue 26 ILE Chi-restraints excluded: chain D residue 139 ILE Chi-restraints excluded: chain D residue 281 ASP Chi-restraints excluded: chain D residue 297 LEU Chi-restraints excluded: chain D residue 299 LYS Chi-restraints excluded: chain E residue 45 ASP Chi-restraints excluded: chain E residue 67 VAL Chi-restraints excluded: chain E residue 92 VAL Chi-restraints excluded: chain E residue 152 ILE Chi-restraints excluded: chain E residue 154 SER Chi-restraints excluded: chain E residue 226 GLU Chi-restraints excluded: chain F residue 4 VAL Chi-restraints excluded: chain F residue 83 GLU Chi-restraints excluded: chain F residue 195 ASP Chi-restraints excluded: chain F residue 261 THR Chi-restraints excluded: chain F residue 275 SER Chi-restraints excluded: chain F residue 288 THR Chi-restraints excluded: chain G residue 29 THR Chi-restraints excluded: chain G residue 115 VAL Chi-restraints excluded: chain G residue 123 LEU Chi-restraints excluded: chain H residue 16 VAL Chi-restraints excluded: chain H residue 124 SER Chi-restraints excluded: chain H residue 139 ILE Chi-restraints excluded: chain H residue 226 ILE Chi-restraints excluded: chain H residue 253 VAL Chi-restraints excluded: chain H residue 282 LEU Chi-restraints excluded: chain H residue 340 VAL Chi-restraints excluded: chain H residue 396 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 257 random chunks: chunk 90 optimal weight: 0.9980 chunk 137 optimal weight: 0.9990 chunk 208 optimal weight: 0.0770 chunk 53 optimal weight: 3.9990 chunk 65 optimal weight: 2.9990 chunk 186 optimal weight: 1.9990 chunk 146 optimal weight: 4.9990 chunk 98 optimal weight: 0.2980 chunk 64 optimal weight: 5.9990 chunk 35 optimal weight: 1.9990 chunk 13 optimal weight: 0.3980 overall best weight: 0.5540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 132 ASN C 11 ASN D 398 ASN E 132 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2653 r_free = 0.2653 target = 0.055000 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2473 r_free = 0.2473 target = 0.047796 restraints weight = 44233.525| |-----------------------------------------------------------------------------| r_work (start): 0.2470 rms_B_bonded: 1.21 r_work: 0.2382 rms_B_bonded: 1.70 restraints_weight: 0.5000 r_work: 0.2263 rms_B_bonded: 2.99 restraints_weight: 0.2500 r_work (final): 0.2263 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8840 moved from start: 0.1662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.113 21984 Z= 0.122 Angle : 0.718 29.182 29916 Z= 0.268 Chirality : 0.043 0.187 3189 Planarity : 0.004 0.045 3748 Dihedral : 9.869 151.953 3138 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 2.66 % Allowed : 12.15 % Favored : 85.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.97 % 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: 0.21 (0.16), residues: 2595 helix: 0.51 (0.16), residues: 1047 sheet: 0.38 (0.25), residues: 411 loop : -0.16 (0.18), residues: 1137 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 403 TYR 0.019 0.001 TYR H 224 PHE 0.015 0.001 PHE F 71 TRP 0.009 0.001 TRP A 216 HIS 0.005 0.001 HIS H 424 Details of bonding type rmsd covalent geometry : bond 0.00276 (21915) covalent geometry : angle 0.50486 (29736) hydrogen bonds : bond 0.04263 ( 876) hydrogen bonds : angle 5.27592 ( 2460) metal coordination : bond 0.01588 ( 65) metal coordination : angle 6.60692 ( 180) Misc. bond : bond 0.00174 ( 4) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5190 Ramachandran restraints generated. 2595 Oldfield, 0 Emsley, 2595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5190 Ramachandran restraints generated. 2595 Oldfield, 0 Emsley, 2595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 354 residues out of total 2255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 294 time to evaluate : 0.880 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 106 LYS cc_start: 0.9175 (OUTLIER) cc_final: 0.8937 (ttpp) REVERT: A 226 GLU cc_start: 0.8446 (OUTLIER) cc_final: 0.7983 (mp0) REVERT: C 32 GLU cc_start: 0.8191 (OUTLIER) cc_final: 0.7928 (mp0) REVERT: C 144 ASP cc_start: 0.8386 (m-30) cc_final: 0.8147 (m-30) REVERT: E 44 ARG cc_start: 0.8849 (ttt-90) cc_final: 0.8645 (ttt-90) REVERT: H 141 LEU cc_start: 0.8519 (mp) cc_final: 0.8261 (tt) REVERT: H 352 GLU cc_start: 0.7487 (tp30) cc_final: 0.7227 (tp30) REVERT: H 410 MET cc_start: 0.8742 (mtp) cc_final: 0.8499 (mtp) outliers start: 60 outliers final: 42 residues processed: 337 average time/residue: 0.1855 time to fit residues: 92.9060 Evaluate side-chains 326 residues out of total 2255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 281 time to evaluate : 0.884 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 106 LYS Chi-restraints excluded: chain A residue 154 SER Chi-restraints excluded: chain A residue 226 GLU Chi-restraints excluded: chain A residue 257 SER Chi-restraints excluded: chain B residue 28 VAL Chi-restraints excluded: chain B residue 261 THR Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 309 LEU Chi-restraints excluded: chain C residue 22 VAL Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 32 GLU Chi-restraints excluded: chain C residue 51 LYS Chi-restraints excluded: chain C residue 71 CYS Chi-restraints excluded: chain C residue 187 SER Chi-restraints excluded: chain D residue 16 VAL Chi-restraints excluded: chain D residue 26 ILE Chi-restraints excluded: chain D residue 139 ILE Chi-restraints excluded: chain D residue 297 LEU Chi-restraints excluded: chain D residue 398 ASN Chi-restraints excluded: chain E residue 45 ASP Chi-restraints excluded: chain E residue 67 VAL Chi-restraints excluded: chain E residue 92 VAL Chi-restraints excluded: chain E residue 152 ILE Chi-restraints excluded: chain E residue 154 SER Chi-restraints excluded: chain E residue 226 GLU Chi-restraints excluded: chain F residue 4 VAL Chi-restraints excluded: chain F residue 82 ILE Chi-restraints excluded: chain F residue 83 GLU Chi-restraints excluded: chain F residue 195 ASP Chi-restraints excluded: chain F residue 261 THR Chi-restraints excluded: chain F residue 275 SER Chi-restraints excluded: chain F residue 288 THR Chi-restraints excluded: chain G residue 29 THR Chi-restraints excluded: chain G residue 105 VAL Chi-restraints excluded: chain G residue 115 VAL Chi-restraints excluded: chain G residue 123 LEU Chi-restraints excluded: chain G residue 152 ILE Chi-restraints excluded: chain G residue 266 SER Chi-restraints excluded: chain H residue 16 VAL Chi-restraints excluded: chain H residue 139 ILE Chi-restraints excluded: chain H residue 226 ILE Chi-restraints excluded: chain H residue 253 VAL Chi-restraints excluded: chain H residue 340 VAL Chi-restraints excluded: chain H residue 396 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 257 random chunks: chunk 44 optimal weight: 3.9990 chunk 221 optimal weight: 4.9990 chunk 190 optimal weight: 2.9990 chunk 138 optimal weight: 2.9990 chunk 215 optimal weight: 1.9990 chunk 129 optimal weight: 3.9990 chunk 30 optimal weight: 2.9990 chunk 161 optimal weight: 1.9990 chunk 80 optimal weight: 0.9990 chunk 96 optimal weight: 3.9990 chunk 227 optimal weight: 1.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 132 ASN E 132 ASN H 160 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2554 r_free = 0.2554 target = 0.051234 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2367 r_free = 0.2367 target = 0.044036 restraints weight = 44634.666| |-----------------------------------------------------------------------------| r_work (start): 0.2367 rms_B_bonded: 1.21 r_work: 0.2276 rms_B_bonded: 1.69 restraints_weight: 0.5000 r_work: 0.2156 rms_B_bonded: 2.94 restraints_weight: 0.2500 r_work (final): 0.2156 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8909 moved from start: 0.1676 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.181 21984 Z= 0.272 Angle : 0.872 33.927 29916 Z= 0.346 Chirality : 0.048 0.196 3189 Planarity : 0.005 0.058 3748 Dihedral : 10.285 158.737 3136 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 3.15 % Allowed : 11.66 % Favored : 85.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.97 % 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: -0.16 (0.16), residues: 2595 helix: 0.19 (0.16), residues: 1032 sheet: 0.34 (0.24), residues: 429 loop : -0.41 (0.18), residues: 1134 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 190 TYR 0.032 0.002 TYR H 224 PHE 0.025 0.002 PHE F 71 TRP 0.012 0.002 TRP C 194 HIS 0.009 0.002 HIS G 95 Details of bonding type rmsd covalent geometry : bond 0.00665 (21915) covalent geometry : angle 0.65360 (29736) hydrogen bonds : bond 0.06174 ( 876) hydrogen bonds : angle 5.68096 ( 2460) metal coordination : bond 0.02714 ( 65) metal coordination : angle 7.47839 ( 180) Misc. bond : bond 0.00213 ( 4) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5190 Ramachandran restraints generated. 2595 Oldfield, 0 Emsley, 2595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5190 Ramachandran restraints generated. 2595 Oldfield, 0 Emsley, 2595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 357 residues out of total 2255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 286 time to evaluate : 0.932 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 106 LYS cc_start: 0.9261 (OUTLIER) cc_final: 0.9002 (mtpp) REVERT: C 32 GLU cc_start: 0.8260 (OUTLIER) cc_final: 0.8029 (mp0) REVERT: H 141 LEU cc_start: 0.8608 (mp) cc_final: 0.8305 (tp) REVERT: H 352 GLU cc_start: 0.7694 (tp30) cc_final: 0.7422 (tp30) outliers start: 71 outliers final: 59 residues processed: 344 average time/residue: 0.1811 time to fit residues: 92.9081 Evaluate side-chains 340 residues out of total 2255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 279 time to evaluate : 0.910 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 106 LYS Chi-restraints excluded: chain A residue 154 SER Chi-restraints excluded: chain A residue 226 GLU Chi-restraints excluded: chain A residue 257 SER Chi-restraints excluded: chain B residue 28 VAL Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 239 CYS Chi-restraints excluded: chain B residue 246 CYS Chi-restraints excluded: chain B residue 251 VAL Chi-restraints excluded: chain B residue 261 THR Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 309 LEU Chi-restraints excluded: chain C residue 22 VAL Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 32 GLU Chi-restraints excluded: chain C residue 51 LYS Chi-restraints excluded: chain C residue 71 CYS Chi-restraints excluded: chain C residue 105 VAL Chi-restraints excluded: chain D residue 16 VAL Chi-restraints excluded: chain D residue 26 ILE Chi-restraints excluded: chain D residue 60 ILE Chi-restraints excluded: chain D residue 139 ILE Chi-restraints excluded: chain D residue 181 MET Chi-restraints excluded: chain D residue 215 LEU Chi-restraints excluded: chain D residue 299 LYS Chi-restraints excluded: chain E residue 45 ASP Chi-restraints excluded: chain E residue 67 VAL Chi-restraints excluded: chain E residue 92 VAL Chi-restraints excluded: chain E residue 152 ILE Chi-restraints excluded: chain E residue 154 SER Chi-restraints excluded: chain E residue 226 GLU Chi-restraints excluded: chain E residue 257 SER Chi-restraints excluded: chain F residue 4 VAL Chi-restraints excluded: chain F residue 28 VAL Chi-restraints excluded: chain F residue 82 ILE Chi-restraints excluded: chain F residue 83 GLU Chi-restraints excluded: chain F residue 104 LEU Chi-restraints excluded: chain F residue 195 ASP Chi-restraints excluded: chain F residue 261 THR Chi-restraints excluded: chain F residue 275 SER Chi-restraints excluded: chain F residue 288 THR Chi-restraints excluded: chain G residue 29 THR Chi-restraints excluded: chain G residue 105 VAL Chi-restraints excluded: chain G residue 115 VAL Chi-restraints excluded: chain G residue 152 ILE Chi-restraints excluded: chain G residue 234 ILE Chi-restraints excluded: chain G residue 266 SER Chi-restraints excluded: chain H residue 16 VAL Chi-restraints excluded: chain H residue 26 ILE Chi-restraints excluded: chain H residue 124 SER Chi-restraints excluded: chain H residue 139 ILE Chi-restraints excluded: chain H residue 226 ILE Chi-restraints excluded: chain H residue 253 VAL Chi-restraints excluded: chain H residue 282 LEU Chi-restraints excluded: chain H residue 286 LYS Chi-restraints excluded: chain H residue 299 LYS Chi-restraints excluded: chain H residue 340 VAL Chi-restraints excluded: chain H residue 396 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 257 random chunks: chunk 66 optimal weight: 0.6980 chunk 44 optimal weight: 2.9990 chunk 24 optimal weight: 3.9990 chunk 165 optimal weight: 0.8980 chunk 125 optimal weight: 0.5980 chunk 119 optimal weight: 1.9990 chunk 117 optimal weight: 0.6980 chunk 181 optimal weight: 0.8980 chunk 130 optimal weight: 3.9990 chunk 139 optimal weight: 1.9990 chunk 192 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 132 ASN E 132 ASN H 160 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2608 r_free = 0.2608 target = 0.053242 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2424 r_free = 0.2424 target = 0.045981 restraints weight = 44423.518| |-----------------------------------------------------------------------------| r_work (start): 0.2422 rms_B_bonded: 1.25 r_work: 0.2332 rms_B_bonded: 1.71 restraints_weight: 0.5000 r_work: 0.2213 rms_B_bonded: 2.97 restraints_weight: 0.2500 r_work (final): 0.2213 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8871 moved from start: 0.1658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.135 21984 Z= 0.147 Angle : 0.781 32.256 29916 Z= 0.294 Chirality : 0.044 0.179 3189 Planarity : 0.004 0.045 3748 Dihedral : 10.041 159.595 3134 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 2.53 % Allowed : 12.77 % Favored : 84.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.97 % 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: -0.02 (0.16), residues: 2595 helix: 0.36 (0.16), residues: 1032 sheet: 0.24 (0.25), residues: 417 loop : -0.32 (0.18), residues: 1146 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 190 TYR 0.022 0.001 TYR H 224 PHE 0.018 0.002 PHE F 71 TRP 0.009 0.001 TRP C 194 HIS 0.004 0.001 HIS D 424 Details of bonding type rmsd covalent geometry : bond 0.00338 (21915) covalent geometry : angle 0.55653 (29736) hydrogen bonds : bond 0.04859 ( 876) hydrogen bonds : angle 5.48655 ( 2460) metal coordination : bond 0.01906 ( 65) metal coordination : angle 7.08247 ( 180) Misc. bond : bond 0.00174 ( 4) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5190 Ramachandran restraints generated. 2595 Oldfield, 0 Emsley, 2595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5190 Ramachandran restraints generated. 2595 Oldfield, 0 Emsley, 2595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 343 residues out of total 2255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 286 time to evaluate : 0.661 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 106 LYS cc_start: 0.9222 (OUTLIER) cc_final: 0.8933 (ttpp) REVERT: A 226 GLU cc_start: 0.8553 (OUTLIER) cc_final: 0.8026 (mp0) REVERT: C 32 GLU cc_start: 0.8235 (OUTLIER) cc_final: 0.7881 (mp0) REVERT: D 349 SER cc_start: 0.8012 (t) cc_final: 0.7736 (m) REVERT: H 141 LEU cc_start: 0.8563 (mp) cc_final: 0.8266 (tp) REVERT: H 352 GLU cc_start: 0.7665 (tp30) cc_final: 0.7378 (tp30) outliers start: 57 outliers final: 47 residues processed: 333 average time/residue: 0.1698 time to fit residues: 83.7445 Evaluate side-chains 332 residues out of total 2255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 282 time to evaluate : 0.898 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 106 LYS Chi-restraints excluded: chain A residue 154 SER Chi-restraints excluded: chain A residue 226 GLU Chi-restraints excluded: chain A residue 257 SER Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 239 CYS Chi-restraints excluded: chain B residue 246 CYS Chi-restraints excluded: chain B residue 261 THR Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 309 LEU Chi-restraints excluded: chain C residue 22 VAL Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 32 GLU Chi-restraints excluded: chain C residue 51 LYS Chi-restraints excluded: chain C residue 71 CYS Chi-restraints excluded: chain D residue 16 VAL Chi-restraints excluded: chain D residue 26 ILE Chi-restraints excluded: chain D residue 139 ILE Chi-restraints excluded: chain D residue 337 ARG Chi-restraints excluded: chain E residue 45 ASP Chi-restraints excluded: chain E residue 67 VAL Chi-restraints excluded: chain E residue 92 VAL Chi-restraints excluded: chain E residue 152 ILE Chi-restraints excluded: chain E residue 154 SER Chi-restraints excluded: chain E residue 226 GLU Chi-restraints excluded: chain E residue 257 SER Chi-restraints excluded: chain F residue 4 VAL Chi-restraints excluded: chain F residue 28 VAL Chi-restraints excluded: chain F residue 82 ILE Chi-restraints excluded: chain F residue 83 GLU Chi-restraints excluded: chain F residue 195 ASP Chi-restraints excluded: chain F residue 261 THR Chi-restraints excluded: chain F residue 275 SER Chi-restraints excluded: chain F residue 288 THR Chi-restraints excluded: chain G residue 29 THR Chi-restraints excluded: chain G residue 105 VAL Chi-restraints excluded: chain G residue 115 VAL Chi-restraints excluded: chain G residue 152 ILE Chi-restraints excluded: chain G residue 266 SER Chi-restraints excluded: chain H residue 16 VAL Chi-restraints excluded: chain H residue 124 SER Chi-restraints excluded: chain H residue 139 ILE Chi-restraints excluded: chain H residue 215 LEU Chi-restraints excluded: chain H residue 226 ILE Chi-restraints excluded: chain H residue 253 VAL Chi-restraints excluded: chain H residue 282 LEU Chi-restraints excluded: chain H residue 340 VAL Chi-restraints excluded: chain H residue 396 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 257 random chunks: chunk 188 optimal weight: 0.0770 chunk 148 optimal weight: 0.7980 chunk 219 optimal weight: 1.9990 chunk 97 optimal weight: 0.5980 chunk 87 optimal weight: 0.0060 chunk 175 optimal weight: 0.0770 chunk 256 optimal weight: 0.0980 chunk 83 optimal weight: 3.9990 chunk 70 optimal weight: 3.9990 chunk 10 optimal weight: 0.9990 chunk 209 optimal weight: 0.9980 overall best weight: 0.1712 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 132 ASN D 398 ASN ** E 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 132 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2695 r_free = 0.2695 target = 0.056642 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2519 r_free = 0.2519 target = 0.049420 restraints weight = 44353.626| |-----------------------------------------------------------------------------| r_work (start): 0.2515 rms_B_bonded: 1.26 r_work: 0.2430 rms_B_bonded: 1.72 restraints_weight: 0.5000 r_work: 0.2313 rms_B_bonded: 3.00 restraints_weight: 0.2500 r_work (final): 0.2313 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8808 moved from start: 0.1873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.090 21984 Z= 0.103 Angle : 0.721 27.058 29916 Z= 0.271 Chirality : 0.042 0.183 3189 Planarity : 0.004 0.047 3748 Dihedral : 9.488 151.806 3134 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 1.82 % Allowed : 13.75 % Favored : 84.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.97 % 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: 0.23 (0.16), residues: 2595 helix: 0.53 (0.16), residues: 1043 sheet: 0.33 (0.25), residues: 429 loop : -0.11 (0.18), residues: 1123 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG H 266 TYR 0.016 0.001 TYR D 316 PHE 0.013 0.001 PHE F 71 TRP 0.009 0.001 TRP A 216 HIS 0.009 0.001 HIS H 214 Details of bonding type rmsd covalent geometry : bond 0.00222 (21915) covalent geometry : angle 0.51710 (29736) hydrogen bonds : bond 0.03728 ( 876) hydrogen bonds : angle 5.20028 ( 2460) metal coordination : bond 0.01245 ( 65) metal coordination : angle 6.49430 ( 180) Misc. bond : bond 0.00134 ( 4) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5190 Ramachandran restraints generated. 2595 Oldfield, 0 Emsley, 2595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5190 Ramachandran restraints generated. 2595 Oldfield, 0 Emsley, 2595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 351 residues out of total 2255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 310 time to evaluate : 0.621 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 106 LYS cc_start: 0.9122 (OUTLIER) cc_final: 0.8916 (ttpp) REVERT: A 226 GLU cc_start: 0.8403 (OUTLIER) cc_final: 0.8040 (mp0) REVERT: C 32 GLU cc_start: 0.8134 (OUTLIER) cc_final: 0.7923 (mp0) REVERT: D 209 GLU cc_start: 0.7986 (tp30) cc_final: 0.7748 (tp30) REVERT: E 226 GLU cc_start: 0.8277 (OUTLIER) cc_final: 0.7877 (mp0) REVERT: H 141 LEU cc_start: 0.8478 (mp) cc_final: 0.8236 (tt) REVERT: H 352 GLU cc_start: 0.7475 (tp30) cc_final: 0.7246 (tp30) REVERT: H 413 ARG cc_start: 0.8789 (mtm-85) cc_final: 0.8588 (mtm-85) outliers start: 41 outliers final: 34 residues processed: 342 average time/residue: 0.1720 time to fit residues: 87.0633 Evaluate side-chains 330 residues out of total 2255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 292 time to evaluate : 0.780 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 106 LYS Chi-restraints excluded: chain A residue 154 SER Chi-restraints excluded: chain A residue 226 GLU Chi-restraints excluded: chain B residue 28 VAL Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 246 CYS Chi-restraints excluded: chain B residue 261 THR Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 309 LEU Chi-restraints excluded: chain C residue 22 VAL Chi-restraints excluded: chain C residue 32 GLU Chi-restraints excluded: chain C residue 51 LYS Chi-restraints excluded: chain C residue 71 CYS Chi-restraints excluded: chain D residue 16 VAL Chi-restraints excluded: chain D residue 26 ILE Chi-restraints excluded: chain D residue 139 ILE Chi-restraints excluded: chain E residue 45 ASP Chi-restraints excluded: chain E residue 67 VAL Chi-restraints excluded: chain E residue 152 ILE Chi-restraints excluded: chain E residue 154 SER Chi-restraints excluded: chain E residue 226 GLU Chi-restraints excluded: chain F residue 4 VAL Chi-restraints excluded: chain F residue 28 VAL Chi-restraints excluded: chain F residue 83 GLU Chi-restraints excluded: chain F residue 195 ASP Chi-restraints excluded: chain F residue 261 THR Chi-restraints excluded: chain F residue 275 SER Chi-restraints excluded: chain G residue 29 THR Chi-restraints excluded: chain G residue 71 CYS Chi-restraints excluded: chain G residue 105 VAL Chi-restraints excluded: chain H residue 16 VAL Chi-restraints excluded: chain H residue 139 ILE Chi-restraints excluded: chain H residue 226 ILE Chi-restraints excluded: chain H residue 282 LEU Chi-restraints excluded: chain H residue 340 VAL Chi-restraints excluded: chain H residue 396 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 257 random chunks: chunk 24 optimal weight: 2.9990 chunk 100 optimal weight: 0.0980 chunk 182 optimal weight: 1.9990 chunk 168 optimal weight: 2.9990 chunk 251 optimal weight: 2.9990 chunk 169 optimal weight: 0.9990 chunk 241 optimal weight: 0.8980 chunk 233 optimal weight: 0.0870 chunk 58 optimal weight: 3.9990 chunk 230 optimal weight: 0.9990 chunk 210 optimal weight: 1.9990 overall best weight: 0.6162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 132 ASN E 132 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2653 r_free = 0.2653 target = 0.054998 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2472 r_free = 0.2472 target = 0.047720 restraints weight = 44527.337| |-----------------------------------------------------------------------------| r_work (start): 0.2473 rms_B_bonded: 1.25 r_work: 0.2385 rms_B_bonded: 1.72 restraints_weight: 0.5000 r_work: 0.2267 rms_B_bonded: 3.00 restraints_weight: 0.2500 r_work (final): 0.2267 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8838 moved from start: 0.1838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.115 21984 Z= 0.130 Angle : 0.734 28.022 29916 Z= 0.283 Chirality : 0.043 0.177 3189 Planarity : 0.004 0.045 3748 Dihedral : 9.466 146.706 3133 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 1.77 % Allowed : 14.15 % Favored : 84.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.97 % 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: 0.22 (0.16), residues: 2595 helix: 0.53 (0.16), residues: 1041 sheet: 0.37 (0.25), residues: 423 loop : -0.15 (0.18), residues: 1131 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG G 190 TYR 0.020 0.001 TYR B 215 PHE 0.016 0.001 PHE F 71 TRP 0.009 0.001 TRP A 216 HIS 0.006 0.001 HIS H 424 Details of bonding type rmsd covalent geometry : bond 0.00300 (21915) covalent geometry : angle 0.53787 (29736) hydrogen bonds : bond 0.04273 ( 876) hydrogen bonds : angle 5.23749 ( 2460) metal coordination : bond 0.01628 ( 65) metal coordination : angle 6.46813 ( 180) Misc. bond : bond 0.00171 ( 4) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5190 Ramachandran restraints generated. 2595 Oldfield, 0 Emsley, 2595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5190 Ramachandran restraints generated. 2595 Oldfield, 0 Emsley, 2595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 331 residues out of total 2255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 291 time to evaluate : 0.659 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 226 GLU cc_start: 0.8456 (OUTLIER) cc_final: 0.8007 (mp0) REVERT: C 32 GLU cc_start: 0.8191 (OUTLIER) cc_final: 0.7929 (mp0) REVERT: D 209 GLU cc_start: 0.8018 (tp30) cc_final: 0.7757 (tp30) REVERT: E 226 GLU cc_start: 0.8338 (OUTLIER) cc_final: 0.7872 (mp0) REVERT: G 144 ASP cc_start: 0.8659 (m-30) cc_final: 0.8192 (m-30) REVERT: H 141 LEU cc_start: 0.8498 (mp) cc_final: 0.8283 (tp) REVERT: H 352 GLU cc_start: 0.7590 (tp30) cc_final: 0.7339 (tp30) outliers start: 40 outliers final: 34 residues processed: 324 average time/residue: 0.1785 time to fit residues: 86.0391 Evaluate side-chains 326 residues out of total 2255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 289 time to evaluate : 0.819 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 154 SER Chi-restraints excluded: chain A residue 226 GLU Chi-restraints excluded: chain B residue 28 VAL Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 261 THR Chi-restraints excluded: chain B residue 309 LEU Chi-restraints excluded: chain C residue 22 VAL Chi-restraints excluded: chain C residue 32 GLU Chi-restraints excluded: chain C residue 51 LYS Chi-restraints excluded: chain C residue 71 CYS Chi-restraints excluded: chain C residue 105 VAL Chi-restraints excluded: chain D residue 16 VAL Chi-restraints excluded: chain D residue 26 ILE Chi-restraints excluded: chain D residue 139 ILE Chi-restraints excluded: chain E residue 45 ASP Chi-restraints excluded: chain E residue 67 VAL Chi-restraints excluded: chain E residue 152 ILE Chi-restraints excluded: chain E residue 154 SER Chi-restraints excluded: chain E residue 226 GLU Chi-restraints excluded: chain F residue 4 VAL Chi-restraints excluded: chain F residue 28 VAL Chi-restraints excluded: chain F residue 83 GLU Chi-restraints excluded: chain F residue 195 ASP Chi-restraints excluded: chain F residue 261 THR Chi-restraints excluded: chain F residue 275 SER Chi-restraints excluded: chain G residue 29 THR Chi-restraints excluded: chain G residue 71 CYS Chi-restraints excluded: chain G residue 105 VAL Chi-restraints excluded: chain H residue 16 VAL Chi-restraints excluded: chain H residue 124 SER Chi-restraints excluded: chain H residue 139 ILE Chi-restraints excluded: chain H residue 226 ILE Chi-restraints excluded: chain H residue 282 LEU Chi-restraints excluded: chain H residue 340 VAL Chi-restraints excluded: chain H residue 396 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 257 random chunks: chunk 155 optimal weight: 0.0980 chunk 256 optimal weight: 0.6980 chunk 62 optimal weight: 1.9990 chunk 47 optimal weight: 1.9990 chunk 172 optimal weight: 0.5980 chunk 245 optimal weight: 0.8980 chunk 156 optimal weight: 0.9990 chunk 251 optimal weight: 2.9990 chunk 102 optimal weight: 0.0370 chunk 192 optimal weight: 0.7980 chunk 165 optimal weight: 1.9990 overall best weight: 0.4458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 132 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2670 r_free = 0.2670 target = 0.055628 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2491 r_free = 0.2491 target = 0.048359 restraints weight = 44559.898| |-----------------------------------------------------------------------------| r_work (start): 0.2489 rms_B_bonded: 1.26 r_work: 0.2402 rms_B_bonded: 1.72 restraints_weight: 0.5000 r_work: 0.2284 rms_B_bonded: 3.01 restraints_weight: 0.2500 r_work (final): 0.2284 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8826 moved from start: 0.1890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.104 21984 Z= 0.115 Angle : 0.720 27.828 29916 Z= 0.275 Chirality : 0.043 0.177 3189 Planarity : 0.004 0.046 3748 Dihedral : 9.253 143.123 3129 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 1.64 % Allowed : 14.55 % Favored : 83.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.97 % 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: 0.22 (0.16), residues: 2595 helix: 0.51 (0.16), residues: 1049 sheet: 0.38 (0.25), residues: 423 loop : -0.14 (0.18), residues: 1123 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG H 403 TYR 0.019 0.001 TYR B 215 PHE 0.015 0.001 PHE D 239 TRP 0.009 0.001 TRP A 216 HIS 0.006 0.001 HIS H 424 Details of bonding type rmsd covalent geometry : bond 0.00258 (21915) covalent geometry : angle 0.52221 (29736) hydrogen bonds : bond 0.04074 ( 876) hydrogen bonds : angle 5.22130 ( 2460) metal coordination : bond 0.01460 ( 65) metal coordination : angle 6.41037 ( 180) Misc. bond : bond 0.00151 ( 4) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4771.34 seconds wall clock time: 82 minutes 48.14 seconds (4968.14 seconds total)