Starting phenix.real_space_refine on Sat Jul 4 14:52:30 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9oyb_71013/07_2026/9oyb_71013.cif Found real_map, /net/cci-nas-00/data/ceres_data/9oyb_71013/07_2026/9oyb_71013.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.14 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9oyb_71013/07_2026/9oyb_71013.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9oyb_71013/07_2026/9oyb_71013.map" model { file = "/net/cci-nas-00/data/ceres_data/9oyb_71013/07_2026/9oyb_71013.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9oyb_71013/07_2026/9oyb_71013.cif" } resolution = 3.14 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= 0.017 sd= 0.651 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 4 6.06 5 P 68 5.49 5 Mg 3 5.21 5 S 112 5.16 5 C 13057 2.51 5 N 3776 2.21 5 O 4054 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 21074 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 2726 Number of conformers: 1 Conformer: "" Number of residues, atoms: 343, 2726 Classifications: {'peptide': 343} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 13, 'TRANS': 329} Chain: "B" Number of atoms: 2856 Number of conformers: 1 Conformer: "" Number of residues, atoms: 367, 2856 Classifications: {'peptide': 367} Link IDs: {'PTRANS': 17, 'TRANS': 349} Chain: "C" Number of atoms: 2873 Number of conformers: 1 Conformer: "" Number of residues, atoms: 369, 2873 Classifications: {'peptide': 369} Link IDs: {'PTRANS': 17, 'TRANS': 351} Chain: "D" Number of atoms: 2799 Number of conformers: 1 Conformer: "" Number of residues, atoms: 360, 2799 Classifications: {'peptide': 360} Link IDs: {'PTRANS': 14, 'TRANS': 345} Chain: "E" Number of atoms: 2602 Number of conformers: 1 Conformer: "" Number of residues, atoms: 334, 2602 Classifications: {'peptide': 334} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 20, 'TRANS': 313} Chain: "F" Number of atoms: 2835 Number of conformers: 1 Conformer: "" Number of residues, atoms: 365, 2835 Classifications: {'peptide': 365} Link IDs: {'PTRANS': 20, 'TRANS': 344} Chain: "G" Number of atoms: 2844 Number of conformers: 1 Conformer: "" Number of residues, atoms: 366, 2844 Classifications: {'peptide': 366} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 20, 'TRANS': 345} Chain: "H" Number of atoms: 613 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 613 Classifications: {'DNA': 30} Link IDs: {'rna3p': 29} Chain: "I" Number of atoms: 411 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 411 Classifications: {'DNA': 20} Link IDs: {'rna3p': 19} Chain: "J" Number of atoms: 230 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 230 Classifications: {'peptide': 28} Link IDs: {'PTRANS': 1, 'TRANS': 26} Chain: "M" Number of atoms: 185 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 185 Classifications: {'DNA': 9} Link IDs: {'rna3p': 8} Chain: "B" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, ' ZN': 1, 'AGS': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, ' ZN': 1, 'AGS': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, ' ZN': 1, 'AGS': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 3209 SG CYS B 64 29.973 83.360 36.019 1.00 65.00 S ATOM 3269 SG CYS B 73 26.387 82.936 36.552 1.00 76.97 S ATOM 3286 SG CYS B 76 28.249 79.741 35.971 1.00 71.73 S ATOM 3308 SG CYS B 79 28.850 81.341 39.117 1.00 74.82 S ATOM 6073 SG CYS C 64 9.698 57.741 68.824 1.00 56.52 S ATOM 6133 SG CYS C 73 8.200 55.499 71.285 1.00 75.52 S ATOM 6150 SG CYS C 76 10.788 53.897 68.842 1.00 62.40 S ATOM 6172 SG CYS C 79 12.089 55.995 71.276 1.00 59.74 S ATOM 8938 SG CYS D 64 34.776 31.360 98.531 1.00 63.49 S ATOM 8998 SG CYS D 73 36.827 29.113 100.485 1.00 68.00 S ATOM 9015 SG CYS D 76 37.701 29.243 96.822 1.00 63.40 S ATOM 9037 SG CYS D 79 38.447 32.249 98.822 1.00 64.64 S ATOM 11661 SG CYS E 50 81.384 33.906 99.412 1.00 68.90 S ATOM 11730 SG CYS E 59 84.716 32.584 98.356 1.00 66.56 S ATOM 11750 SG CYS E 62 82.130 32.518 95.765 1.00 73.26 S ATOM 11771 SG CYS E 65 83.184 35.840 96.753 1.00 65.79 S Time building chain proxies: 5.57, per 1000 atoms: 0.26 Number of scatterers: 21074 At special positions: 0 Unit cell: (123.372, 120.888, 149.868, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 4 29.99 S 112 16.00 P 68 15.00 Mg 3 11.99 O 4054 8.00 N 3776 7.00 C 13057 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.86 Conformation dependent library (CDL) restraints added in 877.1 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN B 701 " pdb="ZN ZN B 701 " - pdb=" SG CYS B 73 " pdb="ZN ZN B 701 " - pdb=" SG CYS B 79 " pdb="ZN ZN B 701 " - pdb=" SG CYS B 76 " pdb="ZN ZN B 701 " - pdb=" SG CYS B 64 " pdb=" ZN C 701 " pdb="ZN ZN C 701 " - pdb=" SG CYS C 79 " pdb="ZN ZN C 701 " - pdb=" SG CYS C 73 " pdb="ZN ZN C 701 " - pdb=" SG CYS C 64 " pdb="ZN ZN C 701 " - pdb=" SG CYS C 76 " pdb=" ZN D 701 " pdb="ZN ZN D 701 " - pdb=" SG CYS D 73 " pdb="ZN ZN D 701 " - pdb=" SG CYS D 76 " pdb="ZN ZN D 701 " - pdb=" SG CYS D 79 " pdb="ZN ZN D 701 " - pdb=" SG CYS D 64 " pdb=" ZN E 401 " pdb="ZN ZN E 401 " - pdb=" SG CYS E 62 " pdb="ZN ZN E 401 " - pdb=" SG CYS E 65 " pdb="ZN ZN E 401 " - pdb=" SG CYS E 59 " pdb="ZN ZN E 401 " - pdb=" SG CYS E 50 " Number of angles added : 24 5032 Ramachandran restraints generated. 2516 Oldfield, 0 Emsley, 2516 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4760 Finding SS restraints... Secondary structure from input PDB file: 124 helices and 15 sheets defined 55.3% alpha, 15.3% beta 28 base pairs and 45 stacking pairs defined. Time for finding SS restraints: 2.54 Creating SS restraints... Processing helix chain 'A' and resid 5 through 7 No H-bonds generated for 'chain 'A' and resid 5 through 7' Processing helix chain 'A' and resid 8 through 16 removed outlier: 3.565A pdb=" N GLN A 12 " --> pdb=" O GLN A 8 " (cutoff:3.500A) Processing helix chain 'A' and resid 27 through 46 Processing helix chain 'A' and resid 60 through 70 removed outlier: 3.624A pdb=" N ILE A 64 " --> pdb=" O ASP A 60 " (cutoff:3.500A) Processing helix chain 'A' and resid 90 through 102 removed outlier: 3.595A pdb=" N GLY A 102 " --> pdb=" O LEU A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 118 through 123 Processing helix chain 'A' and resid 124 through 130 removed outlier: 3.606A pdb=" N THR A 128 " --> pdb=" O ALA A 124 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LEU A 130 " --> pdb=" O TRP A 126 " (cutoff:3.500A) Processing helix chain 'A' and resid 146 through 158 Processing helix chain 'A' and resid 163 through 174 Processing helix chain 'A' and resid 177 through 192 Processing helix chain 'A' and resid 198 through 206 removed outlier: 3.553A pdb=" N ALA A 205 " --> pdb=" O ARG A 201 " (cutoff:3.500A) Processing helix chain 'A' and resid 213 through 224 Processing helix chain 'A' and resid 225 through 240 Processing helix chain 'A' and resid 242 through 265 removed outlier: 3.778A pdb=" N LEU A 246 " --> pdb=" O GLU A 242 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N GLU A 253 " --> pdb=" O THR A 249 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N ALA A 265 " --> pdb=" O LYS A 261 " (cutoff:3.500A) Processing helix chain 'A' and resid 268 through 276 Processing helix chain 'A' and resid 279 through 281 No H-bonds generated for 'chain 'A' and resid 279 through 281' Processing helix chain 'A' and resid 282 through 293 Processing helix chain 'A' and resid 294 through 315 Processing helix chain 'A' and resid 320 through 332 Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'B' and resid 5 through 10 Processing helix chain 'B' and resid 14 through 18 Processing helix chain 'B' and resid 21 through 35 Processing helix chain 'B' and resid 50 through 64 Processing helix chain 'B' and resid 76 through 85 Processing helix chain 'B' and resid 100 through 110 removed outlier: 3.832A pdb=" N ASN B 110 " --> pdb=" O ASP B 106 " (cutoff:3.500A) Processing helix chain 'B' and resid 111 through 113 No H-bonds generated for 'chain 'B' and resid 111 through 113' Processing helix chain 'B' and resid 128 through 131 Processing helix chain 'B' and resid 132 through 145 removed outlier: 4.237A pdb=" N GLU B 145 " --> pdb=" O LYS B 141 " (cutoff:3.500A) Processing helix chain 'B' and resid 158 through 162 removed outlier: 3.660A pdb=" N LYS B 161 " --> pdb=" O ASP B 158 " (cutoff:3.500A) Processing helix chain 'B' and resid 163 through 169 removed outlier: 3.631A pdb=" N LEU B 167 " --> pdb=" O VAL B 164 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ARG B 169 " --> pdb=" O ILE B 166 " (cutoff:3.500A) Processing helix chain 'B' and resid 179 through 194 Processing helix chain 'B' and resid 199 through 211 removed outlier: 3.946A pdb=" N GLU B 211 " --> pdb=" O ALA B 207 " (cutoff:3.500A) Processing helix chain 'B' and resid 213 through 228 Processing helix chain 'B' and resid 233 through 244 Processing helix chain 'B' and resid 247 through 258 Processing helix chain 'B' and resid 260 through 275 Processing helix chain 'B' and resid 277 through 298 Processing helix chain 'B' and resid 299 through 302 removed outlier: 4.010A pdb=" N LEU B 302 " --> pdb=" O PRO B 299 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 299 through 302' Processing helix chain 'B' and resid 303 through 307 removed outlier: 3.530A pdb=" N ALA B 307 " --> pdb=" O ASN B 304 " (cutoff:3.500A) Processing helix chain 'B' and resid 309 through 320 Processing helix chain 'B' and resid 321 through 339 Processing helix chain 'B' and resid 340 through 342 No H-bonds generated for 'chain 'B' and resid 340 through 342' Processing helix chain 'B' and resid 344 through 358 Processing helix chain 'C' and resid 5 through 10 Processing helix chain 'C' and resid 21 through 35 Processing helix chain 'C' and resid 50 through 63 Processing helix chain 'C' and resid 76 through 85 Processing helix chain 'C' and resid 100 through 110 removed outlier: 4.358A pdb=" N ASN C 110 " --> pdb=" O ASP C 106 " (cutoff:3.500A) Processing helix chain 'C' and resid 128 through 131 Processing helix chain 'C' and resid 132 through 145 removed outlier: 4.764A pdb=" N LYS C 141 " --> pdb=" O ASN C 137 " (cutoff:3.500A) removed outlier: 4.661A pdb=" N THR C 142 " --> pdb=" O ALA C 138 " (cutoff:3.500A) Processing helix chain 'C' and resid 158 through 162 removed outlier: 3.577A pdb=" N LYS C 161 " --> pdb=" O ASP C 158 " (cutoff:3.500A) Processing helix chain 'C' and resid 163 through 170 removed outlier: 3.683A pdb=" N ARG C 169 " --> pdb=" O THR C 165 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N CYS C 170 " --> pdb=" O ILE C 166 " (cutoff:3.500A) Processing helix chain 'C' and resid 179 through 195 Processing helix chain 'C' and resid 199 through 211 removed outlier: 4.063A pdb=" N GLU C 211 " --> pdb=" O ALA C 207 " (cutoff:3.500A) Processing helix chain 'C' and resid 213 through 229 Processing helix chain 'C' and resid 233 through 242 Processing helix chain 'C' and resid 245 through 258 removed outlier: 3.568A pdb=" N ALA C 249 " --> pdb=" O ASP C 245 " (cutoff:3.500A) Processing helix chain 'C' and resid 260 through 274 Processing helix chain 'C' and resid 277 through 298 removed outlier: 3.699A pdb=" N LEU C 282 " --> pdb=" O TRP C 278 " (cutoff:3.500A) Processing helix chain 'C' and resid 309 through 320 Processing helix chain 'C' and resid 321 through 339 Processing helix chain 'C' and resid 340 through 342 No H-bonds generated for 'chain 'C' and resid 340 through 342' Processing helix chain 'C' and resid 344 through 359 Processing helix chain 'D' and resid 5 through 10 Processing helix chain 'D' and resid 21 through 34 Processing helix chain 'D' and resid 50 through 63 Processing helix chain 'D' and resid 76 through 84 Processing helix chain 'D' and resid 100 through 111 Processing helix chain 'D' and resid 128 through 131 Processing helix chain 'D' and resid 132 through 139 Processing helix chain 'D' and resid 139 through 145 Processing helix chain 'D' and resid 158 through 162 Processing helix chain 'D' and resid 163 through 170 removed outlier: 3.541A pdb=" N ARG D 169 " --> pdb=" O THR D 165 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N CYS D 170 " --> pdb=" O ILE D 166 " (cutoff:3.500A) Processing helix chain 'D' and resid 179 through 195 Processing helix chain 'D' and resid 199 through 211 removed outlier: 3.853A pdb=" N GLU D 211 " --> pdb=" O ALA D 207 " (cutoff:3.500A) Processing helix chain 'D' and resid 213 through 228 Processing helix chain 'D' and resid 233 through 242 Processing helix chain 'D' and resid 245 through 258 removed outlier: 3.754A pdb=" N ALA D 249 " --> pdb=" O ASP D 245 " (cutoff:3.500A) Processing helix chain 'D' and resid 260 through 274 Processing helix chain 'D' and resid 277 through 298 Processing helix chain 'D' and resid 299 through 302 removed outlier: 3.915A pdb=" N LEU D 302 " --> pdb=" O PRO D 299 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 299 through 302' Processing helix chain 'D' and resid 303 through 307 removed outlier: 3.563A pdb=" N MET D 306 " --> pdb=" O GLY D 303 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ALA D 307 " --> pdb=" O ASN D 304 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 303 through 307' Processing helix chain 'D' and resid 309 through 320 Processing helix chain 'D' and resid 321 through 339 Processing helix chain 'D' and resid 344 through 357 Processing helix chain 'E' and resid 6 through 20 removed outlier: 4.705A pdb=" N ASP E 10 " --> pdb=" O TRP E 6 " (cutoff:3.500A) Processing helix chain 'E' and resid 36 through 49 Processing helix chain 'E' and resid 62 through 71 Processing helix chain 'E' and resid 89 through 101 removed outlier: 3.538A pdb=" N ASN E 101 " --> pdb=" O THR E 97 " (cutoff:3.500A) Processing helix chain 'E' and resid 116 through 120 Processing helix chain 'E' and resid 121 through 134 removed outlier: 3.549A pdb=" N LEU E 129 " --> pdb=" O ALA E 125 " (cutoff:3.500A) removed outlier: 4.641A pdb=" N LYS E 130 " --> pdb=" O ASN E 126 " (cutoff:3.500A) removed outlier: 4.731A pdb=" N THR E 131 " --> pdb=" O ALA E 127 " (cutoff:3.500A) Processing helix chain 'E' and resid 147 through 151 Processing helix chain 'E' and resid 152 through 159 removed outlier: 3.611A pdb=" N ARG E 158 " --> pdb=" O THR E 154 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N CYS E 159 " --> pdb=" O LEU E 155 " (cutoff:3.500A) Processing helix chain 'E' and resid 168 through 180 Processing helix chain 'E' and resid 183 through 194 Processing helix chain 'E' and resid 197 through 206 removed outlier: 3.535A pdb=" N PHE E 205 " --> pdb=" O ALA E 201 " (cutoff:3.500A) Processing helix chain 'E' and resid 208 through 227 Proline residue: E 225 - end of helix Processing helix chain 'E' and resid 228 through 230 No H-bonds generated for 'chain 'E' and resid 228 through 230' Processing helix chain 'E' and resid 231 through 237 removed outlier: 4.537A pdb=" N ALA E 235 " --> pdb=" O SER E 231 " (cutoff:3.500A) Processing helix chain 'E' and resid 240 through 261 Processing helix chain 'E' and resid 270 through 281 Processing helix chain 'E' and resid 282 through 303 Processing helix chain 'E' and resid 307 through 324 Processing helix chain 'F' and resid 7 through 18 removed outlier: 4.209A pdb=" N LYS F 12 " --> pdb=" O GLU F 8 " (cutoff:3.500A) Proline residue: F 13 - end of helix Processing helix chain 'F' and resid 72 through 82 Processing helix chain 'F' and resid 114 through 116 No H-bonds generated for 'chain 'F' and resid 114 through 116' Processing helix chain 'F' and resid 131 through 144 removed outlier: 3.636A pdb=" N THR F 142 " --> pdb=" O LEU F 138 " (cutoff:3.500A) removed outlier: 4.707A pdb=" N PHE F 144 " --> pdb=" O GLU F 140 " (cutoff:3.500A) Processing helix chain 'F' and resid 152 through 157 removed outlier: 3.915A pdb=" N GLY F 157 " --> pdb=" O TYR F 154 " (cutoff:3.500A) Processing helix chain 'F' and resid 196 through 207 Processing helix chain 'F' and resid 259 through 273 removed outlier: 3.739A pdb=" N LEU F 273 " --> pdb=" O ARG F 269 " (cutoff:3.500A) Processing helix chain 'F' and resid 321 through 332 removed outlier: 3.615A pdb=" N LYS F 332 " --> pdb=" O LEU F 328 " (cutoff:3.500A) Processing helix chain 'G' and resid 7 through 18 removed outlier: 4.310A pdb=" N LYS G 12 " --> pdb=" O GLU G 8 " (cutoff:3.500A) Proline residue: G 13 - end of helix removed outlier: 3.768A pdb=" N GLN G 16 " --> pdb=" O LYS G 12 " (cutoff:3.500A) Processing helix chain 'G' and resid 27 through 30 Processing helix chain 'G' and resid 72 through 82 Processing helix chain 'G' and resid 131 through 141 Processing helix chain 'G' and resid 142 through 146 Processing helix chain 'G' and resid 152 through 155 Processing helix chain 'G' and resid 197 through 207 Processing helix chain 'G' and resid 243 through 248 removed outlier: 3.601A pdb=" N VAL G 247 " --> pdb=" O ASP G 243 " (cutoff:3.500A) Processing helix chain 'G' and resid 260 through 271 Processing helix chain 'G' and resid 321 through 332 removed outlier: 3.762A pdb=" N LYS G 332 " --> pdb=" O LEU G 328 " (cutoff:3.500A) Processing helix chain 'J' and resid 4 through 13 Processing helix chain 'J' and resid 21 through 25 removed outlier: 3.509A pdb=" N LEU J 25 " --> pdb=" O PRO J 22 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 2 through 4 removed outlier: 6.942A pdb=" N GLN A 78 " --> pdb=" O LEU A 109 " (cutoff:3.500A) removed outlier: 7.960A pdb=" N ILE A 111 " --> pdb=" O GLN A 78 " (cutoff:3.500A) removed outlier: 6.100A pdb=" N LEU A 80 " --> pdb=" O ILE A 111 " (cutoff:3.500A) removed outlier: 7.347A pdb=" N ARG A 113 " --> pdb=" O LEU A 80 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N LEU A 82 " --> pdb=" O ARG A 113 " (cutoff:3.500A) removed outlier: 7.076A pdb=" N ARG A 77 " --> pdb=" O PHE A 47 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N GLU A 49 " --> pdb=" O ARG A 77 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 161 through 162 removed outlier: 5.957A pdb=" N GLU A 161 " --> pdb=" O LEU A 197 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'B' and resid 90 through 94 removed outlier: 6.356A pdb=" N ILE B 91 " --> pdb=" O LEU B 124 " (cutoff:3.500A) removed outlier: 7.342A pdb=" N ASP B 126 " --> pdb=" O ILE B 91 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N ILE B 93 " --> pdb=" O ASP B 126 " (cutoff:3.500A) removed outlier: 6.099A pdb=" N LYS B 121 " --> pdb=" O LYS B 151 " (cutoff:3.500A) removed outlier: 7.294A pdb=" N LEU B 153 " --> pdb=" O LYS B 121 " (cutoff:3.500A) removed outlier: 6.070A pdb=" N TYR B 123 " --> pdb=" O LEU B 153 " (cutoff:3.500A) removed outlier: 7.280A pdb=" N ALA B 155 " --> pdb=" O TYR B 123 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N ILE B 125 " --> pdb=" O ALA B 155 " (cutoff:3.500A) removed outlier: 6.122A pdb=" N TYR B 41 " --> pdb=" O LEU B 154 " (cutoff:3.500A) removed outlier: 7.777A pdb=" N THR B 156 " --> pdb=" O TYR B 41 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N PHE B 43 " --> pdb=" O THR B 156 " (cutoff:3.500A) removed outlier: 8.246A pdb=" N PHE B 173 " --> pdb=" O ALA B 40 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N LEU B 42 " --> pdb=" O PHE B 173 " (cutoff:3.500A) removed outlier: 7.331A pdb=" N LEU B 175 " --> pdb=" O LEU B 42 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N SER B 44 " --> pdb=" O LEU B 175 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'B' and resid 197 through 198 removed outlier: 6.601A pdb=" N ALA B 197 " --> pdb=" O VAL B 232 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'B' and resid 359 through 361 Processing sheet with id=AA6, first strand: chain 'C' and resid 90 through 94 removed outlier: 6.142A pdb=" N LYS C 121 " --> pdb=" O LYS C 151 " (cutoff:3.500A) removed outlier: 7.400A pdb=" N LEU C 153 " --> pdb=" O LYS C 121 " (cutoff:3.500A) removed outlier: 5.951A pdb=" N TYR C 123 " --> pdb=" O LEU C 153 " (cutoff:3.500A) removed outlier: 7.124A pdb=" N ALA C 155 " --> pdb=" O TYR C 123 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N ILE C 125 " --> pdb=" O ALA C 155 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N TYR C 41 " --> pdb=" O LEU C 154 " (cutoff:3.500A) removed outlier: 7.660A pdb=" N THR C 156 " --> pdb=" O TYR C 41 " (cutoff:3.500A) removed outlier: 6.114A pdb=" N PHE C 43 " --> pdb=" O THR C 156 " (cutoff:3.500A) removed outlier: 7.255A pdb=" N ALA C 40 " --> pdb=" O LEU C 171 " (cutoff:3.500A) removed outlier: 7.831A pdb=" N PHE C 173 " --> pdb=" O ALA C 40 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N LEU C 42 " --> pdb=" O PHE C 173 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 90 through 94 removed outlier: 6.431A pdb=" N ILE D 91 " --> pdb=" O LEU D 124 " (cutoff:3.500A) removed outlier: 7.253A pdb=" N ASP D 126 " --> pdb=" O ILE D 91 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N ILE D 93 " --> pdb=" O ASP D 126 " (cutoff:3.500A) removed outlier: 6.149A pdb=" N LYS D 121 " --> pdb=" O LYS D 151 " (cutoff:3.500A) removed outlier: 7.358A pdb=" N LEU D 153 " --> pdb=" O LYS D 121 " (cutoff:3.500A) removed outlier: 5.858A pdb=" N TYR D 123 " --> pdb=" O LEU D 153 " (cutoff:3.500A) removed outlier: 7.233A pdb=" N ALA D 155 " --> pdb=" O TYR D 123 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N ILE D 125 " --> pdb=" O ALA D 155 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 76 through 79 removed outlier: 6.417A pdb=" N LYS E 110 " --> pdb=" O TRP E 140 " (cutoff:3.500A) removed outlier: 7.792A pdb=" N PHE E 142 " --> pdb=" O LYS E 110 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N VAL E 112 " --> pdb=" O PHE E 142 " (cutoff:3.500A) removed outlier: 7.971A pdb=" N ALA E 144 " --> pdb=" O VAL E 112 " (cutoff:3.500A) removed outlier: 7.104A pdb=" N VAL E 114 " --> pdb=" O ALA E 144 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N LEU E 27 " --> pdb=" O LEU E 143 " (cutoff:3.500A) removed outlier: 7.564A pdb=" N THR E 145 " --> pdb=" O LEU E 27 " (cutoff:3.500A) removed outlier: 5.658A pdb=" N ILE E 29 " --> pdb=" O THR E 145 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'F' and resid 2 through 6 removed outlier: 4.666A pdb=" N ASN G 295 " --> pdb=" O GLY G 280 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N GLY G 280 " --> pdb=" O ASN G 295 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'F' and resid 111 through 112 removed outlier: 3.741A pdb=" N GLY F 66 " --> pdb=" O VAL F 37 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N ASN F 32 " --> pdb=" O THR F 47 " (cutoff:3.500A) removed outlier: 5.274A pdb=" N THR F 47 " --> pdb=" O ASN F 32 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 309 through 310 removed outlier: 4.310A pdb=" N ASP F 351 " --> pdb=" O ALA F 357 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N ALA F 357 " --> pdb=" O ASP F 351 " (cutoff:3.500A) removed outlier: 16.017A pdb=" N SER F 181 " --> pdb=" O THR F 172 " (cutoff:3.500A) removed outlier: 16.053A pdb=" N THR F 172 " --> pdb=" O SER F 181 " (cutoff:3.500A) removed outlier: 14.975A pdb=" N VAL F 170 " --> pdb=" O PRO F 183 " (cutoff:3.500A) removed outlier: 14.221A pdb=" N GLY F 185 " --> pdb=" O ARG F 168 " (cutoff:3.500A) removed outlier: 13.472A pdb=" N ARG F 168 " --> pdb=" O GLY F 185 " (cutoff:3.500A) removed outlier: 8.662A pdb=" N SER F 187 " --> pdb=" O GLU F 166 " (cutoff:3.500A) removed outlier: 8.250A pdb=" N GLU F 166 " --> pdb=" O SER F 187 " (cutoff:3.500A) removed outlier: 5.515A pdb=" N GLY F 164 " --> pdb=" O PRO F 189 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 304 through 306 removed outlier: 3.508A pdb=" N GLU F 304 " --> pdb=" O ILE F 292 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'G' and resid 2 through 6 Processing sheet with id=AB5, first strand: chain 'G' and resid 66 through 71 removed outlier: 6.941A pdb=" N ASN G 32 " --> pdb=" O THR G 47 " (cutoff:3.500A) removed outlier: 5.332A pdb=" N THR G 47 " --> pdb=" O ASN G 32 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'G' and resid 254 through 259 removed outlier: 4.596A pdb=" N ASP G 351 " --> pdb=" O ALA G 357 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N ALA G 357 " --> pdb=" O ASP G 351 " (cutoff:3.500A) removed outlier: 16.088A pdb=" N SER G 181 " --> pdb=" O THR G 172 " (cutoff:3.500A) removed outlier: 16.235A pdb=" N THR G 172 " --> pdb=" O SER G 181 " (cutoff:3.500A) removed outlier: 14.976A pdb=" N VAL G 170 " --> pdb=" O PRO G 183 " (cutoff:3.500A) removed outlier: 13.851A pdb=" N GLY G 185 " --> pdb=" O ARG G 168 " (cutoff:3.500A) removed outlier: 13.854A pdb=" N ARG G 168 " --> pdb=" O GLY G 185 " (cutoff:3.500A) removed outlier: 8.253A pdb=" N SER G 187 " --> pdb=" O GLU G 166 " (cutoff:3.500A) removed outlier: 8.219A pdb=" N GLU G 166 " --> pdb=" O SER G 187 " (cutoff:3.500A) removed outlier: 5.622A pdb=" N GLY G 164 " --> pdb=" O PRO G 189 " (cutoff:3.500A) 1096 hydrogen bonds defined for protein. 3141 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 71 hydrogen bonds 142 hydrogen bond angles 0 basepair planarities 28 basepair parallelities 45 stacking parallelities Total time for adding SS restraints: 4.25 Time building geometry restraints manager: 2.41 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.36: 7198 1.36 - 1.51: 6103 1.51 - 1.65: 8087 1.65 - 1.80: 158 1.80 - 1.95: 28 Bond restraints: 21574 Sorted by residual: bond pdb=" O3A AGS D 702 " pdb=" PA AGS D 702 " ideal model delta sigma weight residual 1.664 1.584 0.080 2.00e-02 2.50e+03 1.61e+01 bond pdb=" O3B AGS D 702 " pdb=" PB AGS D 702 " ideal model delta sigma weight residual 1.673 1.593 0.080 2.00e-02 2.50e+03 1.60e+01 bond pdb=" O3A AGS C 702 " pdb=" PA AGS C 702 " ideal model delta sigma weight residual 1.664 1.586 0.078 2.00e-02 2.50e+03 1.52e+01 bond pdb=" O3B AGS C 702 " pdb=" PB AGS C 702 " ideal model delta sigma weight residual 1.673 1.596 0.077 2.00e-02 2.50e+03 1.47e+01 bond pdb=" O3A AGS B 702 " pdb=" PA AGS B 702 " ideal model delta sigma weight residual 1.664 1.588 0.076 2.00e-02 2.50e+03 1.46e+01 ... (remaining 21569 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.09: 28916 2.09 - 4.19: 535 4.19 - 6.28: 67 6.28 - 8.37: 10 8.37 - 10.47: 10 Bond angle restraints: 29538 Sorted by residual: angle pdb=" N GLY D 20 " pdb=" CA GLY D 20 " pdb=" C GLY D 20 " ideal model delta sigma weight residual 115.08 120.88 -5.80 1.19e+00 7.06e-01 2.38e+01 angle pdb=" N3 DT M 4 " pdb=" C4 DT M 4 " pdb=" O4 DT M 4 " ideal model delta sigma weight residual 119.90 122.50 -2.60 6.00e-01 2.78e+00 1.88e+01 angle pdb=" N3 DT I 8 " pdb=" C4 DT I 8 " pdb=" O4 DT I 8 " ideal model delta sigma weight residual 119.90 122.45 -2.55 6.00e-01 2.78e+00 1.80e+01 angle pdb=" N3 DT I 4 " pdb=" C4 DT I 4 " pdb=" O4 DT I 4 " ideal model delta sigma weight residual 119.90 122.45 -2.55 6.00e-01 2.78e+00 1.80e+01 angle pdb=" N3 DT I 14 " pdb=" C4 DT I 14 " pdb=" O4 DT I 14 " ideal model delta sigma weight residual 119.90 122.42 -2.52 6.00e-01 2.78e+00 1.76e+01 ... (remaining 29533 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.06: 12488 34.06 - 68.13: 543 68.13 - 102.19: 33 102.19 - 136.26: 0 136.26 - 170.32: 2 Dihedral angle restraints: 13066 sinusoidal: 5731 harmonic: 7335 Sorted by residual: dihedral pdb=" CA GLN G 16 " pdb=" C GLN G 16 " pdb=" N VAL G 17 " pdb=" CA VAL G 17 " ideal model delta harmonic sigma weight residual 180.00 156.78 23.22 0 5.00e+00 4.00e-02 2.16e+01 dihedral pdb=" CA SER C 2 " pdb=" C SER C 2 " pdb=" N TYR C 3 " pdb=" CA TYR C 3 " ideal model delta harmonic sigma weight residual 180.00 156.83 23.17 0 5.00e+00 4.00e-02 2.15e+01 dihedral pdb=" CA VAL D 19 " pdb=" C VAL D 19 " pdb=" N GLY D 20 " pdb=" CA GLY D 20 " ideal model delta harmonic sigma weight residual 180.00 158.72 21.28 0 5.00e+00 4.00e-02 1.81e+01 ... (remaining 13063 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.065: 2966 0.065 - 0.130: 410 0.130 - 0.194: 22 0.194 - 0.259: 0 0.259 - 0.324: 3 Chirality restraints: 3401 Sorted by residual: chirality pdb=" C3' AGS B 702 " pdb=" C2' AGS B 702 " pdb=" C4' AGS B 702 " pdb=" O3' AGS B 702 " both_signs ideal model delta sigma weight residual False -2.37 -2.69 0.32 2.00e-01 2.50e+01 2.62e+00 chirality pdb=" C3' AGS C 702 " pdb=" C2' AGS C 702 " pdb=" C4' AGS C 702 " pdb=" O3' AGS C 702 " both_signs ideal model delta sigma weight residual False -2.37 -2.64 0.27 2.00e-01 2.50e+01 1.84e+00 chirality pdb=" C3' AGS D 702 " pdb=" C2' AGS D 702 " pdb=" C4' AGS D 702 " pdb=" O3' AGS D 702 " both_signs ideal model delta sigma weight residual False -2.37 -2.64 0.27 2.00e-01 2.50e+01 1.79e+00 ... (remaining 3398 not shown) Planarity restraints: 3630 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE G 241 " 0.030 5.00e-02 4.00e+02 4.60e-02 3.38e+00 pdb=" N PRO G 242 " -0.080 5.00e-02 4.00e+02 pdb=" CA PRO G 242 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO G 242 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA MET C 1 " -0.009 2.00e-02 2.50e+03 1.80e-02 3.26e+00 pdb=" C MET C 1 " 0.031 2.00e-02 2.50e+03 pdb=" O MET C 1 " -0.012 2.00e-02 2.50e+03 pdb=" N SER C 2 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN A 35 " -0.009 2.00e-02 2.50e+03 1.78e-02 3.17e+00 pdb=" CD GLN A 35 " 0.031 2.00e-02 2.50e+03 pdb=" OE1 GLN A 35 " -0.012 2.00e-02 2.50e+03 pdb=" NE2 GLN A 35 " -0.010 2.00e-02 2.50e+03 ... (remaining 3627 not shown) Histogram of nonbonded interaction distances: 1.83 - 2.44: 6 2.44 - 3.06: 13187 3.06 - 3.67: 31759 3.67 - 4.29: 47412 4.29 - 4.90: 79299 Nonbonded interactions: 171663 Sorted by model distance: nonbonded pdb=" OG1 THR C 52 " pdb="MG MG C 703 " model vdw 1.829 2.170 nonbonded pdb=" OG1 THR D 52 " pdb="MG MG D 703 " model vdw 1.892 2.170 nonbonded pdb=" OG1 THR B 52 " pdb="MG MG B 703 " model vdw 1.895 2.170 nonbonded pdb=" O2G AGS B 702 " pdb="MG MG B 703 " model vdw 1.972 2.170 nonbonded pdb=" O2G AGS D 702 " pdb="MG MG D 703 " model vdw 2.026 2.170 ... (remaining 171658 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 'B' and (resid 2 through 361 or resid 701 through 703)) selection = (chain 'C' and (resid 2 through 361 or resid 701 through 703)) selection = chain 'D' } ncs_group { reference = chain 'F' selection = (chain 'G' and resid 1 through 365) } 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: 5.140 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 0.350 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 25.950 Find NCS groups from input model: 0.430 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.290 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8938 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 : 0.006 0.080 21590 Z= 0.304 Angle : 0.728 13.180 29562 Z= 0.396 Chirality : 0.045 0.324 3401 Planarity : 0.004 0.046 3630 Dihedral : 17.226 170.321 8306 Min Nonbonded Distance : 1.829 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 0.00 % Allowed : 0.85 % Favored : 99.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: 1.40 (0.17), residues: 2516 helix: 1.52 (0.14), residues: 1281 sheet: 1.04 (0.24), residues: 437 loop : 0.02 (0.22), residues: 798 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 47 TYR 0.016 0.002 TYR F 154 PHE 0.022 0.002 PHE C 87 TRP 0.019 0.002 TRP C 10 HIS 0.009 0.002 HIS B 360 Details of bonding type rmsd/Z covalent geometry : bond 0.00587 / 0.30 (21574) covalent geometry : angle 0.70559 / 0.40 (29538) hydrogen bonds : bond 0.13721 / 8.89 ( 1167) hydrogen bonds : angle 5.12871 / 3.74 ( 3283) metal coordination : bond 0.00841 / 0.43 ( 16) metal coordination : angle 6.28577 / 3.80 ( 24) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5032 Ramachandran restraints generated. 2516 Oldfield, 0 Emsley, 2516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5032 Ramachandran restraints generated. 2516 Oldfield, 0 Emsley, 2516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 350 residues out of total 2116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 350 time to evaluate : 0.733 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 GLU cc_start: 0.8074 (mp0) cc_final: 0.7819 (mp0) REVERT: A 277 ARG cc_start: 0.9202 (mtp85) cc_final: 0.8430 (mtp85) REVERT: B 71 THR cc_start: 0.9243 (t) cc_final: 0.9042 (p) REVERT: B 265 MET cc_start: 0.8689 (mmp) cc_final: 0.8433 (mmp) REVERT: C 1 MET cc_start: 0.6045 (ptm) cc_final: 0.5794 (ptm) REVERT: C 248 GLN cc_start: 0.8427 (tt0) cc_final: 0.8126 (tt0) REVERT: C 294 MET cc_start: 0.8899 (mmp) cc_final: 0.8581 (mmp) REVERT: D 137 ASN cc_start: 0.8703 (m-40) cc_final: 0.8470 (m-40) REVERT: D 244 LEU cc_start: 0.8744 (mt) cc_final: 0.8392 (mt) REVERT: D 284 GLU cc_start: 0.7994 (tp30) cc_final: 0.7696 (mm-30) REVERT: E 314 ASP cc_start: 0.8436 (t0) cc_final: 0.8217 (t0) REVERT: F 288 ASN cc_start: 0.7865 (m-40) cc_final: 0.7574 (m-40) REVERT: G 8 GLU cc_start: 0.8353 (pp20) cc_final: 0.8035 (pp20) REVERT: G 12 LYS cc_start: 0.8601 (tppt) cc_final: 0.8358 (tppt) REVERT: G 165 GLU cc_start: 0.7787 (mm-30) cc_final: 0.7513 (mm-30) outliers start: 0 outliers final: 0 residues processed: 350 average time/residue: 0.2004 time to fit residues: 99.5439 Evaluate side-chains 300 residues out of total 2116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 300 time to evaluate : 0.831 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 254 random chunks: chunk 216 optimal weight: 0.8980 chunk 98 optimal weight: 0.6980 chunk 194 optimal weight: 3.9990 chunk 227 optimal weight: 2.9990 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 0.9980 chunk 247 optimal weight: 10.0000 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 0.9980 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 269 ASN ** D 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 56 HIS ** F 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 335 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 9 HIS G 275 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2552 r_free = 0.2552 target = 0.049383 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2257 r_free = 0.2257 target = 0.038809 restraints weight = 47948.644| |-----------------------------------------------------------------------------| r_work (start): 0.2254 rms_B_bonded: 1.39 r_work: 0.2160 rms_B_bonded: 1.85 restraints_weight: 0.5000 r_work: 0.2060 rms_B_bonded: 3.17 restraints_weight: 0.2500 r_work (final): 0.2060 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8940 moved from start: 0.0723 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 21590 Z= 0.177 Angle : 0.638 11.567 29562 Z= 0.323 Chirality : 0.041 0.268 3401 Planarity : 0.004 0.044 3630 Dihedral : 16.257 167.435 3506 Min Nonbonded Distance : 1.853 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 0.71 % Allowed : 6.71 % Favored : 92.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: 1.75 (0.17), residues: 2516 helix: 1.81 (0.15), residues: 1292 sheet: 1.12 (0.24), residues: 440 loop : 0.19 (0.23), residues: 784 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 80 TYR 0.023 0.002 TYR F 310 PHE 0.018 0.001 PHE F 3 TRP 0.019 0.001 TRP C 10 HIS 0.008 0.001 HIS B 360 Details of bonding type rmsd/Z covalent geometry : bond 0.00408 / 0.18 (21574) covalent geometry : angle 0.61550 / 0.32 (29538) hydrogen bonds : bond 0.05010 / 3.34 ( 1167) hydrogen bonds : angle 4.29572 / 3.15 ( 3283) metal coordination : bond 0.00605 / 0.31 ( 16) metal coordination : angle 5.98190 / 3.65 ( 24) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5032 Ramachandran restraints generated. 2516 Oldfield, 0 Emsley, 2516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5032 Ramachandran restraints generated. 2516 Oldfield, 0 Emsley, 2516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 325 residues out of total 2116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 310 time to evaluate : 0.884 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 277 ARG cc_start: 0.9194 (mtp85) cc_final: 0.8350 (mtp85) REVERT: B 265 MET cc_start: 0.8691 (mmp) cc_final: 0.8454 (mmp) REVERT: C 1 MET cc_start: 0.6066 (ptm) cc_final: 0.5774 (ptm) REVERT: C 294 MET cc_start: 0.8904 (mmp) cc_final: 0.8640 (mmp) REVERT: D 137 ASN cc_start: 0.8703 (m-40) cc_final: 0.8474 (m-40) REVERT: D 244 LEU cc_start: 0.8764 (mt) cc_final: 0.8429 (mt) REVERT: D 284 GLU cc_start: 0.8009 (tp30) cc_final: 0.7733 (mm-30) REVERT: E 85 LYS cc_start: 0.8857 (OUTLIER) cc_final: 0.8603 (mtmm) REVERT: F 154 TYR cc_start: 0.9192 (p90) cc_final: 0.8869 (p90) REVERT: F 275 ASN cc_start: 0.8142 (p0) cc_final: 0.7924 (p0) REVERT: F 278 PHE cc_start: 0.8713 (m-80) cc_final: 0.8479 (m-80) REVERT: F 288 ASN cc_start: 0.7833 (m-40) cc_final: 0.7573 (m-40) REVERT: G 8 GLU cc_start: 0.8333 (pp20) cc_final: 0.7927 (pp20) REVERT: G 165 GLU cc_start: 0.7797 (mm-30) cc_final: 0.7537 (mm-30) outliers start: 15 outliers final: 8 residues processed: 316 average time/residue: 0.1959 time to fit residues: 88.3498 Evaluate side-chains 305 residues out of total 2116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 296 time to evaluate : 0.873 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 ASP Chi-restraints excluded: chain D residue 2 SER Chi-restraints excluded: chain D residue 269 ASN Chi-restraints excluded: chain E residue 85 LYS Chi-restraints excluded: chain E residue 161 LEU Chi-restraints excluded: chain F residue 243 ASP Chi-restraints excluded: chain F residue 344 VAL Chi-restraints excluded: chain G residue 51 MET Chi-restraints excluded: chain J residue 28 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 254 random chunks: chunk 172 optimal weight: 0.0870 chunk 194 optimal weight: 1.9990 chunk 135 optimal weight: 1.9990 chunk 253 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 chunk 173 optimal weight: 1.9990 chunk 12 optimal weight: 0.1980 chunk 103 optimal weight: 1.9990 chunk 208 optimal weight: 4.9990 chunk 229 optimal weight: 0.9980 chunk 90 optimal weight: 0.6980 overall best weight: 0.7960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 182 GLN C 269 ASN D 269 ASN ** F 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 348 GLN ** G 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2568 r_free = 0.2568 target = 0.049944 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2270 r_free = 0.2270 target = 0.039201 restraints weight = 47853.697| |-----------------------------------------------------------------------------| r_work (start): 0.2267 rms_B_bonded: 1.46 r_work: 0.2169 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.2068 rms_B_bonded: 3.31 restraints_weight: 0.2500 r_work (final): 0.2068 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8934 moved from start: 0.0957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 21590 Z= 0.141 Angle : 0.583 11.278 29562 Z= 0.296 Chirality : 0.039 0.273 3401 Planarity : 0.004 0.043 3630 Dihedral : 16.187 168.450 3506 Min Nonbonded Distance : 1.878 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 0.99 % Allowed : 8.65 % Favored : 90.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: 1.93 (0.17), residues: 2516 helix: 1.98 (0.15), residues: 1292 sheet: 1.15 (0.24), residues: 440 loop : 0.28 (0.23), residues: 784 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 18 TYR 0.023 0.001 TYR F 310 PHE 0.013 0.001 PHE C 87 TRP 0.017 0.001 TRP C 10 HIS 0.008 0.001 HIS B 360 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.14 (21574) covalent geometry : angle 0.56128 / 0.29 (29538) hydrogen bonds : bond 0.04253 / 2.83 ( 1167) hydrogen bonds : angle 4.01810 / 2.95 ( 3283) metal coordination : bond 0.00402 / 0.19 ( 16) metal coordination : angle 5.52052 / 3.38 ( 24) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5032 Ramachandran restraints generated. 2516 Oldfield, 0 Emsley, 2516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5032 Ramachandran restraints generated. 2516 Oldfield, 0 Emsley, 2516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 337 residues out of total 2116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 316 time to evaluate : 0.869 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 253 GLU cc_start: 0.8025 (OUTLIER) cc_final: 0.7508 (mp0) REVERT: A 277 ARG cc_start: 0.9180 (mtp85) cc_final: 0.8352 (mtp85) REVERT: B 98 ARG cc_start: 0.8875 (mmt90) cc_final: 0.8640 (mmt-90) REVERT: B 265 MET cc_start: 0.8680 (mmp) cc_final: 0.8436 (mmp) REVERT: C 1 MET cc_start: 0.6187 (ptm) cc_final: 0.5873 (ptm) REVERT: D 137 ASN cc_start: 0.8682 (m-40) cc_final: 0.8455 (m-40) REVERT: D 244 LEU cc_start: 0.8785 (mt) cc_final: 0.8529 (mt) REVERT: D 284 GLU cc_start: 0.8102 (tp30) cc_final: 0.7806 (mm-30) REVERT: E 314 ASP cc_start: 0.8324 (t0) cc_final: 0.8121 (t0) REVERT: F 154 TYR cc_start: 0.9185 (p90) cc_final: 0.8892 (p90) REVERT: F 278 PHE cc_start: 0.8695 (m-80) cc_final: 0.8460 (m-80) REVERT: F 288 ASN cc_start: 0.7823 (m-40) cc_final: 0.7571 (m-40) REVERT: G 8 GLU cc_start: 0.8396 (pp20) cc_final: 0.7980 (pp20) REVERT: G 56 ARG cc_start: 0.8946 (mtt90) cc_final: 0.8709 (mtt90) REVERT: G 165 GLU cc_start: 0.7748 (mm-30) cc_final: 0.7483 (tp30) outliers start: 21 outliers final: 11 residues processed: 328 average time/residue: 0.1956 time to fit residues: 91.7407 Evaluate side-chains 316 residues out of total 2116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 304 time to evaluate : 0.789 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 ASP Chi-restraints excluded: chain A residue 253 GLU Chi-restraints excluded: chain B residue 365 LEU Chi-restraints excluded: chain C residue 257 VAL Chi-restraints excluded: chain D residue 2 SER Chi-restraints excluded: chain D residue 252 LEU Chi-restraints excluded: chain D residue 269 ASN Chi-restraints excluded: chain E residue 161 LEU Chi-restraints excluded: chain F residue 243 ASP Chi-restraints excluded: chain F residue 344 VAL Chi-restraints excluded: chain G residue 281 VAL Chi-restraints excluded: chain J residue 28 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 254 random chunks: chunk 191 optimal weight: 3.9990 chunk 177 optimal weight: 2.9990 chunk 118 optimal weight: 1.9990 chunk 212 optimal weight: 4.9990 chunk 4 optimal weight: 3.9990 chunk 144 optimal weight: 4.9990 chunk 171 optimal weight: 0.5980 chunk 13 optimal weight: 6.9990 chunk 179 optimal weight: 3.9990 chunk 14 optimal weight: 1.9990 chunk 51 optimal weight: 0.4980 overall best weight: 1.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 269 ASN D 269 ASN G 15 GLN G 61 GLN ** G 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2532 r_free = 0.2532 target = 0.048553 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2230 r_free = 0.2230 target = 0.037833 restraints weight = 48024.571| |-----------------------------------------------------------------------------| r_work (start): 0.2226 rms_B_bonded: 1.45 r_work: 0.2129 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.2027 rms_B_bonded: 3.26 restraints_weight: 0.2500 r_work (final): 0.2027 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8957 moved from start: 0.1027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 21590 Z= 0.218 Angle : 0.637 11.002 29562 Z= 0.322 Chirality : 0.041 0.267 3401 Planarity : 0.004 0.045 3630 Dihedral : 16.271 169.407 3506 Min Nonbonded Distance : 1.797 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 1.51 % Allowed : 10.16 % Favored : 88.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: 1.83 (0.17), residues: 2516 helix: 1.92 (0.15), residues: 1290 sheet: 1.14 (0.23), residues: 441 loop : 0.16 (0.23), residues: 785 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 263 TYR 0.017 0.002 TYR F 310 PHE 0.013 0.002 PHE C 87 TRP 0.017 0.002 TRP B 10 HIS 0.009 0.001 HIS E 246 Details of bonding type rmsd/Z covalent geometry : bond 0.00516 / 0.22 (21574) covalent geometry : angle 0.61647 / 0.32 (29538) hydrogen bonds : bond 0.04720 / 3.16 ( 1167) hydrogen bonds : angle 4.05259 / 2.97 ( 3283) metal coordination : bond 0.00700 / 0.40 ( 16) metal coordination : angle 5.70485 / 3.49 ( 24) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5032 Ramachandran restraints generated. 2516 Oldfield, 0 Emsley, 2516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5032 Ramachandran restraints generated. 2516 Oldfield, 0 Emsley, 2516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 330 residues out of total 2116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 298 time to evaluate : 0.817 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 253 GLU cc_start: 0.8047 (OUTLIER) cc_final: 0.7529 (mp0) REVERT: A 277 ARG cc_start: 0.9191 (mtp85) cc_final: 0.8461 (mtp85) REVERT: B 98 ARG cc_start: 0.8877 (mmt90) cc_final: 0.8655 (mmt-90) REVERT: B 265 MET cc_start: 0.8687 (mmp) cc_final: 0.8452 (mmp) REVERT: C 1 MET cc_start: 0.6381 (ptm) cc_final: 0.6100 (ptm) REVERT: D 137 ASN cc_start: 0.8732 (m-40) cc_final: 0.8517 (m-40) REVERT: D 171 LEU cc_start: 0.9053 (OUTLIER) cc_final: 0.8745 (mp) REVERT: D 244 LEU cc_start: 0.8847 (mt) cc_final: 0.8596 (mt) REVERT: D 284 GLU cc_start: 0.8129 (tp30) cc_final: 0.7827 (mm-30) REVERT: E 85 LYS cc_start: 0.8912 (mtmm) cc_final: 0.8588 (mtmm) REVERT: E 204 LEU cc_start: 0.8826 (OUTLIER) cc_final: 0.8575 (mp) REVERT: F 154 TYR cc_start: 0.9193 (p90) cc_final: 0.8872 (p90) REVERT: F 278 PHE cc_start: 0.8766 (m-80) cc_final: 0.8468 (m-80) REVERT: F 288 ASN cc_start: 0.7931 (m-40) cc_final: 0.7699 (m-40) REVERT: G 165 GLU cc_start: 0.7751 (mm-30) cc_final: 0.7489 (mm-30) REVERT: G 206 MET cc_start: 0.8598 (OUTLIER) cc_final: 0.8108 (ttm) outliers start: 32 outliers final: 15 residues processed: 318 average time/residue: 0.2014 time to fit residues: 91.9494 Evaluate side-chains 309 residues out of total 2116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 290 time to evaluate : 0.759 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 GLU Chi-restraints excluded: chain A residue 56 ASP Chi-restraints excluded: chain A residue 253 GLU Chi-restraints excluded: chain B residue 65 GLU Chi-restraints excluded: chain B residue 365 LEU Chi-restraints excluded: chain C residue 257 VAL Chi-restraints excluded: chain D residue 2 SER Chi-restraints excluded: chain D residue 171 LEU Chi-restraints excluded: chain D residue 252 LEU Chi-restraints excluded: chain E residue 161 LEU Chi-restraints excluded: chain E residue 204 LEU Chi-restraints excluded: chain F residue 243 ASP Chi-restraints excluded: chain F residue 309 THR Chi-restraints excluded: chain F residue 344 VAL Chi-restraints excluded: chain G residue 6 GLU Chi-restraints excluded: chain G residue 51 MET Chi-restraints excluded: chain G residue 206 MET Chi-restraints excluded: chain G residue 281 VAL Chi-restraints excluded: chain J residue 28 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 254 random chunks: chunk 70 optimal weight: 1.9990 chunk 89 optimal weight: 0.6980 chunk 71 optimal weight: 2.9990 chunk 174 optimal weight: 0.9980 chunk 250 optimal weight: 10.0000 chunk 69 optimal weight: 0.7980 chunk 1 optimal weight: 1.9990 chunk 152 optimal weight: 3.9990 chunk 241 optimal weight: 2.9990 chunk 182 optimal weight: 0.9990 chunk 210 optimal weight: 6.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 204 GLN C 269 ASN D 269 ASN ** G 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2547 r_free = 0.2547 target = 0.049172 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2247 r_free = 0.2247 target = 0.038418 restraints weight = 47755.264| |-----------------------------------------------------------------------------| r_work (start): 0.2242 rms_B_bonded: 1.45 r_work: 0.2145 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.2043 rms_B_bonded: 3.28 restraints_weight: 0.2500 r_work (final): 0.2043 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8948 moved from start: 0.1132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 21590 Z= 0.166 Angle : 0.595 11.242 29562 Z= 0.302 Chirality : 0.039 0.268 3401 Planarity : 0.004 0.044 3630 Dihedral : 16.272 169.585 3506 Min Nonbonded Distance : 1.857 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 1.75 % Allowed : 11.44 % Favored : 86.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: 1.93 (0.17), residues: 2516 helix: 2.01 (0.15), residues: 1291 sheet: 1.10 (0.24), residues: 438 loop : 0.25 (0.23), residues: 787 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 105 TYR 0.019 0.001 TYR F 310 PHE 0.013 0.001 PHE F 3 TRP 0.018 0.001 TRP C 10 HIS 0.007 0.001 HIS B 360 Details of bonding type rmsd/Z covalent geometry : bond 0.00387 / 0.17 (21574) covalent geometry : angle 0.57540 / 0.30 (29538) hydrogen bonds : bond 0.04227 / 2.82 ( 1167) hydrogen bonds : angle 3.95248 / 2.91 ( 3283) metal coordination : bond 0.00492 / 0.27 ( 16) metal coordination : angle 5.40104 / 3.32 ( 24) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5032 Ramachandran restraints generated. 2516 Oldfield, 0 Emsley, 2516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5032 Ramachandran restraints generated. 2516 Oldfield, 0 Emsley, 2516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 340 residues out of total 2116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 303 time to evaluate : 0.812 Fit side-chains revert: symmetry clash REVERT: A 253 GLU cc_start: 0.8036 (OUTLIER) cc_final: 0.7513 (mp0) REVERT: B 51 LYS cc_start: 0.8613 (mttt) cc_final: 0.8413 (mttt) REVERT: C 1 MET cc_start: 0.6374 (ptm) cc_final: 0.6106 (ptm) REVERT: D 137 ASN cc_start: 0.8727 (m-40) cc_final: 0.8511 (m-40) REVERT: D 171 LEU cc_start: 0.9014 (OUTLIER) cc_final: 0.8706 (mp) REVERT: D 244 LEU cc_start: 0.8825 (mt) cc_final: 0.8588 (mt) REVERT: D 284 GLU cc_start: 0.8122 (tp30) cc_final: 0.7874 (mm-30) REVERT: E 204 LEU cc_start: 0.8804 (OUTLIER) cc_final: 0.8545 (mp) REVERT: F 154 TYR cc_start: 0.9214 (p90) cc_final: 0.8914 (p90) REVERT: F 288 ASN cc_start: 0.7922 (m-40) cc_final: 0.7683 (m-40) REVERT: G 2 LYS cc_start: 0.8588 (mtpp) cc_final: 0.8347 (mtpp) REVERT: G 56 ARG cc_start: 0.8926 (mtt90) cc_final: 0.8708 (mtt90) REVERT: G 130 LEU cc_start: 0.8818 (OUTLIER) cc_final: 0.8561 (pp) REVERT: G 165 GLU cc_start: 0.7761 (mm-30) cc_final: 0.7515 (tp30) REVERT: G 206 MET cc_start: 0.8605 (OUTLIER) cc_final: 0.8139 (ttm) outliers start: 37 outliers final: 21 residues processed: 327 average time/residue: 0.1945 time to fit residues: 91.1885 Evaluate side-chains 316 residues out of total 2116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 290 time to evaluate : 0.810 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 15 GLU Chi-restraints excluded: chain A residue 56 ASP Chi-restraints excluded: chain A residue 181 LEU Chi-restraints excluded: chain A residue 253 GLU Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain B residue 365 LEU Chi-restraints excluded: chain C residue 257 VAL Chi-restraints excluded: chain D residue 2 SER Chi-restraints excluded: chain D residue 171 LEU Chi-restraints excluded: chain D residue 252 LEU Chi-restraints excluded: chain D residue 269 ASN Chi-restraints excluded: chain E residue 161 LEU Chi-restraints excluded: chain E residue 204 LEU Chi-restraints excluded: chain F residue 207 LEU Chi-restraints excluded: chain F residue 243 ASP Chi-restraints excluded: chain F residue 305 ILE Chi-restraints excluded: chain F residue 309 THR Chi-restraints excluded: chain F residue 344 VAL Chi-restraints excluded: chain G residue 6 GLU Chi-restraints excluded: chain G residue 41 THR Chi-restraints excluded: chain G residue 51 MET Chi-restraints excluded: chain G residue 99 VAL Chi-restraints excluded: chain G residue 130 LEU Chi-restraints excluded: chain G residue 206 MET Chi-restraints excluded: chain G residue 281 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 254 random chunks: chunk 204 optimal weight: 7.9990 chunk 77 optimal weight: 5.9990 chunk 224 optimal weight: 0.9980 chunk 227 optimal weight: 2.9990 chunk 250 optimal weight: 10.0000 chunk 151 optimal weight: 1.9990 chunk 118 optimal weight: 2.9990 chunk 213 optimal weight: 0.0010 chunk 69 optimal weight: 0.9990 chunk 219 optimal weight: 0.7980 chunk 189 optimal weight: 3.9990 overall best weight: 0.9590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 269 ASN D 269 ASN E 56 HIS G 275 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2553 r_free = 0.2553 target = 0.049395 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2253 r_free = 0.2253 target = 0.038623 restraints weight = 47787.313| |-----------------------------------------------------------------------------| r_work (start): 0.2249 rms_B_bonded: 1.45 r_work: 0.2151 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.2050 rms_B_bonded: 3.29 restraints_weight: 0.2500 r_work (final): 0.2050 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8944 moved from start: 0.1224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 21590 Z= 0.155 Angle : 0.588 11.143 29562 Z= 0.297 Chirality : 0.039 0.313 3401 Planarity : 0.004 0.044 3630 Dihedral : 16.269 169.634 3506 Min Nonbonded Distance : 1.863 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 1.65 % Allowed : 12.29 % Favored : 86.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: 1.96 (0.17), residues: 2516 helix: 2.05 (0.15), residues: 1291 sheet: 1.04 (0.23), residues: 441 loop : 0.29 (0.23), residues: 784 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG F 282 TYR 0.029 0.001 TYR F 310 PHE 0.012 0.001 PHE F 3 TRP 0.017 0.001 TRP C 10 HIS 0.009 0.001 HIS E 56 Details of bonding type rmsd/Z covalent geometry : bond 0.00355 / 0.15 (21574) covalent geometry : angle 0.56831 / 0.30 (29538) hydrogen bonds : bond 0.04124 / 2.76 ( 1167) hydrogen bonds : angle 3.91034 / 2.88 ( 3283) metal coordination : bond 0.00427 / 0.24 ( 16) metal coordination : angle 5.28542 / 3.25 ( 24) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5032 Ramachandran restraints generated. 2516 Oldfield, 0 Emsley, 2516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5032 Ramachandran restraints generated. 2516 Oldfield, 0 Emsley, 2516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 332 residues out of total 2116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 297 time to evaluate : 0.820 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 253 GLU cc_start: 0.8038 (OUTLIER) cc_final: 0.7517 (mp0) REVERT: A 277 ARG cc_start: 0.9188 (mtt-85) cc_final: 0.8561 (mtp85) REVERT: C 1 MET cc_start: 0.6377 (ptm) cc_final: 0.6119 (ptm) REVERT: D 137 ASN cc_start: 0.8725 (m-40) cc_final: 0.8508 (m-40) REVERT: D 171 LEU cc_start: 0.9007 (OUTLIER) cc_final: 0.8718 (mp) REVERT: D 244 LEU cc_start: 0.8809 (mt) cc_final: 0.8596 (mt) REVERT: D 284 GLU cc_start: 0.8126 (tp30) cc_final: 0.7869 (mm-30) REVERT: E 85 LYS cc_start: 0.8835 (mtmm) cc_final: 0.8547 (mtmm) REVERT: E 204 LEU cc_start: 0.8789 (OUTLIER) cc_final: 0.8529 (mp) REVERT: F 154 TYR cc_start: 0.9212 (p90) cc_final: 0.8926 (p90) REVERT: F 254 LYS cc_start: 0.8296 (mtpp) cc_final: 0.7988 (ttpp) REVERT: F 288 ASN cc_start: 0.7903 (m-40) cc_final: 0.7686 (m-40) REVERT: G 130 LEU cc_start: 0.8815 (OUTLIER) cc_final: 0.8567 (pp) REVERT: G 165 GLU cc_start: 0.7759 (mm-30) cc_final: 0.7523 (tp30) REVERT: G 206 MET cc_start: 0.8595 (OUTLIER) cc_final: 0.8142 (ttm) outliers start: 35 outliers final: 22 residues processed: 322 average time/residue: 0.1922 time to fit residues: 88.9669 Evaluate side-chains 320 residues out of total 2116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 293 time to evaluate : 0.514 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 15 GLU Chi-restraints excluded: chain A residue 56 ASP Chi-restraints excluded: chain A residue 181 LEU Chi-restraints excluded: chain A residue 253 GLU Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain B residue 257 VAL Chi-restraints excluded: chain B residue 365 LEU Chi-restraints excluded: chain C residue 257 VAL Chi-restraints excluded: chain D residue 2 SER Chi-restraints excluded: chain D residue 171 LEU Chi-restraints excluded: chain D residue 252 LEU Chi-restraints excluded: chain E residue 161 LEU Chi-restraints excluded: chain E residue 204 LEU Chi-restraints excluded: chain F residue 207 LEU Chi-restraints excluded: chain F residue 243 ASP Chi-restraints excluded: chain F residue 305 ILE Chi-restraints excluded: chain F residue 309 THR Chi-restraints excluded: chain F residue 344 VAL Chi-restraints excluded: chain G residue 6 GLU Chi-restraints excluded: chain G residue 41 THR Chi-restraints excluded: chain G residue 99 VAL Chi-restraints excluded: chain G residue 130 LEU Chi-restraints excluded: chain G residue 206 MET Chi-restraints excluded: chain G residue 281 VAL Chi-restraints excluded: chain J residue 28 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 254 random chunks: chunk 170 optimal weight: 0.9980 chunk 42 optimal weight: 2.9990 chunk 165 optimal weight: 1.9990 chunk 124 optimal weight: 0.9990 chunk 121 optimal weight: 0.9980 chunk 52 optimal weight: 0.7980 chunk 114 optimal weight: 0.9980 chunk 19 optimal weight: 0.9980 chunk 168 optimal weight: 4.9990 chunk 24 optimal weight: 1.9990 chunk 211 optimal weight: 1.9990 overall best weight: 0.9580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 269 ASN ** D 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 56 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2555 r_free = 0.2555 target = 0.049457 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2254 r_free = 0.2254 target = 0.038642 restraints weight = 47814.345| |-----------------------------------------------------------------------------| r_work (start): 0.2252 rms_B_bonded: 1.46 r_work: 0.2154 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.2053 rms_B_bonded: 3.29 restraints_weight: 0.2500 r_work (final): 0.2053 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8942 moved from start: 0.1265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 21590 Z= 0.153 Angle : 0.583 11.064 29562 Z= 0.295 Chirality : 0.039 0.269 3401 Planarity : 0.004 0.065 3630 Dihedral : 16.253 169.712 3506 Min Nonbonded Distance : 1.866 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 1.65 % Allowed : 12.81 % Favored : 85.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: 2.00 (0.17), residues: 2516 helix: 2.09 (0.15), residues: 1291 sheet: 1.00 (0.24), residues: 443 loop : 0.32 (0.23), residues: 782 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG F 279 TYR 0.025 0.001 TYR F 310 PHE 0.014 0.001 PHE G 3 TRP 0.017 0.001 TRP C 10 HIS 0.007 0.001 HIS B 360 Details of bonding type rmsd/Z covalent geometry : bond 0.00353 / 0.15 (21574) covalent geometry : angle 0.56427 / 0.29 (29538) hydrogen bonds : bond 0.04038 / 2.70 ( 1167) hydrogen bonds : angle 3.87555 / 2.85 ( 3283) metal coordination : bond 0.00414 / 0.23 ( 16) metal coordination : angle 5.23487 / 3.21 ( 24) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5032 Ramachandran restraints generated. 2516 Oldfield, 0 Emsley, 2516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5032 Ramachandran restraints generated. 2516 Oldfield, 0 Emsley, 2516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 332 residues out of total 2116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 297 time to evaluate : 0.814 Fit side-chains revert: symmetry clash REVERT: A 253 GLU cc_start: 0.8023 (OUTLIER) cc_final: 0.7498 (mp0) REVERT: A 277 ARG cc_start: 0.9203 (mtt-85) cc_final: 0.8585 (mtp85) REVERT: B 51 LYS cc_start: 0.8626 (mttt) cc_final: 0.8396 (mttt) REVERT: C 1 MET cc_start: 0.6401 (ptm) cc_final: 0.6155 (ptm) REVERT: D 137 ASN cc_start: 0.8712 (m-40) cc_final: 0.8497 (m-40) REVERT: D 171 LEU cc_start: 0.8997 (OUTLIER) cc_final: 0.8721 (mp) REVERT: D 244 LEU cc_start: 0.8793 (mt) cc_final: 0.8576 (mt) REVERT: D 284 GLU cc_start: 0.8129 (tp30) cc_final: 0.7848 (mm-30) REVERT: E 204 LEU cc_start: 0.8785 (OUTLIER) cc_final: 0.8524 (mp) REVERT: E 253 MET cc_start: 0.8898 (ttm) cc_final: 0.8697 (ttp) REVERT: F 154 TYR cc_start: 0.9208 (p90) cc_final: 0.8926 (p90) REVERT: F 254 LYS cc_start: 0.8203 (mtpp) cc_final: 0.7963 (ttpp) REVERT: G 56 ARG cc_start: 0.8920 (mtt90) cc_final: 0.8709 (mtt90) REVERT: G 130 LEU cc_start: 0.8811 (OUTLIER) cc_final: 0.8563 (pp) REVERT: G 206 MET cc_start: 0.8601 (OUTLIER) cc_final: 0.8161 (ttm) outliers start: 35 outliers final: 24 residues processed: 320 average time/residue: 0.1962 time to fit residues: 90.3129 Evaluate side-chains 322 residues out of total 2116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 293 time to evaluate : 0.772 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 15 GLU Chi-restraints excluded: chain A residue 56 ASP Chi-restraints excluded: chain A residue 181 LEU Chi-restraints excluded: chain A residue 253 GLU Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain B residue 257 VAL Chi-restraints excluded: chain B residue 365 LEU Chi-restraints excluded: chain C residue 257 VAL Chi-restraints excluded: chain D residue 2 SER Chi-restraints excluded: chain D residue 171 LEU Chi-restraints excluded: chain D residue 252 LEU Chi-restraints excluded: chain E residue 161 LEU Chi-restraints excluded: chain E residue 204 LEU Chi-restraints excluded: chain E residue 323 LEU Chi-restraints excluded: chain F residue 207 LEU Chi-restraints excluded: chain F residue 243 ASP Chi-restraints excluded: chain F residue 305 ILE Chi-restraints excluded: chain F residue 309 THR Chi-restraints excluded: chain F residue 334 GLU Chi-restraints excluded: chain F residue 344 VAL Chi-restraints excluded: chain G residue 6 GLU Chi-restraints excluded: chain G residue 41 THR Chi-restraints excluded: chain G residue 99 VAL Chi-restraints excluded: chain G residue 130 LEU Chi-restraints excluded: chain G residue 206 MET Chi-restraints excluded: chain G residue 281 VAL Chi-restraints excluded: chain J residue 28 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 254 random chunks: chunk 39 optimal weight: 0.9990 chunk 0 optimal weight: 3.9990 chunk 140 optimal weight: 0.6980 chunk 122 optimal weight: 0.9980 chunk 69 optimal weight: 0.6980 chunk 217 optimal weight: 0.9980 chunk 19 optimal weight: 0.6980 chunk 166 optimal weight: 0.8980 chunk 116 optimal weight: 1.9990 chunk 139 optimal weight: 0.9980 chunk 147 optimal weight: 0.0170 overall best weight: 0.6018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 269 ASN ** D 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 56 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2576 r_free = 0.2576 target = 0.050288 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2278 r_free = 0.2278 target = 0.039464 restraints weight = 47393.107| |-----------------------------------------------------------------------------| r_work (start): 0.2275 rms_B_bonded: 1.46 r_work: 0.2179 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.2078 rms_B_bonded: 3.30 restraints_weight: 0.2500 r_work (final): 0.2078 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8927 moved from start: 0.1390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 21590 Z= 0.124 Angle : 0.564 11.245 29562 Z= 0.286 Chirality : 0.038 0.272 3401 Planarity : 0.004 0.044 3630 Dihedral : 16.193 169.474 3506 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 1.70 % Allowed : 13.14 % Favored : 85.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: 2.10 (0.17), residues: 2516 helix: 2.18 (0.15), residues: 1292 sheet: 1.00 (0.24), residues: 443 loop : 0.38 (0.23), residues: 781 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 263 TYR 0.026 0.001 TYR F 310 PHE 0.011 0.001 PHE G 3 TRP 0.018 0.001 TRP C 10 HIS 0.007 0.001 HIS E 56 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.12 (21574) covalent geometry : angle 0.54633 / 0.29 (29538) hydrogen bonds : bond 0.03691 / 2.47 ( 1167) hydrogen bonds : angle 3.78051 / 2.78 ( 3283) metal coordination : bond 0.00316 / 0.17 ( 16) metal coordination : angle 4.92617 / 3.03 ( 24) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5032 Ramachandran restraints generated. 2516 Oldfield, 0 Emsley, 2516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5032 Ramachandran restraints generated. 2516 Oldfield, 0 Emsley, 2516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 344 residues out of total 2116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 308 time to evaluate : 0.831 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 253 GLU cc_start: 0.8029 (OUTLIER) cc_final: 0.7496 (mp0) REVERT: A 277 ARG cc_start: 0.9201 (mtt-85) cc_final: 0.8589 (mtp85) REVERT: B 51 LYS cc_start: 0.8604 (mttt) cc_final: 0.8385 (mttt) REVERT: C 1 MET cc_start: 0.6368 (ptm) cc_final: 0.6114 (ptm) REVERT: D 137 ASN cc_start: 0.8713 (m-40) cc_final: 0.8507 (m-40) REVERT: D 171 LEU cc_start: 0.8946 (OUTLIER) cc_final: 0.8704 (mp) REVERT: D 244 LEU cc_start: 0.8733 (mt) cc_final: 0.8533 (mt) REVERT: D 284 GLU cc_start: 0.8109 (tp30) cc_final: 0.7833 (mm-30) REVERT: E 57 LYS cc_start: 0.8954 (ttpp) cc_final: 0.8747 (ptmm) REVERT: E 204 LEU cc_start: 0.8739 (OUTLIER) cc_final: 0.8482 (mp) REVERT: E 253 MET cc_start: 0.8896 (ttm) cc_final: 0.8659 (ttp) REVERT: F 154 TYR cc_start: 0.9195 (p90) cc_final: 0.8941 (p90) REVERT: G 56 ARG cc_start: 0.8935 (mtt90) cc_final: 0.8705 (mtt90) REVERT: G 105 ARG cc_start: 0.8398 (ttm110) cc_final: 0.8085 (ttm110) REVERT: G 130 LEU cc_start: 0.8808 (OUTLIER) cc_final: 0.8565 (pp) outliers start: 36 outliers final: 24 residues processed: 334 average time/residue: 0.1804 time to fit residues: 87.0445 Evaluate side-chains 327 residues out of total 2116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 299 time to evaluate : 0.786 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 GLU Chi-restraints excluded: chain A residue 15 GLU Chi-restraints excluded: chain A residue 56 ASP Chi-restraints excluded: chain A residue 181 LEU Chi-restraints excluded: chain A residue 253 GLU Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain B residue 257 VAL Chi-restraints excluded: chain C residue 101 VAL Chi-restraints excluded: chain C residue 257 VAL Chi-restraints excluded: chain D residue 2 SER Chi-restraints excluded: chain D residue 171 LEU Chi-restraints excluded: chain D residue 252 LEU Chi-restraints excluded: chain D residue 269 ASN Chi-restraints excluded: chain E residue 161 LEU Chi-restraints excluded: chain E residue 204 LEU Chi-restraints excluded: chain E residue 323 LEU Chi-restraints excluded: chain F residue 207 LEU Chi-restraints excluded: chain F residue 243 ASP Chi-restraints excluded: chain F residue 305 ILE Chi-restraints excluded: chain F residue 309 THR Chi-restraints excluded: chain F residue 334 GLU Chi-restraints excluded: chain F residue 344 VAL Chi-restraints excluded: chain G residue 6 GLU Chi-restraints excluded: chain G residue 41 THR Chi-restraints excluded: chain G residue 99 VAL Chi-restraints excluded: chain G residue 130 LEU Chi-restraints excluded: chain G residue 281 VAL Chi-restraints excluded: chain J residue 28 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 254 random chunks: chunk 9 optimal weight: 1.9990 chunk 188 optimal weight: 0.9990 chunk 229 optimal weight: 1.9990 chunk 203 optimal weight: 0.9990 chunk 224 optimal weight: 0.8980 chunk 10 optimal weight: 0.9990 chunk 240 optimal weight: 0.8980 chunk 213 optimal weight: 0.0060 chunk 41 optimal weight: 4.9990 chunk 239 optimal weight: 1.9990 chunk 47 optimal weight: 2.9990 overall best weight: 0.7600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 269 ASN ** D 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 56 HIS F 288 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2574 r_free = 0.2574 target = 0.050201 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2275 r_free = 0.2275 target = 0.039377 restraints weight = 47622.879| |-----------------------------------------------------------------------------| r_work (start): 0.2271 rms_B_bonded: 1.46 r_work: 0.2173 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.2072 rms_B_bonded: 3.32 restraints_weight: 0.2500 r_work (final): 0.2072 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8930 moved from start: 0.1416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 21590 Z= 0.138 Angle : 0.576 11.123 29562 Z= 0.293 Chirality : 0.038 0.272 3401 Planarity : 0.004 0.043 3630 Dihedral : 16.173 169.623 3506 Min Nonbonded Distance : 1.889 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 1.42 % Allowed : 13.28 % Favored : 85.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: 2.10 (0.17), residues: 2516 helix: 2.18 (0.15), residues: 1293 sheet: 0.98 (0.23), residues: 449 loop : 0.39 (0.23), residues: 774 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 263 TYR 0.014 0.001 TYR F 310 PHE 0.011 0.001 PHE F 3 TRP 0.016 0.001 TRP C 10 HIS 0.008 0.001 HIS E 56 Details of bonding type rmsd/Z covalent geometry : bond 0.00313 / 0.14 (21574) covalent geometry : angle 0.55823 / 0.29 (29538) hydrogen bonds : bond 0.03786 / 2.54 ( 1167) hydrogen bonds : angle 3.77151 / 2.78 ( 3283) metal coordination : bond 0.00355 / 0.20 ( 16) metal coordination : angle 4.95413 / 3.04 ( 24) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5032 Ramachandran restraints generated. 2516 Oldfield, 0 Emsley, 2516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5032 Ramachandran restraints generated. 2516 Oldfield, 0 Emsley, 2516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 334 residues out of total 2116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 304 time to evaluate : 0.698 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 253 GLU cc_start: 0.8045 (OUTLIER) cc_final: 0.7515 (mp0) REVERT: A 277 ARG cc_start: 0.9192 (mtt-85) cc_final: 0.8585 (mtp85) REVERT: B 51 LYS cc_start: 0.8616 (mttt) cc_final: 0.8379 (mttt) REVERT: C 1 MET cc_start: 0.6390 (ptm) cc_final: 0.6164 (ptm) REVERT: D 137 ASN cc_start: 0.8719 (m-40) cc_final: 0.8478 (m-40) REVERT: D 171 LEU cc_start: 0.8954 (OUTLIER) cc_final: 0.8702 (mp) REVERT: D 284 GLU cc_start: 0.8129 (tp30) cc_final: 0.7843 (mm-30) REVERT: E 204 LEU cc_start: 0.8743 (OUTLIER) cc_final: 0.8487 (mp) REVERT: E 253 MET cc_start: 0.8895 (ttm) cc_final: 0.8654 (ttp) REVERT: F 154 TYR cc_start: 0.9198 (p90) cc_final: 0.8944 (p90) REVERT: F 173 ASP cc_start: 0.8352 (t0) cc_final: 0.8124 (t0) REVERT: G 56 ARG cc_start: 0.8940 (mtt90) cc_final: 0.8695 (mtt90) REVERT: G 105 ARG cc_start: 0.8349 (ttm110) cc_final: 0.8120 (ttm110) REVERT: G 130 LEU cc_start: 0.8808 (OUTLIER) cc_final: 0.8559 (pp) outliers start: 30 outliers final: 23 residues processed: 324 average time/residue: 0.1801 time to fit residues: 84.9388 Evaluate side-chains 321 residues out of total 2116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 294 time to evaluate : 0.791 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 7 GLU Chi-restraints excluded: chain A residue 15 GLU Chi-restraints excluded: chain A residue 56 ASP Chi-restraints excluded: chain A residue 181 LEU Chi-restraints excluded: chain A residue 253 GLU Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain C residue 101 VAL Chi-restraints excluded: chain C residue 257 VAL Chi-restraints excluded: chain C residue 313 MET Chi-restraints excluded: chain D residue 2 SER Chi-restraints excluded: chain D residue 171 LEU Chi-restraints excluded: chain D residue 252 LEU Chi-restraints excluded: chain D residue 269 ASN Chi-restraints excluded: chain E residue 161 LEU Chi-restraints excluded: chain E residue 204 LEU Chi-restraints excluded: chain E residue 323 LEU Chi-restraints excluded: chain F residue 243 ASP Chi-restraints excluded: chain F residue 305 ILE Chi-restraints excluded: chain F residue 309 THR Chi-restraints excluded: chain F residue 334 GLU Chi-restraints excluded: chain F residue 344 VAL Chi-restraints excluded: chain G residue 6 GLU Chi-restraints excluded: chain G residue 99 VAL Chi-restraints excluded: chain G residue 130 LEU Chi-restraints excluded: chain G residue 281 VAL Chi-restraints excluded: chain J residue 28 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 254 random chunks: chunk 69 optimal weight: 0.7980 chunk 160 optimal weight: 0.0980 chunk 50 optimal weight: 2.9990 chunk 106 optimal weight: 2.9990 chunk 152 optimal weight: 2.9990 chunk 147 optimal weight: 4.9990 chunk 20 optimal weight: 0.9980 chunk 237 optimal weight: 0.9980 chunk 3 optimal weight: 1.9990 chunk 156 optimal weight: 0.9980 chunk 38 optimal weight: 3.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 56 HIS F 288 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2574 r_free = 0.2574 target = 0.050206 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.2274 r_free = 0.2274 target = 0.039366 restraints weight = 47604.650| |-----------------------------------------------------------------------------| r_work (start): 0.2270 rms_B_bonded: 1.46 r_work: 0.2173 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.2072 rms_B_bonded: 3.31 restraints_weight: 0.2500 r_work (final): 0.2072 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8929 moved from start: 0.1451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 21590 Z= 0.139 Angle : 0.581 10.960 29562 Z= 0.296 Chirality : 0.038 0.273 3401 Planarity : 0.004 0.043 3630 Dihedral : 16.158 169.765 3506 Min Nonbonded Distance : 1.889 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 1.37 % Allowed : 13.52 % Favored : 85.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.10 (0.17), residues: 2516 helix: 2.18 (0.15), residues: 1291 sheet: 0.97 (0.23), residues: 449 loop : 0.41 (0.23), residues: 776 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 263 TYR 0.020 0.001 TYR F 310 PHE 0.011 0.001 PHE F 3 TRP 0.016 0.001 TRP C 10 HIS 0.009 0.001 HIS E 56 Details of bonding type rmsd/Z covalent geometry : bond 0.00316 / 0.14 (21574) covalent geometry : angle 0.56404 / 0.29 (29538) hydrogen bonds : bond 0.03789 / 2.54 ( 1167) hydrogen bonds : angle 3.77195 / 2.78 ( 3283) metal coordination : bond 0.00370 / 0.21 ( 16) metal coordination : angle 4.96623 / 3.04 ( 24) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5032 Ramachandran restraints generated. 2516 Oldfield, 0 Emsley, 2516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5032 Ramachandran restraints generated. 2516 Oldfield, 0 Emsley, 2516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 328 residues out of total 2116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 299 time to evaluate : 0.678 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 253 GLU cc_start: 0.8045 (OUTLIER) cc_final: 0.7516 (mp0) REVERT: A 277 ARG cc_start: 0.9198 (mtt-85) cc_final: 0.8587 (mtp85) REVERT: B 51 LYS cc_start: 0.8602 (mttt) cc_final: 0.8365 (mttt) REVERT: C 1 MET cc_start: 0.6420 (ptm) cc_final: 0.6191 (ptm) REVERT: D 137 ASN cc_start: 0.8721 (m-40) cc_final: 0.8485 (m-40) REVERT: D 171 LEU cc_start: 0.8952 (OUTLIER) cc_final: 0.8699 (mp) REVERT: E 204 LEU cc_start: 0.8740 (OUTLIER) cc_final: 0.8488 (mp) REVERT: E 253 MET cc_start: 0.8900 (ttm) cc_final: 0.8657 (ttp) REVERT: F 154 TYR cc_start: 0.9197 (p90) cc_final: 0.8947 (p90) REVERT: F 173 ASP cc_start: 0.8351 (t0) cc_final: 0.8135 (t0) REVERT: G 56 ARG cc_start: 0.8948 (mtt90) cc_final: 0.8699 (mtt90) REVERT: G 105 ARG cc_start: 0.8354 (ttm110) cc_final: 0.8111 (ttm110) REVERT: G 130 LEU cc_start: 0.8809 (OUTLIER) cc_final: 0.8562 (pp) outliers start: 29 outliers final: 23 residues processed: 319 average time/residue: 0.1795 time to fit residues: 82.8413 Evaluate side-chains 322 residues out of total 2116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 295 time to evaluate : 0.656 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 7 GLU Chi-restraints excluded: chain A residue 56 ASP Chi-restraints excluded: chain A residue 181 LEU Chi-restraints excluded: chain A residue 253 GLU Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain B residue 257 VAL Chi-restraints excluded: chain C residue 101 VAL Chi-restraints excluded: chain C residue 257 VAL Chi-restraints excluded: chain C residue 313 MET Chi-restraints excluded: chain D residue 2 SER Chi-restraints excluded: chain D residue 171 LEU Chi-restraints excluded: chain D residue 252 LEU Chi-restraints excluded: chain D residue 269 ASN Chi-restraints excluded: chain E residue 161 LEU Chi-restraints excluded: chain E residue 204 LEU Chi-restraints excluded: chain E residue 281 LEU Chi-restraints excluded: chain E residue 323 LEU Chi-restraints excluded: chain F residue 188 LEU Chi-restraints excluded: chain F residue 243 ASP Chi-restraints excluded: chain F residue 305 ILE Chi-restraints excluded: chain F residue 309 THR Chi-restraints excluded: chain F residue 344 VAL Chi-restraints excluded: chain G residue 6 GLU Chi-restraints excluded: chain G residue 99 VAL Chi-restraints excluded: chain G residue 130 LEU Chi-restraints excluded: chain J residue 28 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 254 random chunks: chunk 242 optimal weight: 0.5980 chunk 238 optimal weight: 2.9990 chunk 141 optimal weight: 0.0370 chunk 58 optimal weight: 0.0030 chunk 205 optimal weight: 0.7980 chunk 148 optimal weight: 3.9990 chunk 199 optimal weight: 0.9980 chunk 138 optimal weight: 0.7980 chunk 32 optimal weight: 2.9990 chunk 241 optimal weight: 1.9990 chunk 226 optimal weight: 2.9990 overall best weight: 0.4468 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 269 ASN ** D 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 288 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2597 r_free = 0.2597 target = 0.051085 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2310 r_free = 0.2310 target = 0.040553 restraints weight = 47541.211| |-----------------------------------------------------------------------------| r_work (start): 0.2306 rms_B_bonded: 1.31 r_work: 0.2217 rms_B_bonded: 1.77 restraints_weight: 0.5000 r_work: 0.2123 rms_B_bonded: 3.04 restraints_weight: 0.2500 r_work (final): 0.2123 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8902 moved from start: 0.1561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 21590 Z= 0.115 Angle : 0.566 11.019 29562 Z= 0.288 Chirality : 0.038 0.276 3401 Planarity : 0.004 0.078 3630 Dihedral : 16.107 169.582 3506 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 1.28 % Allowed : 13.99 % Favored : 84.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: 2.19 (0.17), residues: 2516 helix: 2.26 (0.15), residues: 1291 sheet: 0.99 (0.24), residues: 448 loop : 0.44 (0.23), residues: 777 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG F 279 TYR 0.019 0.001 TYR F 310 PHE 0.011 0.001 PHE G 3 TRP 0.018 0.001 TRP C 10 HIS 0.006 0.001 HIS B 360 Details of bonding type rmsd/Z covalent geometry : bond 0.00252 / 0.12 (21574) covalent geometry : angle 0.55027 / 0.29 (29538) hydrogen bonds : bond 0.03500 / 2.34 ( 1167) hydrogen bonds : angle 3.67833 / 2.70 ( 3283) metal coordination : bond 0.00268 / 0.15 ( 16) metal coordination : angle 4.74070 / 2.91 ( 24) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4744.80 seconds wall clock time: 82 minutes 6.17 seconds (4926.17 seconds total)