Starting phenix.real_space_refine on Fri Aug 7 12:13:47 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9oyb_71013/08_2026/9oyb_71013.cif Found real_map, /net/cci-nas-00/data/ceres_data/9oyb_71013/08_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 { model { file = "/net/cci-nas-00/data/ceres_data/9oyb_71013/08_2026/9oyb_71013.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9oyb_71013/08_2026/9oyb_71013.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9oyb_71013/08_2026/9oyb_71013.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9oyb_71013/08_2026/9oyb_71013.map" } 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/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: 4.67, per 1000 atoms: 0.22 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: 1.79 Conformation dependent library (CDL) restraints added in 896.3 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: 2.69 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: 4.13 Time building geometry restraints manager: 2.28 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: 2.970 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.390 Check model and map are aligned: 0.070 Set scattering table: 0.050 Process input model: 24.400 Find NCS groups from input model: 0.450 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.730 ------------------------------------------------------------------------------- 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= 0.397 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 0.70633 / 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 : 0.829 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: 0.7820 (mp0) 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: 0.2070 time to fit residues: 102.6253 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 : 0.888 ------------------------------------------------------------------------------- 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 ** F 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 9 HIS ** 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 = 0.2553 r_free = 0.2553 target = 0.049406 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2258 r_free = 0.2258 target = 0.038825 restraints weight = 47957.226| |-----------------------------------------------------------------------------| r_work (start): 0.2254 rms_B_bonded: 1.40 r_work: 0.2160 rms_B_bonded: 1.86 restraints_weight: 0.5000 r_work: 0.2060 rms_B_bonded: 3.18 restraints_weight: 0.2500 r_work (final): 0.2060 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8939 moved from start: 0.0736 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= 0.176 Angle : 0.642 11.512 29562 Z= 0.324 Chirality : 0.041 0.294 3401 Planarity : 0.004 0.045 3630 Dihedral : 16.240 168.421 3506 Min Nonbonded Distance : 1.854 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 0.61 % Allowed : 6.90 % Favored : 92.49 % 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: 1.13 (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 0.019 0.001 PHE F 3 TRP 0.019 0.002 TRP C 10 HIS 0.008 0.001 HIS B 360 Details of bonding type rmsd/Z covalent geometry : bond 0.00404 / 0.18 (21574) covalent geometry : angle 0.61898 / 0.32 (29538) hydrogen bonds : bond 0.04886 / 3.26 ( 1167) hydrogen bonds : angle 4.28136 / 3.14 ( 3283) metal coordination : bond 0.00619 / 0.32 ( 16) metal coordination : angle 5.97432 / 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 323 residues out of total 2116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 310 time to evaluate : 0.823 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 277 ARG cc_start: 0.9227 (mtp85) cc_final: 0.8429 (mtp85) REVERT: B 265 MET cc_start: 0.8682 (mmp) cc_final: 0.8445 (mmp) REVERT: C 1 MET cc_start: 0.6075 (ptm) cc_final: 0.5776 (ptm) REVERT: C 294 MET cc_start: 0.8901 (mmp) cc_final: 0.8637 (mmp) REVERT: D 137 ASN cc_start: 0.8697 (m-40) cc_final: 0.8468 (m-40) REVERT: D 244 LEU cc_start: 0.8760 (mt) cc_final: 0.8426 (mt) REVERT: D 284 GLU cc_start: 0.8011 (tp30) cc_final: 0.7731 (mm-30) REVERT: E 85 LYS cc_start: 0.8860 (mttp) cc_final: 0.8623 (mtmm) REVERT: F 154 TYR cc_start: 0.9190 (p90) cc_final: 0.8871 (p90) REVERT: F 275 ASN cc_start: 0.8130 (p0) cc_final: 0.7923 (p0) REVERT: F 278 PHE cc_start: 0.8707 (m-80) cc_final: 0.8476 (m-80) REVERT: F 288 ASN cc_start: 0.7834 (m-40) cc_final: 0.7573 (m-40) REVERT: F 308 VAL cc_start: 0.9000 (t) cc_final: 0.8799 (m) REVERT: G 8 GLU cc_start: 0.8344 (pp20) cc_final: 0.7925 (pp20) REVERT: G 165 GLU cc_start: 0.7800 (mm-30) cc_final: 0.7531 (mm-30) outliers start: 13 outliers final: 7 residues processed: 315 average time/residue: 0.2038 time to fit residues: 91.6340 Evaluate side-chains 303 residues out of total 2116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 296 time to evaluate : 0.824 ------------------------------------------------------------------------------- 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 161 LEU Chi-restraints excluded: chain F residue 243 ASP 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: 0.0980 chunk 194 optimal weight: 2.9990 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: 0.9990 chunk 103 optimal weight: 1.9990 chunk 208 optimal weight: 3.9990 chunk 229 optimal weight: 0.6980 chunk 90 optimal weight: 0.9980 overall best weight: 0.9584 ------------------------------------------------------------------------------- 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 = 0.2559 r_free = 0.2559 target = 0.049597 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2260 r_free = 0.2260 target = 0.038860 restraints weight = 47950.972| |-----------------------------------------------------------------------------| r_work (start): 0.2256 rms_B_bonded: 1.45 r_work: 0.2159 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.2058 rms_B_bonded: 3.29 restraints_weight: 0.2500 r_work (final): 0.2058 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8940 moved from start: 0.0935 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= 0.155 Angle : 0.599 11.385 29562 Z= 0.302 Chirality : 0.040 0.295 3401 Planarity : 0.004 0.045 3630 Dihedral : 16.180 169.532 3506 Min Nonbonded Distance : 1.857 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 1.04 % Allowed : 8.55 % Favored : 90.41 % 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: 1.88 (0.17), residues: 2516 helix: 1.95 (0.15), residues: 1292 sheet: 1.14 (0.24), residues: 434 loop : 0.23 (0.23), residues: 790 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 18 TYR 0.024 0.001 TYR F 310 PHE 0.012 0.001 PHE G 3 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 0.00353 / 0.15 (21574) covalent geometry : angle 0.57720 / 0.30 (29538) hydrogen bonds : bond 0.04377 / 2.92 ( 1167) hydrogen bonds : angle 4.03396 / 2.96 ( 3283) metal coordination : bond 0.00461 / 0.23 ( 16) metal coordination : angle 5.62550 / 3.44 ( 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 338 residues out of total 2116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 316 time to evaluate : 0.824 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 253 GLU cc_start: 0.8013 (OUTLIER) cc_final: 0.7507 (mp0) REVERT: A 277 ARG cc_start: 0.9218 (mtp85) cc_final: 0.8422 (mtp85) REVERT: B 98 ARG cc_start: 0.8873 (mmt90) cc_final: 0.8636 (mmt-90) REVERT: B 265 MET cc_start: 0.8695 (mmp) cc_final: 0.8452 (mmp) REVERT: C 1 MET cc_start: 0.6229 (ptm) cc_final: 0.5925 (ptm) REVERT: D 137 ASN cc_start: 0.8695 (m-40) cc_final: 0.8480 (m-40) REVERT: D 244 LEU cc_start: 0.8784 (mt) cc_final: 0.8540 (mt) REVERT: D 284 GLU cc_start: 0.8107 (tp30) cc_final: 0.7815 (mm-30) REVERT: E 314 ASP cc_start: 0.8329 (t0) cc_final: 0.8119 (t0) REVERT: F 154 TYR cc_start: 0.9188 (p90) cc_final: 0.8887 (p90) REVERT: F 278 PHE cc_start: 0.8693 (m-80) cc_final: 0.8458 (m-80) REVERT: F 288 ASN cc_start: 0.7827 (m-40) cc_final: 0.7577 (m-40) REVERT: G 8 GLU cc_start: 0.8399 (pp20) cc_final: 0.7991 (pp20) REVERT: G 56 ARG cc_start: 0.8940 (mtt90) cc_final: 0.8705 (mtt90) REVERT: G 165 GLU cc_start: 0.7763 (mm-30) cc_final: 0.7535 (tp30) outliers start: 22 outliers final: 12 residues processed: 329 average time/residue: 0.1984 time to fit residues: 93.6343 Evaluate side-chains 314 residues out of total 2116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 301 time to evaluate : 0.803 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 ASP 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 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: 0.9990 chunk 177 optimal weight: 2.9990 chunk 118 optimal weight: 0.8980 chunk 212 optimal weight: 0.7980 chunk 4 optimal weight: 3.9990 chunk 144 optimal weight: 4.9990 chunk 171 optimal weight: 0.8980 chunk 13 optimal weight: 2.9990 chunk 179 optimal weight: 2.9990 chunk 14 optimal weight: 1.9990 chunk 51 optimal weight: 0.5980 overall best weight: 0.8382 ------------------------------------------------------------------------------- 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 = 0.2565 r_free = 0.2565 target = 0.049830 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2266 r_free = 0.2266 target = 0.039075 restraints weight = 47860.246| |-----------------------------------------------------------------------------| r_work (start): 0.2262 rms_B_bonded: 1.45 r_work: 0.2165 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.2064 rms_B_bonded: 3.31 restraints_weight: 0.2500 r_work (final): 0.2064 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8936 moved from start: 0.1094 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= 0.143 Angle : 0.583 11.475 29562 Z= 0.295 Chirality : 0.039 0.297 3401 Planarity : 0.004 0.043 3630 Dihedral : 16.178 169.736 3506 Min Nonbonded Distance : 1.874 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 1.42 % Allowed : 10.21 % Favored : 88.37 % 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: 1.98 (0.17), residues: 2516 helix: 2.04 (0.15), residues: 1292 sheet: 1.13 (0.24), residues: 438 loop : 0.28 (0.23), residues: 786 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 263 TYR 0.021 0.001 TYR F 310 PHE 0.012 0.001 PHE F 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 0.00323 / 0.14 (21574) covalent geometry : angle 0.56448 / 0.29 (29538) hydrogen bonds : bond 0.04104 / 2.74 ( 1167) hydrogen bonds : angle 3.93676 / 2.89 ( 3283) metal coordination : bond 0.00406 / 0.23 ( 16) metal coordination : angle 5.18015 / 3.17 ( 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 337 residues out of total 2116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 307 time to evaluate : 0.829 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 253 GLU cc_start: 0.8045 (OUTLIER) cc_final: 0.7518 (mp0) REVERT: A 277 ARG cc_start: 0.9210 (mtp85) cc_final: 0.8415 (mtp85) REVERT: B 51 LYS cc_start: 0.8609 (mttt) cc_final: 0.8382 (mttt) REVERT: B 98 ARG cc_start: 0.8863 (mmt90) cc_final: 0.8642 (mmt-90) REVERT: B 265 MET cc_start: 0.8678 (mmp) cc_final: 0.8448 (mmp) REVERT: C 1 MET cc_start: 0.6250 (ptm) cc_final: 0.5968 (ptm) REVERT: C 117 ARG cc_start: 0.8752 (mtp85) cc_final: 0.8394 (ttp-110) REVERT: D 137 ASN cc_start: 0.8694 (m-40) cc_final: 0.8480 (m-40) REVERT: D 171 LEU cc_start: 0.8984 (OUTLIER) cc_final: 0.8690 (mp) REVERT: D 244 LEU cc_start: 0.8768 (mt) cc_final: 0.8521 (mt) REVERT: D 284 GLU cc_start: 0.8106 (tp30) cc_final: 0.7798 (mm-30) REVERT: E 204 LEU cc_start: 0.8774 (OUTLIER) cc_final: 0.8519 (mp) REVERT: E 314 ASP cc_start: 0.8367 (t0) cc_final: 0.8125 (t0) REVERT: F 24 ARG cc_start: 0.9240 (mmm-85) cc_final: 0.8488 (mmm-85) REVERT: F 154 TYR cc_start: 0.9209 (p90) cc_final: 0.8902 (p90) REVERT: F 173 ASP cc_start: 0.8446 (t0) cc_final: 0.8050 (t0) REVERT: F 288 ASN cc_start: 0.7862 (m-40) cc_final: 0.7607 (m-40) REVERT: G 56 ARG cc_start: 0.8940 (mtt90) cc_final: 0.8669 (mtt90) REVERT: G 165 GLU cc_start: 0.7754 (mm-30) cc_final: 0.7499 (mm-30) outliers start: 30 outliers final: 15 residues processed: 327 average time/residue: 0.1996 time to fit residues: 93.3290 Evaluate side-chains 310 residues out of total 2116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 292 time to evaluate : 0.812 ------------------------------------------------------------------------------- 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 A residue 256 LEU Chi-restraints excluded: chain B residue 101 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 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 41 THR Chi-restraints excluded: chain G residue 281 VAL 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: 0.9990 chunk 71 optimal weight: 0.7980 chunk 174 optimal weight: 2.9990 chunk 250 optimal weight: 10.0000 chunk 69 optimal weight: 2.9990 chunk 1 optimal weight: 2.9990 chunk 152 optimal weight: 4.9990 chunk 241 optimal weight: 2.9990 chunk 182 optimal weight: 0.3980 chunk 210 optimal weight: 0.7980 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 204 GLN C 269 ASN D 269 ASN E 56 HIS ** 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 = 0.2559 r_free = 0.2559 target = 0.049609 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2259 r_free = 0.2259 target = 0.038828 restraints weight = 47834.187| |-----------------------------------------------------------------------------| r_work (start): 0.2255 rms_B_bonded: 1.46 r_work: 0.2159 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.2058 rms_B_bonded: 3.29 restraints_weight: 0.2500 r_work (final): 0.2058 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8939 moved from start: 0.1158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 21590 Z= 0.156 Angle : 0.589 11.161 29562 Z= 0.297 Chirality : 0.039 0.296 3401 Planarity : 0.004 0.043 3630 Dihedral : 16.195 170.151 3506 Min Nonbonded Distance : 1.859 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 1.75 % Allowed : 11.11 % Favored : 87.15 % 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: 2.01 (0.17), residues: 2516 helix: 2.08 (0.15), residues: 1291 sheet: 1.12 (0.23), residues: 439 loop : 0.30 (0.23), residues: 786 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 263 TYR 0.019 0.001 TYR F 310 PHE 0.012 0.001 PHE G 3 TRP 0.016 0.001 TRP C 10 HIS 0.007 0.001 HIS E 56 Details of bonding type rmsd/Z covalent geometry : bond 0.00360 / 0.16 (21574) covalent geometry : angle 0.57000 / 0.30 (29538) hydrogen bonds : bond 0.04103 / 2.74 ( 1167) hydrogen bonds : angle 3.89937 / 2.87 ( 3283) metal coordination : bond 0.00428 / 0.24 ( 16) metal coordination : angle 5.22334 / 3.20 ( 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 334 residues out of total 2116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 297 time to evaluate : 0.759 Fit side-chains revert: symmetry clash REVERT: A 253 GLU cc_start: 0.8049 (OUTLIER) cc_final: 0.7521 (mp0) REVERT: A 277 ARG cc_start: 0.9200 (mtp85) cc_final: 0.8421 (mtp85) REVERT: B 98 ARG cc_start: 0.8883 (mmt90) cc_final: 0.8655 (mmt-90) REVERT: B 265 MET cc_start: 0.8675 (mmp) cc_final: 0.8455 (mmp) REVERT: C 1 MET cc_start: 0.6310 (ptm) cc_final: 0.6036 (ptm) REVERT: D 137 ASN cc_start: 0.8712 (m-40) cc_final: 0.8495 (m-40) REVERT: D 171 LEU cc_start: 0.8994 (OUTLIER) cc_final: 0.8709 (mp) REVERT: D 244 LEU cc_start: 0.8770 (mt) cc_final: 0.8544 (mt) REVERT: D 284 GLU cc_start: 0.8122 (tp30) cc_final: 0.7872 (mm-30) REVERT: E 85 LYS cc_start: 0.8814 (mtmm) cc_final: 0.8555 (mtmm) REVERT: E 204 LEU cc_start: 0.8777 (OUTLIER) cc_final: 0.8515 (mp) REVERT: F 24 ARG cc_start: 0.9189 (mmm-85) cc_final: 0.8511 (mmm-85) REVERT: F 154 TYR cc_start: 0.9212 (p90) cc_final: 0.8924 (p90) REVERT: F 288 ASN cc_start: 0.7920 (m-40) cc_final: 0.7691 (m-40) REVERT: G 56 ARG cc_start: 0.8939 (mtt90) cc_final: 0.8659 (mtt90) REVERT: G 130 LEU cc_start: 0.8814 (OUTLIER) cc_final: 0.8552 (pp) REVERT: G 165 GLU cc_start: 0.7751 (mm-30) cc_final: 0.7482 (tp30) REVERT: G 206 MET cc_start: 0.8581 (OUTLIER) cc_final: 0.8122 (ttm) outliers start: 37 outliers final: 21 residues processed: 324 average time/residue: 0.1972 time to fit residues: 91.8597 Evaluate side-chains 318 residues out of total 2116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 292 time to evaluate : 0.777 ------------------------------------------------------------------------------- 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 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 254 random chunks: chunk 204 optimal weight: 7.9990 chunk 77 optimal weight: 2.9990 chunk 224 optimal weight: 0.9980 chunk 227 optimal weight: 3.9990 chunk 250 optimal weight: 10.0000 chunk 151 optimal weight: 0.6980 chunk 118 optimal weight: 0.6980 chunk 213 optimal weight: 0.3980 chunk 69 optimal weight: 0.8980 chunk 219 optimal weight: 3.9990 chunk 189 optimal weight: 3.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 269 ASN D 269 ASN E 56 HIS ** 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 = 0.2569 r_free = 0.2569 target = 0.049975 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2270 r_free = 0.2270 target = 0.039196 restraints weight = 47765.149| |-----------------------------------------------------------------------------| r_work (start): 0.2267 rms_B_bonded: 1.46 r_work: 0.2170 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.2070 rms_B_bonded: 3.29 restraints_weight: 0.2500 r_work (final): 0.2070 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8932 moved from start: 0.1237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 21590 Z= 0.134 Angle : 0.575 11.476 29562 Z= 0.290 Chirality : 0.039 0.298 3401 Planarity : 0.004 0.043 3630 Dihedral : 16.187 170.179 3506 Min Nonbonded Distance : 1.884 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 1.42 % Allowed : 11.77 % 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: 2.05 (0.17), residues: 2516 helix: 2.13 (0.15), residues: 1291 sheet: 1.02 (0.24), residues: 443 loop : 0.36 (0.23), residues: 782 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 263 TYR 0.030 0.001 TYR F 310 PHE 0.012 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 0.00302 / 0.13 (21574) covalent geometry : angle 0.55651 / 0.29 (29538) hydrogen bonds : bond 0.03914 / 2.62 ( 1167) hydrogen bonds : angle 3.84927 / 2.83 ( 3283) metal coordination : bond 0.00337 / 0.18 ( 16) metal coordination : angle 5.03986 / 3.09 ( 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 329 residues out of total 2116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 299 time to evaluate : 0.814 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 253 GLU cc_start: 0.8034 (OUTLIER) cc_final: 0.7507 (mp0) REVERT: A 277 ARG cc_start: 0.9192 (mtp85) cc_final: 0.8410 (mtp85) REVERT: B 51 LYS cc_start: 0.8627 (mttt) cc_final: 0.8395 (mttt) REVERT: B 265 MET cc_start: 0.8661 (mmp) cc_final: 0.8440 (mmp) REVERT: C 1 MET cc_start: 0.6305 (ptm) cc_final: 0.6028 (ptm) REVERT: C 256 MET cc_start: 0.8822 (ttp) cc_final: 0.8612 (ttm) REVERT: D 137 ASN cc_start: 0.8706 (m-40) cc_final: 0.8491 (m-40) REVERT: D 171 LEU cc_start: 0.8972 (OUTLIER) cc_final: 0.8700 (mp) REVERT: D 244 LEU cc_start: 0.8772 (mt) cc_final: 0.8548 (mt) REVERT: D 284 GLU cc_start: 0.8118 (tp30) cc_final: 0.7868 (mm-30) REVERT: E 85 LYS cc_start: 0.8815 (mtmm) cc_final: 0.8530 (mtmm) REVERT: E 204 LEU cc_start: 0.8762 (OUTLIER) cc_final: 0.8499 (mp) REVERT: F 154 TYR cc_start: 0.9220 (p90) cc_final: 0.8954 (p90) REVERT: F 173 ASP cc_start: 0.8403 (t0) cc_final: 0.8102 (t0) REVERT: F 254 LYS cc_start: 0.8215 (mtpp) cc_final: 0.8012 (ttpp) REVERT: F 288 ASN cc_start: 0.7918 (m-40) cc_final: 0.7672 (m-40) REVERT: G 56 ARG cc_start: 0.8926 (mtt90) cc_final: 0.8624 (mtt90) REVERT: G 165 GLU cc_start: 0.7738 (mm-30) cc_final: 0.7485 (tp30) REVERT: G 206 MET cc_start: 0.8562 (OUTLIER) cc_final: 0.8138 (ttm) outliers start: 30 outliers final: 20 residues processed: 320 average time/residue: 0.1903 time to fit residues: 87.8501 Evaluate side-chains 319 residues out of total 2116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 295 time to evaluate : 0.793 ------------------------------------------------------------------------------- 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 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 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: 0.6980 chunk 42 optimal weight: 2.9990 chunk 165 optimal weight: 1.9990 chunk 124 optimal weight: 0.9980 chunk 121 optimal weight: 0.7980 chunk 52 optimal weight: 1.9990 chunk 114 optimal weight: 0.8980 chunk 19 optimal weight: 0.8980 chunk 168 optimal weight: 5.9990 chunk 24 optimal weight: 0.9980 chunk 211 optimal weight: 0.9980 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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 E 246 HIS ** 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 = 0.2569 r_free = 0.2569 target = 0.050013 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2270 r_free = 0.2270 target = 0.039184 restraints weight = 47762.094| |-----------------------------------------------------------------------------| r_work (start): 0.2266 rms_B_bonded: 1.46 r_work: 0.2168 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.2067 rms_B_bonded: 3.30 restraints_weight: 0.2500 r_work (final): 0.2067 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8933 moved from start: 0.1293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 21590 Z= 0.142 Angle : 0.580 11.262 29562 Z= 0.291 Chirality : 0.039 0.298 3401 Planarity : 0.004 0.074 3630 Dihedral : 16.178 170.407 3506 Min Nonbonded Distance : 1.874 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 1.70 % Allowed : 12.29 % Favored : 86.01 % 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: 2.08 (0.17), residues: 2516 helix: 2.15 (0.15), residues: 1292 sheet: 1.05 (0.24), residues: 441 loop : 0.36 (0.23), residues: 783 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG F 279 TYR 0.028 0.001 TYR F 310 PHE 0.012 0.001 PHE G 3 TRP 0.016 0.001 TRP C 10 HIS 0.007 0.001 HIS E 56 Details of bonding type rmsd/Z covalent geometry : bond 0.00325 / 0.14 (21574) covalent geometry : angle 0.56244 / 0.29 (29538) hydrogen bonds : bond 0.03913 / 2.61 ( 1167) hydrogen bonds : angle 3.81832 / 2.81 ( 3283) metal coordination : bond 0.00382 / 0.21 ( 16) metal coordination : angle 5.03929 / 3.08 ( 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 343 residues out of total 2116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 307 time to evaluate : 0.685 Fit side-chains revert: symmetry clash REVERT: A 253 GLU cc_start: 0.8043 (OUTLIER) cc_final: 0.7516 (mp0) REVERT: A 277 ARG cc_start: 0.9193 (mtp85) cc_final: 0.8420 (mtp85) REVERT: B 51 LYS cc_start: 0.8602 (mttt) cc_final: 0.8381 (mttt) REVERT: B 265 MET cc_start: 0.8660 (mmp) cc_final: 0.8444 (mmp) REVERT: C 1 MET cc_start: 0.6345 (ptm) cc_final: 0.6076 (ptm) REVERT: C 256 MET cc_start: 0.8826 (ttp) cc_final: 0.8620 (ttm) REVERT: D 137 ASN cc_start: 0.8716 (m-40) cc_final: 0.8502 (m-40) REVERT: D 171 LEU cc_start: 0.8972 (OUTLIER) cc_final: 0.8698 (mp) REVERT: D 244 LEU cc_start: 0.8733 (mt) cc_final: 0.8518 (mt) REVERT: D 284 GLU cc_start: 0.8130 (tp30) cc_final: 0.7850 (mm-30) REVERT: E 204 LEU cc_start: 0.8755 (OUTLIER) cc_final: 0.8491 (mp) REVERT: F 24 ARG cc_start: 0.9226 (mmm-85) cc_final: 0.8515 (mmm-85) REVERT: F 154 TYR cc_start: 0.9218 (p90) cc_final: 0.8952 (p90) REVERT: F 173 ASP cc_start: 0.8382 (t0) cc_final: 0.8140 (t0) REVERT: F 254 LYS cc_start: 0.8112 (mtpp) cc_final: 0.7713 (ttmm) REVERT: F 288 ASN cc_start: 0.7919 (m-40) cc_final: 0.7689 (m-40) REVERT: G 56 ARG cc_start: 0.8919 (mtt90) cc_final: 0.8605 (mtt90) REVERT: G 130 LEU cc_start: 0.8814 (OUTLIER) cc_final: 0.8548 (pp) REVERT: G 206 MET cc_start: 0.8561 (OUTLIER) cc_final: 0.8109 (ttm) outliers start: 36 outliers final: 21 residues processed: 333 average time/residue: 0.1720 time to fit residues: 82.7985 Evaluate side-chains 320 residues out of total 2116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 294 time to evaluate : 0.664 ------------------------------------------------------------------------------- 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 253 GLU Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain B residue 101 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 319 PHE 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 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: 2.9990 chunk 69 optimal weight: 2.9990 chunk 217 optimal weight: 0.9980 chunk 19 optimal weight: 0.7980 chunk 166 optimal weight: 0.9990 chunk 116 optimal weight: 1.9990 chunk 139 optimal weight: 0.7980 chunk 147 optimal weight: 2.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- 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 E 246 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 = 0.2567 r_free = 0.2567 target = 0.049925 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2267 r_free = 0.2267 target = 0.039104 restraints weight = 47380.843| |-----------------------------------------------------------------------------| r_work (start): 0.2263 rms_B_bonded: 1.46 r_work: 0.2166 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.2065 rms_B_bonded: 3.31 restraints_weight: 0.2500 r_work (final): 0.2065 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8933 moved from start: 0.1340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 21590 Z= 0.143 Angle : 0.583 11.608 29562 Z= 0.293 Chirality : 0.039 0.299 3401 Planarity : 0.004 0.045 3630 Dihedral : 16.157 170.508 3506 Min Nonbonded Distance : 1.879 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 1.56 % Allowed : 12.67 % Favored : 85.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 2.07 (0.17), residues: 2516 helix: 2.15 (0.15), residues: 1293 sheet: 1.03 (0.24), residues: 439 loop : 0.36 (0.23), residues: 784 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 263 TYR 0.025 0.001 TYR F 310 PHE 0.012 0.001 PHE F 3 TRP 0.015 0.001 TRP C 10 HIS 0.009 0.001 HIS E 56 Details of bonding type rmsd/Z covalent geometry : bond 0.00326 / 0.14 (21574) covalent geometry : angle 0.56584 / 0.29 (29538) hydrogen bonds : bond 0.03877 / 2.60 ( 1167) hydrogen bonds : angle 3.78792 / 2.79 ( 3283) metal coordination : bond 0.00382 / 0.20 ( 16) metal coordination : angle 4.99800 / 3.06 ( 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 331 residues out of total 2116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 298 time to evaluate : 0.870 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 253 GLU cc_start: 0.8042 (OUTLIER) cc_final: 0.7514 (mp0) REVERT: A 277 ARG cc_start: 0.9189 (mtp85) cc_final: 0.8410 (mtp85) REVERT: B 51 LYS cc_start: 0.8590 (mttt) cc_final: 0.8377 (mttt) REVERT: B 265 MET cc_start: 0.8653 (mmp) cc_final: 0.8441 (mmp) REVERT: C 1 MET cc_start: 0.6363 (ptm) cc_final: 0.6096 (ptm) REVERT: C 256 MET cc_start: 0.8827 (ttp) cc_final: 0.8620 (ttm) REVERT: D 137 ASN cc_start: 0.8719 (m-40) cc_final: 0.8504 (m-40) REVERT: D 171 LEU cc_start: 0.8965 (OUTLIER) cc_final: 0.8700 (mp) REVERT: D 284 GLU cc_start: 0.8129 (tp30) cc_final: 0.7844 (mm-30) REVERT: E 85 LYS cc_start: 0.8713 (mtmm) cc_final: 0.8440 (mtmm) REVERT: E 204 LEU cc_start: 0.8752 (OUTLIER) cc_final: 0.8404 (mp) REVERT: F 24 ARG cc_start: 0.9202 (mmm-85) cc_final: 0.8565 (mmm-85) REVERT: F 154 TYR cc_start: 0.9202 (p90) cc_final: 0.8938 (p90) REVERT: F 288 ASN cc_start: 0.7915 (m-40) cc_final: 0.7689 (m-40) REVERT: G 56 ARG cc_start: 0.8907 (mtt90) cc_final: 0.8623 (mtt90) REVERT: G 105 ARG cc_start: 0.8403 (ttm110) cc_final: 0.8194 (ttm110) REVERT: G 130 LEU cc_start: 0.8804 (OUTLIER) cc_final: 0.8549 (pp) REVERT: G 206 MET cc_start: 0.8550 (OUTLIER) cc_final: 0.8107 (ttm) outliers start: 33 outliers final: 24 residues processed: 320 average time/residue: 0.1792 time to fit residues: 82.6014 Evaluate side-chains 329 residues out of total 2116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 300 time to evaluate : 0.603 ------------------------------------------------------------------------------- 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 365 LEU 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 247 VAL 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 206 MET 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: 0.7980 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: 4.9990 chunk 213 optimal weight: 0.9980 chunk 41 optimal weight: 1.9990 chunk 239 optimal weight: 1.9990 chunk 47 optimal weight: 0.8980 overall best weight: 0.9182 ------------------------------------------------------------------------------- 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 ** G 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2567 r_free = 0.2567 target = 0.049912 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2266 r_free = 0.2266 target = 0.039071 restraints weight = 47644.936| |-----------------------------------------------------------------------------| r_work (start): 0.2262 rms_B_bonded: 1.45 r_work: 0.2166 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.2066 rms_B_bonded: 3.29 restraints_weight: 0.2500 r_work (final): 0.2066 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8934 moved from start: 0.1355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 21590 Z= 0.149 Angle : 0.591 11.755 29562 Z= 0.298 Chirality : 0.039 0.299 3401 Planarity : 0.004 0.079 3630 Dihedral : 16.145 170.619 3506 Min Nonbonded Distance : 1.872 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 1.56 % Allowed : 12.95 % Favored : 85.49 % 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: 2.07 (0.17), residues: 2516 helix: 2.15 (0.15), residues: 1293 sheet: 1.02 (0.24), residues: 439 loop : 0.35 (0.23), residues: 784 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG F 279 TYR 0.016 0.001 TYR F 310 PHE 0.011 0.001 PHE F 3 TRP 0.015 0.001 TRP C 10 HIS 0.008 0.001 HIS E 56 Details of bonding type rmsd/Z covalent geometry : bond 0.00344 / 0.15 (21574) covalent geometry : angle 0.57401 / 0.30 (29538) hydrogen bonds : bond 0.03924 / 2.63 ( 1167) hydrogen bonds : angle 3.79023 / 2.79 ( 3283) metal coordination : bond 0.00395 / 0.22 ( 16) metal coordination : angle 5.03626 / 3.09 ( 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 333 residues out of total 2116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 300 time to evaluate : 0.747 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 253 GLU cc_start: 0.8042 (OUTLIER) cc_final: 0.7517 (mp0) REVERT: A 277 ARG cc_start: 0.9187 (mtp85) cc_final: 0.8406 (mtp85) REVERT: B 51 LYS cc_start: 0.8591 (mttt) cc_final: 0.8382 (mttt) REVERT: B 265 MET cc_start: 0.8660 (mmp) cc_final: 0.8449 (mmp) REVERT: C 1 MET cc_start: 0.6387 (ptm) cc_final: 0.6120 (ptm) REVERT: C 256 MET cc_start: 0.8834 (ttp) cc_final: 0.8623 (ttm) REVERT: D 137 ASN cc_start: 0.8725 (m-40) cc_final: 0.8508 (m-40) REVERT: D 171 LEU cc_start: 0.8972 (OUTLIER) cc_final: 0.8709 (mp) REVERT: E 85 LYS cc_start: 0.8733 (mtmm) cc_final: 0.8518 (mtmm) REVERT: E 204 LEU cc_start: 0.8756 (OUTLIER) cc_final: 0.8502 (mp) REVERT: F 24 ARG cc_start: 0.9183 (mmm-85) cc_final: 0.8584 (mmm-85) REVERT: F 154 TYR cc_start: 0.9202 (p90) cc_final: 0.8939 (p90) REVERT: F 173 ASP cc_start: 0.8362 (t0) cc_final: 0.8153 (t0) REVERT: F 288 ASN cc_start: 0.7943 (m-40) cc_final: 0.7600 (m110) REVERT: G 56 ARG cc_start: 0.8906 (mtt90) cc_final: 0.8622 (mtt90) REVERT: G 105 ARG cc_start: 0.8348 (ttm110) cc_final: 0.8114 (ttm110) REVERT: G 130 LEU cc_start: 0.8806 (OUTLIER) cc_final: 0.8552 (pp) REVERT: G 206 MET cc_start: 0.8555 (OUTLIER) cc_final: 0.8113 (ttm) outliers start: 33 outliers final: 22 residues processed: 321 average time/residue: 0.1738 time to fit residues: 80.5557 Evaluate side-chains 317 residues out of total 2116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 290 time to evaluate : 0.785 ------------------------------------------------------------------------------- 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 65 GLU Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain B residue 365 LEU 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 207 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 99 VAL Chi-restraints excluded: chain G residue 130 LEU Chi-restraints excluded: chain G residue 206 MET 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: 2.9990 chunk 160 optimal weight: 0.6980 chunk 50 optimal weight: 1.9990 chunk 106 optimal weight: 1.9990 chunk 152 optimal weight: 3.9990 chunk 147 optimal weight: 0.9980 chunk 20 optimal weight: 0.9990 chunk 237 optimal weight: 0.7980 chunk 3 optimal weight: 0.7980 chunk 156 optimal weight: 0.6980 chunk 38 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 204 GLN ** D 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2573 r_free = 0.2573 target = 0.050161 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2273 r_free = 0.2273 target = 0.039298 restraints weight = 47692.617| |-----------------------------------------------------------------------------| r_work (start): 0.2269 rms_B_bonded: 1.46 r_work: 0.2172 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.2072 rms_B_bonded: 3.30 restraints_weight: 0.2500 r_work (final): 0.2072 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8930 moved from start: 0.1401 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 : 0.586 11.857 29562 Z= 0.296 Chirality : 0.039 0.300 3401 Planarity : 0.004 0.044 3630 Dihedral : 16.113 170.618 3506 Min Nonbonded Distance : 1.889 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 1.37 % Allowed : 13.28 % Favored : 85.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 2.09 (0.17), residues: 2516 helix: 2.17 (0.15), residues: 1292 sheet: 0.95 (0.23), residues: 446 loop : 0.41 (0.23), residues: 778 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 263 TYR 0.022 0.001 TYR F 310 PHE 0.011 0.001 PHE F 3 TRP 0.016 0.001 TRP C 10 HIS 0.006 0.001 HIS B 360 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.14 (21574) covalent geometry : angle 0.56931 / 0.30 (29538) hydrogen bonds : bond 0.03817 / 2.56 ( 1167) hydrogen bonds : angle 3.76355 / 2.77 ( 3283) metal coordination : bond 0.00364 / 0.20 ( 16) metal coordination : angle 4.95516 / 3.05 ( 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 : 0.761 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 253 GLU cc_start: 0.8031 (OUTLIER) cc_final: 0.7505 (mp0) REVERT: A 277 ARG cc_start: 0.9194 (mtp85) cc_final: 0.8413 (mtp85) REVERT: B 51 LYS cc_start: 0.8585 (mttt) cc_final: 0.8374 (mttt) REVERT: B 265 MET cc_start: 0.8650 (mmp) cc_final: 0.8439 (mmp) REVERT: C 1 MET cc_start: 0.6379 (ptm) cc_final: 0.6114 (ptm) REVERT: C 256 MET cc_start: 0.8834 (ttp) cc_final: 0.8625 (ttm) REVERT: D 137 ASN cc_start: 0.8719 (m-40) cc_final: 0.8500 (m-40) REVERT: D 171 LEU cc_start: 0.8959 (OUTLIER) cc_final: 0.8698 (mp) REVERT: E 204 LEU cc_start: 0.8748 (OUTLIER) cc_final: 0.8495 (mp) REVERT: F 24 ARG cc_start: 0.9180 (mmm-85) cc_final: 0.8560 (mmm-85) REVERT: F 154 TYR cc_start: 0.9200 (p90) cc_final: 0.8944 (p90) REVERT: F 173 ASP cc_start: 0.8345 (t0) cc_final: 0.8143 (t0) REVERT: F 288 ASN cc_start: 0.7929 (m-40) cc_final: 0.7593 (m110) REVERT: G 56 ARG cc_start: 0.8900 (mtt90) cc_final: 0.8618 (mtt90) REVERT: G 105 ARG cc_start: 0.8366 (ttm110) cc_final: 0.8139 (ttm110) REVERT: G 130 LEU cc_start: 0.8809 (OUTLIER) cc_final: 0.8552 (pp) REVERT: G 206 MET cc_start: 0.8530 (OUTLIER) cc_final: 0.8115 (ttm) REVERT: G 254 LYS cc_start: 0.9005 (mtmt) cc_final: 0.8801 (mtmt) outliers start: 29 outliers final: 20 residues processed: 318 average time/residue: 0.1990 time to fit residues: 91.0020 Evaluate side-chains 318 residues out of total 2116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 293 time to evaluate : 0.729 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET 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 365 LEU 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 207 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 99 VAL Chi-restraints excluded: chain G residue 130 LEU Chi-restraints excluded: chain G residue 206 MET 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: 0.9980 chunk 238 optimal weight: 0.0030 chunk 141 optimal weight: 1.9990 chunk 58 optimal weight: 3.9990 chunk 205 optimal weight: 3.9990 chunk 148 optimal weight: 0.7980 chunk 199 optimal weight: 0.0670 chunk 138 optimal weight: 4.9990 chunk 32 optimal weight: 0.9980 chunk 241 optimal weight: 1.9990 chunk 226 optimal weight: 0.9980 overall best weight: 0.5728 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 269 ASN ** D 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2588 r_free = 0.2588 target = 0.050725 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2299 r_free = 0.2299 target = 0.040172 restraints weight = 47766.188| |-----------------------------------------------------------------------------| r_work (start): 0.2295 rms_B_bonded: 1.31 r_work: 0.2207 rms_B_bonded: 1.78 restraints_weight: 0.5000 r_work: 0.2111 rms_B_bonded: 3.06 restraints_weight: 0.2500 r_work (final): 0.2111 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8909 moved from start: 0.1474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 21590 Z= 0.123 Angle : 0.573 11.828 29562 Z= 0.291 Chirality : 0.038 0.303 3401 Planarity : 0.004 0.043 3630 Dihedral : 16.080 170.496 3506 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 1.42 % Allowed : 13.23 % Favored : 85.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 2.14 (0.17), residues: 2516 helix: 2.22 (0.15), residues: 1290 sheet: 0.97 (0.24), residues: 448 loop : 0.41 (0.23), residues: 778 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 263 TYR 0.022 0.001 TYR F 310 PHE 0.011 0.001 PHE G 3 TRP 0.017 0.001 TRP C 10 HIS 0.006 0.001 HIS B 290 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.12 (21574) covalent geometry : angle 0.55698 / 0.29 (29538) hydrogen bonds : bond 0.03637 / 2.44 ( 1167) hydrogen bonds : angle 3.71954 / 2.74 ( 3283) metal coordination : bond 0.00287 / 0.16 ( 16) metal coordination : angle 4.81959 / 2.97 ( 24) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4757.51 seconds wall clock time: 82 minutes 18.41 seconds (4938.41 seconds total)