Starting phenix.real_space_refine on Sat Jul 4 14:16:44 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9oyc_71014/07_2026/9oyc_71014.cif Found real_map, /net/cci-nas-00/data/ceres_data/9oyc_71014/07_2026/9oyc_71014.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.71 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9oyc_71014/07_2026/9oyc_71014.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9oyc_71014/07_2026/9oyc_71014.map" model { file = "/net/cci-nas-00/data/ceres_data/9oyc_71014/07_2026/9oyc_71014.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9oyc_71014/07_2026/9oyc_71014.cif" } resolution = 2.71 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= 0.018 sd= 0.728 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 60 5.49 5 Mg 3 5.21 5 S 112 5.16 5 C 12968 2.51 5 N 3745 2.21 5 O 4002 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 20894 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: 2840 Number of conformers: 1 Conformer: "" Number of residues, atoms: 365, 2840 Classifications: {'peptide': 365} Link IDs: {'PTRANS': 16, 'TRANS': 348} 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: 532 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 532 Classifications: {'DNA': 26} Link IDs: {'rna3p': 25} 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: 102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 102 Classifications: {'DNA': 5} Link IDs: {'rna3p': 4} 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 28.915 84.408 38.144 1.00 44.26 S ATOM 3269 SG CYS B 73 25.362 83.864 38.514 1.00 57.03 S ATOM 3286 SG CYS B 76 27.328 80.720 38.133 1.00 46.09 S ATOM 3308 SG CYS B 79 27.797 82.590 41.310 1.00 46.09 S ATOM 6057 SG CYS C 64 9.108 59.131 71.457 1.00 46.24 S ATOM 6117 SG CYS C 73 7.529 56.586 73.792 1.00 50.34 S ATOM 6134 SG CYS C 76 9.985 55.210 71.377 1.00 45.29 S ATOM 6156 SG CYS C 79 11.466 57.312 73.701 1.00 49.13 S ATOM 8922 SG CYS D 64 33.913 33.272 101.480 1.00 41.13 S ATOM 8982 SG CYS D 73 35.748 30.836 103.486 1.00 48.02 S ATOM 8999 SG CYS D 76 36.622 30.979 99.813 1.00 41.32 S ATOM 9021 SG CYS D 79 37.641 33.903 101.830 1.00 45.98 S ATOM 11645 SG CYS E 50 80.357 34.787 102.111 1.00 43.18 S ATOM 11714 SG CYS E 59 83.704 33.486 101.151 1.00 46.17 S ATOM 11734 SG CYS E 62 81.116 33.494 98.472 1.00 44.85 S ATOM 11755 SG CYS E 65 82.321 36.783 99.556 1.00 44.35 S Time building chain proxies: 4.93, per 1000 atoms: 0.24 Number of scatterers: 20894 At special positions: 0 Unit cell: (123.372, 123.372, 151.524, 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 60 15.00 Mg 3 11.99 O 4002 8.00 N 3745 7.00 C 12968 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: 1.93 Conformation dependent library (CDL) restraints added in 854.7 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 76 " pdb="ZN ZN C 701 " - pdb=" SG CYS C 73 " pdb="ZN ZN C 701 " - pdb=" SG CYS C 64 " pdb=" ZN D 701 " pdb="ZN ZN D 701 " - pdb=" SG CYS D 64 " 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 E 401 " 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 62 " pdb="ZN ZN E 401 " - pdb=" SG CYS E 50 " Number of angles added : 24 5028 Ramachandran restraints generated. 2514 Oldfield, 0 Emsley, 2514 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4756 Finding SS restraints... Secondary structure from input PDB file: 130 helices and 15 sheets defined 56.5% alpha, 15.3% beta 24 base pairs and 40 stacking pairs defined. Time for finding SS restraints: 2.58 Creating SS restraints... Processing helix chain 'A' and resid 5 through 16 removed outlier: 4.579A pdb=" N ARG A 10 " --> pdb=" O PRO A 6 " (cutoff:3.500A) removed outlier: 5.243A pdb=" N ALA A 11 " --> pdb=" O GLU A 7 " (cutoff:3.500A) Processing helix chain 'A' and resid 27 through 45 Processing helix chain 'A' and resid 60 through 70 removed outlier: 3.627A pdb=" N ILE A 64 " --> pdb=" O ASP A 60 " (cutoff:3.500A) Processing helix chain 'A' and resid 90 through 103 removed outlier: 3.554A pdb=" N GLY A 102 " --> pdb=" O LEU A 98 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N LEU A 103 " --> pdb=" O THR A 99 " (cutoff:3.500A) Processing helix chain 'A' and resid 118 through 123 Processing helix chain 'A' and resid 124 through 130 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 Processing helix chain 'A' and resid 213 through 224 removed outlier: 3.527A pdb=" N TRP A 217 " --> pdb=" O THR A 213 " (cutoff:3.500A) Processing helix chain 'A' and resid 225 through 240 Processing helix chain 'A' and resid 242 through 265 removed outlier: 3.820A pdb=" N LEU A 246 " --> pdb=" O GLU A 242 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N GLU A 253 " --> pdb=" O THR A 249 " (cutoff:3.500A) removed outlier: 4.156A 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 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 337 through 343 removed outlier: 3.627A pdb=" N ILE A 341 " --> pdb=" O ALA A 337 " (cutoff:3.500A) 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: 3.847A 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: 4.180A pdb=" N GLU B 145 " --> pdb=" O LYS B 141 " (cutoff:3.500A) Processing helix chain 'B' and resid 158 through 162 Processing helix chain 'B' and resid 163 through 169 removed outlier: 3.695A pdb=" N LEU B 167 " --> pdb=" O VAL B 164 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ARG B 169 " --> pdb=" O ILE B 166 " (cutoff:3.500A) Processing helix chain 'B' and resid 179 through 195 Processing helix chain 'B' and resid 199 through 211 removed outlier: 3.912A pdb=" N GLU B 211 " --> pdb=" O ALA B 207 " (cutoff:3.500A) Processing helix chain 'B' and resid 213 through 229 Processing helix chain 'B' and resid 233 through 245 Processing helix chain 'B' and resid 247 through 259 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: 3.777A 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 308 removed outlier: 3.853A pdb=" N ALA B 307 " --> pdb=" O ASN B 304 " (cutoff:3.500A) removed outlier: 5.395A pdb=" N ALA B 308 " --> pdb=" O ASP B 305 " (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 14 through 18 Processing helix chain 'C' and resid 21 through 35 Processing helix chain 'C' and resid 50 through 64 Processing helix chain 'C' and resid 76 through 85 Processing helix chain 'C' and resid 100 through 110 removed outlier: 4.176A 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: 4.687A pdb=" N LYS C 141 " --> pdb=" O ASN C 137 " (cutoff:3.500A) removed outlier: 4.769A pdb=" N THR C 142 " --> pdb=" O ALA C 138 " (cutoff:3.500A) Processing helix chain 'C' and resid 158 through 162 Processing helix chain 'C' and resid 163 through 170 removed outlier: 3.595A 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: 4.081A pdb=" N GLU C 211 " --> pdb=" O ALA C 207 " (cutoff:3.500A) Processing helix chain 'C' and resid 213 through 228 Processing helix chain 'C' and resid 233 through 242 Processing helix chain 'C' and resid 245 through 258 removed outlier: 3.507A pdb=" N ALA C 249 " --> pdb=" O ASP C 245 " (cutoff:3.500A) Processing helix chain 'C' and resid 260 through 274 removed outlier: 3.514A pdb=" N ARG C 274 " --> pdb=" O GLU C 270 " (cutoff:3.500A) Processing helix chain 'C' and resid 277 through 298 Processing helix chain 'C' and resid 299 through 302 removed outlier: 4.260A pdb=" N LEU C 302 " --> pdb=" O PRO C 299 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 299 through 302' 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 14 through 18 Processing helix chain 'D' and resid 21 through 35 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: 3.580A pdb=" N ARG D 169 " --> pdb=" O THR D 165 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N CYS D 170 " --> pdb=" O ILE D 166 " (cutoff:3.500A) Processing helix chain 'D' and resid 179 through 194 Processing helix chain 'D' and resid 199 through 211 removed outlier: 3.823A 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 Processing helix chain 'D' and resid 260 through 275 Processing helix chain 'D' and resid 277 through 298 Processing helix chain 'D' and resid 299 through 302 removed outlier: 3.607A 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: 3.655A pdb=" N ALA D 307 " --> pdb=" O ASN D 304 " (cutoff:3.500A) Processing helix chain 'D' and resid 309 through 320 Processing helix chain 'D' and resid 321 through 339 Processing helix chain 'D' and resid 340 through 342 No H-bonds generated for 'chain 'D' and resid 340 through 342' Processing helix chain 'D' and resid 344 through 357 Processing helix chain 'D' and resid 358 through 360 No H-bonds generated for 'chain 'D' and resid 358 through 360' Processing helix chain 'E' and resid 6 through 20 removed outlier: 4.599A pdb=" N ASP E 10 " --> pdb=" O TRP E 6 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N SER E 17 " --> pdb=" O LYS E 13 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N TYR E 18 " --> pdb=" O LEU E 14 " (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: 3.551A 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 127 Processing helix chain 'E' and resid 128 through 134 Processing helix chain 'E' and resid 147 through 151 Processing helix chain 'E' and resid 152 through 159 removed outlier: 3.720A pdb=" N CYS E 159 " --> pdb=" O LEU E 155 " (cutoff:3.500A) Processing helix chain 'E' and resid 168 through 178 removed outlier: 3.586A pdb=" N ARG E 178 " --> pdb=" O THR E 174 " (cutoff:3.500A) Processing helix chain 'E' and resid 183 through 194 Processing helix chain 'E' and resid 197 through 206 removed outlier: 3.578A 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 231 Processing helix chain 'E' and resid 232 through 237 Processing helix chain 'E' and resid 240 through 260 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 323 Processing helix chain 'F' and resid 7 through 18 removed outlier: 4.571A 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 27 through 30 Processing helix chain 'F' and resid 72 through 81 Processing helix chain 'F' and resid 112 through 116 Processing helix chain 'F' and resid 131 through 144 removed outlier: 4.772A pdb=" N PHE F 144 " --> pdb=" O GLU F 140 " (cutoff:3.500A) Processing helix chain 'F' and resid 152 through 157 removed outlier: 3.667A 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 243 through 248 removed outlier: 4.191A pdb=" N VAL F 247 " --> pdb=" O ASP F 243 " (cutoff:3.500A) Processing helix chain 'F' and resid 259 through 273 removed outlier: 3.810A pdb=" N LEU F 273 " --> pdb=" O ARG F 269 " (cutoff:3.500A) Processing helix chain 'F' and resid 321 through 332 Processing helix chain 'G' and resid 7 through 18 removed outlier: 4.517A pdb=" N LYS G 12 " --> pdb=" O GLU G 8 " (cutoff:3.500A) Proline residue: G 13 - end of helix Processing helix chain 'G' and resid 28 through 30 No H-bonds generated for 'chain 'G' and resid 28 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 Processing helix chain 'G' and resid 260 through 271 Processing helix chain 'G' and resid 321 through 332 removed outlier: 3.625A 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: 3.508A 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: 6.468A pdb=" N GLU A 49 " --> pdb=" O THR A 79 " (cutoff:3.500A) removed outlier: 7.787A pdb=" N LEU A 81 " --> pdb=" O GLU A 49 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N HIS A 51 " --> pdb=" O LEU A 81 " (cutoff:3.500A) removed outlier: 7.878A pdb=" N LEU A 83 " --> pdb=" O HIS A 51 " (cutoff:3.500A) removed outlier: 7.113A pdb=" N PHE A 53 " --> pdb=" O LEU A 83 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 161 through 162 removed outlier: 6.451A 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: 6.435A pdb=" N ILE B 91 " --> pdb=" O LEU B 124 " (cutoff:3.500A) removed outlier: 7.363A pdb=" N ASP B 126 " --> pdb=" O ILE B 91 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N ILE B 93 " --> pdb=" O ASP B 126 " (cutoff:3.500A) removed outlier: 6.135A pdb=" N LYS B 121 " --> pdb=" O LYS B 151 " (cutoff:3.500A) removed outlier: 7.479A pdb=" N LEU B 153 " --> pdb=" O LYS B 121 " (cutoff:3.500A) removed outlier: 6.005A pdb=" N TYR B 123 " --> pdb=" O LEU B 153 " (cutoff:3.500A) removed outlier: 7.191A pdb=" N ALA B 155 " --> pdb=" O TYR B 123 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N ILE B 125 " --> pdb=" O ALA B 155 " (cutoff:3.500A) removed outlier: 8.111A pdb=" N PHE B 173 " --> pdb=" O ALA B 40 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N LEU B 42 " --> pdb=" O PHE B 173 " (cutoff:3.500A) removed outlier: 7.225A pdb=" N LEU B 175 " --> pdb=" O LEU B 42 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N SER B 44 " --> pdb=" O LEU B 175 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 197 through 198 removed outlier: 6.519A 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: 6.175A pdb=" N LYS C 121 " --> pdb=" O LYS C 151 " (cutoff:3.500A) removed outlier: 7.332A pdb=" N LEU C 153 " --> pdb=" O LYS C 121 " (cutoff:3.500A) removed outlier: 5.868A pdb=" N TYR C 123 " --> pdb=" O LEU C 153 " (cutoff:3.500A) removed outlier: 7.240A pdb=" N ALA C 155 " --> pdb=" O TYR C 123 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N ILE C 125 " --> pdb=" O ALA C 155 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 90 through 94 removed outlier: 6.399A pdb=" N ILE D 91 " --> pdb=" O LEU D 124 " (cutoff:3.500A) removed outlier: 7.349A pdb=" N ASP D 126 " --> pdb=" O ILE D 91 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N ILE D 93 " --> pdb=" O ASP D 126 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N LYS D 121 " --> pdb=" O LYS D 151 " (cutoff:3.500A) removed outlier: 7.533A pdb=" N LEU D 153 " --> pdb=" O LYS D 121 " (cutoff:3.500A) removed outlier: 6.049A pdb=" N TYR D 123 " --> pdb=" O LEU D 153 " (cutoff:3.500A) removed outlier: 7.451A pdb=" N ALA D 155 " --> pdb=" O TYR D 123 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N ILE D 125 " --> pdb=" O ALA D 155 " (cutoff:3.500A) removed outlier: 7.126A pdb=" N ALA D 40 " --> pdb=" O LEU D 171 " (cutoff:3.500A) removed outlier: 7.766A pdb=" N PHE D 173 " --> pdb=" O ALA D 40 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N LEU D 42 " --> pdb=" O PHE D 173 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 76 through 79 removed outlier: 6.479A pdb=" N LYS E 110 " --> pdb=" O TRP E 140 " (cutoff:3.500A) removed outlier: 7.815A pdb=" N PHE E 142 " --> pdb=" O LYS E 110 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N VAL E 112 " --> pdb=" O PHE E 142 " (cutoff:3.500A) removed outlier: 8.004A pdb=" N ALA E 144 " --> pdb=" O VAL E 112 " (cutoff:3.500A) removed outlier: 7.141A pdb=" N VAL E 114 " --> pdb=" O ALA E 144 " (cutoff:3.500A) removed outlier: 6.164A pdb=" N LEU E 27 " --> pdb=" O LEU E 143 " (cutoff:3.500A) removed outlier: 7.498A pdb=" N THR E 145 " --> pdb=" O LEU E 27 " (cutoff:3.500A) removed outlier: 5.681A 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: 3.546A pdb=" N GLU F 93 " --> pdb=" O ARG F 96 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N ASN G 295 " --> pdb=" O GLY G 280 " (cutoff:3.500A) removed outlier: 5.935A pdb=" N GLY G 280 " --> pdb=" O ASN G 295 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'F' and resid 66 through 71 removed outlier: 6.360A pdb=" N ASN F 32 " --> pdb=" O THR F 47 " (cutoff:3.500A) removed outlier: 5.192A 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: 4.487A pdb=" N ASP F 351 " --> pdb=" O ALA F 357 " (cutoff:3.500A) removed outlier: 7.331A pdb=" N ALA F 357 " --> pdb=" O ASP F 351 " (cutoff:3.500A) removed outlier: 16.026A 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: 15.053A pdb=" N VAL F 170 " --> pdb=" O PRO F 183 " (cutoff:3.500A) removed outlier: 13.989A pdb=" N GLY F 185 " --> pdb=" O ARG F 168 " (cutoff:3.500A) removed outlier: 13.176A pdb=" N ARG F 168 " --> pdb=" O GLY F 185 " (cutoff:3.500A) removed outlier: 8.769A pdb=" N SER F 187 " --> pdb=" O GLU F 166 " (cutoff:3.500A) removed outlier: 8.577A pdb=" N GLU F 166 " --> pdb=" O SER F 187 " (cutoff:3.500A) removed outlier: 4.777A 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 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: 3.648A pdb=" N GLY G 66 " --> pdb=" O VAL G 37 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N ASN G 32 " --> pdb=" O THR G 47 " (cutoff:3.500A) removed outlier: 5.277A 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: 4.653A pdb=" N ASP G 351 " --> pdb=" O ALA G 357 " (cutoff:3.500A) removed outlier: 7.289A pdb=" N ALA G 357 " --> pdb=" O ASP G 351 " (cutoff:3.500A) removed outlier: 5.221A pdb=" N GLU G 165 " --> pdb=" O ILE G 184 " (cutoff:3.500A) removed outlier: 9.078A pdb=" N GLN G 186 " --> pdb=" O GLU G 163 " (cutoff:3.500A) removed outlier: 7.661A pdb=" N GLU G 163 " --> pdb=" O GLN G 186 " (cutoff:3.500A) removed outlier: 9.352A pdb=" N LEU G 188 " --> pdb=" O GLU G 161 " (cutoff:3.500A) removed outlier: 10.636A pdb=" N GLU G 161 " --> pdb=" O LEU G 188 " (cutoff:3.500A) removed outlier: 13.408A pdb=" N SER G 190 " --> pdb=" O LEU G 159 " (cutoff:3.500A) removed outlier: 14.069A pdb=" N LEU G 159 " --> pdb=" O SER G 190 " (cutoff:3.500A) removed outlier: 13.342A pdb=" N SER G 192 " --> pdb=" O GLY G 157 " (cutoff:3.500A) removed outlier: 12.949A pdb=" N GLY G 157 " --> pdb=" O SER G 192 " (cutoff:3.500A) 1123 hydrogen bonds defined for protein. 3192 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 62 hydrogen bonds 124 hydrogen bond angles 0 basepair planarities 24 basepair parallelities 40 stacking parallelities Total time for adding SS restraints: 4.24 Time building geometry restraints manager: 2.48 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.36: 7142 1.36 - 1.51: 5663 1.51 - 1.65: 8382 1.65 - 1.80: 135 1.80 - 1.95: 51 Bond restraints: 21373 Sorted by residual: bond pdb=" O3B AGS C 702 " pdb=" PB AGS C 702 " ideal model delta sigma weight residual 1.673 1.588 0.085 2.00e-02 2.50e+03 1.80e+01 bond pdb=" O3B AGS D 702 " pdb=" PB AGS D 702 " ideal model delta sigma weight residual 1.673 1.589 0.084 2.00e-02 2.50e+03 1.76e+01 bond pdb=" O3B AGS B 702 " pdb=" PB AGS B 702 " ideal model delta sigma weight residual 1.673 1.592 0.081 2.00e-02 2.50e+03 1.66e+01 bond pdb=" O3A AGS B 702 " pdb=" PA AGS B 702 " ideal model delta sigma weight residual 1.664 1.584 0.080 2.00e-02 2.50e+03 1.59e+01 bond pdb=" O3A AGS C 702 " pdb=" PA AGS C 702 " ideal model delta sigma weight residual 1.664 1.589 0.075 2.00e-02 2.50e+03 1.40e+01 ... (remaining 21368 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.99: 28655 1.99 - 3.99: 498 3.99 - 5.98: 55 5.98 - 7.98: 10 7.98 - 9.97: 12 Bond angle restraints: 29230 Sorted by residual: angle pdb=" N3 DT I 8 " pdb=" C4 DT I 8 " pdb=" O4 DT I 8 " ideal model delta sigma weight residual 119.90 122.60 -2.70 6.00e-01 2.78e+00 2.02e+01 angle pdb=" N3 DT I 14 " pdb=" C4 DT I 14 " pdb=" O4 DT I 14 " ideal model delta sigma weight residual 119.90 122.50 -2.60 6.00e-01 2.78e+00 1.88e+01 angle pdb=" N3 DT H 25 " pdb=" C4 DT H 25 " pdb=" O4 DT H 25 " ideal model delta sigma weight residual 119.90 122.48 -2.58 6.00e-01 2.78e+00 1.85e+01 angle pdb=" N3 DT H 27 " pdb=" C4 DT H 27 " pdb=" O4 DT H 27 " ideal model delta sigma weight residual 119.90 122.46 -2.56 6.00e-01 2.78e+00 1.82e+01 angle pdb=" N3 DT H 19 " pdb=" C4 DT H 19 " pdb=" O4 DT H 19 " ideal model delta sigma weight residual 119.90 122.42 -2.52 6.00e-01 2.78e+00 1.77e+01 ... (remaining 29225 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.99: 11560 17.99 - 35.98: 987 35.98 - 53.97: 299 53.97 - 71.95: 92 71.95 - 89.94: 24 Dihedral angle restraints: 12962 sinusoidal: 5633 harmonic: 7329 Sorted by residual: dihedral pdb=" CA VAL B 19 " pdb=" C VAL B 19 " pdb=" N GLY B 20 " pdb=" CA GLY B 20 " ideal model delta harmonic sigma weight residual 180.00 158.02 21.98 0 5.00e+00 4.00e-02 1.93e+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 180.00 158.49 21.51 0 5.00e+00 4.00e-02 1.85e+01 dihedral pdb=" CA ALA G 114 " pdb=" C ALA G 114 " pdb=" N ASP G 115 " pdb=" CA ASP G 115 " ideal model delta harmonic sigma weight residual 180.00 161.62 18.38 0 5.00e+00 4.00e-02 1.35e+01 ... (remaining 12959 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.063: 2961 0.063 - 0.126: 391 0.126 - 0.189: 12 0.189 - 0.252: 0 0.252 - 0.314: 3 Chirality restraints: 3367 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 -2.68 0.31 2.00e-01 2.50e+01 2.47e+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 -2.68 0.31 2.00e-01 2.50e+01 2.46e+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 -2.68 0.31 2.00e-01 2.50e+01 2.40e+00 ... (remaining 3364 not shown) Planarity restraints: 3618 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG C 47 " -0.143 9.50e-02 1.11e+02 6.46e-02 3.22e+00 pdb=" NE ARG C 47 " 0.013 2.00e-02 2.50e+03 pdb=" CZ ARG C 47 " -0.013 2.00e-02 2.50e+03 pdb=" NH1 ARG C 47 " 0.006 2.00e-02 2.50e+03 pdb=" NH2 ARG C 47 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE G 241 " 0.028 5.00e-02 4.00e+02 4.19e-02 2.81e+00 pdb=" N PRO G 242 " -0.072 5.00e-02 4.00e+02 pdb=" CA PRO G 242 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO G 242 " 0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU G 248 " 0.026 5.00e-02 4.00e+02 3.94e-02 2.49e+00 pdb=" N PRO G 249 " -0.068 5.00e-02 4.00e+02 pdb=" CA PRO G 249 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO G 249 " 0.022 5.00e-02 4.00e+02 ... (remaining 3615 not shown) Histogram of nonbonded interaction distances: 1.94 - 2.53: 9 2.53 - 3.13: 15113 3.13 - 3.72: 32677 3.72 - 4.31: 46549 4.31 - 4.90: 77893 Nonbonded interactions: 172241 Sorted by model distance: nonbonded pdb=" O2G AGS B 702 " pdb="MG MG B 703 " model vdw 1.943 2.170 nonbonded pdb=" OG1 THR C 52 " pdb="MG MG C 703 " model vdw 1.984 2.170 nonbonded pdb=" OG1 THR B 52 " pdb="MG MG B 703 " model vdw 2.010 2.170 nonbonded pdb=" OG1 THR D 52 " pdb="MG MG D 703 " model vdw 2.024 2.170 nonbonded pdb=" O2G AGS C 702 " pdb="MG MG C 703 " model vdw 2.024 2.170 ... (remaining 172236 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: 3.000 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.320 Check model and map are aligned: 0.060 Set scattering table: 0.030 Process input model: 24.770 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:6.450 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.140 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8882 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 : 0.004 0.088 21389 Z= 0.247 Angle : 0.667 12.804 29254 Z= 0.365 Chirality : 0.042 0.314 3367 Planarity : 0.005 0.065 3618 Dihedral : 15.919 89.942 8206 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 0.00 % Allowed : 0.28 % Favored : 99.72 % 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: 1.67 (0.17), residues: 2514 helix: 1.65 (0.15), residues: 1280 sheet: 1.51 (0.23), residues: 434 loop : 0.10 (0.22), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG C 47 TYR 0.012 0.001 TYR G 284 PHE 0.021 0.002 PHE D 136 TRP 0.016 0.002 TRP D 10 HIS 0.007 0.001 HIS B 23 Details of bonding type rmsd/Z covalent geometry : bond 0.00448 / 0.25 (21373) covalent geometry : angle 0.64573 / 0.36 (29230) hydrogen bonds : bond 0.13638 / 9.29 ( 1185) hydrogen bonds : angle 4.88551 / 3.57 ( 3316) metal coordination : bond 0.00550 / 0.24 ( 16) metal coordination : angle 5.88428 / 3.63 ( 24) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5028 Ramachandran restraints generated. 2514 Oldfield, 0 Emsley, 2514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5028 Ramachandran restraints generated. 2514 Oldfield, 0 Emsley, 2514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 421 residues out of total 2114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 421 time to evaluate : 0.684 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 161 GLU cc_start: 0.8642 (mt-10) cc_final: 0.8232 (mt-10) REVERT: F 162 THR cc_start: 0.8611 (m) cc_final: 0.8404 (p) REVERT: F 167 LEU cc_start: 0.9106 (tp) cc_final: 0.8904 (tp) REVERT: G 204 MET cc_start: 0.9037 (mmm) cc_final: 0.8609 (mmm) outliers start: 0 outliers final: 0 residues processed: 421 average time/residue: 0.8710 time to fit residues: 401.4420 Evaluate side-chains 328 residues out of total 2114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 328 time to evaluate : 0.647 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 253 random chunks: chunk 216 optimal weight: 4.9990 chunk 98 optimal weight: 1.9990 chunk 194 optimal weight: 2.9990 chunk 227 optimal weight: 0.9980 chunk 107 optimal weight: 0.7980 chunk 10 optimal weight: 0.0370 chunk 66 optimal weight: 1.9990 chunk 247 optimal weight: 8.9990 chunk 130 optimal weight: 0.9980 chunk 124 optimal weight: 0.6980 chunk 103 optimal weight: 0.6980 overall best weight: 0.6458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 136 GLN A 140 GLN A 263 GLN A 266 HIS B 30 ASN B 110 ASN B 186 GLN B 223 GLN C 186 GLN C 269 ASN D 13 GLN D 23 HIS D 110 ASN D 160 GLN D 186 GLN E 56 HIS E 206 GLN E 299 GLN F 63 HIS F 329 ASN G 16 GLN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2539 r_free = 0.2539 target = 0.050783 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2301 r_free = 0.2301 target = 0.041738 restraints weight = 38124.044| |-----------------------------------------------------------------------------| r_work (start): 0.2299 rms_B_bonded: 1.08 r_work: 0.2206 rms_B_bonded: 1.51 restraints_weight: 0.5000 r_work: 0.2115 rms_B_bonded: 2.59 restraints_weight: 0.2500 r_work (final): 0.2115 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8907 moved from start: 0.1012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 21389 Z= 0.142 Angle : 0.595 11.381 29254 Z= 0.303 Chirality : 0.039 0.183 3367 Planarity : 0.005 0.048 3618 Dihedral : 14.546 61.812 3412 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 2.46 % Allowed : 9.70 % Favored : 87.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.84 (0.17), residues: 2514 helix: 1.81 (0.15), residues: 1303 sheet: 1.37 (0.24), residues: 437 loop : 0.22 (0.23), residues: 774 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 263 TYR 0.015 0.001 TYR F 284 PHE 0.018 0.001 PHE G 230 TRP 0.017 0.001 TRP C 10 HIS 0.011 0.001 HIS E 56 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.14 (21373) covalent geometry : angle 0.57390 / 0.30 (29230) hydrogen bonds : bond 0.04492 / 3.00 ( 1185) hydrogen bonds : angle 4.06440 / 2.99 ( 3316) metal coordination : bond 0.00362 / 0.15 ( 16) metal coordination : angle 5.57060 / 3.40 ( 24) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5028 Ramachandran restraints generated. 2514 Oldfield, 0 Emsley, 2514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5028 Ramachandran restraints generated. 2514 Oldfield, 0 Emsley, 2514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 390 residues out of total 2114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 338 time to evaluate : 0.757 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 77 ARG cc_start: 0.8815 (OUTLIER) cc_final: 0.7999 (ttp80) REVERT: A 161 GLU cc_start: 0.8568 (mt-10) cc_final: 0.8365 (mt-10) REVERT: B 136 PHE cc_start: 0.8305 (OUTLIER) cc_final: 0.7742 (t80) REVERT: B 214 LEU cc_start: 0.9149 (OUTLIER) cc_final: 0.8812 (tt) REVERT: B 247 ASP cc_start: 0.8221 (p0) cc_final: 0.7861 (p0) REVERT: C 306 MET cc_start: 0.9050 (OUTLIER) cc_final: 0.8807 (mtm) REVERT: D 277 GLU cc_start: 0.8629 (OUTLIER) cc_final: 0.8322 (tt0) REVERT: F 173 ASP cc_start: 0.8504 (m-30) cc_final: 0.8141 (m-30) REVERT: F 351 ASP cc_start: 0.7898 (t70) cc_final: 0.7587 (t0) REVERT: G 95 GLU cc_start: 0.7529 (mm-30) cc_final: 0.7309 (mm-30) REVERT: G 149 GLN cc_start: 0.8129 (OUTLIER) cc_final: 0.7918 (mt0) REVERT: G 204 MET cc_start: 0.8989 (mmm) cc_final: 0.8568 (mmm) REVERT: G 289 GLN cc_start: 0.8860 (OUTLIER) cc_final: 0.8656 (tt0) outliers start: 52 outliers final: 11 residues processed: 354 average time/residue: 0.8218 time to fit residues: 318.2750 Evaluate side-chains 334 residues out of total 2114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 316 time to evaluate : 0.776 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 ARG Chi-restraints excluded: chain A residue 136 GLN Chi-restraints excluded: chain B residue 136 PHE Chi-restraints excluded: chain B residue 214 LEU Chi-restraints excluded: chain C residue 157 THR Chi-restraints excluded: chain C residue 306 MET Chi-restraints excluded: chain D residue 86 ARG Chi-restraints excluded: chain D residue 93 ILE Chi-restraints excluded: chain D residue 277 GLU Chi-restraints excluded: chain E residue 83 LYS Chi-restraints excluded: chain E residue 276 GLU Chi-restraints excluded: chain F residue 84 GLU Chi-restraints excluded: chain F residue 262 LEU Chi-restraints excluded: chain F residue 293 THR Chi-restraints excluded: chain G residue 149 GLN Chi-restraints excluded: chain G residue 261 ASP Chi-restraints excluded: chain G residue 289 GLN Chi-restraints excluded: chain J residue 28 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 253 random chunks: chunk 77 optimal weight: 0.8980 chunk 210 optimal weight: 0.9980 chunk 163 optimal weight: 1.9990 chunk 40 optimal weight: 5.9990 chunk 117 optimal weight: 2.9990 chunk 63 optimal weight: 1.9990 chunk 164 optimal weight: 1.9990 chunk 23 optimal weight: 3.9990 chunk 218 optimal weight: 2.9990 chunk 173 optimal weight: 2.9990 chunk 91 optimal weight: 2.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 40 GLN A 157 GLN A 263 GLN B 110 ASN C 137 ASN C 269 ASN D 110 ASN D 160 GLN E 56 HIS E 86 ASN F 61 GLN G 16 GLN G 295 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2471 r_free = 0.2471 target = 0.048159 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2225 r_free = 0.2225 target = 0.039129 restraints weight = 38317.173| |-----------------------------------------------------------------------------| r_work (start): 0.2223 rms_B_bonded: 1.07 r_work: 0.2128 rms_B_bonded: 1.50 restraints_weight: 0.5000 r_work: 0.2034 rms_B_bonded: 2.55 restraints_weight: 0.2500 r_work (final): 0.2034 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8951 moved from start: 0.1252 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.110 21389 Z= 0.235 Angle : 0.675 13.426 29254 Z= 0.341 Chirality : 0.042 0.159 3367 Planarity : 0.006 0.057 3618 Dihedral : 14.621 62.559 3412 Min Nonbonded Distance : 1.900 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 2.74 % Allowed : 11.26 % Favored : 86.00 % 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: 1.65 (0.17), residues: 2514 helix: 1.64 (0.15), residues: 1303 sheet: 1.52 (0.24), residues: 420 loop : 0.04 (0.22), residues: 791 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG F 205 TYR 0.016 0.002 TYR D 3 PHE 0.018 0.002 PHE D 136 TRP 0.017 0.002 TRP C 10 HIS 0.011 0.002 HIS E 56 Details of bonding type rmsd/Z covalent geometry : bond 0.00562 / 0.23 (21373) covalent geometry : angle 0.65334 / 0.34 (29230) hydrogen bonds : bond 0.05309 / 3.58 ( 1185) hydrogen bonds : angle 4.05208 / 2.97 ( 3316) metal coordination : bond 0.00613 / 0.28 ( 16) metal coordination : angle 5.96141 / 3.74 ( 24) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5028 Ramachandran restraints generated. 2514 Oldfield, 0 Emsley, 2514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5028 Ramachandran restraints generated. 2514 Oldfield, 0 Emsley, 2514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 377 residues out of total 2114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 319 time to evaluate : 0.804 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 77 ARG cc_start: 0.8944 (OUTLIER) cc_final: 0.7626 (ttp80) REVERT: A 318 GLN cc_start: 0.8935 (OUTLIER) cc_final: 0.8454 (tm-30) REVERT: B 124 LEU cc_start: 0.9110 (OUTLIER) cc_final: 0.8792 (tt) REVERT: B 214 LEU cc_start: 0.9210 (OUTLIER) cc_final: 0.8886 (tt) REVERT: B 247 ASP cc_start: 0.8350 (p0) cc_final: 0.8047 (p0) REVERT: D 277 GLU cc_start: 0.8753 (OUTLIER) cc_final: 0.8432 (tt0) REVERT: F 136 LYS cc_start: 0.8920 (OUTLIER) cc_final: 0.8587 (ttpp) REVERT: F 173 ASP cc_start: 0.8557 (m-30) cc_final: 0.8198 (m-30) REVERT: G 95 GLU cc_start: 0.7635 (mm-30) cc_final: 0.7397 (mm-30) REVERT: G 204 MET cc_start: 0.9018 (mmm) cc_final: 0.8611 (mmm) outliers start: 58 outliers final: 22 residues processed: 345 average time/residue: 0.8084 time to fit residues: 305.8013 Evaluate side-chains 339 residues out of total 2114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 311 time to evaluate : 0.823 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 77 ARG Chi-restraints excluded: chain A residue 136 GLN Chi-restraints excluded: chain A residue 318 GLN Chi-restraints excluded: chain B residue 124 LEU Chi-restraints excluded: chain B residue 214 LEU Chi-restraints excluded: chain B residue 235 GLN Chi-restraints excluded: chain B residue 311 LEU Chi-restraints excluded: chain C residue 101 VAL Chi-restraints excluded: chain C residue 157 THR Chi-restraints excluded: chain D residue 93 ILE Chi-restraints excluded: chain D residue 277 GLU Chi-restraints excluded: chain E residue 52 GLN Chi-restraints excluded: chain E residue 83 LYS Chi-restraints excluded: chain E residue 276 GLU Chi-restraints excluded: chain F residue 53 MET Chi-restraints excluded: chain F residue 136 LYS Chi-restraints excluded: chain F residue 262 LEU Chi-restraints excluded: chain F residue 293 THR Chi-restraints excluded: chain F residue 315 MET Chi-restraints excluded: chain F residue 339 MET Chi-restraints excluded: chain G residue 64 GLU Chi-restraints excluded: chain G residue 123 GLN Chi-restraints excluded: chain G residue 142 THR Chi-restraints excluded: chain G residue 261 ASP Chi-restraints excluded: chain G residue 334 GLU Chi-restraints excluded: chain G residue 338 MET Chi-restraints excluded: chain J residue 28 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 253 random chunks: chunk 138 optimal weight: 1.9990 chunk 25 optimal weight: 0.9990 chunk 75 optimal weight: 0.5980 chunk 26 optimal weight: 0.7980 chunk 144 optimal weight: 3.9990 chunk 128 optimal weight: 2.9990 chunk 220 optimal weight: 1.9990 chunk 250 optimal weight: 6.9990 chunk 181 optimal weight: 6.9990 chunk 157 optimal weight: 1.9990 chunk 156 optimal weight: 0.8980 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 136 GLN C 137 ASN C 182 GLN C 269 ASN D 110 ASN D 160 GLN E 56 HIS E 86 ASN G 16 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2491 r_free = 0.2491 target = 0.048904 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2248 r_free = 0.2248 target = 0.039854 restraints weight = 38014.043| |-----------------------------------------------------------------------------| r_work (start): 0.2246 rms_B_bonded: 1.07 r_work: 0.2152 rms_B_bonded: 1.49 restraints_weight: 0.5000 r_work: 0.2060 rms_B_bonded: 2.55 restraints_weight: 0.2500 r_work (final): 0.2060 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8938 moved from start: 0.1330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 21389 Z= 0.175 Angle : 0.602 10.383 29254 Z= 0.305 Chirality : 0.040 0.168 3367 Planarity : 0.005 0.057 3618 Dihedral : 14.639 61.834 3412 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 2.51 % Allowed : 12.77 % Favored : 84.72 % 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: 1.74 (0.17), residues: 2514 helix: 1.73 (0.15), residues: 1305 sheet: 1.43 (0.24), residues: 425 loop : 0.13 (0.23), residues: 784 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG F 205 TYR 0.018 0.002 TYR G 284 PHE 0.013 0.001 PHE F 3 TRP 0.018 0.002 TRP C 10 HIS 0.011 0.001 HIS E 56 Details of bonding type rmsd/Z covalent geometry : bond 0.00409 / 0.17 (21373) covalent geometry : angle 0.58172 / 0.30 (29230) hydrogen bonds : bond 0.04537 / 3.05 ( 1185) hydrogen bonds : angle 3.92335 / 2.88 ( 3316) metal coordination : bond 0.00403 / 0.18 ( 16) metal coordination : angle 5.48425 / 3.45 ( 24) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5028 Ramachandran restraints generated. 2514 Oldfield, 0 Emsley, 2514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5028 Ramachandran restraints generated. 2514 Oldfield, 0 Emsley, 2514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 367 residues out of total 2114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 314 time to evaluate : 0.791 Fit side-chains revert: symmetry clash REVERT: A 77 ARG cc_start: 0.8881 (OUTLIER) cc_final: 0.8225 (ttp-170) REVERT: A 136 GLN cc_start: 0.9189 (OUTLIER) cc_final: 0.8989 (tt0) REVERT: A 259 ASN cc_start: 0.8387 (m-40) cc_final: 0.7948 (m110) REVERT: A 318 GLN cc_start: 0.8905 (OUTLIER) cc_final: 0.8447 (tm-30) REVERT: B 124 LEU cc_start: 0.9109 (OUTLIER) cc_final: 0.8797 (tt) REVERT: B 136 PHE cc_start: 0.8707 (OUTLIER) cc_final: 0.8322 (t80) REVERT: B 214 LEU cc_start: 0.9170 (OUTLIER) cc_final: 0.8842 (tt) REVERT: B 247 ASP cc_start: 0.8325 (p0) cc_final: 0.8011 (p0) REVERT: B 362 ARG cc_start: 0.9106 (OUTLIER) cc_final: 0.7149 (mtt180) REVERT: D 277 GLU cc_start: 0.8689 (OUTLIER) cc_final: 0.8375 (tt0) REVERT: F 56 ARG cc_start: 0.8713 (OUTLIER) cc_final: 0.8143 (mtp180) REVERT: F 136 LYS cc_start: 0.8854 (OUTLIER) cc_final: 0.8649 (tttm) REVERT: F 173 ASP cc_start: 0.8494 (m-30) cc_final: 0.8168 (m-30) REVERT: F 182 MET cc_start: 0.8856 (OUTLIER) cc_final: 0.8569 (mtm) REVERT: F 351 ASP cc_start: 0.7922 (t70) cc_final: 0.7649 (t0) REVERT: G 11 LEU cc_start: 0.9200 (OUTLIER) cc_final: 0.8925 (mp) REVERT: G 95 GLU cc_start: 0.7632 (mm-30) cc_final: 0.7414 (mm-30) REVERT: G 204 MET cc_start: 0.9016 (mmm) cc_final: 0.8628 (mmm) outliers start: 53 outliers final: 22 residues processed: 338 average time/residue: 0.8572 time to fit residues: 318.0589 Evaluate side-chains 339 residues out of total 2114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 305 time to evaluate : 0.778 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 LEU Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 77 ARG Chi-restraints excluded: chain A residue 136 GLN Chi-restraints excluded: chain A residue 318 GLN Chi-restraints excluded: chain B residue 124 LEU Chi-restraints excluded: chain B residue 136 PHE Chi-restraints excluded: chain B residue 214 LEU Chi-restraints excluded: chain B residue 235 GLN Chi-restraints excluded: chain B residue 337 LYS Chi-restraints excluded: chain B residue 362 ARG Chi-restraints excluded: chain C residue 101 VAL Chi-restraints excluded: chain C residue 157 THR Chi-restraints excluded: chain D residue 93 ILE Chi-restraints excluded: chain D residue 277 GLU Chi-restraints excluded: chain E residue 52 GLN Chi-restraints excluded: chain E residue 83 LYS Chi-restraints excluded: chain E residue 276 GLU Chi-restraints excluded: chain F residue 52 GLU Chi-restraints excluded: chain F residue 53 MET Chi-restraints excluded: chain F residue 56 ARG Chi-restraints excluded: chain F residue 84 GLU Chi-restraints excluded: chain F residue 136 LYS Chi-restraints excluded: chain F residue 182 MET Chi-restraints excluded: chain F residue 262 LEU Chi-restraints excluded: chain F residue 293 THR Chi-restraints excluded: chain F residue 339 MET Chi-restraints excluded: chain G residue 11 LEU Chi-restraints excluded: chain G residue 64 GLU Chi-restraints excluded: chain G residue 123 GLN Chi-restraints excluded: chain G residue 142 THR Chi-restraints excluded: chain G residue 261 ASP Chi-restraints excluded: chain G residue 334 GLU Chi-restraints excluded: chain J residue 28 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 253 random chunks: chunk 160 optimal weight: 0.9980 chunk 166 optimal weight: 1.9990 chunk 86 optimal weight: 0.5980 chunk 147 optimal weight: 0.6980 chunk 40 optimal weight: 3.9990 chunk 105 optimal weight: 1.9990 chunk 82 optimal weight: 0.6980 chunk 196 optimal weight: 2.9990 chunk 62 optimal weight: 1.9990 chunk 48 optimal weight: 2.9990 chunk 50 optimal weight: 0.0970 overall best weight: 0.6178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 137 ASN C 269 ASN D 110 ASN D 160 GLN E 56 HIS E 86 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2515 r_free = 0.2515 target = 0.049828 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2274 r_free = 0.2274 target = 0.040759 restraints weight = 37881.695| |-----------------------------------------------------------------------------| r_work (start): 0.2273 rms_B_bonded: 1.07 r_work: 0.2180 rms_B_bonded: 1.50 restraints_weight: 0.5000 r_work: 0.2089 rms_B_bonded: 2.57 restraints_weight: 0.2500 r_work (final): 0.2089 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8923 moved from start: 0.1409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 21389 Z= 0.132 Angle : 0.560 9.144 29254 Z= 0.285 Chirality : 0.038 0.150 3367 Planarity : 0.005 0.053 3618 Dihedral : 14.589 61.021 3412 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 2.65 % Allowed : 13.43 % Favored : 83.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.94 (0.17), residues: 2514 helix: 1.98 (0.15), residues: 1290 sheet: 1.40 (0.24), residues: 427 loop : 0.16 (0.22), residues: 797 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG F 205 TYR 0.011 0.001 TYR D 3 PHE 0.023 0.001 PHE G 230 TRP 0.018 0.001 TRP C 10 HIS 0.012 0.001 HIS E 56 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.13 (21373) covalent geometry : angle 0.54014 / 0.28 (29230) hydrogen bonds : bond 0.04078 / 2.74 ( 1185) hydrogen bonds : angle 3.83577 / 2.82 ( 3316) metal coordination : bond 0.00284 / 0.13 ( 16) metal coordination : angle 5.18260 / 3.26 ( 24) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5028 Ramachandran restraints generated. 2514 Oldfield, 0 Emsley, 2514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5028 Ramachandran restraints generated. 2514 Oldfield, 0 Emsley, 2514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 371 residues out of total 2114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 315 time to evaluate : 0.797 Fit side-chains revert: symmetry clash REVERT: A 77 ARG cc_start: 0.8844 (OUTLIER) cc_final: 0.8299 (ttp-170) REVERT: A 259 ASN cc_start: 0.8368 (m-40) cc_final: 0.7949 (m110) REVERT: A 275 LYS cc_start: 0.9005 (OUTLIER) cc_final: 0.8688 (ttpp) REVERT: A 318 GLN cc_start: 0.8897 (OUTLIER) cc_final: 0.8424 (tm-30) REVERT: B 124 LEU cc_start: 0.9086 (OUTLIER) cc_final: 0.8774 (tt) REVERT: B 136 PHE cc_start: 0.8723 (OUTLIER) cc_final: 0.8361 (t80) REVERT: B 214 LEU cc_start: 0.9135 (OUTLIER) cc_final: 0.8815 (tt) REVERT: B 247 ASP cc_start: 0.8273 (p0) cc_final: 0.7954 (p0) REVERT: B 362 ARG cc_start: 0.9081 (OUTLIER) cc_final: 0.7572 (mtm180) REVERT: C 263 ARG cc_start: 0.8347 (tpt-90) cc_final: 0.7971 (ttt-90) REVERT: D 86 ARG cc_start: 0.8869 (OUTLIER) cc_final: 0.7898 (ptm160) REVERT: D 277 GLU cc_start: 0.8649 (OUTLIER) cc_final: 0.8361 (tt0) REVERT: D 330 GLN cc_start: 0.8964 (OUTLIER) cc_final: 0.8561 (tm-30) REVERT: E 146 ARG cc_start: 0.8838 (OUTLIER) cc_final: 0.8397 (ptp-170) REVERT: F 6 GLU cc_start: 0.7922 (OUTLIER) cc_final: 0.6948 (tm-30) REVERT: F 121 ASP cc_start: 0.7606 (t0) cc_final: 0.7309 (t0) REVERT: F 173 ASP cc_start: 0.8395 (m-30) cc_final: 0.8077 (m-30) REVERT: F 182 MET cc_start: 0.8796 (OUTLIER) cc_final: 0.8444 (mtm) REVERT: G 11 LEU cc_start: 0.9151 (OUTLIER) cc_final: 0.8859 (mp) REVERT: G 95 GLU cc_start: 0.7612 (mm-30) cc_final: 0.7400 (mm-30) REVERT: G 204 MET cc_start: 0.9005 (mmm) cc_final: 0.8546 (mmm) outliers start: 56 outliers final: 16 residues processed: 342 average time/residue: 0.8473 time to fit residues: 318.5472 Evaluate side-chains 337 residues out of total 2114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 307 time to evaluate : 0.780 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 LEU Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 77 ARG Chi-restraints excluded: chain A residue 275 LYS Chi-restraints excluded: chain A residue 318 GLN Chi-restraints excluded: chain B residue 124 LEU Chi-restraints excluded: chain B residue 136 PHE Chi-restraints excluded: chain B residue 214 LEU Chi-restraints excluded: chain B residue 235 GLN Chi-restraints excluded: chain B residue 362 ARG Chi-restraints excluded: chain C residue 101 VAL Chi-restraints excluded: chain C residue 157 THR Chi-restraints excluded: chain D residue 2 SER Chi-restraints excluded: chain D residue 86 ARG Chi-restraints excluded: chain D residue 93 ILE Chi-restraints excluded: chain D residue 277 GLU Chi-restraints excluded: chain D residue 330 GLN Chi-restraints excluded: chain E residue 52 GLN Chi-restraints excluded: chain E residue 83 LYS Chi-restraints excluded: chain E residue 146 ARG Chi-restraints excluded: chain F residue 6 GLU Chi-restraints excluded: chain F residue 52 GLU Chi-restraints excluded: chain F residue 53 MET Chi-restraints excluded: chain F residue 182 MET Chi-restraints excluded: chain F residue 339 MET Chi-restraints excluded: chain G residue 11 LEU Chi-restraints excluded: chain G residue 64 GLU Chi-restraints excluded: chain G residue 142 THR Chi-restraints excluded: chain G residue 334 GLU Chi-restraints excluded: chain J residue 28 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 253 random chunks: chunk 249 optimal weight: 10.0000 chunk 128 optimal weight: 4.9990 chunk 15 optimal weight: 0.6980 chunk 220 optimal weight: 3.9990 chunk 165 optimal weight: 2.9990 chunk 170 optimal weight: 0.2980 chunk 158 optimal weight: 0.0770 chunk 234 optimal weight: 2.9990 chunk 87 optimal weight: 2.9990 chunk 145 optimal weight: 0.7980 chunk 51 optimal weight: 2.9990 overall best weight: 0.9740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 137 ASN C 269 ASN D 110 ASN D 160 GLN E 56 HIS E 86 ASN G 275 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2497 r_free = 0.2497 target = 0.049149 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2255 r_free = 0.2255 target = 0.040099 restraints weight = 37718.580| |-----------------------------------------------------------------------------| r_work (start): 0.2253 rms_B_bonded: 1.07 r_work: 0.2159 rms_B_bonded: 1.49 restraints_weight: 0.5000 r_work: 0.2067 rms_B_bonded: 2.55 restraints_weight: 0.2500 r_work (final): 0.2067 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8934 moved from start: 0.1454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 21389 Z= 0.166 Angle : 0.592 9.907 29254 Z= 0.300 Chirality : 0.039 0.159 3367 Planarity : 0.005 0.055 3618 Dihedral : 14.612 60.499 3412 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 2.70 % Allowed : 14.00 % Favored : 83.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.84 (0.17), residues: 2514 helix: 1.83 (0.15), residues: 1314 sheet: 1.45 (0.24), residues: 422 loop : 0.11 (0.23), residues: 778 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG D 208 TYR 0.013 0.001 TYR E 47 PHE 0.050 0.002 PHE G 230 TRP 0.015 0.002 TRP C 10 HIS 0.010 0.001 HIS E 56 Details of bonding type rmsd/Z covalent geometry : bond 0.00388 / 0.17 (21373) covalent geometry : angle 0.57258 / 0.30 (29230) hydrogen bonds : bond 0.04383 / 2.95 ( 1185) hydrogen bonds : angle 3.83755 / 2.81 ( 3316) metal coordination : bond 0.00337 / 0.15 ( 16) metal coordination : angle 5.24007 / 3.32 ( 24) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5028 Ramachandran restraints generated. 2514 Oldfield, 0 Emsley, 2514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5028 Ramachandran restraints generated. 2514 Oldfield, 0 Emsley, 2514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 373 residues out of total 2114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 316 time to evaluate : 0.823 Fit side-chains revert: symmetry clash REVERT: A 77 ARG cc_start: 0.8879 (OUTLIER) cc_final: 0.7907 (ttp80) REVERT: A 259 ASN cc_start: 0.8363 (m-40) cc_final: 0.7936 (m110) REVERT: A 275 LYS cc_start: 0.9000 (OUTLIER) cc_final: 0.8676 (ttpp) REVERT: A 318 GLN cc_start: 0.8895 (OUTLIER) cc_final: 0.8440 (tm-30) REVERT: B 124 LEU cc_start: 0.9096 (OUTLIER) cc_final: 0.8795 (tt) REVERT: B 136 PHE cc_start: 0.8772 (OUTLIER) cc_final: 0.8380 (t80) REVERT: B 158 ASP cc_start: 0.8712 (OUTLIER) cc_final: 0.8454 (m-30) REVERT: B 214 LEU cc_start: 0.9141 (OUTLIER) cc_final: 0.8815 (tt) REVERT: B 247 ASP cc_start: 0.8301 (p0) cc_final: 0.7996 (p0) REVERT: B 362 ARG cc_start: 0.9081 (OUTLIER) cc_final: 0.7127 (mtm180) REVERT: C 133 ARG cc_start: 0.9032 (OUTLIER) cc_final: 0.6979 (mmm160) REVERT: C 263 ARG cc_start: 0.8452 (tpt-90) cc_final: 0.8103 (ttt-90) REVERT: D 86 ARG cc_start: 0.8915 (OUTLIER) cc_final: 0.7810 (ptm160) REVERT: D 277 GLU cc_start: 0.8674 (OUTLIER) cc_final: 0.8384 (tt0) REVERT: D 330 GLN cc_start: 0.8970 (OUTLIER) cc_final: 0.8558 (tm-30) REVERT: E 99 LYS cc_start: 0.8944 (OUTLIER) cc_final: 0.8662 (mtpt) REVERT: E 146 ARG cc_start: 0.8851 (OUTLIER) cc_final: 0.8415 (ptp-170) REVERT: F 6 GLU cc_start: 0.7961 (OUTLIER) cc_final: 0.6915 (tm-30) REVERT: F 39 ASP cc_start: 0.8407 (p0) cc_final: 0.8201 (p0) REVERT: F 56 ARG cc_start: 0.8696 (OUTLIER) cc_final: 0.8138 (mtp180) REVERT: F 121 ASP cc_start: 0.7613 (t0) cc_final: 0.7318 (t0) REVERT: F 173 ASP cc_start: 0.8390 (m-30) cc_final: 0.8084 (m-30) REVERT: F 182 MET cc_start: 0.8848 (OUTLIER) cc_final: 0.8534 (mtm) REVERT: G 11 LEU cc_start: 0.9163 (OUTLIER) cc_final: 0.8831 (mp) REVERT: G 95 GLU cc_start: 0.7639 (mm-30) cc_final: 0.7428 (mm-30) REVERT: G 204 MET cc_start: 0.9011 (mmm) cc_final: 0.8547 (mmm) outliers start: 57 outliers final: 21 residues processed: 348 average time/residue: 0.8308 time to fit residues: 318.2460 Evaluate side-chains 341 residues out of total 2114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 302 time to evaluate : 0.817 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 LEU Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 77 ARG Chi-restraints excluded: chain A residue 94 ASN Chi-restraints excluded: chain A residue 275 LYS Chi-restraints excluded: chain A residue 318 GLN Chi-restraints excluded: chain B residue 124 LEU Chi-restraints excluded: chain B residue 136 PHE Chi-restraints excluded: chain B residue 158 ASP Chi-restraints excluded: chain B residue 214 LEU Chi-restraints excluded: chain B residue 235 GLN Chi-restraints excluded: chain B residue 362 ARG Chi-restraints excluded: chain C residue 101 VAL Chi-restraints excluded: chain C residue 133 ARG Chi-restraints excluded: chain C residue 157 THR Chi-restraints excluded: chain D residue 2 SER Chi-restraints excluded: chain D residue 86 ARG Chi-restraints excluded: chain D residue 93 ILE Chi-restraints excluded: chain D residue 277 GLU Chi-restraints excluded: chain D residue 330 GLN Chi-restraints excluded: chain E residue 52 GLN Chi-restraints excluded: chain E residue 83 LYS Chi-restraints excluded: chain E residue 99 LYS Chi-restraints excluded: chain E residue 119 LEU Chi-restraints excluded: chain E residue 146 ARG Chi-restraints excluded: chain F residue 6 GLU Chi-restraints excluded: chain F residue 52 GLU Chi-restraints excluded: chain F residue 53 MET Chi-restraints excluded: chain F residue 56 ARG Chi-restraints excluded: chain F residue 69 THR Chi-restraints excluded: chain F residue 84 GLU Chi-restraints excluded: chain F residue 182 MET Chi-restraints excluded: chain F residue 262 LEU Chi-restraints excluded: chain F residue 293 THR Chi-restraints excluded: chain F residue 339 MET Chi-restraints excluded: chain G residue 11 LEU Chi-restraints excluded: chain G residue 64 GLU Chi-restraints excluded: chain G residue 334 GLU Chi-restraints excluded: chain J residue 28 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 253 random chunks: chunk 218 optimal weight: 1.9990 chunk 25 optimal weight: 0.6980 chunk 103 optimal weight: 0.8980 chunk 176 optimal weight: 0.1980 chunk 4 optimal weight: 1.9990 chunk 87 optimal weight: 0.5980 chunk 203 optimal weight: 2.9990 chunk 172 optimal weight: 0.9980 chunk 220 optimal weight: 0.8980 chunk 182 optimal weight: 0.6980 chunk 1 optimal weight: 0.5980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 330 GLN C 137 ASN C 269 ASN D 21 GLN D 110 ASN D 160 GLN E 56 HIS E 86 ASN E 259 HIS ** G 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2522 r_free = 0.2522 target = 0.050143 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2281 r_free = 0.2281 target = 0.041034 restraints weight = 37933.716| |-----------------------------------------------------------------------------| r_work (start): 0.2280 rms_B_bonded: 1.08 r_work: 0.2187 rms_B_bonded: 1.51 restraints_weight: 0.5000 r_work: 0.2096 rms_B_bonded: 2.58 restraints_weight: 0.2500 r_work (final): 0.2096 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8917 moved from start: 0.1516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 21389 Z= 0.126 Angle : 0.553 8.855 29254 Z= 0.282 Chirality : 0.038 0.196 3367 Planarity : 0.005 0.053 3618 Dihedral : 14.539 60.796 3412 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 2.55 % Allowed : 14.81 % Favored : 82.64 % 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: 1.99 (0.17), residues: 2514 helix: 2.05 (0.15), residues: 1291 sheet: 1.23 (0.24), residues: 435 loop : 0.20 (0.23), residues: 788 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG D 208 TYR 0.018 0.001 TYR G 284 PHE 0.047 0.001 PHE G 230 TRP 0.017 0.001 TRP C 10 HIS 0.010 0.001 HIS E 56 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.13 (21373) covalent geometry : angle 0.53492 / 0.28 (29230) hydrogen bonds : bond 0.03900 / 2.61 ( 1185) hydrogen bonds : angle 3.76290 / 2.75 ( 3316) metal coordination : bond 0.00227 / 0.11 ( 16) metal coordination : angle 4.99166 / 3.17 ( 24) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5028 Ramachandran restraints generated. 2514 Oldfield, 0 Emsley, 2514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5028 Ramachandran restraints generated. 2514 Oldfield, 0 Emsley, 2514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 367 residues out of total 2114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 313 time to evaluate : 0.818 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 77 ARG cc_start: 0.8819 (OUTLIER) cc_final: 0.8276 (ttp-170) REVERT: A 259 ASN cc_start: 0.8339 (m-40) cc_final: 0.7925 (m110) REVERT: A 275 LYS cc_start: 0.9017 (OUTLIER) cc_final: 0.8710 (ttpp) REVERT: A 318 GLN cc_start: 0.8893 (OUTLIER) cc_final: 0.8434 (tm-30) REVERT: B 124 LEU cc_start: 0.9083 (OUTLIER) cc_final: 0.8785 (tt) REVERT: B 136 PHE cc_start: 0.8795 (OUTLIER) cc_final: 0.8395 (t80) REVERT: B 247 ASP cc_start: 0.8264 (p0) cc_final: 0.7954 (p0) REVERT: B 362 ARG cc_start: 0.9066 (OUTLIER) cc_final: 0.7117 (mtm180) REVERT: C 133 ARG cc_start: 0.8995 (OUTLIER) cc_final: 0.6927 (mmm160) REVERT: C 263 ARG cc_start: 0.8477 (tpt-90) cc_final: 0.8175 (ttt-90) REVERT: D 86 ARG cc_start: 0.8906 (OUTLIER) cc_final: 0.7821 (ptm160) REVERT: D 277 GLU cc_start: 0.8614 (OUTLIER) cc_final: 0.8356 (tt0) REVERT: D 330 GLN cc_start: 0.8960 (OUTLIER) cc_final: 0.8534 (tm-30) REVERT: E 99 LYS cc_start: 0.8915 (OUTLIER) cc_final: 0.8623 (mtpt) REVERT: F 6 GLU cc_start: 0.7958 (OUTLIER) cc_final: 0.6976 (tm-30) REVERT: F 121 ASP cc_start: 0.7580 (t0) cc_final: 0.7303 (t0) REVERT: F 173 ASP cc_start: 0.8318 (m-30) cc_final: 0.8041 (m-30) REVERT: F 182 MET cc_start: 0.8776 (OUTLIER) cc_final: 0.8415 (mtm) REVERT: F 264 LYS cc_start: 0.9137 (OUTLIER) cc_final: 0.8640 (ttpp) REVERT: G 11 LEU cc_start: 0.9117 (OUTLIER) cc_final: 0.8788 (mp) REVERT: G 95 GLU cc_start: 0.7607 (mm-30) cc_final: 0.7396 (mm-30) REVERT: G 204 MET cc_start: 0.8998 (mmm) cc_final: 0.8456 (mmm) outliers start: 54 outliers final: 20 residues processed: 343 average time/residue: 0.8092 time to fit residues: 303.9780 Evaluate side-chains 336 residues out of total 2114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 301 time to evaluate : 0.765 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 LEU Chi-restraints excluded: chain A residue 77 ARG Chi-restraints excluded: chain A residue 94 ASN Chi-restraints excluded: chain A residue 275 LYS Chi-restraints excluded: chain A residue 318 GLN Chi-restraints excluded: chain B residue 124 LEU Chi-restraints excluded: chain B residue 136 PHE Chi-restraints excluded: chain B residue 235 GLN Chi-restraints excluded: chain B residue 257 VAL Chi-restraints excluded: chain B residue 362 ARG Chi-restraints excluded: chain C residue 101 VAL Chi-restraints excluded: chain C residue 133 ARG Chi-restraints excluded: chain C residue 157 THR Chi-restraints excluded: chain D residue 2 SER Chi-restraints excluded: chain D residue 86 ARG Chi-restraints excluded: chain D residue 93 ILE Chi-restraints excluded: chain D residue 102 GLU Chi-restraints excluded: chain D residue 277 GLU Chi-restraints excluded: chain D residue 330 GLN Chi-restraints excluded: chain E residue 52 GLN Chi-restraints excluded: chain E residue 83 LYS Chi-restraints excluded: chain E residue 99 LYS Chi-restraints excluded: chain E residue 119 LEU Chi-restraints excluded: chain F residue 6 GLU Chi-restraints excluded: chain F residue 52 GLU Chi-restraints excluded: chain F residue 53 MET Chi-restraints excluded: chain F residue 69 THR Chi-restraints excluded: chain F residue 182 MET Chi-restraints excluded: chain F residue 262 LEU Chi-restraints excluded: chain F residue 264 LYS Chi-restraints excluded: chain F residue 339 MET Chi-restraints excluded: chain G residue 11 LEU Chi-restraints excluded: chain G residue 64 GLU Chi-restraints excluded: chain G residue 334 GLU Chi-restraints excluded: chain J residue 28 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 253 random chunks: chunk 214 optimal weight: 0.9980 chunk 190 optimal weight: 2.9990 chunk 123 optimal weight: 0.1980 chunk 117 optimal weight: 0.0670 chunk 245 optimal weight: 1.9990 chunk 186 optimal weight: 0.8980 chunk 219 optimal weight: 0.0870 chunk 207 optimal weight: 1.9990 chunk 185 optimal weight: 3.9990 chunk 50 optimal weight: 0.9990 chunk 104 optimal weight: 0.6980 overall best weight: 0.3896 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 136 GLN B 290 HIS B 330 GLN C 137 ASN C 269 ASN D 110 ASN D 160 GLN E 56 HIS E 86 ASN G 16 GLN G 91 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2543 r_free = 0.2543 target = 0.051004 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2305 r_free = 0.2305 target = 0.041930 restraints weight = 37620.833| |-----------------------------------------------------------------------------| r_work (start): 0.2304 rms_B_bonded: 1.07 r_work: 0.2212 rms_B_bonded: 1.51 restraints_weight: 0.5000 r_work: 0.2121 rms_B_bonded: 2.58 restraints_weight: 0.2500 r_work (final): 0.2121 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8903 moved from start: 0.1616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 21389 Z= 0.113 Angle : 0.538 8.351 29254 Z= 0.275 Chirality : 0.037 0.177 3367 Planarity : 0.004 0.055 3618 Dihedral : 14.478 61.403 3412 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 2.32 % Allowed : 15.42 % Favored : 82.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.10 (0.17), residues: 2514 helix: 2.18 (0.15), residues: 1291 sheet: 1.24 (0.24), residues: 435 loop : 0.23 (0.23), residues: 788 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG D 208 TYR 0.010 0.001 TYR E 47 PHE 0.042 0.001 PHE G 230 TRP 0.017 0.001 TRP C 10 HIS 0.009 0.001 HIS E 56 Details of bonding type rmsd/Z covalent geometry : bond 0.00245 / 0.11 (21373) covalent geometry : angle 0.52023 / 0.27 (29230) hydrogen bonds : bond 0.03644 / 2.44 ( 1185) hydrogen bonds : angle 3.68995 / 2.70 ( 3316) metal coordination : bond 0.00210 / 0.10 ( 16) metal coordination : angle 4.81645 / 3.04 ( 24) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5028 Ramachandran restraints generated. 2514 Oldfield, 0 Emsley, 2514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5028 Ramachandran restraints generated. 2514 Oldfield, 0 Emsley, 2514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 365 residues out of total 2114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 316 time to evaluate : 0.781 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 77 ARG cc_start: 0.8797 (OUTLIER) cc_final: 0.8225 (ttp-170) REVERT: A 259 ASN cc_start: 0.8320 (m-40) cc_final: 0.7920 (m110) REVERT: A 318 GLN cc_start: 0.8862 (OUTLIER) cc_final: 0.8408 (tm-30) REVERT: B 124 LEU cc_start: 0.9082 (OUTLIER) cc_final: 0.8808 (tt) REVERT: B 136 PHE cc_start: 0.8789 (OUTLIER) cc_final: 0.8368 (t80) REVERT: B 214 LEU cc_start: 0.9185 (OUTLIER) cc_final: 0.8684 (tt) REVERT: B 247 ASP cc_start: 0.8218 (p0) cc_final: 0.7910 (p0) REVERT: B 362 ARG cc_start: 0.9050 (OUTLIER) cc_final: 0.7135 (mtm180) REVERT: C 133 ARG cc_start: 0.8981 (OUTLIER) cc_final: 0.6897 (mmm160) REVERT: C 263 ARG cc_start: 0.8422 (tpt-90) cc_final: 0.8126 (ttt-90) REVERT: D 330 GLN cc_start: 0.8948 (OUTLIER) cc_final: 0.8518 (tm-30) REVERT: E 99 LYS cc_start: 0.8895 (OUTLIER) cc_final: 0.8583 (mtpt) REVERT: F 6 GLU cc_start: 0.7964 (OUTLIER) cc_final: 0.6905 (tm-30) REVERT: F 56 ARG cc_start: 0.8648 (OUTLIER) cc_final: 0.8094 (mtp180) REVERT: F 121 ASP cc_start: 0.7521 (t0) cc_final: 0.7253 (t0) REVERT: F 173 ASP cc_start: 0.8236 (m-30) cc_final: 0.8016 (m-30) REVERT: F 182 MET cc_start: 0.8725 (OUTLIER) cc_final: 0.8354 (mtm) REVERT: G 48 ASP cc_start: 0.8061 (t0) cc_final: 0.7672 (t0) REVERT: G 95 GLU cc_start: 0.7579 (mm-30) cc_final: 0.7377 (mm-30) REVERT: G 204 MET cc_start: 0.8989 (mmm) cc_final: 0.8486 (mmm) outliers start: 49 outliers final: 20 residues processed: 340 average time/residue: 0.8152 time to fit residues: 304.6400 Evaluate side-chains 339 residues out of total 2114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 307 time to evaluate : 0.735 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 LEU Chi-restraints excluded: chain A residue 77 ARG Chi-restraints excluded: chain A residue 94 ASN Chi-restraints excluded: chain A residue 318 GLN Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 124 LEU Chi-restraints excluded: chain B residue 136 PHE Chi-restraints excluded: chain B residue 214 LEU Chi-restraints excluded: chain B residue 257 VAL Chi-restraints excluded: chain B residue 362 ARG Chi-restraints excluded: chain C residue 101 VAL Chi-restraints excluded: chain C residue 133 ARG Chi-restraints excluded: chain C residue 257 VAL Chi-restraints excluded: chain D residue 2 SER Chi-restraints excluded: chain D residue 93 ILE Chi-restraints excluded: chain D residue 102 GLU Chi-restraints excluded: chain D residue 330 GLN Chi-restraints excluded: chain E residue 52 GLN Chi-restraints excluded: chain E residue 83 LYS Chi-restraints excluded: chain E residue 99 LYS Chi-restraints excluded: chain F residue 6 GLU Chi-restraints excluded: chain F residue 52 GLU Chi-restraints excluded: chain F residue 56 ARG Chi-restraints excluded: chain F residue 69 THR Chi-restraints excluded: chain F residue 84 GLU Chi-restraints excluded: chain F residue 182 MET Chi-restraints excluded: chain F residue 250 LYS Chi-restraints excluded: chain F residue 262 LEU Chi-restraints excluded: chain F residue 339 MET Chi-restraints excluded: chain G residue 64 GLU Chi-restraints excluded: chain G residue 334 GLU Chi-restraints excluded: chain J residue 28 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 253 random chunks: chunk 192 optimal weight: 1.9990 chunk 66 optimal weight: 0.9990 chunk 223 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 194 optimal weight: 2.9990 chunk 161 optimal weight: 0.6980 chunk 164 optimal weight: 0.6980 chunk 170 optimal weight: 0.9990 chunk 114 optimal weight: 2.9990 chunk 160 optimal weight: 0.0670 chunk 52 optimal weight: 1.9990 overall best weight: 0.6922 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 136 GLN A 263 GLN C 137 ASN C 269 ASN D 110 ASN D 160 GLN E 56 HIS E 86 ASN G 16 GLN G 91 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2526 r_free = 0.2526 target = 0.050364 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2286 r_free = 0.2286 target = 0.041255 restraints weight = 37705.721| |-----------------------------------------------------------------------------| r_work (start): 0.2285 rms_B_bonded: 1.07 r_work: 0.2192 rms_B_bonded: 1.50 restraints_weight: 0.5000 r_work: 0.2101 rms_B_bonded: 2.58 restraints_weight: 0.2500 r_work (final): 0.2101 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8915 moved from start: 0.1601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 21389 Z= 0.138 Angle : 0.569 8.815 29254 Z= 0.288 Chirality : 0.038 0.177 3367 Planarity : 0.005 0.058 3618 Dihedral : 14.472 60.627 3412 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 2.13 % Allowed : 15.80 % Favored : 82.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: 2514 helix: 2.15 (0.15), residues: 1291 sheet: 1.28 (0.24), residues: 434 loop : 0.18 (0.22), residues: 789 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG D 208 TYR 0.012 0.001 TYR E 47 PHE 0.052 0.001 PHE G 230 TRP 0.014 0.001 TRP C 10 HIS 0.010 0.001 HIS E 56 Details of bonding type rmsd/Z covalent geometry : bond 0.00316 / 0.14 (21373) covalent geometry : angle 0.55139 / 0.29 (29230) hydrogen bonds : bond 0.03929 / 2.63 ( 1185) hydrogen bonds : angle 3.69909 / 2.71 ( 3316) metal coordination : bond 0.00238 / 0.11 ( 16) metal coordination : angle 4.87605 / 3.11 ( 24) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5028 Ramachandran restraints generated. 2514 Oldfield, 0 Emsley, 2514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5028 Ramachandran restraints generated. 2514 Oldfield, 0 Emsley, 2514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 356 residues out of total 2114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 311 time to evaluate : 0.802 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 77 ARG cc_start: 0.8829 (OUTLIER) cc_final: 0.7976 (ttp80) REVERT: A 259 ASN cc_start: 0.8334 (m-40) cc_final: 0.7914 (m110) REVERT: A 318 GLN cc_start: 0.8866 (OUTLIER) cc_final: 0.8393 (tm-30) REVERT: B 124 LEU cc_start: 0.9087 (OUTLIER) cc_final: 0.8805 (tt) REVERT: B 158 ASP cc_start: 0.8672 (OUTLIER) cc_final: 0.8444 (m-30) REVERT: B 214 LEU cc_start: 0.9193 (OUTLIER) cc_final: 0.8661 (tt) REVERT: B 247 ASP cc_start: 0.8262 (p0) cc_final: 0.7956 (p0) REVERT: B 362 ARG cc_start: 0.9055 (OUTLIER) cc_final: 0.7134 (mtm180) REVERT: C 133 ARG cc_start: 0.8999 (OUTLIER) cc_final: 0.6931 (mmm160) REVERT: C 263 ARG cc_start: 0.8446 (tpt-90) cc_final: 0.8125 (ttt-90) REVERT: D 330 GLN cc_start: 0.8956 (OUTLIER) cc_final: 0.8525 (tm-30) REVERT: E 99 LYS cc_start: 0.8912 (OUTLIER) cc_final: 0.8606 (mtpt) REVERT: F 6 GLU cc_start: 0.8017 (OUTLIER) cc_final: 0.7035 (tm-30) REVERT: F 56 ARG cc_start: 0.8670 (OUTLIER) cc_final: 0.8124 (mtp180) REVERT: F 121 ASP cc_start: 0.7553 (t0) cc_final: 0.7286 (t0) REVERT: F 173 ASP cc_start: 0.8261 (m-30) cc_final: 0.8041 (m-30) REVERT: F 182 MET cc_start: 0.8766 (OUTLIER) cc_final: 0.8396 (mtm) REVERT: F 264 LYS cc_start: 0.9143 (OUTLIER) cc_final: 0.8649 (ttpp) REVERT: F 351 ASP cc_start: 0.7514 (t70) cc_final: 0.7313 (t0) REVERT: G 48 ASP cc_start: 0.8106 (t0) cc_final: 0.7748 (t0) REVERT: G 95 GLU cc_start: 0.7594 (mm-30) cc_final: 0.7392 (mm-30) REVERT: G 204 MET cc_start: 0.8996 (mmm) cc_final: 0.8472 (mmm) outliers start: 45 outliers final: 21 residues processed: 336 average time/residue: 0.7924 time to fit residues: 292.6527 Evaluate side-chains 338 residues out of total 2114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 304 time to evaluate : 0.772 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 LEU Chi-restraints excluded: chain A residue 77 ARG Chi-restraints excluded: chain A residue 94 ASN Chi-restraints excluded: chain A residue 318 GLN Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 124 LEU Chi-restraints excluded: chain B residue 136 PHE Chi-restraints excluded: chain B residue 158 ASP Chi-restraints excluded: chain B residue 214 LEU Chi-restraints excluded: chain B residue 257 VAL Chi-restraints excluded: chain B residue 362 ARG Chi-restraints excluded: chain C residue 101 VAL Chi-restraints excluded: chain C residue 133 ARG Chi-restraints excluded: chain C residue 244 LEU Chi-restraints excluded: chain C residue 351 MET Chi-restraints excluded: chain D residue 2 SER Chi-restraints excluded: chain D residue 93 ILE Chi-restraints excluded: chain D residue 102 GLU Chi-restraints excluded: chain D residue 330 GLN Chi-restraints excluded: chain E residue 52 GLN Chi-restraints excluded: chain E residue 83 LYS Chi-restraints excluded: chain E residue 99 LYS Chi-restraints excluded: chain E residue 119 LEU Chi-restraints excluded: chain F residue 6 GLU Chi-restraints excluded: chain F residue 52 GLU Chi-restraints excluded: chain F residue 56 ARG Chi-restraints excluded: chain F residue 69 THR Chi-restraints excluded: chain F residue 84 GLU Chi-restraints excluded: chain F residue 182 MET Chi-restraints excluded: chain F residue 226 HIS Chi-restraints excluded: chain F residue 264 LYS Chi-restraints excluded: chain F residue 293 THR Chi-restraints excluded: chain F residue 339 MET Chi-restraints excluded: chain G residue 64 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 253 random chunks: chunk 110 optimal weight: 0.8980 chunk 233 optimal weight: 4.9990 chunk 244 optimal weight: 6.9990 chunk 45 optimal weight: 2.9990 chunk 142 optimal weight: 0.3980 chunk 64 optimal weight: 0.8980 chunk 34 optimal weight: 2.9990 chunk 87 optimal weight: 3.9990 chunk 42 optimal weight: 1.9990 chunk 146 optimal weight: 1.9990 chunk 145 optimal weight: 0.6980 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 136 GLN A 263 GLN B 330 GLN C 137 ASN C 269 ASN D 110 ASN D 160 GLN E 56 HIS E 86 ASN G 16 GLN G 91 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2505 r_free = 0.2505 target = 0.049467 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2262 r_free = 0.2262 target = 0.040362 restraints weight = 37912.946| |-----------------------------------------------------------------------------| r_work (start): 0.2260 rms_B_bonded: 1.08 r_work: 0.2166 rms_B_bonded: 1.50 restraints_weight: 0.5000 r_work: 0.2074 rms_B_bonded: 2.56 restraints_weight: 0.2500 r_work (final): 0.2074 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8930 moved from start: 0.1592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 21389 Z= 0.167 Angle : 0.606 9.628 29254 Z= 0.307 Chirality : 0.040 0.170 3367 Planarity : 0.005 0.059 3618 Dihedral : 14.512 59.893 3412 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 2.22 % Allowed : 15.85 % Favored : 81.93 % 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: 1.95 (0.17), residues: 2514 helix: 2.00 (0.15), residues: 1301 sheet: 1.29 (0.24), residues: 434 loop : 0.16 (0.23), residues: 779 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG D 208 TYR 0.015 0.002 TYR G 284 PHE 0.053 0.002 PHE G 230 TRP 0.012 0.002 TRP D 10 HIS 0.010 0.001 HIS E 56 Details of bonding type rmsd/Z covalent geometry : bond 0.00392 / 0.17 (21373) covalent geometry : angle 0.58803 / 0.31 (29230) hydrogen bonds : bond 0.04293 / 2.89 ( 1185) hydrogen bonds : angle 3.80105 / 2.77 ( 3316) metal coordination : bond 0.00304 / 0.14 ( 16) metal coordination : angle 5.10150 / 3.26 ( 24) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5028 Ramachandran restraints generated. 2514 Oldfield, 0 Emsley, 2514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5028 Ramachandran restraints generated. 2514 Oldfield, 0 Emsley, 2514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 354 residues out of total 2114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 307 time to evaluate : 0.576 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 77 ARG cc_start: 0.8868 (OUTLIER) cc_final: 0.7900 (ttp80) REVERT: A 259 ASN cc_start: 0.8346 (m-40) cc_final: 0.7918 (m110) REVERT: A 274 ASP cc_start: 0.8647 (m-30) cc_final: 0.8413 (m-30) REVERT: A 318 GLN cc_start: 0.8890 (OUTLIER) cc_final: 0.8411 (tm-30) REVERT: B 124 LEU cc_start: 0.9103 (OUTLIER) cc_final: 0.8821 (tt) REVERT: B 158 ASP cc_start: 0.8738 (OUTLIER) cc_final: 0.8530 (m-30) REVERT: B 247 ASP cc_start: 0.8312 (p0) cc_final: 0.8021 (p0) REVERT: B 362 ARG cc_start: 0.9068 (OUTLIER) cc_final: 0.7129 (mtm180) REVERT: C 133 ARG cc_start: 0.9019 (OUTLIER) cc_final: 0.6960 (mmm160) REVERT: C 263 ARG cc_start: 0.8497 (tpt-90) cc_final: 0.8134 (ttt-90) REVERT: D 330 GLN cc_start: 0.8972 (OUTLIER) cc_final: 0.8547 (tm-30) REVERT: E 99 LYS cc_start: 0.8934 (OUTLIER) cc_final: 0.8624 (mtpt) REVERT: F 6 GLU cc_start: 0.8054 (OUTLIER) cc_final: 0.7036 (tm-30) REVERT: F 56 ARG cc_start: 0.8682 (OUTLIER) cc_final: 0.8125 (mtp180) REVERT: F 121 ASP cc_start: 0.7592 (t0) cc_final: 0.7322 (t0) REVERT: F 173 ASP cc_start: 0.8353 (m-30) cc_final: 0.8096 (m-30) REVERT: F 182 MET cc_start: 0.8833 (OUTLIER) cc_final: 0.8511 (mtm) REVERT: F 264 LYS cc_start: 0.9150 (OUTLIER) cc_final: 0.8657 (ttpp) REVERT: G 48 ASP cc_start: 0.8153 (t0) cc_final: 0.7782 (t0) REVERT: G 95 GLU cc_start: 0.7611 (mm-30) cc_final: 0.7402 (mm-30) REVERT: G 204 MET cc_start: 0.9003 (mmm) cc_final: 0.8565 (mmm) outliers start: 47 outliers final: 23 residues processed: 335 average time/residue: 0.8213 time to fit residues: 302.0727 Evaluate side-chains 340 residues out of total 2114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 305 time to evaluate : 0.626 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 LEU Chi-restraints excluded: chain A residue 77 ARG Chi-restraints excluded: chain A residue 94 ASN Chi-restraints excluded: chain A residue 318 GLN Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 124 LEU Chi-restraints excluded: chain B residue 136 PHE Chi-restraints excluded: chain B residue 158 ASP Chi-restraints excluded: chain B residue 214 LEU Chi-restraints excluded: chain B residue 257 VAL Chi-restraints excluded: chain B residue 362 ARG Chi-restraints excluded: chain C residue 101 VAL Chi-restraints excluded: chain C residue 133 ARG Chi-restraints excluded: chain C residue 351 MET Chi-restraints excluded: chain D residue 2 SER Chi-restraints excluded: chain D residue 93 ILE Chi-restraints excluded: chain D residue 330 GLN Chi-restraints excluded: chain E residue 52 GLN Chi-restraints excluded: chain E residue 83 LYS Chi-restraints excluded: chain E residue 99 LYS Chi-restraints excluded: chain E residue 119 LEU Chi-restraints excluded: chain E residue 253 MET Chi-restraints excluded: chain F residue 6 GLU Chi-restraints excluded: chain F residue 52 GLU Chi-restraints excluded: chain F residue 56 ARG Chi-restraints excluded: chain F residue 69 THR Chi-restraints excluded: chain F residue 84 GLU Chi-restraints excluded: chain F residue 182 MET Chi-restraints excluded: chain F residue 226 HIS Chi-restraints excluded: chain F residue 250 LYS Chi-restraints excluded: chain F residue 262 LEU Chi-restraints excluded: chain F residue 264 LYS Chi-restraints excluded: chain F residue 293 THR Chi-restraints excluded: chain G residue 64 GLU Chi-restraints excluded: chain J residue 28 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 253 random chunks: chunk 114 optimal weight: 0.9980 chunk 1 optimal weight: 2.9990 chunk 123 optimal weight: 0.8980 chunk 252 optimal weight: 0.0040 chunk 149 optimal weight: 4.9990 chunk 188 optimal weight: 0.8980 chunk 200 optimal weight: 2.9990 chunk 59 optimal weight: 0.5980 chunk 157 optimal weight: 0.9990 chunk 28 optimal weight: 2.9990 chunk 204 optimal weight: 0.6980 overall best weight: 0.6192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 136 GLN A 263 GLN C 137 ASN C 269 ASN D 110 ASN D 160 GLN E 54 GLN E 56 HIS E 86 ASN F 61 GLN G 16 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2525 r_free = 0.2525 target = 0.050297 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2285 r_free = 0.2285 target = 0.041183 restraints weight = 37669.390| |-----------------------------------------------------------------------------| r_work (start): 0.2284 rms_B_bonded: 1.08 r_work: 0.2191 rms_B_bonded: 1.50 restraints_weight: 0.5000 r_work: 0.2099 rms_B_bonded: 2.57 restraints_weight: 0.2500 r_work (final): 0.2099 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8916 moved from start: 0.1629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 21389 Z= 0.131 Angle : 0.571 9.432 29254 Z= 0.290 Chirality : 0.038 0.158 3367 Planarity : 0.005 0.060 3618 Dihedral : 14.490 60.482 3412 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 1.94 % Allowed : 16.13 % Favored : 81.93 % 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: 2.04 (0.17), residues: 2514 helix: 2.10 (0.15), residues: 1290 sheet: 1.28 (0.24), residues: 434 loop : 0.20 (0.22), residues: 790 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG D 208 TYR 0.011 0.001 TYR E 47 PHE 0.046 0.001 PHE G 230 TRP 0.016 0.001 TRP C 10 HIS 0.010 0.001 HIS E 56 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.13 (21373) covalent geometry : angle 0.55337 / 0.29 (29230) hydrogen bonds : bond 0.03902 / 2.62 ( 1185) hydrogen bonds : angle 3.74320 / 2.74 ( 3316) metal coordination : bond 0.00245 / 0.11 ( 16) metal coordination : angle 4.93911 / 3.15 ( 24) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7493.82 seconds wall clock time: 128 minutes 21.38 seconds (7701.38 seconds total)