Starting phenix.real_space_refine on Fri Jun 5 14:12:33 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9oyc_71014/06_2026/9oyc_71014.cif Found real_map, /net/cci-nas-00/data/ceres_data/9oyc_71014/06_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_71014/06_2026/9oyc_71014.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9oyc_71014/06_2026/9oyc_71014.map" model { file = "/net/cci-nas-00/data/ceres_data/9oyc_71014/06_2026/9oyc_71014.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9oyc_71014/06_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-6079/lib/python3.9/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: 5.25, per 1000 atoms: 0.25 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: 1.86 Conformation dependent library (CDL) restraints added in 976.8 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: 2.96 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: 4.13 Time building geometry restraints manager: 2.42 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=" C ARG G 240 " pdb=" N PHE G 241 " ideal model delta sigma weight residual 1.339 1.252 0.088 5.57e-02 3.22e+02 2.48e+00 bond pdb=" CB VAL B 257 " pdb=" CG1 VAL B 257 " ideal model delta sigma weight residual 1.521 1.470 0.051 3.30e-02 9.18e+02 2.41e+00 bond pdb=" CB MET E 253 " pdb=" CG MET E 253 " ideal model delta sigma weight residual 1.520 1.485 0.035 3.00e-02 1.11e+03 1.39e+00 bond pdb=" CB THR F 69 " pdb=" CG2 THR F 69 " ideal model delta sigma weight residual 1.521 1.485 0.036 3.30e-02 9.18e+02 1.21e+00 bond pdb=" N ARG F 279 " pdb=" CA ARG F 279 " ideal model delta sigma weight residual 1.460 1.475 -0.015 1.48e-02 4.57e+03 1.08e+00 ... (remaining 21368 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.72: 28617 1.72 - 3.44: 542 3.44 - 5.16: 60 5.16 - 6.88: 10 6.88 - 8.60: 1 Bond angle restraints: 29230 Sorted by residual: angle pdb=" N GLU G 50 " pdb=" CA GLU G 50 " pdb=" C GLU G 50 " ideal model delta sigma weight residual 114.04 109.72 4.32 1.24e+00 6.50e-01 1.21e+01 angle pdb=" C ASP F 48 " pdb=" N LEU F 49 " pdb=" CA LEU F 49 " ideal model delta sigma weight residual 121.54 128.09 -6.55 1.91e+00 2.74e-01 1.18e+01 angle pdb=" CA ARG B 208 " pdb=" CB ARG B 208 " pdb=" CG ARG B 208 " ideal model delta sigma weight residual 114.10 120.10 -6.00 2.00e+00 2.50e-01 9.01e+00 angle pdb=" C ALA G 38 " pdb=" N ASP G 39 " pdb=" CA ASP G 39 " ideal model delta sigma weight residual 121.54 127.08 -5.54 1.91e+00 2.74e-01 8.41e+00 angle pdb=" CB MET E 253 " pdb=" CG MET E 253 " pdb=" SD MET E 253 " ideal model delta sigma weight residual 112.70 104.10 8.60 3.00e+00 1.11e-01 8.22e+00 ... (remaining 29225 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.37: 12098 26.37 - 52.74: 673 52.74 - 79.11: 120 79.11 - 105.47: 15 105.47 - 131.84: 2 Dihedral angle restraints: 12908 sinusoidal: 5579 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=" O1A AGS B 702 " pdb=" O3A AGS B 702 " pdb=" PA AGS B 702 " pdb=" PB AGS B 702 " ideal model delta sinusoidal sigma weight residual -67.73 64.11 -131.84 1 3.00e+01 1.11e-03 1.78e+01 ... (remaining 12905 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 2062 0.030 - 0.061: 925 0.061 - 0.091: 256 0.091 - 0.122: 120 0.122 - 0.152: 10 Chirality restraints: 3373 Sorted by residual: chirality pdb=" CA ASP G 39 " pdb=" N ASP G 39 " pdb=" C ASP G 39 " pdb=" CB ASP G 39 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.80e-01 chirality pdb=" CA VAL F 195 " pdb=" N VAL F 195 " pdb=" C VAL F 195 " pdb=" CB VAL F 195 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.48e-01 chirality pdb=" CG LEU A 327 " pdb=" CB LEU A 327 " pdb=" CD1 LEU A 327 " pdb=" CD2 LEU A 327 " both_signs ideal model delta sigma weight residual False -2.59 -2.72 0.13 2.00e-01 2.50e+01 4.37e-01 ... (remaining 3370 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: 3.200 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: 0.020 Extract box with map and model: 0.330 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 25.290 Find NCS groups from input model: 0.370 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:10.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.730 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8823 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= 0.162 Angle : 0.601 12.804 29254 Z= 0.306 Chirality : 0.039 0.152 3373 Planarity : 0.005 0.065 3618 Dihedral : 16.060 131.842 8152 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 0.00378 / 0.16 (21373) covalent geometry : angle 0.57752 / 0.30 (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 : 0.894 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: 0.9575 time to fit residues: 439.1286 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 : 0.792 ------------------------------------------------------------------------------- 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: 2.9990 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... Flipped N/Q/H residues before XYZ refinement: 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 329 ASN G 16 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2540 r_free = 0.2540 target = 0.050839 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2302 r_free = 0.2302 target = 0.041787 restraints weight = 38069.767| |-----------------------------------------------------------------------------| r_work (start): 0.2301 rms_B_bonded: 1.08 r_work: 0.2207 rms_B_bonded: 1.51 restraints_weight: 0.5000 r_work: 0.2115 rms_B_bonded: 2.58 restraints_weight: 0.2500 r_work (final): 0.2115 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8848 moved from start: 0.1023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 21389 Z= 0.139 Angle : 0.578 11.600 29254 Z= 0.292 Chirality : 0.038 0.178 3373 Planarity : 0.005 0.046 3618 Dihedral : 14.917 135.679 3358 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 2.37 % Allowed : 9.89 % Favored : 87.75 % 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: 1.87 (0.17), residues: 2514 helix: 1.84 (0.15), residues: 1304 sheet: 1.36 (0.23), residues: 442 loop : 0.23 (0.23), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG F 205 TYR 0.012 0.001 TYR F 284 PHE 0.018 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 0.00315 / 0.14 (21373) covalent geometry : angle 0.55546 / 0.29 (29230) hydrogen bonds : bond 0.04420 / 2.97 ( 1185) hydrogen bonds : angle 4.02007 / 2.95 ( 3316) metal coordination : bond 0.00394 / 0.16 ( 16) metal coordination : angle 5.55905 / 3.41 ( 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: 50 poor density : 340 time to evaluate : 0.965 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 77 ARG cc_start: 0.8817 (OUTLIER) cc_final: 0.8003 (ttp80) REVERT: A 259 ASN cc_start: 0.8377 (m-40) cc_final: 0.7897 (m110) REVERT: B 214 LEU cc_start: 0.9153 (OUTLIER) cc_final: 0.8823 (tt) REVERT: B 247 ASP cc_start: 0.8218 (p0) cc_final: 0.7849 (p0) REVERT: C 306 MET cc_start: 0.9050 (OUTLIER) cc_final: 0.8808 (mtm) REVERT: D 277 GLU cc_start: 0.8640 (OUTLIER) cc_final: 0.8347 (tt0) REVERT: F 173 ASP cc_start: 0.8479 (m-30) cc_final: 0.8121 (m-30) REVERT: F 351 ASP cc_start: 0.7861 (t70) cc_final: 0.7558 (t0) REVERT: G 95 GLU cc_start: 0.7528 (mm-30) cc_final: 0.7311 (mm-30) REVERT: G 149 GLN cc_start: 0.8133 (OUTLIER) cc_final: 0.7918 (mt0) REVERT: G 204 MET cc_start: 0.8993 (mmm) cc_final: 0.8466 (mmm) REVERT: G 289 GLN cc_start: 0.8862 (OUTLIER) cc_final: 0.8655 (tt0) outliers start: 50 outliers final: 10 residues processed: 357 average time/residue: 0.9179 time to fit residues: 358.5730 Evaluate side-chains 335 residues out of total 2114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 319 time to evaluate : 0.810 ------------------------------------------------------------------------------- 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 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 250 LYS 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: 2.9990 chunk 163 optimal weight: 1.9990 chunk 40 optimal weight: 5.9990 chunk 117 optimal weight: 2.9990 chunk 63 optimal weight: 2.9990 chunk 164 optimal weight: 0.9990 chunk 23 optimal weight: 2.9990 chunk 218 optimal weight: 2.9990 chunk 173 optimal weight: 3.9990 chunk 91 optimal weight: 2.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 40 GLN A 157 GLN A 263 GLN B 110 ASN C 137 ASN C 182 GLN C 269 ASN D 110 ASN D 160 GLN E 56 HIS E 86 ASN F 61 GLN F 63 HIS G 16 GLN G 295 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2446 r_free = 0.2446 target = 0.047167 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2199 r_free = 0.2199 target = 0.038206 restraints weight = 38598.995| |-----------------------------------------------------------------------------| r_work (start): 0.2197 rms_B_bonded: 1.07 r_work: 0.2101 rms_B_bonded: 1.49 restraints_weight: 0.5000 r_work: 0.2008 rms_B_bonded: 2.53 restraints_weight: 0.2500 r_work (final): 0.2008 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8912 moved from start: 0.1347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.123 21389 Z= 0.287 Angle : 0.721 14.793 29254 Z= 0.363 Chirality : 0.045 0.196 3373 Planarity : 0.006 0.058 3618 Dihedral : 15.085 130.883 3358 Min Nonbonded Distance : 1.886 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 2.79 % Allowed : 11.64 % Favored : 85.57 % 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: 1.52 (0.17), residues: 2514 helix: 1.54 (0.14), residues: 1297 sheet: 1.45 (0.23), residues: 430 loop : -0.03 (0.22), residues: 787 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG F 205 TYR 0.015 0.002 TYR E 47 PHE 0.020 0.002 PHE G 278 TRP 0.016 0.003 TRP C 10 HIS 0.010 0.002 HIS E 56 Details of bonding type rmsd/Z covalent geometry : bond 0.00700 / 0.29 (21373) covalent geometry : angle 0.69930 / 0.36 (29230) hydrogen bonds : bond 0.05631 / 3.81 ( 1185) hydrogen bonds : angle 4.12561 / 3.02 ( 3316) metal coordination : bond 0.00662 / 0.31 ( 16) metal coordination : angle 6.18820 / 3.88 ( 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 371 residues out of total 2114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 312 time to evaluate : 0.839 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 77 ARG cc_start: 0.8964 (OUTLIER) cc_final: 0.7532 (ttp80) REVERT: A 136 GLN cc_start: 0.9208 (OUTLIER) cc_final: 0.8993 (mt0) REVERT: A 259 ASN cc_start: 0.8416 (m-40) cc_final: 0.7963 (m110) REVERT: A 318 GLN cc_start: 0.8944 (OUTLIER) cc_final: 0.8457 (tm-30) REVERT: B 124 LEU cc_start: 0.9118 (OUTLIER) cc_final: 0.8821 (tt) REVERT: B 136 PHE cc_start: 0.8784 (OUTLIER) cc_final: 0.8464 (t80) REVERT: B 214 LEU cc_start: 0.9230 (OUTLIER) cc_final: 0.8888 (tt) REVERT: D 277 GLU cc_start: 0.8787 (OUTLIER) cc_final: 0.8451 (tt0) REVERT: G 95 GLU cc_start: 0.7674 (mm-30) cc_final: 0.7430 (mm-30) REVERT: G 149 GLN cc_start: 0.8204 (OUTLIER) cc_final: 0.7995 (mt0) REVERT: G 204 MET cc_start: 0.9021 (mmm) cc_final: 0.8599 (mmm) REVERT: G 362 MET cc_start: 0.8987 (OUTLIER) cc_final: 0.8385 (mpp) outliers start: 59 outliers final: 16 residues processed: 339 average time/residue: 0.9330 time to fit residues: 346.2010 Evaluate side-chains 327 residues out of total 2114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 302 time to evaluate : 0.670 ------------------------------------------------------------------------------- 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 136 PHE Chi-restraints excluded: chain B residue 214 LEU Chi-restraints excluded: chain B residue 235 GLN 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 276 GLU Chi-restraints excluded: chain F residue 53 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 64 GLU Chi-restraints excluded: chain G residue 123 GLN Chi-restraints excluded: chain G residue 149 GLN Chi-restraints excluded: chain G residue 261 ASP Chi-restraints excluded: chain G residue 334 GLU Chi-restraints excluded: chain G residue 362 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: 0.9980 chunk 25 optimal weight: 0.5980 chunk 75 optimal weight: 1.9990 chunk 26 optimal weight: 0.5980 chunk 144 optimal weight: 2.9990 chunk 128 optimal weight: 3.9990 chunk 220 optimal weight: 0.6980 chunk 250 optimal weight: 1.9990 chunk 181 optimal weight: 0.0470 chunk 157 optimal weight: 0.7980 chunk 156 optimal weight: 2.9990 overall best weight: 0.5478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 136 GLN C 137 ASN C 269 ASN D 21 GLN 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 = 0.2518 r_free = 0.2518 target = 0.049999 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2280 r_free = 0.2280 target = 0.040950 restraints weight = 37939.755| |-----------------------------------------------------------------------------| r_work (start): 0.2278 rms_B_bonded: 1.07 r_work: 0.2184 rms_B_bonded: 1.51 restraints_weight: 0.5000 r_work: 0.2093 rms_B_bonded: 2.57 restraints_weight: 0.2500 r_work (final): 0.2093 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8863 moved from start: 0.1379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 21389 Z= 0.126 Angle : 0.552 9.391 29254 Z= 0.280 Chirality : 0.038 0.166 3373 Planarity : 0.005 0.052 3618 Dihedral : 15.043 135.191 3358 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 2.13 % Allowed : 13.29 % Favored : 84.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.91 (0.17), residues: 2514 helix: 1.91 (0.15), residues: 1295 sheet: 1.43 (0.24), residues: 429 loop : 0.17 (0.23), residues: 790 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG F 205 TYR 0.017 0.001 TYR G 284 PHE 0.012 0.001 PHE F 3 TRP 0.018 0.001 TRP C 10 HIS 0.010 0.001 HIS E 56 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.13 (21373) covalent geometry : angle 0.53140 / 0.28 (29230) hydrogen bonds : bond 0.03936 / 2.65 ( 1185) hydrogen bonds : angle 3.82292 / 2.81 ( 3316) metal coordination : bond 0.00305 / 0.14 ( 16) metal coordination : angle 5.24008 / 3.29 ( 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 363 residues out of total 2114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 318 time to evaluate : 0.840 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 77 ARG cc_start: 0.8815 (OUTLIER) cc_final: 0.8313 (ttp-170) REVERT: A 259 ASN cc_start: 0.8360 (m-40) cc_final: 0.7922 (m110) REVERT: A 318 GLN cc_start: 0.8891 (OUTLIER) cc_final: 0.8458 (tm-30) REVERT: B 124 LEU cc_start: 0.9089 (OUTLIER) cc_final: 0.8786 (tt) REVERT: B 136 PHE cc_start: 0.8778 (OUTLIER) cc_final: 0.8405 (t80) REVERT: B 214 LEU cc_start: 0.9135 (OUTLIER) cc_final: 0.8838 (tt) REVERT: B 247 ASP cc_start: 0.8258 (p0) cc_final: 0.7937 (p0) REVERT: B 362 ARG cc_start: 0.9061 (OUTLIER) cc_final: 0.7561 (mtm180) REVERT: C 133 ARG cc_start: 0.8986 (OUTLIER) cc_final: 0.6938 (mmm160) REVERT: C 256 MET cc_start: 0.8634 (ttm) cc_final: 0.8352 (ttm) REVERT: D 277 GLU cc_start: 0.8644 (OUTLIER) cc_final: 0.8367 (tt0) REVERT: F 6 GLU cc_start: 0.7977 (OUTLIER) cc_final: 0.6950 (tm-30) REVERT: F 173 ASP cc_start: 0.8416 (m-30) cc_final: 0.8116 (m-30) REVERT: F 351 ASP cc_start: 0.7855 (t70) cc_final: 0.7601 (t0) REVERT: G 95 GLU cc_start: 0.7601 (mm-30) cc_final: 0.7389 (mm-30) REVERT: G 204 MET cc_start: 0.9006 (mmm) cc_final: 0.8533 (mmm) outliers start: 45 outliers final: 13 residues processed: 338 average time/residue: 0.9417 time to fit residues: 346.9500 Evaluate side-chains 326 residues out of total 2114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 304 time to evaluate : 0.803 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 ARG 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 133 ARG 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 F residue 6 GLU Chi-restraints excluded: chain F residue 52 GLU Chi-restraints excluded: chain F residue 250 LYS Chi-restraints excluded: chain F residue 262 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 253 random chunks: chunk 160 optimal weight: 0.5980 chunk 166 optimal weight: 1.9990 chunk 86 optimal weight: 0.0020 chunk 147 optimal weight: 0.0570 chunk 40 optimal weight: 0.0030 chunk 105 optimal weight: 0.7980 chunk 82 optimal weight: 1.9990 chunk 196 optimal weight: 0.9980 chunk 62 optimal weight: 2.9990 chunk 48 optimal weight: 3.9990 chunk 50 optimal weight: 0.7980 overall best weight: 0.2916 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 290 HIS C 137 ASN C 269 ASN D 110 ASN D 160 GLN E 56 HIS E 86 ASN E 259 HIS G 275 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2562 r_free = 0.2562 target = 0.051728 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2327 r_free = 0.2327 target = 0.042664 restraints weight = 37877.777| |-----------------------------------------------------------------------------| r_work (start): 0.2325 rms_B_bonded: 1.07 r_work: 0.2234 rms_B_bonded: 1.51 restraints_weight: 0.5000 r_work: 0.2143 rms_B_bonded: 2.58 restraints_weight: 0.2500 r_work (final): 0.2143 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8833 moved from start: 0.1537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 21389 Z= 0.104 Angle : 0.515 8.549 29254 Z= 0.261 Chirality : 0.037 0.151 3373 Planarity : 0.004 0.050 3618 Dihedral : 14.899 135.898 3358 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 2.13 % Allowed : 13.72 % Favored : 84.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.17 (0.17), residues: 2514 helix: 2.23 (0.15), residues: 1281 sheet: 1.25 (0.24), residues: 445 loop : 0.30 (0.23), residues: 788 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG F 205 TYR 0.012 0.001 TYR D 3 PHE 0.026 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 0.00227 / 0.10 (21373) covalent geometry : angle 0.49689 / 0.26 (29230) hydrogen bonds : bond 0.03431 / 2.29 ( 1185) hydrogen bonds : angle 3.63018 / 2.67 ( 3316) metal coordination : bond 0.00228 / 0.11 ( 16) metal coordination : angle 4.81462 / 3.01 ( 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 366 residues out of total 2114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 321 time to evaluate : 0.665 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 77 ARG cc_start: 0.8801 (OUTLIER) cc_final: 0.8261 (ttp-170) REVERT: A 259 ASN cc_start: 0.8304 (m-40) cc_final: 0.7901 (m110) REVERT: A 318 GLN cc_start: 0.8851 (OUTLIER) cc_final: 0.8416 (tm-30) REVERT: B 124 LEU cc_start: 0.9074 (OUTLIER) cc_final: 0.8802 (tt) REVERT: B 136 PHE cc_start: 0.8763 (OUTLIER) cc_final: 0.8384 (t80) REVERT: B 247 ASP cc_start: 0.8173 (p0) cc_final: 0.7860 (p0) REVERT: B 362 ARG cc_start: 0.9030 (OUTLIER) cc_final: 0.7079 (mtm180) REVERT: C 133 ARG cc_start: 0.8955 (OUTLIER) cc_final: 0.7535 (mmt180) REVERT: C 256 MET cc_start: 0.8633 (ttm) cc_final: 0.8342 (ttm) REVERT: D 86 ARG cc_start: 0.8862 (OUTLIER) cc_final: 0.7931 (ptm160) REVERT: E 99 LYS cc_start: 0.8910 (OUTLIER) cc_final: 0.8611 (mtpt) REVERT: F 6 GLU cc_start: 0.7981 (OUTLIER) cc_final: 0.6943 (tm-30) REVERT: F 173 ASP cc_start: 0.8207 (m-30) cc_final: 0.7985 (m-30) REVERT: G 11 LEU cc_start: 0.9110 (OUTLIER) cc_final: 0.8809 (mp) REVERT: G 48 ASP cc_start: 0.8080 (t0) cc_final: 0.7677 (t0) REVERT: G 204 MET cc_start: 0.9004 (mmm) cc_final: 0.8494 (mmm) outliers start: 45 outliers final: 14 residues processed: 345 average time/residue: 0.9300 time to fit residues: 349.4741 Evaluate side-chains 329 residues out of total 2114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 305 time to evaluate : 0.859 ------------------------------------------------------------------------------- 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 318 GLN Chi-restraints excluded: chain B residue 124 LEU Chi-restraints excluded: chain B residue 136 PHE 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 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 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 53 MET Chi-restraints excluded: chain F residue 250 LYS Chi-restraints excluded: chain F residue 262 LEU 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 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: 3.9990 chunk 128 optimal weight: 4.9990 chunk 15 optimal weight: 0.9990 chunk 220 optimal weight: 0.6980 chunk 165 optimal weight: 2.9990 chunk 170 optimal weight: 0.4980 chunk 158 optimal weight: 0.6980 chunk 234 optimal weight: 1.9990 chunk 87 optimal weight: 0.9980 chunk 145 optimal weight: 1.9990 chunk 51 optimal weight: 4.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 204 GLN 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: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2521 r_free = 0.2521 target = 0.050099 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2280 r_free = 0.2280 target = 0.041004 restraints weight = 37635.489| |-----------------------------------------------------------------------------| r_work (start): 0.2279 rms_B_bonded: 1.07 r_work: 0.2186 rms_B_bonded: 1.50 restraints_weight: 0.5000 r_work: 0.2094 rms_B_bonded: 2.57 restraints_weight: 0.2500 r_work (final): 0.2094 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8863 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 0.058 21389 Z= 0.147 Angle : 0.561 9.701 29254 Z= 0.283 Chirality : 0.038 0.143 3373 Planarity : 0.005 0.051 3618 Dihedral : 14.887 133.541 3358 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 2.37 % Allowed : 14.47 % Favored : 83.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.08 (0.17), residues: 2514 helix: 2.13 (0.15), residues: 1300 sheet: 1.36 (0.24), residues: 439 loop : 0.16 (0.23), residues: 775 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG F 205 TYR 0.018 0.001 TYR D 3 PHE 0.050 0.001 PHE G 230 TRP 0.013 0.001 TRP D 10 HIS 0.010 0.001 HIS E 56 Details of bonding type rmsd/Z covalent geometry : bond 0.00344 / 0.15 (21373) covalent geometry : angle 0.54305 / 0.28 (29230) hydrogen bonds : bond 0.03996 / 2.69 ( 1185) hydrogen bonds : angle 3.71399 / 2.72 ( 3316) metal coordination : bond 0.00289 / 0.13 ( 16) metal coordination : angle 4.97782 / 3.17 ( 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 359 residues out of total 2114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 309 time to evaluate : 0.823 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 77 ARG cc_start: 0.8853 (OUTLIER) cc_final: 0.8005 (ttp80) REVERT: A 259 ASN cc_start: 0.8351 (m-40) cc_final: 0.7923 (m110) REVERT: A 318 GLN cc_start: 0.8864 (OUTLIER) cc_final: 0.8416 (tm-30) REVERT: B 124 LEU cc_start: 0.9099 (OUTLIER) cc_final: 0.8827 (tt) REVERT: B 136 PHE cc_start: 0.8814 (OUTLIER) cc_final: 0.8430 (t80) REVERT: B 214 LEU cc_start: 0.9231 (OUTLIER) cc_final: 0.8696 (tt) REVERT: B 247 ASP cc_start: 0.8232 (p0) cc_final: 0.7920 (p0) REVERT: B 362 ARG cc_start: 0.9065 (OUTLIER) cc_final: 0.7242 (mtt180) REVERT: C 133 ARG cc_start: 0.9006 (OUTLIER) cc_final: 0.6929 (mmm160) REVERT: D 86 ARG cc_start: 0.8918 (OUTLIER) cc_final: 0.8017 (ptm160) REVERT: D 330 GLN cc_start: 0.8960 (OUTLIER) cc_final: 0.8524 (tm-30) REVERT: E 99 LYS cc_start: 0.8939 (OUTLIER) cc_final: 0.8638 (mtpt) REVERT: F 6 GLU cc_start: 0.8010 (OUTLIER) cc_final: 0.7032 (tm-30) REVERT: F 39 ASP cc_start: 0.8401 (p0) cc_final: 0.8178 (p0) REVERT: F 56 ARG cc_start: 0.8675 (OUTLIER) cc_final: 0.8109 (mtp180) REVERT: F 173 ASP cc_start: 0.8294 (m-30) cc_final: 0.8049 (m-30) REVERT: G 11 LEU cc_start: 0.9134 (OUTLIER) cc_final: 0.8787 (mp) REVERT: G 48 ASP cc_start: 0.8147 (t0) cc_final: 0.7754 (t0) REVERT: G 204 MET cc_start: 0.9010 (mmm) cc_final: 0.8473 (mmm) outliers start: 50 outliers final: 21 residues processed: 335 average time/residue: 0.9493 time to fit residues: 346.9656 Evaluate side-chains 332 residues out of total 2114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 298 time to evaluate : 0.815 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 ARG 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 337 LYS 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 86 ARG 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 53 MET Chi-restraints excluded: chain F residue 56 ARG Chi-restraints excluded: chain F residue 69 THR 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 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 334 GLU Chi-restraints excluded: chain G residue 338 MET 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: 3.9990 chunk 25 optimal weight: 0.6980 chunk 103 optimal weight: 1.9990 chunk 176 optimal weight: 0.9980 chunk 4 optimal weight: 1.9990 chunk 87 optimal weight: 2.9990 chunk 203 optimal weight: 4.9990 chunk 172 optimal weight: 0.7980 chunk 220 optimal weight: 1.9990 chunk 182 optimal weight: 0.9990 chunk 1 optimal weight: 0.6980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 263 GLN 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: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2515 r_free = 0.2515 target = 0.049811 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2272 r_free = 0.2272 target = 0.040708 restraints weight = 37955.198| |-----------------------------------------------------------------------------| r_work (start): 0.2271 rms_B_bonded: 1.07 r_work: 0.2178 rms_B_bonded: 1.50 restraints_weight: 0.5000 r_work: 0.2086 rms_B_bonded: 2.56 restraints_weight: 0.2500 r_work (final): 0.2086 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8868 moved from start: 0.1529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 21389 Z= 0.153 Angle : 0.569 9.253 29254 Z= 0.288 Chirality : 0.038 0.157 3373 Planarity : 0.005 0.052 3618 Dihedral : 14.909 133.096 3358 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 2.46 % Allowed : 14.38 % Favored : 83.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.03 (0.17), residues: 2514 helix: 2.09 (0.15), residues: 1296 sheet: 1.33 (0.24), residues: 439 loop : 0.16 (0.23), residues: 779 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG F 105 TYR 0.015 0.001 TYR D 3 PHE 0.048 0.001 PHE G 230 TRP 0.013 0.001 TRP D 10 HIS 0.009 0.001 HIS E 56 Details of bonding type rmsd/Z covalent geometry : bond 0.00357 / 0.15 (21373) covalent geometry : angle 0.55101 / 0.29 (29230) hydrogen bonds : bond 0.04053 / 2.73 ( 1185) hydrogen bonds : angle 3.73671 / 2.73 ( 3316) metal coordination : bond 0.00303 / 0.14 ( 16) metal coordination : angle 5.00499 / 3.21 ( 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 365 residues out of total 2114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 313 time to evaluate : 0.741 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 77 ARG cc_start: 0.8867 (OUTLIER) cc_final: 0.7927 (ttp80) REVERT: A 259 ASN cc_start: 0.8345 (m-40) cc_final: 0.7915 (m110) REVERT: A 318 GLN cc_start: 0.8876 (OUTLIER) cc_final: 0.8403 (tm-30) REVERT: B 124 LEU cc_start: 0.9104 (OUTLIER) cc_final: 0.8824 (tt) REVERT: B 247 ASP cc_start: 0.8270 (p0) cc_final: 0.7967 (p0) REVERT: B 362 ARG cc_start: 0.9055 (OUTLIER) cc_final: 0.7261 (mtt180) REVERT: C 133 ARG cc_start: 0.9024 (OUTLIER) cc_final: 0.6945 (mmm160) REVERT: D 86 ARG cc_start: 0.8939 (OUTLIER) cc_final: 0.7877 (ptm160) REVERT: D 330 GLN cc_start: 0.8965 (OUTLIER) cc_final: 0.8526 (tm-30) REVERT: E 99 LYS cc_start: 0.8944 (OUTLIER) cc_final: 0.8636 (mtpt) REVERT: F 6 GLU cc_start: 0.8015 (OUTLIER) cc_final: 0.6857 (tm-30) REVERT: F 56 ARG cc_start: 0.8687 (OUTLIER) cc_final: 0.8119 (mtp180) REVERT: F 173 ASP cc_start: 0.8338 (m-30) cc_final: 0.8091 (m-30) REVERT: F 264 LYS cc_start: 0.9164 (OUTLIER) cc_final: 0.8667 (ttpp) REVERT: G 11 LEU cc_start: 0.9129 (OUTLIER) cc_final: 0.8770 (mp) REVERT: G 204 MET cc_start: 0.9012 (mmm) cc_final: 0.8455 (mmm) REVERT: G 261 ASP cc_start: 0.8643 (OUTLIER) cc_final: 0.8389 (t0) outliers start: 52 outliers final: 26 residues processed: 341 average time/residue: 0.9131 time to fit residues: 340.1223 Evaluate side-chains 340 residues out of total 2114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 301 time to evaluate : 0.800 ------------------------------------------------------------------------------- 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 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 244 LEU Chi-restraints excluded: chain C residue 351 MET 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 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 56 ARG Chi-restraints excluded: chain F residue 69 THR Chi-restraints excluded: chain F residue 84 GLU Chi-restraints excluded: chain F residue 250 LYS 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 11 LEU Chi-restraints excluded: chain G residue 64 GLU 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 253 random chunks: chunk 214 optimal weight: 0.5980 chunk 190 optimal weight: 0.0970 chunk 123 optimal weight: 0.4980 chunk 117 optimal weight: 0.9990 chunk 245 optimal weight: 2.9990 chunk 186 optimal weight: 1.9990 chunk 219 optimal weight: 0.9980 chunk 207 optimal weight: 0.9980 chunk 185 optimal weight: 2.9990 chunk 50 optimal weight: 0.8980 chunk 104 optimal weight: 0.7980 overall best weight: 0.5778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2534 r_free = 0.2534 target = 0.050609 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2294 r_free = 0.2294 target = 0.041490 restraints weight = 37569.368| |-----------------------------------------------------------------------------| r_work (start): 0.2292 rms_B_bonded: 1.07 r_work: 0.2199 rms_B_bonded: 1.51 restraints_weight: 0.5000 r_work: 0.2108 rms_B_bonded: 2.56 restraints_weight: 0.2500 r_work (final): 0.2108 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8854 moved from start: 0.1594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 21389 Z= 0.128 Angle : 0.553 8.798 29254 Z= 0.279 Chirality : 0.037 0.169 3373 Planarity : 0.004 0.051 3618 Dihedral : 14.891 133.661 3358 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 2.41 % Allowed : 14.85 % Favored : 82.73 % 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: 2.17 (0.15), residues: 1295 sheet: 1.29 (0.24), residues: 439 loop : 0.19 (0.23), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG F 240 TYR 0.014 0.001 TYR D 3 PHE 0.045 0.001 PHE G 230 TRP 0.014 0.001 TRP D 10 HIS 0.010 0.001 HIS E 56 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.13 (21373) covalent geometry : angle 0.53573 / 0.28 (29230) hydrogen bonds : bond 0.03740 / 2.51 ( 1185) hydrogen bonds : angle 3.67450 / 2.70 ( 3316) metal coordination : bond 0.00246 / 0.12 ( 16) metal coordination : angle 4.84703 / 3.09 ( 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 360 residues out of total 2114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 309 time to evaluate : 0.901 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 77 ARG cc_start: 0.8824 (OUTLIER) cc_final: 0.8293 (ttp-170) REVERT: A 259 ASN cc_start: 0.8322 (m-40) cc_final: 0.7903 (m110) REVERT: A 318 GLN cc_start: 0.8854 (OUTLIER) cc_final: 0.8396 (tm-30) REVERT: B 124 LEU cc_start: 0.9085 (OUTLIER) cc_final: 0.8815 (tt) REVERT: B 247 ASP cc_start: 0.8235 (p0) cc_final: 0.7926 (p0) REVERT: B 362 ARG cc_start: 0.9039 (OUTLIER) cc_final: 0.7271 (mtt180) REVERT: C 133 ARG cc_start: 0.8994 (OUTLIER) cc_final: 0.6929 (mmm160) REVERT: D 86 ARG cc_start: 0.8923 (OUTLIER) cc_final: 0.7976 (ptm160) REVERT: D 330 GLN cc_start: 0.8958 (OUTLIER) cc_final: 0.8518 (tm-30) REVERT: E 99 LYS cc_start: 0.8923 (OUTLIER) cc_final: 0.8615 (mtpt) REVERT: F 6 GLU cc_start: 0.8055 (OUTLIER) cc_final: 0.6963 (tm-30) REVERT: F 56 ARG cc_start: 0.8669 (OUTLIER) cc_final: 0.8113 (mtp180) REVERT: F 173 ASP cc_start: 0.8276 (m-30) cc_final: 0.8064 (m-30) REVERT: F 264 LYS cc_start: 0.9151 (OUTLIER) cc_final: 0.8653 (ttpp) REVERT: G 11 LEU cc_start: 0.9143 (OUTLIER) cc_final: 0.8788 (mp) REVERT: G 48 ASP cc_start: 0.8128 (t0) cc_final: 0.7785 (t0) REVERT: G 204 MET cc_start: 0.8994 (mmm) cc_final: 0.8461 (mmm) REVERT: G 261 ASP cc_start: 0.8638 (OUTLIER) cc_final: 0.8382 (t0) outliers start: 51 outliers final: 20 residues processed: 336 average time/residue: 0.9407 time to fit residues: 344.5893 Evaluate side-chains 337 residues out of total 2114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 304 time to evaluate : 0.721 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 351 MET 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 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 56 ARG Chi-restraints excluded: chain F residue 69 THR Chi-restraints excluded: chain F residue 84 GLU 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 261 ASP 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: 0.6980 chunk 66 optimal weight: 0.4980 chunk 223 optimal weight: 2.9990 chunk 33 optimal weight: 0.7980 chunk 194 optimal weight: 0.9980 chunk 161 optimal weight: 0.6980 chunk 164 optimal weight: 0.4980 chunk 170 optimal weight: 0.6980 chunk 114 optimal weight: 1.9990 chunk 160 optimal weight: 0.9980 chunk 52 optimal weight: 1.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2533 r_free = 0.2533 target = 0.050613 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2293 r_free = 0.2293 target = 0.041473 restraints weight = 37671.783| |-----------------------------------------------------------------------------| r_work (start): 0.2292 rms_B_bonded: 1.07 r_work: 0.2199 rms_B_bonded: 1.50 restraints_weight: 0.5000 r_work: 0.2108 rms_B_bonded: 2.57 restraints_weight: 0.2500 r_work (final): 0.2108 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8854 moved from start: 0.1610 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= 0.133 Angle : 0.556 8.811 29254 Z= 0.282 Chirality : 0.038 0.177 3373 Planarity : 0.004 0.051 3618 Dihedral : 14.879 133.283 3358 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 2.03 % Allowed : 15.56 % Favored : 82.40 % 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: 2.09 (0.17), residues: 2514 helix: 2.17 (0.15), residues: 1291 sheet: 1.24 (0.24), residues: 441 loop : 0.21 (0.23), residues: 782 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG F 240 TYR 0.013 0.001 TYR D 3 PHE 0.038 0.001 PHE G 230 TRP 0.013 0.001 TRP D 10 HIS 0.010 0.001 HIS E 56 Details of bonding type rmsd/Z covalent geometry : bond 0.00306 / 0.13 (21373) covalent geometry : angle 0.53913 / 0.28 (29230) hydrogen bonds : bond 0.03778 / 2.54 ( 1185) hydrogen bonds : angle 3.67984 / 2.69 ( 3316) metal coordination : bond 0.00250 / 0.12 ( 16) metal coordination : angle 4.80935 / 3.07 ( 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 351 residues out of total 2114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 308 time to evaluate : 0.855 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 77 ARG cc_start: 0.8832 (OUTLIER) cc_final: 0.8273 (ttp-170) REVERT: A 259 ASN cc_start: 0.8324 (m-40) cc_final: 0.7902 (m110) REVERT: A 318 GLN cc_start: 0.8865 (OUTLIER) cc_final: 0.8397 (tm-30) REVERT: B 124 LEU cc_start: 0.9097 (OUTLIER) cc_final: 0.8828 (tt) REVERT: B 247 ASP cc_start: 0.8236 (p0) cc_final: 0.7930 (p0) REVERT: B 362 ARG cc_start: 0.9040 (OUTLIER) cc_final: 0.7264 (mtt180) REVERT: C 133 ARG cc_start: 0.9004 (OUTLIER) cc_final: 0.6939 (mmm160) REVERT: D 86 ARG cc_start: 0.8933 (OUTLIER) cc_final: 0.7976 (ptm160) REVERT: D 330 GLN cc_start: 0.8958 (OUTLIER) cc_final: 0.8515 (tm-30) REVERT: E 99 LYS cc_start: 0.8924 (OUTLIER) cc_final: 0.8618 (mtpt) REVERT: F 6 GLU cc_start: 0.8061 (OUTLIER) cc_final: 0.6973 (tm-30) REVERT: F 56 ARG cc_start: 0.8660 (OUTLIER) cc_final: 0.8098 (mtp180) REVERT: F 173 ASP cc_start: 0.8267 (m-30) cc_final: 0.8054 (m-30) REVERT: F 264 LYS cc_start: 0.9155 (OUTLIER) cc_final: 0.8657 (ttpp) REVERT: G 11 LEU cc_start: 0.9109 (OUTLIER) cc_final: 0.8749 (mp) REVERT: G 14 LEU cc_start: 0.8678 (OUTLIER) cc_final: 0.8462 (mp) REVERT: G 48 ASP cc_start: 0.8077 (t0) cc_final: 0.7757 (t0) REVERT: G 204 MET cc_start: 0.8991 (mmm) cc_final: 0.8466 (mmm) REVERT: G 261 ASP cc_start: 0.8643 (OUTLIER) cc_final: 0.8386 (t0) outliers start: 43 outliers final: 19 residues processed: 332 average time/residue: 0.9297 time to fit residues: 337.1067 Evaluate side-chains 333 residues out of total 2114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 300 time to evaluate : 0.828 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 124 LEU Chi-restraints excluded: chain B residue 136 PHE Chi-restraints excluded: chain B residue 214 LEU 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 86 ARG 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 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 262 LEU Chi-restraints excluded: chain F residue 264 LYS Chi-restraints excluded: chain F residue 293 THR Chi-restraints excluded: chain G residue 11 LEU Chi-restraints excluded: chain G residue 14 LEU Chi-restraints excluded: chain G residue 64 GLU Chi-restraints excluded: chain G residue 261 ASP Chi-restraints excluded: chain G residue 334 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 253 random chunks: chunk 110 optimal weight: 3.9990 chunk 233 optimal weight: 0.0870 chunk 244 optimal weight: 0.0030 chunk 45 optimal weight: 3.9990 chunk 142 optimal weight: 0.2980 chunk 64 optimal weight: 1.9990 chunk 34 optimal weight: 2.9990 chunk 87 optimal weight: 3.9990 chunk 42 optimal weight: 0.9980 chunk 146 optimal weight: 1.9990 chunk 145 optimal weight: 1.9990 overall best weight: 0.6770 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 58 ASN 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 91 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2532 r_free = 0.2532 target = 0.050557 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2291 r_free = 0.2291 target = 0.041407 restraints weight = 37866.002| |-----------------------------------------------------------------------------| r_work (start): 0.2290 rms_B_bonded: 1.08 r_work: 0.2196 rms_B_bonded: 1.51 restraints_weight: 0.5000 r_work: 0.2105 rms_B_bonded: 2.57 restraints_weight: 0.2500 r_work (final): 0.2105 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8856 moved from start: 0.1640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 21389 Z= 0.138 Angle : 0.572 8.992 29254 Z= 0.290 Chirality : 0.038 0.255 3373 Planarity : 0.005 0.051 3618 Dihedral : 14.880 132.917 3358 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 1.94 % Allowed : 15.89 % Favored : 82.17 % 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: 2.06 (0.17), residues: 2514 helix: 2.14 (0.15), residues: 1295 sheet: 1.25 (0.24), residues: 441 loop : 0.17 (0.23), residues: 778 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG F 240 TYR 0.013 0.001 TYR D 3 PHE 0.012 0.001 PHE F 3 TRP 0.013 0.001 TRP B 10 HIS 0.010 0.001 HIS E 56 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.14 (21373) covalent geometry : angle 0.55481 / 0.29 (29230) hydrogen bonds : bond 0.03869 / 2.61 ( 1185) hydrogen bonds : angle 3.72320 / 2.72 ( 3316) metal coordination : bond 0.00257 / 0.12 ( 16) metal coordination : angle 4.86692 / 3.11 ( 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 346 residues out of total 2114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 305 time to evaluate : 0.855 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 77 ARG cc_start: 0.8835 (OUTLIER) cc_final: 0.8299 (ttp-170) REVERT: A 259 ASN cc_start: 0.8325 (m-40) cc_final: 0.7900 (m110) REVERT: A 318 GLN cc_start: 0.8867 (OUTLIER) cc_final: 0.8392 (tm-30) REVERT: B 124 LEU cc_start: 0.9099 (OUTLIER) cc_final: 0.8826 (tt) REVERT: B 247 ASP cc_start: 0.8245 (p0) cc_final: 0.7939 (p0) REVERT: B 362 ARG cc_start: 0.9037 (OUTLIER) cc_final: 0.7260 (mtt180) REVERT: C 133 ARG cc_start: 0.9009 (OUTLIER) cc_final: 0.6933 (mmm160) REVERT: D 86 ARG cc_start: 0.8940 (OUTLIER) cc_final: 0.7973 (ptm160) REVERT: D 330 GLN cc_start: 0.8960 (OUTLIER) cc_final: 0.8513 (tm-30) REVERT: E 99 LYS cc_start: 0.8924 (OUTLIER) cc_final: 0.8620 (mtpt) REVERT: F 6 GLU cc_start: 0.8047 (OUTLIER) cc_final: 0.7001 (tm-30) REVERT: F 56 ARG cc_start: 0.8668 (OUTLIER) cc_final: 0.8125 (mtp180) REVERT: F 173 ASP cc_start: 0.8275 (m-30) cc_final: 0.8056 (m-30) REVERT: F 264 LYS cc_start: 0.9156 (OUTLIER) cc_final: 0.8662 (ttpp) REVERT: G 11 LEU cc_start: 0.9090 (OUTLIER) cc_final: 0.8734 (mp) REVERT: G 48 ASP cc_start: 0.8039 (t0) cc_final: 0.7732 (t0) REVERT: G 204 MET cc_start: 0.8990 (mmm) cc_final: 0.8464 (mmm) REVERT: G 261 ASP cc_start: 0.8644 (OUTLIER) cc_final: 0.8387 (t0) outliers start: 41 outliers final: 23 residues processed: 328 average time/residue: 0.9225 time to fit residues: 330.7373 Evaluate side-chains 337 residues out of total 2114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 301 time to evaluate : 0.771 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 337 LYS 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 252 LEU Chi-restraints excluded: chain C residue 351 MET 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 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 56 ARG Chi-restraints excluded: chain F residue 69 THR 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 11 LEU Chi-restraints excluded: chain G residue 64 GLU Chi-restraints excluded: chain G residue 88 ILE Chi-restraints excluded: chain G residue 261 ASP 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: 1.9990 chunk 1 optimal weight: 0.0870 chunk 123 optimal weight: 0.8980 chunk 252 optimal weight: 3.9990 chunk 149 optimal weight: 0.9980 chunk 188 optimal weight: 0.7980 chunk 200 optimal weight: 2.9990 chunk 59 optimal weight: 0.9980 chunk 157 optimal weight: 0.9990 chunk 28 optimal weight: 0.8980 chunk 204 optimal weight: 0.8980 overall best weight: 0.7158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 ** both conformations clash, **PLEASE CHECK MANUALLY** G 91 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2526 r_free = 0.2526 target = 0.050315 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2285 r_free = 0.2285 target = 0.041178 restraints weight = 37729.524| |-----------------------------------------------------------------------------| r_work (start): 0.2284 rms_B_bonded: 1.08 r_work: 0.2190 rms_B_bonded: 1.51 restraints_weight: 0.5000 r_work: 0.2100 rms_B_bonded: 2.57 restraints_weight: 0.2500 r_work (final): 0.2100 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8859 moved from start: 0.1634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 21389 Z= 0.143 Angle : 0.570 9.019 29254 Z= 0.289 Chirality : 0.038 0.253 3373 Planarity : 0.005 0.051 3618 Dihedral : 14.884 132.672 3358 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 2.27 % Allowed : 15.66 % Favored : 82.07 % 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: 2.06 (0.17), residues: 2514 helix: 2.14 (0.15), residues: 1290 sheet: 1.26 (0.24), residues: 442 loop : 0.19 (0.23), residues: 782 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG F 240 TYR 0.015 0.001 TYR G 284 PHE 0.011 0.001 PHE F 3 TRP 0.013 0.001 TRP B 10 HIS 0.010 0.001 HIS E 56 Details of bonding type rmsd/Z covalent geometry : bond 0.00332 / 0.14 (21373) covalent geometry : angle 0.55278 / 0.29 (29230) hydrogen bonds : bond 0.03907 / 2.63 ( 1185) hydrogen bonds : angle 3.72418 / 2.72 ( 3316) metal coordination : bond 0.00270 / 0.13 ( 16) metal coordination : angle 4.89085 / 3.13 ( 24) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8162.13 seconds wall clock time: 139 minutes 20.34 seconds (8360.34 seconds total)