Starting phenix.real_space_refine on Sat Mar 7 14:46:59 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7stb_25423/03_2026/7stb_25423_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/7stb_25423/03_2026/7stb_25423.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.72 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7stb_25423/03_2026/7stb_25423.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7stb_25423/03_2026/7stb_25423.map" model { file = "/net/cci-nas-00/data/ceres_data/7stb_25423/03_2026/7stb_25423_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7stb_25423/03_2026/7stb_25423_trim.cif" } resolution = 2.72 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= -0.001 sd= 0.042 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 P 49 5.49 5 Mg 4 5.21 5 S 119 5.16 5 C 14313 2.51 5 N 3904 2.21 5 O 4425 1.98 5 H 22555 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 30 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 45369 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 8378 Number of conformers: 1 Conformer: "" Number of residues, atoms: 515, 8378 Classifications: {'peptide': 515} Link IDs: {'PTRANS': 19, 'TRANS': 495} Chain breaks: 3 Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Chain: "B" Number of atoms: 5027 Number of conformers: 1 Conformer: "" Number of residues, atoms: 315, 5027 Classifications: {'peptide': 315} Link IDs: {'PTRANS': 9, 'TRANS': 305} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 5196 Number of conformers: 1 Conformer: "" Number of residues, atoms: 327, 5196 Classifications: {'peptide': 327} Link IDs: {'PTRANS': 12, 'TRANS': 314} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "D" Number of atoms: 5304 Number of conformers: 1 Conformer: "" Number of residues, atoms: 333, 5304 Classifications: {'peptide': 333} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 12, 'TRANS': 320} Chain: "E" Number of atoms: 5525 Number of conformers: 1 Conformer: "" Number of residues, atoms: 342, 5525 Classifications: {'peptide': 342} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 14, 'TRANS': 327} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "F" Number of atoms: 4539 Number of conformers: 1 Conformer: "" Number of residues, atoms: 288, 4539 Classifications: {'peptide': 288} Link IDs: {'PTRANS': 3, 'TRANS': 284} Chain breaks: 2 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "G" Number of atoms: 5428 Number of conformers: 1 Conformer: "" Number of residues, atoms: 340, 5428 Classifications: {'peptide': 340} Link IDs: {'PTRANS': 11, 'TRANS': 328} Chain breaks: 3 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 10 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "H" Number of atoms: 4710 Number of conformers: 1 Conformer: "" Number of residues, atoms: 293, 4710 Classifications: {'peptide': 293} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 11, 'TRANS': 281} Chain breaks: 6 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "J" Number of atoms: 804 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 804 Classifications: {'DNA': 25} Link IDs: {'rna3p': 24} Chain: "I" Number of atoms: 303 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 303 Classifications: {'DNA': 11} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 10} Unresolved chain link angles: 1 Unresolved chain link dihedrals: 2 Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {' DA%5*END:plan': 1, ' DA%5*END:plan2': 1} Unresolved non-hydrogen planarities: 13 Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 7.17, per 1000 atoms: 0.16 Number of scatterers: 45369 At special positions: 0 Unit cell: (128.856, 122.248, 145.376, 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) S 119 16.00 P 49 15.00 Mg 4 11.99 O 4425 8.00 N 3904 7.00 C 14313 6.00 H 22555 1.00 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: 3.76 Conformation dependent library (CDL) restraints added in 1.0 seconds 5414 Ramachandran restraints generated. 2707 Oldfield, 0 Emsley, 2707 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5266 Finding SS restraints... Secondary structure from input PDB file: 135 helices and 16 sheets defined 54.6% alpha, 17.3% beta 7 base pairs and 27 stacking pairs defined. Time for finding SS restraints: 7.64 Creating SS restraints... Processing helix chain 'A' and resid 65 through 70 Processing helix chain 'A' and resid 74 through 78 removed outlier: 3.572A pdb=" N VAL A 78 " --> pdb=" O LEU A 75 " (cutoff:3.500A) Processing helix chain 'A' and resid 81 through 96 Processing helix chain 'A' and resid 114 through 131 removed outlier: 3.610A pdb=" N ILE A 125 " --> pdb=" O GLU A 121 " (cutoff:3.500A) Proline residue: A 128 - end of helix Processing helix chain 'A' and resid 161 through 163 No H-bonds generated for 'chain 'A' and resid 161 through 163' Processing helix chain 'A' and resid 164 through 174 Processing helix chain 'A' and resid 175 through 176 No H-bonds generated for 'chain 'A' and resid 175 through 176' Processing helix chain 'A' and resid 177 through 181 Processing helix chain 'A' and resid 194 through 211 Processing helix chain 'A' and resid 238 through 242 Processing helix chain 'A' and resid 245 through 250 Processing helix chain 'A' and resid 251 through 256 Processing helix chain 'A' and resid 269 through 284 Processing helix chain 'A' and resid 285 through 291 Processing helix chain 'A' and resid 296 through 306 removed outlier: 3.757A pdb=" N VAL A 300 " --> pdb=" O LYS A 296 " (cutoff:3.500A) Processing helix chain 'A' and resid 310 through 324 Processing helix chain 'A' and resid 338 through 349 Processing helix chain 'A' and resid 355 through 367 Processing helix chain 'A' and resid 367 through 373 removed outlier: 3.786A pdb=" N LYS A 373 " --> pdb=" O ASN A 369 " (cutoff:3.500A) Processing helix chain 'A' and resid 373 through 384 removed outlier: 3.990A pdb=" N LYS A 377 " --> pdb=" O LYS A 373 " (cutoff:3.500A) Processing helix chain 'A' and resid 385 through 387 No H-bonds generated for 'chain 'A' and resid 385 through 387' Processing helix chain 'A' and resid 393 through 408 removed outlier: 3.678A pdb=" N ALA A 397 " --> pdb=" O SER A 393 " (cutoff:3.500A) Processing helix chain 'A' and resid 413 through 431 removed outlier: 3.603A pdb=" N ILE A 431 " --> pdb=" O THR A 427 " (cutoff:3.500A) Processing helix chain 'A' and resid 445 through 472 Processing helix chain 'A' and resid 476 through 483 Processing helix chain 'A' and resid 483 through 509 Proline residue: A 489 - end of helix Processing helix chain 'A' and resid 523 through 528 Processing helix chain 'A' and resid 566 through 590 Processing helix chain 'A' and resid 599 through 605 Processing helix chain 'B' and resid 10 through 15 Processing helix chain 'B' and resid 19 through 23 Processing helix chain 'B' and resid 26 through 40 Processing helix chain 'B' and resid 54 through 68 Processing helix chain 'B' and resid 70 through 74 Processing helix chain 'B' and resid 85 through 99 removed outlier: 4.132A pdb=" N ILE B 93 " --> pdb=" O VAL B 89 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N LYS B 94 " --> pdb=" O ARG B 90 " (cutoff:3.500A) Processing helix chain 'B' and resid 116 through 119 Processing helix chain 'B' and resid 120 through 134 removed outlier: 3.704A pdb=" N ARG B 129 " --> pdb=" O GLN B 125 " (cutoff:3.500A) Processing helix chain 'B' and resid 146 through 150 Processing helix chain 'B' and resid 151 through 156 Processing helix chain 'B' and resid 167 through 183 Processing helix chain 'B' and resid 187 through 199 removed outlier: 3.642A pdb=" N LEU B 191 " --> pdb=" O THR B 187 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N GLU B 199 " --> pdb=" O ILE B 195 " (cutoff:3.500A) Processing helix chain 'B' and resid 201 through 217 Processing helix chain 'B' and resid 220 through 228 Processing helix chain 'B' and resid 231 through 241 Processing helix chain 'B' and resid 244 through 256 Processing helix chain 'B' and resid 262 through 277 Processing helix chain 'B' and resid 281 through 301 Processing helix chain 'B' and resid 305 through 321 removed outlier: 3.660A pdb=" N LEU B 309 " --> pdb=" O THR B 305 " (cutoff:3.500A) Processing helix chain 'C' and resid 9 through 13 removed outlier: 3.687A pdb=" N ASN C 12 " --> pdb=" O SER C 9 " (cutoff:3.500A) Processing helix chain 'C' and resid 14 through 19 Processing helix chain 'C' and resid 23 through 27 Processing helix chain 'C' and resid 30 through 44 Processing helix chain 'C' and resid 58 through 71 Processing helix chain 'C' and resid 74 through 78 Processing helix chain 'C' and resid 89 through 102 removed outlier: 3.967A pdb=" N ILE C 97 " --> pdb=" O VAL C 93 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N LYS C 98 " --> pdb=" O ARG C 94 " (cutoff:3.500A) Processing helix chain 'C' and resid 118 through 122 Processing helix chain 'C' and resid 123 through 137 removed outlier: 4.109A pdb=" N ARG C 132 " --> pdb=" O ASN C 128 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N VAL C 133 " --> pdb=" O ALA C 129 " (cutoff:3.500A) Processing helix chain 'C' and resid 149 through 153 removed outlier: 3.686A pdb=" N LYS C 152 " --> pdb=" O TYR C 149 " (cutoff:3.500A) Processing helix chain 'C' and resid 154 through 161 Processing helix chain 'C' and resid 170 through 185 Processing helix chain 'C' and resid 190 through 202 removed outlier: 3.610A pdb=" N ASN C 202 " --> pdb=" O ILE C 198 " (cutoff:3.500A) Processing helix chain 'C' and resid 204 through 219 Processing helix chain 'C' and resid 228 through 237 Processing helix chain 'C' and resid 240 through 254 Processing helix chain 'C' and resid 255 through 270 removed outlier: 4.069A pdb=" N LYS C 270 " --> pdb=" O VAL C 266 " (cutoff:3.500A) Processing helix chain 'C' and resid 273 through 286 Processing helix chain 'C' and resid 292 through 313 removed outlier: 3.908A pdb=" N ARG C 296 " --> pdb=" O ASN C 292 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LYS C 312 " --> pdb=" O TYR C 308 " (cutoff:3.500A) Processing helix chain 'C' and resid 315 through 332 Processing helix chain 'D' and resid 26 through 31 Processing helix chain 'D' and resid 35 through 39 Processing helix chain 'D' and resid 42 through 52 removed outlier: 4.499A pdb=" N VAL D 48 " --> pdb=" O HIS D 44 " (cutoff:3.500A) Processing helix chain 'D' and resid 53 through 55 No H-bonds generated for 'chain 'D' and resid 53 through 55' Processing helix chain 'D' and resid 70 through 91 removed outlier: 3.602A pdb=" N THR D 74 " --> pdb=" O GLY D 70 " (cutoff:3.500A) Proline residue: D 85 - end of helix removed outlier: 4.085A pdb=" N LYS D 89 " --> pdb=" O PRO D 85 " (cutoff:3.500A) removed outlier: 4.675A pdb=" N SER D 90 " --> pdb=" O ASP D 86 " (cutoff:3.500A) Processing helix chain 'D' and resid 102 through 116 removed outlier: 3.859A pdb=" N VAL D 110 " --> pdb=" O VAL D 106 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N LYS D 111 " --> pdb=" O ARG D 107 " (cutoff:3.500A) Processing helix chain 'D' and resid 122 through 129 removed outlier: 3.561A pdb=" N LEU D 126 " --> pdb=" O SER D 122 " (cutoff:3.500A) Processing helix chain 'D' and resid 141 through 145 Processing helix chain 'D' and resid 146 through 153 Processing helix chain 'D' and resid 153 through 160 removed outlier: 3.622A pdb=" N GLU D 158 " --> pdb=" O ARG D 154 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N TYR D 160 " --> pdb=" O THR D 156 " (cutoff:3.500A) Processing helix chain 'D' and resid 172 through 176 Processing helix chain 'D' and resid 177 through 184 Processing helix chain 'D' and resid 197 through 209 Processing helix chain 'D' and resid 215 through 225 Processing helix chain 'D' and resid 227 through 246 Processing helix chain 'D' and resid 252 through 261 removed outlier: 3.678A pdb=" N VAL D 256 " --> pdb=" O THR D 252 " (cutoff:3.500A) Processing helix chain 'D' and resid 264 through 277 Processing helix chain 'D' and resid 279 through 292 Processing helix chain 'D' and resid 296 through 311 Processing helix chain 'D' and resid 315 through 335 removed outlier: 3.595A pdb=" N TRP D 324 " --> pdb=" O ASN D 320 " (cutoff:3.500A) Processing helix chain 'D' and resid 338 through 353 Processing helix chain 'E' and resid 3 through 8 removed outlier: 3.516A pdb=" N TYR E 8 " --> pdb=" O TRP E 4 " (cutoff:3.500A) Processing helix chain 'E' and resid 19 through 32 removed outlier: 4.331A pdb=" N GLN E 32 " --> pdb=" O SER E 28 " (cutoff:3.500A) Processing helix chain 'E' and resid 48 through 62 Processing helix chain 'E' and resid 63 through 65 No H-bonds generated for 'chain 'E' and resid 63 through 65' Processing helix chain 'E' and resid 97 through 103 removed outlier: 6.890A pdb=" N ASN E 103 " --> pdb=" O ASP E 100 " (cutoff:3.500A) Processing helix chain 'E' and resid 104 through 112 removed outlier: 3.904A pdb=" N VAL E 108 " --> pdb=" O ASN E 104 " (cutoff:3.500A) Processing helix chain 'E' and resid 112 through 119 Processing helix chain 'E' and resid 142 through 146 Processing helix chain 'E' and resid 147 through 161 removed outlier: 3.559A pdb=" N ARG E 155 " --> pdb=" O GLN E 151 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N ARG E 156 " --> pdb=" O ALA E 152 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N THR E 157 " --> pdb=" O ALA E 153 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N TYR E 161 " --> pdb=" O THR E 157 " (cutoff:3.500A) Processing helix chain 'E' and resid 178 through 185 Processing helix chain 'E' and resid 194 through 209 Processing helix chain 'E' and resid 216 through 227 Processing helix chain 'E' and resid 229 through 244 Processing helix chain 'E' and resid 257 through 273 Processing helix chain 'E' and resid 275 through 292 removed outlier: 3.650A pdb=" N ALA E 284 " --> pdb=" O ILE E 280 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N VAL E 285 " --> pdb=" O GLU E 281 " (cutoff:3.500A) Processing helix chain 'E' and resid 295 through 308 Processing helix chain 'E' and resid 314 through 335 Processing helix chain 'E' and resid 338 through 354 Processing helix chain 'F' and resid 17 through 26 removed outlier: 3.606A pdb=" N ILE F 21 " --> pdb=" O HIS F 17 " (cutoff:3.500A) Processing helix chain 'F' and resid 27 through 32 Proline residue: F 30 - end of helix No H-bonds generated for 'chain 'F' and resid 27 through 32' Processing helix chain 'F' and resid 65 through 67 No H-bonds generated for 'chain 'F' and resid 65 through 67' Processing helix chain 'F' and resid 88 through 93 removed outlier: 3.570A pdb=" N VAL F 93 " --> pdb=" O ILE F 89 " (cutoff:3.500A) Processing helix chain 'F' and resid 141 through 145 removed outlier: 4.304A pdb=" N LEU F 145 " --> pdb=" O THR F 142 " (cutoff:3.500A) Processing helix chain 'F' and resid 159 through 173 Processing helix chain 'F' and resid 239 through 243 Processing helix chain 'F' and resid 245 through 251 removed outlier: 3.823A pdb=" N ILE F 251 " --> pdb=" O LYS F 247 " (cutoff:3.500A) Processing helix chain 'F' and resid 317 through 328 Processing helix chain 'G' and resid 9 through 27 Processing helix chain 'G' and resid 59 through 61 No H-bonds generated for 'chain 'G' and resid 59 through 61' Processing helix chain 'G' and resid 68 through 71 Processing helix chain 'G' and resid 74 through 76 No H-bonds generated for 'chain 'G' and resid 74 through 76' Processing helix chain 'G' and resid 98 through 106 Processing helix chain 'G' and resid 127 through 131 Processing helix chain 'G' and resid 161 through 174 Processing helix chain 'G' and resid 188 through 205 Processing helix chain 'G' and resid 234 through 244 removed outlier: 3.755A pdb=" N ASN G 243 " --> pdb=" O ASN G 239 " (cutoff:3.500A) Processing helix chain 'G' and resid 326 through 333 Processing helix chain 'G' and resid 334 through 339 Proline residue: G 337 - end of helix No H-bonds generated for 'chain 'G' and resid 334 through 339' Processing helix chain 'H' and resid 12 through 28 Processing helix chain 'H' and resid 75 through 77 No H-bonds generated for 'chain 'H' and resid 75 through 77' Processing helix chain 'H' and resid 86 through 90 Processing helix chain 'H' and resid 97 through 115 removed outlier: 3.939A pdb=" N SER H 115 " --> pdb=" O MET H 111 " (cutoff:3.500A) Processing helix chain 'H' and resid 213 through 220 removed outlier: 3.711A pdb=" N ILE H 220 " --> pdb=" O GLN H 216 " (cutoff:3.500A) Processing helix chain 'H' and resid 242 through 252 Processing helix chain 'H' and resid 253 through 256 removed outlier: 3.972A pdb=" N TYR H 256 " --> pdb=" O VAL H 253 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 253 through 256' Processing helix chain 'H' and resid 412 through 423 Processing sheet with id=AA1, first strand: chain 'A' and resid 148 through 150 removed outlier: 6.247A pdb=" N ILE A 184 " --> pdb=" O VAL A 220 " (cutoff:3.500A) removed outlier: 7.414A pdb=" N CYS A 222 " --> pdb=" O ILE A 184 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N ILE A 186 " --> pdb=" O CYS A 222 " (cutoff:3.500A) removed outlier: 7.575A pdb=" N THR A 224 " --> pdb=" O ILE A 186 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 226 through 227 Processing sheet with id=AA3, first strand: chain 'B' and resid 75 through 78 removed outlier: 3.540A pdb=" N LEU B 113 " --> pdb=" O ALA B 141 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N ILE B 46 " --> pdb=" O LEU B 161 " (cutoff:3.500A) removed outlier: 7.283A pdb=" N TYR B 163 " --> pdb=" O ILE B 46 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N SER B 48 " --> pdb=" O TYR B 163 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 79 through 82 removed outlier: 6.145A pdb=" N LYS C 112 " --> pdb=" O ARG C 142 " (cutoff:3.500A) removed outlier: 7.541A pdb=" N CYS C 144 " --> pdb=" O LYS C 112 " (cutoff:3.500A) removed outlier: 6.171A pdb=" N ILE C 114 " --> pdb=" O CYS C 144 " (cutoff:3.500A) removed outlier: 7.434A pdb=" N LEU C 146 " --> pdb=" O ILE C 114 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N LEU C 116 " --> pdb=" O LEU C 146 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N LEU C 49 " --> pdb=" O VAL C 145 " (cutoff:3.500A) removed outlier: 8.012A pdb=" N ALA C 147 " --> pdb=" O LEU C 49 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N PHE C 51 " --> pdb=" O ALA C 147 " (cutoff:3.500A) removed outlier: 5.987A pdb=" N LEU C 50 " --> pdb=" O PHE C 164 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 188 through 189 removed outlier: 6.997A pdb=" N LYS C 188 " --> pdb=" O ILE C 227 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'D' and resid 92 through 95 removed outlier: 6.172A pdb=" N LEU D 62 " --> pdb=" O PHE D 187 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 69 through 76 removed outlier: 3.695A pdb=" N ARG E 73 " --> pdb=" O LEU E 85 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LEU E 85 " --> pdb=" O ARG E 73 " (cutoff:3.500A) removed outlier: 6.139A pdb=" N LYS E 136 " --> pdb=" O ARG E 166 " (cutoff:3.500A) removed outlier: 7.278A pdb=" N ILE E 168 " --> pdb=" O LYS E 136 " (cutoff:3.500A) removed outlier: 5.849A pdb=" N VAL E 138 " --> pdb=" O ILE E 168 " (cutoff:3.500A) removed outlier: 7.661A pdb=" N VAL E 170 " --> pdb=" O VAL E 138 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N ILE E 140 " --> pdb=" O VAL E 170 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 212 through 213 removed outlier: 6.475A pdb=" N GLN E 212 " --> pdb=" O LEU E 248 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'F' and resid 69 through 72 removed outlier: 3.660A pdb=" N SER F 127 " --> pdb=" O CYS H 295 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N HIS H 291 " --> pdb=" O GLU F 131 " (cutoff:3.500A) removed outlier: 4.970A pdb=" N LEU H 281 " --> pdb=" O TRP H 296 " (cutoff:3.500A) removed outlier: 5.781A pdb=" N ASN H 286 " --> pdb=" O HIS H 261 " (cutoff:3.500A) removed outlier: 8.265A pdb=" N HIS H 261 " --> pdb=" O ASN H 286 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N HIS H 406 " --> pdb=" O GLY H 266 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'F' and resid 79 through 85 removed outlier: 5.948A pdb=" N ASP F 36 " --> pdb=" O GLU F 51 " (cutoff:3.500A) removed outlier: 4.920A pdb=" N GLU F 51 " --> pdb=" O ASP F 36 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N VAL F 305 " --> pdb=" O LEU F 61 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N LYS F 216 " --> pdb=" O ILE F 157 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 232 through 238 removed outlier: 3.634A pdb=" N GLU F 189 " --> pdb=" O GLU F 185 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N GLU G 63 " --> pdb=" O THR G 6 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'G' and resid 78 through 82 removed outlier: 4.304A pdb=" N SER G 93 " --> pdb=" O ILE G 155 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'G' and resid 78 through 82 removed outlier: 7.222A pdb=" N ASP G 29 " --> pdb=" O MET G 44 " (cutoff:3.500A) removed outlier: 5.831A pdb=" N MET G 44 " --> pdb=" O ASP G 29 " (cutoff:3.500A) removed outlier: 4.918A pdb=" N GLN G 365 " --> pdb=" O ASN G 348 " (cutoff:3.500A) removed outlier: 6.171A pdb=" N ASN G 348 " --> pdb=" O GLN G 365 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'G' and resid 320 through 325 removed outlier: 3.623A pdb=" N SER G 283 " --> pdb=" O LYS H 206 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LYS H 206 " --> pdb=" O SER G 283 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N LYS H 122 " --> pdb=" O GLY H 157 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N LEU H 123 " --> pdb=" O LEU H 3 " (cutoff:3.500A) removed outlier: 5.369A pdb=" N LEU H 3 " --> pdb=" O LEU H 123 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N LEU H 79 " --> pdb=" O ILE H 6 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'G' and resid 320 through 325 removed outlier: 3.623A pdb=" N SER G 283 " --> pdb=" O LYS H 206 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LYS H 206 " --> pdb=" O SER G 283 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N ASN H 96 " --> pdb=" O PRO H 208 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N GLY H 462 " --> pdb=" O LEU H 444 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N SER H 443 " --> pdb=" O GLU H 427 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N GLU H 427 " --> pdb=" O SER H 443 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'G' and resid 270 through 271 removed outlier: 6.363A pdb=" N VAL G 270 " --> pdb=" O LEU G 278 " (cutoff:3.500A) 1282 hydrogen bonds defined for protein. 3663 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 15 hydrogen bonds 30 hydrogen bond angles 0 basepair planarities 7 basepair parallelities 27 stacking parallelities Total time for adding SS restraints: 10.95 Time building geometry restraints manager: 5.16 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.06: 22500 1.06 - 1.28: 3801 1.28 - 1.50: 9706 1.50 - 1.73: 9639 1.73 - 1.95: 179 Bond restraints: 45825 Sorted by residual: bond pdb=" CB PRO E 63 " pdb=" CG PRO E 63 " ideal model delta sigma weight residual 1.492 1.650 -0.158 5.00e-02 4.00e+02 9.98e+00 bond pdb=" CG PRO E 63 " pdb=" CD PRO E 63 " ideal model delta sigma weight residual 1.503 1.403 0.100 3.40e-02 8.65e+02 8.73e+00 bond pdb=" N PRO E 63 " pdb=" CD PRO E 63 " ideal model delta sigma weight residual 1.473 1.500 -0.027 1.40e-02 5.10e+03 3.77e+00 bond pdb=" N MET G 1 " pdb=" CA MET G 1 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.09e+00 bond pdb=" N MET G 1 " pdb=" H MET G 1 " ideal model delta sigma weight residual 0.860 0.890 -0.030 2.00e-02 2.50e+03 2.21e+00 ... (remaining 45820 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.01: 82903 3.01 - 6.03: 83 6.03 - 9.04: 2 9.04 - 12.05: 1 12.05 - 15.06: 1 Bond angle restraints: 82990 Sorted by residual: angle pdb=" CA PRO E 63 " pdb=" N PRO E 63 " pdb=" CD PRO E 63 " ideal model delta sigma weight residual 112.00 96.94 15.06 1.40e+00 5.10e-01 1.16e+02 angle pdb=" N PRO E 63 " pdb=" CD PRO E 63 " pdb=" CG PRO E 63 " ideal model delta sigma weight residual 103.20 94.36 8.84 1.50e+00 4.44e-01 3.48e+01 angle pdb=" CA PRO E 63 " pdb=" CB PRO E 63 " pdb=" CG PRO E 63 " ideal model delta sigma weight residual 104.50 98.74 5.76 1.90e+00 2.77e-01 9.18e+00 angle pdb=" O3' DA I 0 " pdb=" P DC I 1 " pdb=" O5' DC I 1 " ideal model delta sigma weight residual 104.00 99.72 4.28 1.50e+00 4.44e-01 8.12e+00 angle pdb=" C GLY E 62 " pdb=" N PRO E 63 " pdb=" CD PRO E 63 " ideal model delta sigma weight residual 125.00 136.68 -11.68 4.10e+00 5.95e-02 8.12e+00 ... (remaining 82985 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.32: 20561 31.32 - 62.63: 642 62.63 - 93.95: 29 93.95 - 125.26: 2 125.26 - 156.58: 3 Dihedral angle restraints: 21237 sinusoidal: 11945 harmonic: 9292 Sorted by residual: dihedral pdb=" O1B ADP E 401 " pdb=" O3A ADP E 401 " pdb=" PB ADP E 401 " pdb=" PA ADP E 401 " ideal model delta sinusoidal sigma weight residual 300.00 179.41 120.59 1 2.00e+01 2.50e-03 3.62e+01 dihedral pdb=" O1A AGS D 402 " pdb=" O3A AGS D 402 " pdb=" PA AGS D 402 " pdb=" PB AGS D 402 " ideal model delta sinusoidal sigma weight residual -67.73 77.93 -145.66 1 3.00e+01 1.11e-03 1.95e+01 dihedral pdb=" O1A AGS C 402 " pdb=" O3A AGS C 402 " pdb=" PA AGS C 402 " pdb=" PB AGS C 402 " ideal model delta sinusoidal sigma weight residual -67.73 74.68 -142.41 1 3.00e+01 1.11e-03 1.91e+01 ... (remaining 21234 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 2542 0.032 - 0.063: 708 0.063 - 0.095: 225 0.095 - 0.126: 151 0.126 - 0.158: 18 Chirality restraints: 3644 Sorted by residual: chirality pdb=" CA ILE F 41 " pdb=" N ILE F 41 " pdb=" C ILE F 41 " pdb=" CB ILE F 41 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.24e-01 chirality pdb=" CA PRO E 63 " pdb=" N PRO E 63 " pdb=" C PRO E 63 " pdb=" CB PRO E 63 " both_signs ideal model delta sigma weight residual False 2.72 2.58 0.14 2.00e-01 2.50e+01 5.13e-01 chirality pdb=" CA ILE F 269 " pdb=" N ILE F 269 " pdb=" C ILE F 269 " pdb=" CB ILE F 269 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.13e-01 ... (remaining 3641 not shown) Planarity restraints: 6533 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY E 62 " 0.054 5.00e-02 4.00e+02 7.31e-02 8.54e+00 pdb=" N PRO E 63 " -0.126 5.00e-02 4.00e+02 pdb=" CA PRO E 63 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO E 63 " 0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG D 32 " -0.034 5.00e-02 4.00e+02 5.11e-02 4.17e+00 pdb=" N PRO D 33 " 0.088 5.00e-02 4.00e+02 pdb=" CA PRO D 33 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO D 33 " -0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 162 " -0.124 9.50e-02 1.11e+02 4.15e-02 2.06e+00 pdb=" NE ARG B 162 " 0.009 2.00e-02 2.50e+03 pdb=" CZ ARG B 162 " -0.007 2.00e-02 2.50e+03 pdb=" NH1 ARG B 162 " 0.000 2.00e-02 2.50e+03 pdb=" NH2 ARG B 162 " -0.000 2.00e-02 2.50e+03 pdb="HH11 ARG B 162 " 0.003 2.00e-02 2.50e+03 pdb="HH12 ARG B 162 " -0.000 2.00e-02 2.50e+03 pdb="HH21 ARG B 162 " 0.000 2.00e-02 2.50e+03 pdb="HH22 ARG B 162 " -0.000 2.00e-02 2.50e+03 ... (remaining 6530 not shown) Histogram of nonbonded interaction distances: 1.59 - 2.19: 2204 2.19 - 2.80: 93519 2.80 - 3.40: 124855 3.40 - 4.00: 167163 4.00 - 4.60: 259721 Nonbonded interactions: 647462 Sorted by model distance: nonbonded pdb=" O PHE A 387 " pdb=" HD1 HIS A 438 " model vdw 1.593 2.450 nonbonded pdb=" OD1 ASP A 402 " pdb="HH12 ARG E 331 " model vdw 1.594 2.450 nonbonded pdb=" O ARG H 20 " pdb="HD21 ASN H 24 " model vdw 1.595 2.450 nonbonded pdb=" HG1 THR A 224 " pdb=" O3G AGS A 901 " model vdw 1.596 2.450 nonbonded pdb=" H LYS D 34 " pdb=" OE2 GLU D 38 " model vdw 1.598 2.450 ... (remaining 647457 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 4.030 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: 0.190 Extract box with map and model: 0.610 Check model and map are aligned: 0.130 Set scattering table: 0.120 Process input model: 44.730 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:7.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 57.870 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7424 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 : 0.002 0.158 23270 Z= 0.095 Angle : 0.448 15.063 31605 Z= 0.246 Chirality : 0.039 0.158 3644 Planarity : 0.003 0.073 3878 Dihedral : 14.255 156.576 8866 Min Nonbonded Distance : 1.875 Molprobity Statistics. All-atom Clashscore : 4.07 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.62 % Favored : 97.34 % Rotamer: Outliers : 0.00 % Allowed : 0.16 % Favored : 99.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.20 (0.17), residues: 2707 helix: 2.46 (0.15), residues: 1297 sheet: 0.99 (0.22), residues: 562 loop : 0.25 (0.24), residues: 848 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 162 TYR 0.008 0.001 TYR E 287 PHE 0.015 0.001 PHE F 236 TRP 0.006 0.001 TRP G 42 HIS 0.006 0.001 HIS D 340 Details of bonding type rmsd covalent geometry : bond 0.00226 (23270) covalent geometry : angle 0.44798 (31605) hydrogen bonds : bond 0.13949 ( 1271) hydrogen bonds : angle 5.45335 ( 3693) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5414 Ramachandran restraints generated. 2707 Oldfield, 0 Emsley, 2707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5414 Ramachandran restraints generated. 2707 Oldfield, 0 Emsley, 2707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 116 is missing expected H atoms. Skipping. Residue LEU 509 is missing expected H atoms. Skipping. Residue MET 520 is missing expected H atoms. Skipping. Residue SER 547 is missing expected H atoms. Skipping. Residue MET 590 is missing expected H atoms. Skipping. Residue THR 600 is missing expected H atoms. Skipping. Residue LEU 7 is missing expected H atoms. Skipping. Residue THR 56 is missing expected H atoms. Skipping. Residue SER 9 is missing expected H atoms. Skipping. Residue THR 60 is missing expected H atoms. Skipping. Residue THR 72 is missing expected H atoms. Skipping. Residue SER 2 is missing expected H atoms. Skipping. Residue LEU 7 is missing expected H atoms. Skipping. Residue LEU 51 is missing expected H atoms. Skipping. Residue LEU 187 is missing expected H atoms. Skipping. Residue MET 319 is missing expected H atoms. Skipping. Residue LYS 269 is missing expected H atoms. Skipping. Residue SER 448 is missing expected H atoms. Skipping. Residue LYS 457 is missing expected H atoms. Skipping. Evaluate side-chains 410 residues out of total 2495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 410 time to evaluate : 1.260 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 2 residues processed: 410 average time/residue: 1.5830 time to fit residues: 733.8265 Evaluate side-chains 184 residues out of total 2495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 182 time to evaluate : 1.132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 139 ASP Chi-restraints excluded: chain F residue 143 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 275 random chunks: chunk 197 optimal weight: 2.9990 chunk 215 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 132 optimal weight: 4.9990 chunk 261 optimal weight: 6.9990 chunk 248 optimal weight: 9.9990 chunk 207 optimal weight: 5.9990 chunk 155 optimal weight: 4.9990 chunk 244 optimal weight: 6.9990 chunk 183 optimal weight: 1.9990 chunk 111 optimal weight: 3.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 65 GLN A 411 ASN B 146 GLN B 208 ASN B 250 GLN C 30 GLN C 291 GLN D 128 ASN E 19 ASN E 118 GLN ** F 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 69 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.102643 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.079550 restraints weight = 144332.621| |-----------------------------------------------------------------------------| r_work (start): 0.3440 rms_B_bonded: 2.95 r_work: 0.3332 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3332 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7915 moved from start: 0.2172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 23270 Z= 0.223 Angle : 0.572 6.352 31605 Z= 0.313 Chirality : 0.042 0.207 3644 Planarity : 0.004 0.049 3878 Dihedral : 12.775 153.629 3406 Min Nonbonded Distance : 1.659 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.21 % Favored : 96.75 % Rotamer: Outliers : 1.29 % Allowed : 9.53 % Favored : 89.18 % 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: 1.64 (0.17), residues: 2707 helix: 1.95 (0.15), residues: 1315 sheet: 0.75 (0.22), residues: 570 loop : 0.00 (0.23), residues: 822 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 165 TYR 0.012 0.001 TYR H 422 PHE 0.020 0.002 PHE G 152 TRP 0.008 0.001 TRP G 16 HIS 0.008 0.001 HIS E 341 Details of bonding type rmsd covalent geometry : bond 0.00505 (23270) covalent geometry : angle 0.57175 (31605) hydrogen bonds : bond 0.04959 ( 1271) hydrogen bonds : angle 4.67165 ( 3693) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5414 Ramachandran restraints generated. 2707 Oldfield, 0 Emsley, 2707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5414 Ramachandran restraints generated. 2707 Oldfield, 0 Emsley, 2707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 116 is missing expected H atoms. Skipping. Residue LEU 509 is missing expected H atoms. Skipping. Residue MET 520 is missing expected H atoms. Skipping. Residue SER 547 is missing expected H atoms. Skipping. Residue MET 590 is missing expected H atoms. Skipping. Residue THR 600 is missing expected H atoms. Skipping. Residue LEU 7 is missing expected H atoms. Skipping. Residue THR 56 is missing expected H atoms. Skipping. Residue SER 9 is missing expected H atoms. Skipping. Residue THR 60 is missing expected H atoms. Skipping. Residue THR 72 is missing expected H atoms. Skipping. Residue SER 2 is missing expected H atoms. Skipping. Residue LEU 7 is missing expected H atoms. Skipping. Residue LEU 51 is missing expected H atoms. Skipping. Residue LEU 187 is missing expected H atoms. Skipping. Residue MET 319 is missing expected H atoms. Skipping. Residue LYS 269 is missing expected H atoms. Skipping. Residue SER 448 is missing expected H atoms. Skipping. Residue LYS 457 is missing expected H atoms. Skipping. Evaluate side-chains 221 residues out of total 2495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 189 time to evaluate : 1.158 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 68 GLU cc_start: 0.8353 (tp30) cc_final: 0.7902 (tp30) REVERT: A 365 GLU cc_start: 0.8176 (tm-30) cc_final: 0.7911 (pp20) REVERT: B 77 GLU cc_start: 0.8416 (OUTLIER) cc_final: 0.8182 (tp30) REVERT: D 24 GLN cc_start: 0.6463 (tt0) cc_final: 0.5990 (mm-40) REVERT: E 118 GLN cc_start: 0.8373 (mt0) cc_final: 0.7940 (tm-30) REVERT: F 20 HIS cc_start: 0.6807 (m-70) cc_final: 0.6360 (m90) REVERT: F 238 ASP cc_start: 0.7391 (t0) cc_final: 0.7162 (t0) REVERT: G 198 THR cc_start: 0.8116 (m) cc_final: 0.7723 (t) outliers start: 32 outliers final: 11 residues processed: 212 average time/residue: 1.5661 time to fit residues: 378.3080 Evaluate side-chains 174 residues out of total 2495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 162 time to evaluate : 1.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 336 THR Chi-restraints excluded: chain A residue 483 GLU Chi-restraints excluded: chain A residue 584 TYR Chi-restraints excluded: chain B residue 77 GLU Chi-restraints excluded: chain B residue 87 ASP Chi-restraints excluded: chain B residue 204 GLN Chi-restraints excluded: chain D residue 82 LEU Chi-restraints excluded: chain D residue 86 ASP Chi-restraints excluded: chain F residue 106 CYS Chi-restraints excluded: chain F residue 143 ASN Chi-restraints excluded: chain F residue 306 ILE Chi-restraints excluded: chain G residue 91 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 275 random chunks: chunk 25 optimal weight: 3.9990 chunk 62 optimal weight: 3.9990 chunk 181 optimal weight: 5.9990 chunk 35 optimal weight: 0.6980 chunk 105 optimal weight: 3.9990 chunk 255 optimal weight: 4.9990 chunk 221 optimal weight: 0.0770 chunk 97 optimal weight: 3.9990 chunk 76 optimal weight: 3.9990 chunk 112 optimal weight: 1.9990 chunk 158 optimal weight: 0.9990 overall best weight: 1.5544 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 89 GLN A 411 ASN ** A 436 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 146 GLN F 17 HIS ** F 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 199 GLN G 247 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.102411 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.079347 restraints weight = 143946.714| |-----------------------------------------------------------------------------| r_work (start): 0.3438 rms_B_bonded: 2.96 r_work: 0.3330 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3330 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7905 moved from start: 0.2492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 23270 Z= 0.147 Angle : 0.513 5.897 31605 Z= 0.276 Chirality : 0.040 0.171 3644 Planarity : 0.004 0.044 3878 Dihedral : 12.639 153.689 3404 Min Nonbonded Distance : 1.713 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.96 % Favored : 97.01 % Rotamer: Outliers : 1.05 % Allowed : 10.95 % Favored : 88.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.57 (0.17), residues: 2707 helix: 1.98 (0.15), residues: 1311 sheet: 0.67 (0.22), residues: 568 loop : -0.14 (0.23), residues: 828 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 78 TYR 0.010 0.001 TYR G 148 PHE 0.015 0.001 PHE G 152 TRP 0.014 0.001 TRP A 294 HIS 0.005 0.001 HIS D 340 Details of bonding type rmsd covalent geometry : bond 0.00332 (23270) covalent geometry : angle 0.51287 (31605) hydrogen bonds : bond 0.04181 ( 1271) hydrogen bonds : angle 4.44026 ( 3693) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5414 Ramachandran restraints generated. 2707 Oldfield, 0 Emsley, 2707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5414 Ramachandran restraints generated. 2707 Oldfield, 0 Emsley, 2707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 116 is missing expected H atoms. Skipping. Residue LEU 509 is missing expected H atoms. Skipping. Residue MET 520 is missing expected H atoms. Skipping. Residue SER 547 is missing expected H atoms. Skipping. Residue MET 590 is missing expected H atoms. Skipping. Residue THR 600 is missing expected H atoms. Skipping. Residue LEU 7 is missing expected H atoms. Skipping. Residue THR 56 is missing expected H atoms. Skipping. Residue SER 9 is missing expected H atoms. Skipping. Residue THR 60 is missing expected H atoms. Skipping. Residue THR 72 is missing expected H atoms. Skipping. Residue SER 2 is missing expected H atoms. Skipping. Residue LEU 7 is missing expected H atoms. Skipping. Residue LEU 51 is missing expected H atoms. Skipping. Residue LEU 187 is missing expected H atoms. Skipping. Residue MET 319 is missing expected H atoms. Skipping. Residue LYS 269 is missing expected H atoms. Skipping. Residue SER 448 is missing expected H atoms. Skipping. Residue LYS 457 is missing expected H atoms. Skipping. Evaluate side-chains 199 residues out of total 2495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 173 time to evaluate : 1.263 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 68 GLU cc_start: 0.8413 (tp30) cc_final: 0.7938 (tp30) REVERT: A 238 PHE cc_start: 0.5604 (OUTLIER) cc_final: 0.5213 (m-80) REVERT: A 365 GLU cc_start: 0.8158 (tm-30) cc_final: 0.7919 (pp20) REVERT: A 523 PHE cc_start: 0.7549 (m-10) cc_final: 0.7317 (m-10) REVERT: A 584 TYR cc_start: 0.6391 (OUTLIER) cc_final: 0.6179 (t80) REVERT: B 202 MET cc_start: 0.8131 (tpt) cc_final: 0.7912 (tpt) REVERT: D 24 GLN cc_start: 0.6491 (tt0) cc_final: 0.6029 (mm-40) REVERT: D 81 GLU cc_start: 0.7993 (mp0) cc_final: 0.7740 (mp0) REVERT: E 118 GLN cc_start: 0.8322 (mt0) cc_final: 0.7922 (tm-30) REVERT: F 238 ASP cc_start: 0.7309 (t0) cc_final: 0.7079 (t0) REVERT: G 193 ASP cc_start: 0.8024 (m-30) cc_final: 0.7776 (m-30) outliers start: 26 outliers final: 12 residues processed: 189 average time/residue: 1.4068 time to fit residues: 306.8990 Evaluate side-chains 170 residues out of total 2495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 156 time to evaluate : 1.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 287 MET Chi-restraints excluded: chain A residue 336 THR Chi-restraints excluded: chain A residue 483 GLU Chi-restraints excluded: chain A residue 584 TYR Chi-restraints excluded: chain B residue 87 ASP Chi-restraints excluded: chain D residue 82 LEU Chi-restraints excluded: chain D residue 221 LEU Chi-restraints excluded: chain F residue 106 CYS Chi-restraints excluded: chain F residue 143 ASN Chi-restraints excluded: chain F residue 259 MET Chi-restraints excluded: chain F residue 306 ILE Chi-restraints excluded: chain G residue 91 LEU Chi-restraints excluded: chain H residue 1 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 275 random chunks: chunk 42 optimal weight: 4.9990 chunk 208 optimal weight: 4.9990 chunk 197 optimal weight: 0.9990 chunk 229 optimal weight: 3.9990 chunk 263 optimal weight: 4.9990 chunk 60 optimal weight: 0.8980 chunk 193 optimal weight: 2.9990 chunk 198 optimal weight: 5.9990 chunk 21 optimal weight: 4.9990 chunk 103 optimal weight: 2.9990 chunk 146 optimal weight: 0.8980 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 89 GLN A 411 ASN ** A 436 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 146 GLN D 124 HIS ** F 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 199 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.101286 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.078210 restraints weight = 144412.959| |-----------------------------------------------------------------------------| r_work (start): 0.3414 rms_B_bonded: 3.05 r_work: 0.3304 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3304 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7944 moved from start: 0.2770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 23270 Z= 0.163 Angle : 0.513 5.996 31605 Z= 0.276 Chirality : 0.040 0.167 3644 Planarity : 0.004 0.046 3878 Dihedral : 12.721 154.155 3404 Min Nonbonded Distance : 1.707 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.18 % Favored : 96.79 % Rotamer: Outliers : 1.41 % Allowed : 11.31 % Favored : 87.28 % 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: 1.49 (0.17), residues: 2707 helix: 1.93 (0.15), residues: 1319 sheet: 0.58 (0.21), residues: 575 loop : -0.20 (0.23), residues: 813 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 165 TYR 0.012 0.001 TYR A 501 PHE 0.016 0.001 PHE G 152 TRP 0.008 0.001 TRP G 42 HIS 0.006 0.001 HIS D 340 Details of bonding type rmsd covalent geometry : bond 0.00370 (23270) covalent geometry : angle 0.51288 (31605) hydrogen bonds : bond 0.03995 ( 1271) hydrogen bonds : angle 4.37052 ( 3693) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5414 Ramachandran restraints generated. 2707 Oldfield, 0 Emsley, 2707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5414 Ramachandran restraints generated. 2707 Oldfield, 0 Emsley, 2707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 116 is missing expected H atoms. Skipping. Residue LEU 509 is missing expected H atoms. Skipping. Residue MET 520 is missing expected H atoms. Skipping. Residue SER 547 is missing expected H atoms. Skipping. Residue MET 590 is missing expected H atoms. Skipping. Residue THR 600 is missing expected H atoms. Skipping. Residue LEU 7 is missing expected H atoms. Skipping. Residue THR 56 is missing expected H atoms. Skipping. Residue SER 9 is missing expected H atoms. Skipping. Residue THR 60 is missing expected H atoms. Skipping. Residue THR 72 is missing expected H atoms. Skipping. Residue SER 2 is missing expected H atoms. Skipping. Residue LEU 7 is missing expected H atoms. Skipping. Residue LEU 51 is missing expected H atoms. Skipping. Residue LEU 187 is missing expected H atoms. Skipping. Residue MET 319 is missing expected H atoms. Skipping. Residue LYS 269 is missing expected H atoms. Skipping. Residue SER 448 is missing expected H atoms. Skipping. Residue LYS 457 is missing expected H atoms. Skipping. Evaluate side-chains 200 residues out of total 2495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 165 time to evaluate : 1.265 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 68 GLU cc_start: 0.8477 (tp30) cc_final: 0.7932 (tp30) REVERT: A 238 PHE cc_start: 0.5627 (OUTLIER) cc_final: 0.5224 (m-80) REVERT: A 365 GLU cc_start: 0.8092 (tm-30) cc_final: 0.7855 (pp20) REVERT: D 24 GLN cc_start: 0.6588 (tt0) cc_final: 0.6108 (mm-40) REVERT: D 81 GLU cc_start: 0.8077 (mp0) cc_final: 0.7856 (mp0) REVERT: E 118 GLN cc_start: 0.8320 (mt0) cc_final: 0.7910 (tm-30) REVERT: F 20 HIS cc_start: 0.6832 (m-70) cc_final: 0.6385 (m90) REVERT: G 167 LYS cc_start: 0.8446 (OUTLIER) cc_final: 0.8039 (mppt) REVERT: G 193 ASP cc_start: 0.8081 (m-30) cc_final: 0.7810 (m-30) REVERT: H 231 MET cc_start: 0.6765 (OUTLIER) cc_final: 0.6239 (pmt) outliers start: 35 outliers final: 12 residues processed: 189 average time/residue: 1.5031 time to fit residues: 325.2488 Evaluate side-chains 173 residues out of total 2495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 158 time to evaluate : 1.234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 336 THR Chi-restraints excluded: chain A residue 483 GLU Chi-restraints excluded: chain A residue 584 TYR Chi-restraints excluded: chain B residue 87 ASP Chi-restraints excluded: chain B residue 204 GLN Chi-restraints excluded: chain D residue 82 LEU Chi-restraints excluded: chain D residue 221 LEU Chi-restraints excluded: chain E residue 272 LYS Chi-restraints excluded: chain F residue 106 CYS Chi-restraints excluded: chain F residue 259 MET Chi-restraints excluded: chain F residue 306 ILE Chi-restraints excluded: chain G residue 91 LEU Chi-restraints excluded: chain G residue 167 LYS Chi-restraints excluded: chain H residue 231 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 275 random chunks: chunk 147 optimal weight: 4.9990 chunk 49 optimal weight: 9.9990 chunk 40 optimal weight: 3.9990 chunk 15 optimal weight: 0.4980 chunk 0 optimal weight: 3.9990 chunk 193 optimal weight: 4.9990 chunk 130 optimal weight: 3.9990 chunk 19 optimal weight: 3.9990 chunk 156 optimal weight: 0.9980 chunk 182 optimal weight: 5.9990 chunk 247 optimal weight: 3.9990 overall best weight: 2.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 89 GLN A 411 ASN ** A 436 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 146 GLN C 167 GLN ** E 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 199 GLN G 247 ASN H 8 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.098947 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.075990 restraints weight = 144906.617| |-----------------------------------------------------------------------------| r_work (start): 0.3358 rms_B_bonded: 3.03 r_work: 0.3249 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3249 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8016 moved from start: 0.3087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 23270 Z= 0.222 Angle : 0.546 6.146 31605 Z= 0.297 Chirality : 0.042 0.197 3644 Planarity : 0.004 0.058 3878 Dihedral : 12.924 153.942 3402 Min Nonbonded Distance : 1.714 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.55 % Favored : 96.42 % Rotamer: Outliers : 1.45 % Allowed : 11.75 % Favored : 86.79 % 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: 1.22 (0.17), residues: 2707 helix: 1.72 (0.15), residues: 1313 sheet: 0.48 (0.21), residues: 568 loop : -0.34 (0.22), residues: 826 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 165 TYR 0.013 0.001 TYR G 229 PHE 0.023 0.002 PHE G 152 TRP 0.011 0.001 TRP G 16 HIS 0.008 0.001 HIS D 340 Details of bonding type rmsd covalent geometry : bond 0.00506 (23270) covalent geometry : angle 0.54619 (31605) hydrogen bonds : bond 0.04423 ( 1271) hydrogen bonds : angle 4.48209 ( 3693) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5414 Ramachandran restraints generated. 2707 Oldfield, 0 Emsley, 2707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5414 Ramachandran restraints generated. 2707 Oldfield, 0 Emsley, 2707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 116 is missing expected H atoms. Skipping. Residue LEU 509 is missing expected H atoms. Skipping. Residue MET 520 is missing expected H atoms. Skipping. Residue SER 547 is missing expected H atoms. Skipping. Residue MET 590 is missing expected H atoms. Skipping. Residue THR 600 is missing expected H atoms. Skipping. Residue LEU 7 is missing expected H atoms. Skipping. Residue THR 56 is missing expected H atoms. Skipping. Residue SER 9 is missing expected H atoms. Skipping. Residue THR 60 is missing expected H atoms. Skipping. Residue THR 72 is missing expected H atoms. Skipping. Residue SER 2 is missing expected H atoms. Skipping. Residue LEU 7 is missing expected H atoms. Skipping. Residue LEU 51 is missing expected H atoms. Skipping. Residue LEU 187 is missing expected H atoms. Skipping. Residue MET 319 is missing expected H atoms. Skipping. Residue LYS 269 is missing expected H atoms. Skipping. Residue SER 448 is missing expected H atoms. Skipping. Residue LYS 457 is missing expected H atoms. Skipping. Evaluate side-chains 194 residues out of total 2495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 158 time to evaluate : 1.017 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 68 GLU cc_start: 0.8568 (tp30) cc_final: 0.8018 (tp30) REVERT: A 238 PHE cc_start: 0.5695 (OUTLIER) cc_final: 0.5279 (m-80) REVERT: D 24 GLN cc_start: 0.6899 (tt0) cc_final: 0.6350 (mm-40) REVERT: E 118 GLN cc_start: 0.8307 (mt0) cc_final: 0.7938 (tm-30) REVERT: F 20 HIS cc_start: 0.6808 (m-70) cc_final: 0.6345 (m90) REVERT: G 167 LYS cc_start: 0.8457 (OUTLIER) cc_final: 0.8052 (mppt) REVERT: G 193 ASP cc_start: 0.8087 (m-30) cc_final: 0.7724 (m-30) REVERT: H 231 MET cc_start: 0.6827 (OUTLIER) cc_final: 0.6493 (pmt) outliers start: 36 outliers final: 22 residues processed: 179 average time/residue: 1.3473 time to fit residues: 276.8580 Evaluate side-chains 179 residues out of total 2495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 154 time to evaluate : 1.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 HIS Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 336 THR Chi-restraints excluded: chain A residue 416 SER Chi-restraints excluded: chain A residue 483 GLU Chi-restraints excluded: chain A residue 497 TYR Chi-restraints excluded: chain A residue 584 TYR Chi-restraints excluded: chain B residue 77 GLU Chi-restraints excluded: chain B residue 87 ASP Chi-restraints excluded: chain B residue 204 GLN Chi-restraints excluded: chain C residue 167 GLN Chi-restraints excluded: chain D residue 82 LEU Chi-restraints excluded: chain E residue 174 MET Chi-restraints excluded: chain E residue 272 LYS Chi-restraints excluded: chain F residue 25 LEU Chi-restraints excluded: chain F residue 38 LEU Chi-restraints excluded: chain F residue 51 GLU Chi-restraints excluded: chain F residue 106 CYS Chi-restraints excluded: chain F residue 259 MET Chi-restraints excluded: chain F residue 306 ILE Chi-restraints excluded: chain G residue 91 LEU Chi-restraints excluded: chain G residue 167 LYS Chi-restraints excluded: chain G residue 198 THR Chi-restraints excluded: chain G residue 284 MET Chi-restraints excluded: chain H residue 231 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 275 random chunks: chunk 26 optimal weight: 3.9990 chunk 21 optimal weight: 3.9990 chunk 64 optimal weight: 2.9990 chunk 126 optimal weight: 5.9990 chunk 78 optimal weight: 0.9990 chunk 157 optimal weight: 2.9990 chunk 187 optimal weight: 4.9990 chunk 98 optimal weight: 2.9990 chunk 235 optimal weight: 0.8980 chunk 195 optimal weight: 0.8980 chunk 86 optimal weight: 0.9980 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 89 GLN A 411 ASN ** A 436 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 146 GLN C 167 GLN E 227 ASN ** F 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.099928 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.077106 restraints weight = 144264.216| |-----------------------------------------------------------------------------| r_work (start): 0.3385 rms_B_bonded: 2.99 r_work: 0.3279 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3279 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7988 moved from start: 0.3130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 23270 Z= 0.137 Angle : 0.504 6.162 31605 Z= 0.272 Chirality : 0.040 0.168 3644 Planarity : 0.004 0.047 3878 Dihedral : 12.877 153.877 3402 Min Nonbonded Distance : 1.740 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.32 % Favored : 96.64 % Rotamer: Outliers : 1.01 % Allowed : 12.64 % Favored : 86.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.36 (0.17), residues: 2707 helix: 1.85 (0.15), residues: 1320 sheet: 0.47 (0.22), residues: 567 loop : -0.27 (0.23), residues: 820 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 149 TYR 0.011 0.001 TYR A 501 PHE 0.016 0.001 PHE C 166 TRP 0.015 0.001 TRP A 294 HIS 0.004 0.001 HIS D 340 Details of bonding type rmsd covalent geometry : bond 0.00310 (23270) covalent geometry : angle 0.50448 (31605) hydrogen bonds : bond 0.03868 ( 1271) hydrogen bonds : angle 4.31365 ( 3693) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5414 Ramachandran restraints generated. 2707 Oldfield, 0 Emsley, 2707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5414 Ramachandran restraints generated. 2707 Oldfield, 0 Emsley, 2707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 116 is missing expected H atoms. Skipping. Residue LEU 509 is missing expected H atoms. Skipping. Residue MET 520 is missing expected H atoms. Skipping. Residue SER 547 is missing expected H atoms. Skipping. Residue MET 590 is missing expected H atoms. Skipping. Residue THR 600 is missing expected H atoms. Skipping. Residue LEU 7 is missing expected H atoms. Skipping. Residue THR 56 is missing expected H atoms. Skipping. Residue SER 9 is missing expected H atoms. Skipping. Residue THR 60 is missing expected H atoms. Skipping. Residue THR 72 is missing expected H atoms. Skipping. Residue SER 2 is missing expected H atoms. Skipping. Residue LEU 7 is missing expected H atoms. Skipping. Residue LEU 51 is missing expected H atoms. Skipping. Residue LEU 187 is missing expected H atoms. Skipping. Residue MET 319 is missing expected H atoms. Skipping. Residue LYS 269 is missing expected H atoms. Skipping. Residue SER 448 is missing expected H atoms. Skipping. Residue LYS 457 is missing expected H atoms. Skipping. Evaluate side-chains 186 residues out of total 2495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 161 time to evaluate : 1.248 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 68 GLU cc_start: 0.8535 (tp30) cc_final: 0.7971 (tp30) REVERT: A 238 PHE cc_start: 0.5644 (OUTLIER) cc_final: 0.5247 (m-80) REVERT: A 365 GLU cc_start: 0.8145 (tm-30) cc_final: 0.7852 (pp20) REVERT: D 24 GLN cc_start: 0.6839 (tt0) cc_final: 0.6327 (mm-40) REVERT: E 118 GLN cc_start: 0.8309 (mt0) cc_final: 0.7928 (tm-30) REVERT: F 20 HIS cc_start: 0.6773 (m-70) cc_final: 0.6324 (m90) REVERT: G 193 ASP cc_start: 0.8115 (m-30) cc_final: 0.7766 (m-30) outliers start: 25 outliers final: 17 residues processed: 176 average time/residue: 1.1566 time to fit residues: 236.7716 Evaluate side-chains 173 residues out of total 2495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 155 time to evaluate : 1.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 HIS Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 336 THR Chi-restraints excluded: chain A residue 411 ASN Chi-restraints excluded: chain A residue 483 GLU Chi-restraints excluded: chain B residue 87 ASP Chi-restraints excluded: chain B residue 204 GLN Chi-restraints excluded: chain D residue 82 LEU Chi-restraints excluded: chain E residue 174 MET Chi-restraints excluded: chain E residue 272 LYS Chi-restraints excluded: chain F residue 25 LEU Chi-restraints excluded: chain F residue 38 LEU Chi-restraints excluded: chain F residue 51 GLU Chi-restraints excluded: chain F residue 106 CYS Chi-restraints excluded: chain F residue 143 ASN Chi-restraints excluded: chain F residue 259 MET Chi-restraints excluded: chain F residue 306 ILE Chi-restraints excluded: chain G residue 91 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 275 random chunks: chunk 232 optimal weight: 0.6980 chunk 266 optimal weight: 10.0000 chunk 165 optimal weight: 6.9990 chunk 205 optimal weight: 3.9990 chunk 176 optimal weight: 3.9990 chunk 24 optimal weight: 1.9990 chunk 107 optimal weight: 2.9990 chunk 29 optimal weight: 3.9990 chunk 38 optimal weight: 1.9990 chunk 240 optimal weight: 0.9980 chunk 41 optimal weight: 4.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 89 GLN ** A 436 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 250 GLN ** F 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.099562 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.076751 restraints weight = 144153.765| |-----------------------------------------------------------------------------| r_work (start): 0.3376 rms_B_bonded: 2.99 r_work: 0.3269 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3269 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7998 moved from start: 0.3205 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 23270 Z= 0.159 Angle : 0.509 6.483 31605 Z= 0.274 Chirality : 0.040 0.164 3644 Planarity : 0.004 0.049 3878 Dihedral : 12.908 153.924 3402 Min Nonbonded Distance : 1.729 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.73 % Favored : 96.23 % Rotamer: Outliers : 1.01 % Allowed : 13.21 % Favored : 85.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.33 (0.17), residues: 2707 helix: 1.84 (0.15), residues: 1322 sheet: 0.42 (0.21), residues: 568 loop : -0.28 (0.23), residues: 817 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 149 TYR 0.011 0.001 TYR G 148 PHE 0.015 0.001 PHE G 152 TRP 0.009 0.001 TRP A 294 HIS 0.005 0.001 HIS D 340 Details of bonding type rmsd covalent geometry : bond 0.00361 (23270) covalent geometry : angle 0.50911 (31605) hydrogen bonds : bond 0.03892 ( 1271) hydrogen bonds : angle 4.29771 ( 3693) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5414 Ramachandran restraints generated. 2707 Oldfield, 0 Emsley, 2707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5414 Ramachandran restraints generated. 2707 Oldfield, 0 Emsley, 2707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 116 is missing expected H atoms. Skipping. Residue LEU 509 is missing expected H atoms. Skipping. Residue MET 520 is missing expected H atoms. Skipping. Residue SER 547 is missing expected H atoms. Skipping. Residue MET 590 is missing expected H atoms. Skipping. Residue THR 600 is missing expected H atoms. Skipping. Residue LEU 7 is missing expected H atoms. Skipping. Residue THR 56 is missing expected H atoms. Skipping. Residue SER 9 is missing expected H atoms. Skipping. Residue THR 60 is missing expected H atoms. Skipping. Residue THR 72 is missing expected H atoms. Skipping. Residue SER 2 is missing expected H atoms. Skipping. Residue LEU 7 is missing expected H atoms. Skipping. Residue LEU 51 is missing expected H atoms. Skipping. Residue LEU 187 is missing expected H atoms. Skipping. Residue MET 319 is missing expected H atoms. Skipping. Residue LYS 269 is missing expected H atoms. Skipping. Residue SER 448 is missing expected H atoms. Skipping. Residue LYS 457 is missing expected H atoms. Skipping. Evaluate side-chains 181 residues out of total 2495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 156 time to evaluate : 1.342 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 68 GLU cc_start: 0.8549 (tp30) cc_final: 0.7980 (tp30) REVERT: A 238 PHE cc_start: 0.5681 (OUTLIER) cc_final: 0.5286 (m-80) REVERT: A 365 GLU cc_start: 0.8141 (tm-30) cc_final: 0.7874 (pp20) REVERT: D 24 GLN cc_start: 0.6859 (tt0) cc_final: 0.6367 (mm-40) REVERT: E 118 GLN cc_start: 0.8317 (mt0) cc_final: 0.7942 (tm-30) REVERT: F 20 HIS cc_start: 0.6774 (m-70) cc_final: 0.6307 (m90) REVERT: G 167 LYS cc_start: 0.8457 (OUTLIER) cc_final: 0.8048 (mppt) REVERT: G 193 ASP cc_start: 0.8123 (m-30) cc_final: 0.7799 (m-30) REVERT: H 231 MET cc_start: 0.6578 (OUTLIER) cc_final: 0.5940 (pmt) outliers start: 25 outliers final: 16 residues processed: 171 average time/residue: 1.3493 time to fit residues: 265.7208 Evaluate side-chains 171 residues out of total 2495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 152 time to evaluate : 1.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 HIS Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 336 THR Chi-restraints excluded: chain A residue 483 GLU Chi-restraints excluded: chain B residue 87 ASP Chi-restraints excluded: chain B residue 204 GLN Chi-restraints excluded: chain E residue 174 MET Chi-restraints excluded: chain E residue 272 LYS Chi-restraints excluded: chain F residue 25 LEU Chi-restraints excluded: chain F residue 38 LEU Chi-restraints excluded: chain F residue 51 GLU Chi-restraints excluded: chain F residue 106 CYS Chi-restraints excluded: chain F residue 143 ASN Chi-restraints excluded: chain F residue 259 MET Chi-restraints excluded: chain F residue 306 ILE Chi-restraints excluded: chain G residue 91 LEU Chi-restraints excluded: chain G residue 167 LYS Chi-restraints excluded: chain G residue 284 MET Chi-restraints excluded: chain H residue 231 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 275 random chunks: chunk 72 optimal weight: 4.9990 chunk 99 optimal weight: 4.9990 chunk 11 optimal weight: 3.9990 chunk 257 optimal weight: 0.9990 chunk 112 optimal weight: 3.9990 chunk 25 optimal weight: 1.9990 chunk 0 optimal weight: 1.9990 chunk 168 optimal weight: 5.9990 chunk 23 optimal weight: 0.9980 chunk 232 optimal weight: 0.6980 chunk 211 optimal weight: 0.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 89 GLN ** A 436 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.100982 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.078555 restraints weight = 144784.564| |-----------------------------------------------------------------------------| r_work (start): 0.3404 rms_B_bonded: 2.92 r_work: 0.3294 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3294 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7954 moved from start: 0.3257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 23270 Z= 0.122 Angle : 0.498 8.075 31605 Z= 0.266 Chirality : 0.040 0.162 3644 Planarity : 0.004 0.051 3878 Dihedral : 12.890 154.023 3402 Min Nonbonded Distance : 1.745 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.18 % Favored : 96.79 % Rotamer: Outliers : 0.93 % Allowed : 13.21 % Favored : 85.86 % 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: 1.46 (0.17), residues: 2707 helix: 1.94 (0.15), residues: 1322 sheet: 0.46 (0.22), residues: 566 loop : -0.19 (0.23), residues: 819 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 149 TYR 0.010 0.001 TYR G 148 PHE 0.014 0.001 PHE A 523 TRP 0.009 0.001 TRP G 42 HIS 0.004 0.001 HIS D 340 Details of bonding type rmsd covalent geometry : bond 0.00276 (23270) covalent geometry : angle 0.49811 (31605) hydrogen bonds : bond 0.03599 ( 1271) hydrogen bonds : angle 4.20630 ( 3693) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5414 Ramachandran restraints generated. 2707 Oldfield, 0 Emsley, 2707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5414 Ramachandran restraints generated. 2707 Oldfield, 0 Emsley, 2707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 116 is missing expected H atoms. Skipping. Residue LEU 509 is missing expected H atoms. Skipping. Residue MET 520 is missing expected H atoms. Skipping. Residue SER 547 is missing expected H atoms. Skipping. Residue MET 590 is missing expected H atoms. Skipping. Residue THR 600 is missing expected H atoms. Skipping. Residue LEU 7 is missing expected H atoms. Skipping. Residue THR 56 is missing expected H atoms. Skipping. Residue SER 9 is missing expected H atoms. Skipping. Residue THR 60 is missing expected H atoms. Skipping. Residue THR 72 is missing expected H atoms. Skipping. Residue SER 2 is missing expected H atoms. Skipping. Residue LEU 7 is missing expected H atoms. Skipping. Residue LEU 51 is missing expected H atoms. Skipping. Residue LEU 187 is missing expected H atoms. Skipping. Residue MET 319 is missing expected H atoms. Skipping. Residue LYS 269 is missing expected H atoms. Skipping. Residue SER 448 is missing expected H atoms. Skipping. Residue LYS 457 is missing expected H atoms. Skipping. Evaluate side-chains 178 residues out of total 2495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 155 time to evaluate : 0.934 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 68 GLU cc_start: 0.8526 (tp30) cc_final: 0.7940 (tp30) REVERT: A 238 PHE cc_start: 0.5597 (OUTLIER) cc_final: 0.5207 (m-80) REVERT: A 365 GLU cc_start: 0.8249 (tm-30) cc_final: 0.7878 (pp20) REVERT: D 24 GLN cc_start: 0.6837 (tt0) cc_final: 0.6344 (mm-40) REVERT: E 118 GLN cc_start: 0.8288 (mt0) cc_final: 0.7940 (tm-30) REVERT: F 20 HIS cc_start: 0.6780 (m-70) cc_final: 0.6313 (m90) REVERT: G 167 LYS cc_start: 0.8436 (OUTLIER) cc_final: 0.8037 (mppt) REVERT: G 193 ASP cc_start: 0.8136 (m-30) cc_final: 0.7815 (m-30) REVERT: H 231 MET cc_start: 0.6576 (OUTLIER) cc_final: 0.6015 (pmt) outliers start: 23 outliers final: 12 residues processed: 168 average time/residue: 1.1133 time to fit residues: 215.8744 Evaluate side-chains 169 residues out of total 2495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 154 time to evaluate : 0.793 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 HIS Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 336 THR Chi-restraints excluded: chain A residue 483 GLU Chi-restraints excluded: chain D residue 221 LEU Chi-restraints excluded: chain E residue 174 MET Chi-restraints excluded: chain E residue 272 LYS Chi-restraints excluded: chain F residue 25 LEU Chi-restraints excluded: chain F residue 106 CYS Chi-restraints excluded: chain F residue 259 MET Chi-restraints excluded: chain F residue 306 ILE Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain G residue 91 LEU Chi-restraints excluded: chain G residue 167 LYS Chi-restraints excluded: chain H residue 231 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 275 random chunks: chunk 179 optimal weight: 2.9990 chunk 219 optimal weight: 1.9990 chunk 180 optimal weight: 0.5980 chunk 62 optimal weight: 3.9990 chunk 40 optimal weight: 5.9990 chunk 203 optimal weight: 3.9990 chunk 198 optimal weight: 2.9990 chunk 56 optimal weight: 2.9990 chunk 186 optimal weight: 0.6980 chunk 266 optimal weight: 1.9990 chunk 176 optimal weight: 1.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 89 GLN ** A 436 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.099688 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.077030 restraints weight = 143965.021| |-----------------------------------------------------------------------------| r_work (start): 0.3382 rms_B_bonded: 2.98 r_work: 0.3274 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3274 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7991 moved from start: 0.3315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 23270 Z= 0.141 Angle : 0.506 8.100 31605 Z= 0.270 Chirality : 0.040 0.153 3644 Planarity : 0.004 0.049 3878 Dihedral : 12.912 154.298 3402 Min Nonbonded Distance : 1.733 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.62 % Favored : 96.34 % Rotamer: Outliers : 1.05 % Allowed : 13.33 % Favored : 85.62 % 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: 1.43 (0.17), residues: 2707 helix: 1.95 (0.15), residues: 1322 sheet: 0.43 (0.21), residues: 567 loop : -0.24 (0.23), residues: 818 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 149 TYR 0.016 0.001 TYR A 501 PHE 0.030 0.001 PHE A 523 TRP 0.009 0.001 TRP A 294 HIS 0.005 0.001 HIS D 340 Details of bonding type rmsd covalent geometry : bond 0.00322 (23270) covalent geometry : angle 0.50600 (31605) hydrogen bonds : bond 0.03678 ( 1271) hydrogen bonds : angle 4.20772 ( 3693) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5414 Ramachandran restraints generated. 2707 Oldfield, 0 Emsley, 2707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5414 Ramachandran restraints generated. 2707 Oldfield, 0 Emsley, 2707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 116 is missing expected H atoms. Skipping. Residue LEU 509 is missing expected H atoms. Skipping. Residue MET 520 is missing expected H atoms. Skipping. Residue SER 547 is missing expected H atoms. Skipping. Residue MET 590 is missing expected H atoms. Skipping. Residue THR 600 is missing expected H atoms. Skipping. Residue LEU 7 is missing expected H atoms. Skipping. Residue THR 56 is missing expected H atoms. Skipping. Residue SER 9 is missing expected H atoms. Skipping. Residue THR 60 is missing expected H atoms. Skipping. Residue THR 72 is missing expected H atoms. Skipping. Residue SER 2 is missing expected H atoms. Skipping. Residue LEU 7 is missing expected H atoms. Skipping. Residue LEU 51 is missing expected H atoms. Skipping. Residue LEU 187 is missing expected H atoms. Skipping. Residue MET 319 is missing expected H atoms. Skipping. Residue LYS 269 is missing expected H atoms. Skipping. Residue SER 448 is missing expected H atoms. Skipping. Residue LYS 457 is missing expected H atoms. Skipping. Evaluate side-chains 184 residues out of total 2495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 158 time to evaluate : 0.798 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 68 GLU cc_start: 0.8547 (tp30) cc_final: 0.7969 (tp30) REVERT: A 238 PHE cc_start: 0.5701 (OUTLIER) cc_final: 0.5285 (m-80) REVERT: A 365 GLU cc_start: 0.8254 (tm-30) cc_final: 0.7876 (pp20) REVERT: D 24 GLN cc_start: 0.6914 (tt0) cc_final: 0.6113 (mp10) REVERT: E 118 GLN cc_start: 0.8300 (mt0) cc_final: 0.7947 (tm-30) REVERT: F 20 HIS cc_start: 0.6804 (m-70) cc_final: 0.6351 (m90) REVERT: F 238 ASP cc_start: 0.7312 (t0) cc_final: 0.7059 (t0) REVERT: G 167 LYS cc_start: 0.8448 (OUTLIER) cc_final: 0.8032 (mppt) REVERT: G 193 ASP cc_start: 0.8118 (m-30) cc_final: 0.7784 (m-30) REVERT: H 231 MET cc_start: 0.6565 (OUTLIER) cc_final: 0.6022 (pmt) outliers start: 26 outliers final: 17 residues processed: 173 average time/residue: 0.9425 time to fit residues: 189.8003 Evaluate side-chains 172 residues out of total 2495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 152 time to evaluate : 0.768 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 HIS Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 336 THR Chi-restraints excluded: chain A residue 483 GLU Chi-restraints excluded: chain A residue 497 TYR Chi-restraints excluded: chain B residue 175 LEU Chi-restraints excluded: chain D residue 221 LEU Chi-restraints excluded: chain E residue 174 MET Chi-restraints excluded: chain E residue 272 LYS Chi-restraints excluded: chain F residue 25 LEU Chi-restraints excluded: chain F residue 38 LEU Chi-restraints excluded: chain F residue 106 CYS Chi-restraints excluded: chain F residue 125 PHE Chi-restraints excluded: chain F residue 143 ASN Chi-restraints excluded: chain F residue 259 MET Chi-restraints excluded: chain F residue 306 ILE Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain G residue 91 LEU Chi-restraints excluded: chain G residue 167 LYS Chi-restraints excluded: chain H residue 231 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 275 random chunks: chunk 197 optimal weight: 2.9990 chunk 13 optimal weight: 1.9990 chunk 235 optimal weight: 3.9990 chunk 69 optimal weight: 2.9990 chunk 254 optimal weight: 0.0970 chunk 215 optimal weight: 1.9990 chunk 37 optimal weight: 5.9990 chunk 165 optimal weight: 0.1980 chunk 113 optimal weight: 2.9990 chunk 272 optimal weight: 3.9990 chunk 191 optimal weight: 0.0570 overall best weight: 0.8700 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 89 GLN ** A 436 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.100432 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.077733 restraints weight = 144578.260| |-----------------------------------------------------------------------------| r_work (start): 0.3396 rms_B_bonded: 2.99 r_work: 0.3288 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3288 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7973 moved from start: 0.3352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 23270 Z= 0.110 Angle : 0.500 8.045 31605 Z= 0.266 Chirality : 0.039 0.156 3644 Planarity : 0.003 0.043 3878 Dihedral : 12.882 154.528 3402 Min Nonbonded Distance : 1.758 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.25 % Favored : 96.71 % Rotamer: Outliers : 0.73 % Allowed : 13.77 % Favored : 85.50 % 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: 1.51 (0.17), residues: 2707 helix: 2.02 (0.15), residues: 1322 sheet: 0.46 (0.22), residues: 566 loop : -0.20 (0.23), residues: 819 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 272 TYR 0.009 0.001 TYR F 179 PHE 0.027 0.001 PHE A 523 TRP 0.012 0.001 TRP A 294 HIS 0.004 0.001 HIS D 340 Details of bonding type rmsd covalent geometry : bond 0.00249 (23270) covalent geometry : angle 0.50021 (31605) hydrogen bonds : bond 0.03433 ( 1271) hydrogen bonds : angle 4.15625 ( 3693) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5414 Ramachandran restraints generated. 2707 Oldfield, 0 Emsley, 2707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5414 Ramachandran restraints generated. 2707 Oldfield, 0 Emsley, 2707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 116 is missing expected H atoms. Skipping. Residue LEU 509 is missing expected H atoms. Skipping. Residue MET 520 is missing expected H atoms. Skipping. Residue SER 547 is missing expected H atoms. Skipping. Residue MET 590 is missing expected H atoms. Skipping. Residue THR 600 is missing expected H atoms. Skipping. Residue LEU 7 is missing expected H atoms. Skipping. Residue THR 56 is missing expected H atoms. Skipping. Residue SER 9 is missing expected H atoms. Skipping. Residue THR 60 is missing expected H atoms. Skipping. Residue THR 72 is missing expected H atoms. Skipping. Residue SER 2 is missing expected H atoms. Skipping. Residue LEU 7 is missing expected H atoms. Skipping. Residue LEU 51 is missing expected H atoms. Skipping. Residue LEU 187 is missing expected H atoms. Skipping. Residue MET 319 is missing expected H atoms. Skipping. Residue LYS 269 is missing expected H atoms. Skipping. Residue SER 448 is missing expected H atoms. Skipping. Residue LYS 457 is missing expected H atoms. Skipping. Evaluate side-chains 175 residues out of total 2495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 157 time to evaluate : 0.711 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 68 GLU cc_start: 0.8530 (tp30) cc_final: 0.7945 (tp30) REVERT: A 238 PHE cc_start: 0.5677 (OUTLIER) cc_final: 0.5262 (m-80) REVERT: A 365 GLU cc_start: 0.8258 (tm-30) cc_final: 0.7851 (pp20) REVERT: D 24 GLN cc_start: 0.6850 (tt0) cc_final: 0.6343 (mm-40) REVERT: E 118 GLN cc_start: 0.8293 (mt0) cc_final: 0.7941 (tm-30) REVERT: F 20 HIS cc_start: 0.6794 (m-70) cc_final: 0.6341 (m90) REVERT: F 238 ASP cc_start: 0.7272 (t0) cc_final: 0.7051 (t0) REVERT: G 167 LYS cc_start: 0.8458 (OUTLIER) cc_final: 0.8047 (mppt) REVERT: G 193 ASP cc_start: 0.8121 (m-30) cc_final: 0.7787 (m-30) REVERT: H 231 MET cc_start: 0.6483 (OUTLIER) cc_final: 0.5950 (pmt) outliers start: 18 outliers final: 9 residues processed: 167 average time/residue: 0.8477 time to fit residues: 164.3335 Evaluate side-chains 164 residues out of total 2495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 152 time to evaluate : 0.711 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 483 GLU Chi-restraints excluded: chain A residue 497 TYR Chi-restraints excluded: chain E residue 174 MET Chi-restraints excluded: chain E residue 272 LYS Chi-restraints excluded: chain F residue 106 CYS Chi-restraints excluded: chain F residue 125 PHE Chi-restraints excluded: chain F residue 259 MET Chi-restraints excluded: chain F residue 306 ILE Chi-restraints excluded: chain G residue 91 LEU Chi-restraints excluded: chain G residue 167 LYS Chi-restraints excluded: chain H residue 231 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 275 random chunks: chunk 272 optimal weight: 4.9990 chunk 237 optimal weight: 1.9990 chunk 208 optimal weight: 0.6980 chunk 121 optimal weight: 0.7980 chunk 136 optimal weight: 5.9990 chunk 55 optimal weight: 0.6980 chunk 265 optimal weight: 4.9990 chunk 195 optimal weight: 4.9990 chunk 200 optimal weight: 3.9990 chunk 77 optimal weight: 2.9990 chunk 36 optimal weight: 0.7980 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 89 GLN ** A 436 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 247 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.100394 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.077739 restraints weight = 144164.343| |-----------------------------------------------------------------------------| r_work (start): 0.3397 rms_B_bonded: 2.99 r_work: 0.3290 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3290 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7976 moved from start: 0.3389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 23270 Z= 0.117 Angle : 0.507 10.787 31605 Z= 0.268 Chirality : 0.039 0.157 3644 Planarity : 0.004 0.062 3878 Dihedral : 12.876 154.907 3402 Min Nonbonded Distance : 1.754 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.25 % Favored : 96.71 % Rotamer: Outliers : 0.81 % Allowed : 13.85 % Favored : 85.34 % 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: 1.53 (0.17), residues: 2707 helix: 2.05 (0.15), residues: 1322 sheet: 0.45 (0.22), residues: 566 loop : -0.19 (0.23), residues: 819 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG F 149 TYR 0.009 0.001 TYR F 179 PHE 0.026 0.001 PHE A 523 TRP 0.016 0.001 TRP A 294 HIS 0.004 0.001 HIS D 340 Details of bonding type rmsd covalent geometry : bond 0.00266 (23270) covalent geometry : angle 0.50694 (31605) hydrogen bonds : bond 0.03413 ( 1271) hydrogen bonds : angle 4.12673 ( 3693) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11228.70 seconds wall clock time: 190 minutes 47.12 seconds (11447.12 seconds total)