Starting phenix.real_space_refine on Thu Jun 19 07:07:39 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8fs7_29416/06_2025/8fs7_29416.cif Found real_map, /net/cci-nas-00/data/ceres_data/8fs7_29416/06_2025/8fs7_29416.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.85 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8fs7_29416/06_2025/8fs7_29416.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8fs7_29416/06_2025/8fs7_29416.map" model { file = "/net/cci-nas-00/data/ceres_data/8fs7_29416/06_2025/8fs7_29416.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8fs7_29416/06_2025/8fs7_29416.cif" } resolution = 2.85 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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= -0.000 sd= 0.045 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: 6 Type Number sf(0) Gaussians P 71 5.49 5 Mg 4 5.21 5 S 114 5.16 5 C 13864 2.51 5 N 3819 2.21 5 O 4323 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 33 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 22195 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 3580 Number of conformers: 1 Conformer: "" Number of residues, atoms: 439, 3580 Classifications: {'peptide': 439} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 17, 'TRANS': 421} Chain breaks: 2 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "B" Number of atoms: 2503 Number of conformers: 1 Conformer: "" Number of residues, atoms: 319, 2503 Classifications: {'peptide': 319} Link IDs: {'PTRANS': 9, 'TRANS': 309} Chain: "C" Number of atoms: 2586 Number of conformers: 1 Conformer: "" Number of residues, atoms: 327, 2586 Classifications: {'peptide': 327} Link IDs: {'PTRANS': 12, 'TRANS': 314} Chain: "D" Number of atoms: 2616 Number of conformers: 1 Conformer: "" Number of residues, atoms: 330, 2616 Classifications: {'peptide': 330} Link IDs: {'PTRANS': 12, 'TRANS': 317} Chain: "E" Number of atoms: 2668 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2668 Classifications: {'peptide': 338} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 14, 'TRANS': 323} Chain breaks: 1 Chain: "F" Number of atoms: 2276 Number of conformers: 1 Conformer: "" Number of residues, atoms: 282, 2276 Classifications: {'peptide': 282} Link IDs: {'PTRANS': 9, 'TRANS': 272} Chain breaks: 6 Chain: "G" Number of atoms: 2315 Number of conformers: 1 Conformer: "" Number of residues, atoms: 292, 2315 Classifications: {'peptide': 292} Link IDs: {'PTRANS': 5, 'TRANS': 286} Chain breaks: 2 Chain: "H" Number of atoms: 2330 Number of conformers: 1 Conformer: "" Number of residues, atoms: 289, 2330 Classifications: {'peptide': 289} Link IDs: {'PTRANS': 10, 'TRANS': 278} Chain breaks: 4 Chain: "I" Number of atoms: 652 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 652 Classifications: {'DNA': 32} Link IDs: {'rna3p': 31} Chain breaks: 1 Chain: "J" Number of atoms: 313 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 313 Classifications: {'DNA': 16} Link IDs: {'rna3p': 15} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {' DA:plan': 1, ' DA:plan2': 1} Unresolved non-hydrogen planarities: 13 Chain: "K" Number of atoms: 201 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 201 Classifications: {'DNA': 10} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 9} 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: 14.58, per 1000 atoms: 0.66 Number of scatterers: 22195 At special positions: 0 Unit cell: (113.436, 120.888, 139.932, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 114 16.00 P 71 15.00 Mg 4 11.99 O 4323 8.00 N 3819 7.00 C 13864 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 5.61 Conformation dependent library (CDL) restraints added in 2.9 seconds 5140 Ramachandran restraints generated. 2570 Oldfield, 0 Emsley, 2570 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5004 Finding SS restraints... Secondary structure from input PDB file: 116 helices and 16 sheets defined 52.1% alpha, 16.9% beta 22 base pairs and 47 stacking pairs defined. Time for finding SS restraints: 8.85 Creating SS restraints... Processing helix chain 'A' and resid 65 through 70 Processing helix chain 'A' and resid 74 through 78 removed outlier: 3.557A pdb=" N GLN A 77 " --> pdb=" O CYS A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 81 through 96 removed outlier: 3.643A pdb=" N ALA A 91 " --> pdb=" O ASP A 87 " (cutoff:3.500A) Processing helix chain 'A' and resid 114 through 131 removed outlier: 3.560A pdb=" N VAL A 118 " --> pdb=" O SER A 114 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ILE A 119 " --> pdb=" O LYS A 115 " (cutoff:3.500A) removed outlier: 3.676A 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 194 through 210 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 284 through 291 Processing helix chain 'A' and resid 296 through 308 removed outlier: 3.612A 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 372 Processing helix chain 'A' and resid 373 through 384 removed outlier: 3.850A 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: 3.572A pdb=" N ALA A 397 " --> pdb=" O SER A 393 " (cutoff:3.500A) Processing helix chain 'A' and resid 413 through 431 removed outlier: 3.557A pdb=" N ASN A 417 " --> pdb=" O LEU A 413 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ILE A 431 " --> pdb=" O THR A 427 " (cutoff:3.500A) Processing helix chain 'A' and resid 445 through 468 Processing helix chain 'A' and resid 476 through 483 Processing helix chain 'A' and resid 486 through 499 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 55 through 68 Processing helix chain 'B' and resid 69 through 72 removed outlier: 3.832A pdb=" N ALA B 72 " --> pdb=" O ARG B 69 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 69 through 72' Processing helix chain 'B' and resid 85 through 99 Processing helix chain 'B' and resid 116 through 119 removed outlier: 3.504A pdb=" N MET B 119 " --> pdb=" O ALA B 116 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 116 through 119' Processing helix chain 'B' and resid 120 through 134 Processing helix chain 'B' and resid 146 through 150 removed outlier: 3.659A pdb=" N LYS B 149 " --> pdb=" O GLN B 146 " (cutoff:3.500A) Processing helix chain 'B' and resid 151 through 157 removed outlier: 3.927A pdb=" N ARG B 157 " --> pdb=" O PRO B 153 " (cutoff:3.500A) Processing helix chain 'B' and resid 167 through 183 Processing helix chain 'B' and resid 187 through 199 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 257 Processing helix chain 'B' and resid 262 through 276 Processing helix chain 'B' and resid 281 through 302 Processing helix chain 'B' and resid 305 through 322 removed outlier: 3.833A pdb=" N LEU B 309 " --> pdb=" O THR B 305 " (cutoff:3.500A) Processing helix chain 'C' and resid 9 through 13 removed outlier: 3.725A pdb=" N LEU C 13 " --> pdb=" O LYS C 10 " (cutoff:3.500A) 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 101 removed outlier: 3.927A pdb=" N ILE C 97 " --> pdb=" O VAL C 93 " (cutoff:3.500A) removed outlier: 4.344A 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: 4.111A pdb=" N ARG C 132 " --> pdb=" O ASN C 128 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N VAL C 133 " --> pdb=" O ALA C 129 " (cutoff:3.500A) Processing helix chain 'C' and resid 149 through 153 removed outlier: 3.733A 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 186 removed outlier: 3.508A pdb=" N ILE C 174 " --> pdb=" O PRO C 170 " (cutoff:3.500A) Processing helix chain 'C' and resid 190 through 202 removed outlier: 3.555A pdb=" N ASN C 202 " --> pdb=" O ILE C 198 " (cutoff:3.500A) Processing helix chain 'C' and resid 204 through 219 removed outlier: 3.598A pdb=" N VAL C 208 " --> pdb=" O ASP C 204 " (cutoff:3.500A) 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 271 removed outlier: 4.049A pdb=" N LYS C 270 " --> pdb=" O VAL C 266 " (cutoff:3.500A) Processing helix chain 'C' and resid 273 through 287 removed outlier: 3.912A pdb=" N ASP C 287 " --> pdb=" O LYS C 283 " (cutoff:3.500A) Processing helix chain 'C' and resid 293 through 313 removed outlier: 3.794A pdb=" N VAL C 297 " --> pdb=" O GLU C 293 " (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 42 through 55 removed outlier: 3.572A pdb=" N LYS D 54 " --> pdb=" O LYS D 50 " (cutoff:3.500A) Processing helix chain 'D' and resid 70 through 91 Proline residue: D 85 - end of helix removed outlier: 4.617A pdb=" N LYS D 89 " --> pdb=" O PRO D 85 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N SER D 90 " --> pdb=" O ASP D 86 " (cutoff:3.500A) Processing helix chain 'D' and resid 102 through 116 removed outlier: 3.744A pdb=" N VAL D 110 " --> pdb=" O VAL D 106 " (cutoff:3.500A) removed outlier: 4.697A pdb=" N LYS D 111 " --> pdb=" O ARG D 107 " (cutoff:3.500A) Processing helix chain 'D' and resid 122 through 129 Processing helix chain 'D' and resid 141 through 145 Processing helix chain 'D' and resid 146 through 160 removed outlier: 4.371A pdb=" N ARG D 155 " --> pdb=" O SER D 151 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N THR D 156 " --> pdb=" O ALA D 152 " (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 193 through 208 removed outlier: 5.257A pdb=" N ASP D 199 " --> pdb=" O SER D 195 " (cutoff:3.500A) removed outlier: 5.502A pdb=" N ARG D 200 " --> pdb=" O ASN D 196 " (cutoff:3.500A) Processing helix chain 'D' and resid 217 through 224 Processing helix chain 'D' and resid 227 through 246 removed outlier: 3.809A pdb=" N GLY D 231 " --> pdb=" O ASP D 227 " (cutoff:3.500A) Processing helix chain 'D' and resid 252 through 261 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 334 Processing helix chain 'D' and resid 338 through 352 Processing helix chain 'E' and resid 3 through 8 Processing helix chain 'E' and resid 12 through 16 Processing helix chain 'E' and resid 20 through 32 removed outlier: 4.469A pdb=" N GLN E 32 " --> pdb=" O SER E 28 " (cutoff:3.500A) Processing helix chain 'E' and resid 33 through 36 Processing helix chain 'E' and resid 48 through 62 Processing helix chain 'E' and resid 104 through 118 removed outlier: 3.881A pdb=" N VAL E 108 " --> pdb=" O ASN E 104 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ILE E 109 " --> pdb=" O ASP E 105 " (cutoff:3.500A) Processing helix chain 'E' and resid 142 through 146 removed outlier: 3.800A pdb=" N LEU E 146 " --> pdb=" O ALA E 143 " (cutoff:3.500A) Processing helix chain 'E' and resid 149 through 161 removed outlier: 4.027A pdb=" N ARG E 156 " --> pdb=" O ALA E 152 " (cutoff:3.500A) Processing helix chain 'E' and resid 178 through 184 Processing helix chain 'E' and resid 194 through 209 Processing helix chain 'E' and resid 216 through 226 removed outlier: 3.581A pdb=" N LYS E 220 " --> pdb=" O LYS E 216 " (cutoff:3.500A) 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 Processing helix chain 'E' and resid 295 through 309 Processing helix chain 'E' and resid 314 through 334 Processing helix chain 'E' and resid 337 through 354 removed outlier: 4.427A pdb=" N HIS E 341 " --> pdb=" O LYS E 337 " (cutoff:3.500A) Processing helix chain 'F' and resid 12 through 30 removed outlier: 3.663A pdb=" N TYR F 16 " --> pdb=" O ALA F 12 " (cutoff:3.500A) Processing helix chain 'F' and resid 75 through 77 No H-bonds generated for 'chain 'F' and resid 75 through 77' Processing helix chain 'F' and resid 86 through 90 Processing helix chain 'F' and resid 96 through 113 removed outlier: 3.518A pdb=" N LEU F 100 " --> pdb=" O ASN F 96 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N MET F 111 " --> pdb=" O TYR F 107 " (cutoff:3.500A) Processing helix chain 'F' and resid 213 through 219 Processing helix chain 'F' and resid 240 through 252 removed outlier: 4.404A pdb=" N SER F 244 " --> pdb=" O GLY F 240 " (cutoff:3.500A) removed outlier: 4.642A pdb=" N ALA F 245 " --> pdb=" O GLU F 241 " (cutoff:3.500A) Processing helix chain 'F' and resid 412 through 425 removed outlier: 3.617A pdb=" N ALA F 424 " --> pdb=" O LYS F 420 " (cutoff:3.500A) Processing helix chain 'G' and resid 17 through 27 removed outlier: 3.716A pdb=" N ILE G 21 " --> pdb=" O HIS G 17 " (cutoff:3.500A) Processing helix chain 'G' and resid 65 through 67 No H-bonds generated for 'chain 'G' and resid 65 through 67' Processing helix chain 'G' and resid 86 through 93 Processing helix chain 'G' and resid 160 through 173 Processing helix chain 'G' and resid 239 through 243 Processing helix chain 'G' and resid 244 through 246 No H-bonds generated for 'chain 'G' and resid 244 through 246' Processing helix chain 'G' and resid 318 through 330 removed outlier: 4.067A pdb=" N THR G 322 " --> pdb=" O GLU G 318 " (cutoff:3.500A) Processing helix chain 'H' and resid 9 through 27 Processing helix chain 'H' and resid 98 through 103 Processing helix chain 'H' and resid 234 through 244 Processing helix chain 'H' and resid 326 through 336 removed outlier: 4.075A pdb=" N GLY H 336 " --> pdb=" O PHE H 332 " (cutoff:3.500A) Processing helix chain 'H' and resid 337 through 339 No H-bonds generated for 'chain 'H' and resid 337 through 339' Processing sheet with id=AA1, first strand: chain 'A' and resid 148 through 150 removed outlier: 6.131A pdb=" N ILE A 184 " --> pdb=" O VAL A 220 " (cutoff:3.500A) removed outlier: 7.392A pdb=" N CYS A 222 " --> pdb=" O ILE A 184 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N ILE A 186 " --> pdb=" O CYS A 222 " (cutoff:3.500A) removed outlier: 7.783A pdb=" N THR A 224 " --> pdb=" O ILE A 186 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N SER A 108 " --> pdb=" O ILE A 263 " (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 109 through 114 removed outlier: 6.235A pdb=" N LYS B 109 " --> pdb=" O ARG B 139 " (cutoff:3.500A) removed outlier: 7.289A pdb=" N ALA B 141 " --> pdb=" O LYS B 109 " (cutoff:3.500A) removed outlier: 6.153A pdb=" N VAL B 111 " --> pdb=" O ALA B 141 " (cutoff:3.500A) removed outlier: 7.417A pdb=" N ALA B 143 " --> pdb=" O VAL B 111 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N LEU B 113 " --> pdb=" O ALA B 143 " (cutoff:3.500A) removed outlier: 5.840A pdb=" N ILE B 46 " --> pdb=" O LEU B 161 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N TYR B 163 " --> pdb=" O ILE B 46 " (cutoff:3.500A) removed outlier: 6.391A 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: 6.052A 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: 7.127A 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: 6.197A pdb=" N LYS D 135 " --> pdb=" O ARG D 165 " (cutoff:3.500A) removed outlier: 7.610A pdb=" N CYS D 167 " --> pdb=" O LYS D 135 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N ILE D 137 " --> pdb=" O CYS D 167 " (cutoff:3.500A) removed outlier: 7.769A pdb=" N ILE D 169 " --> pdb=" O ILE D 137 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N LEU D 139 " --> pdb=" O ILE D 169 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 93 through 96 removed outlier: 6.066A pdb=" N LEU E 94 " --> pdb=" O ILE E 139 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N LEU E 39 " --> pdb=" O MET E 169 " (cutoff:3.500A) removed outlier: 8.066A pdb=" N CYS E 171 " --> pdb=" O LEU E 39 " (cutoff:3.500A) removed outlier: 6.021A pdb=" N LEU E 41 " --> pdb=" O CYS E 171 " (cutoff:3.500A) removed outlier: 6.042A pdb=" N LEU E 40 " --> pdb=" O ILE E 188 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 69 through 75 Processing sheet with id=AA9, first strand: chain 'F' and resid 79 through 83 removed outlier: 3.911A pdb=" N LEU F 79 " --> pdb=" O ILE F 6 " (cutoff:3.500A) removed outlier: 5.200A pdb=" N LEU F 3 " --> pdb=" O LEU F 123 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N LYS F 122 " --> pdb=" O GLY F 157 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N VAL F 207 " --> pdb=" O LEU F 156 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N LEU F 68 " --> pdb=" O SER F 46 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N GLU F 427 " --> pdb=" O SER F 443 " (cutoff:3.500A) removed outlier: 4.741A pdb=" N VAL F 428 " --> pdb=" O LEU F 235 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'F' and resid 79 through 83 removed outlier: 3.911A pdb=" N LEU F 79 " --> pdb=" O ILE F 6 " (cutoff:3.500A) removed outlier: 5.200A pdb=" N LEU F 3 " --> pdb=" O LEU F 123 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N LYS F 122 " --> pdb=" O GLY F 157 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N VAL F 207 " --> pdb=" O LEU F 156 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N SER H 283 " --> pdb=" O LYS F 206 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLU H 251 " --> pdb=" O PHE H 266 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 405 through 406 Processing sheet with id=AB3, first strand: chain 'F' and resid 405 through 406 removed outlier: 3.591A pdb=" N ARG G 129 " --> pdb=" O GLU F 293 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'G' and resid 80 through 85 removed outlier: 7.189A pdb=" N ASP G 36 " --> pdb=" O GLU G 51 " (cutoff:3.500A) removed outlier: 5.912A pdb=" N GLU G 51 " --> pdb=" O ASP G 36 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N PHE G 48 " --> pdb=" O LEU G 60 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ILE G 56 " --> pdb=" O ASN G 52 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N VAL G 305 " --> pdb=" O LEU G 61 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ILE G 304 " --> pdb=" O SER G 271 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N SER G 271 " --> pdb=" O ILE G 304 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ILE G 306 " --> pdb=" O ILE G 269 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N VAL G 264 " --> pdb=" O ASP G 260 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N LYS G 216 " --> pdb=" O ILE G 157 " (cutoff:3.500A) removed outlier: 7.668A pdb=" N LYS G 159 " --> pdb=" O LEU G 214 " (cutoff:3.500A) removed outlier: 7.378A pdb=" N LEU G 214 " --> pdb=" O LYS G 159 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'G' and resid 232 through 238 removed outlier: 4.633A pdb=" N PHE G 192 " --> pdb=" O LEU G 207 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LYS G 204 " --> pdb=" O GLU H 147 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N PHE H 3 " --> pdb=" O VAL H 120 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'H' and resid 78 through 80 Processing sheet with id=AB7, first strand: chain 'H' and resid 78 through 80 removed outlier: 7.174A pdb=" N ASP H 29 " --> pdb=" O MET H 44 " (cutoff:3.500A) removed outlier: 5.774A pdb=" N MET H 44 " --> pdb=" O ASP H 29 " (cutoff:3.500A) removed outlier: 4.875A pdb=" N GLN H 365 " --> pdb=" O ASN H 348 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N ASN H 348 " --> pdb=" O GLN H 365 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N PHE H 353 " --> pdb=" O ASN H 228 " (cutoff:3.500A) 1182 hydrogen bonds defined for protein. 3396 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 55 hydrogen bonds 110 hydrogen bond angles 0 basepair planarities 22 basepair parallelities 47 stacking parallelities Total time for adding SS restraints: 9.91 Time building geometry restraints manager: 6.44 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.36: 7207 1.36 - 1.51: 6083 1.51 - 1.66: 9230 1.66 - 1.80: 79 1.80 - 1.95: 90 Bond restraints: 22689 Sorted by residual: bond pdb=" N SER E 90 " pdb=" CA SER E 90 " ideal model delta sigma weight residual 1.456 1.487 -0.031 1.04e-02 9.25e+03 8.84e+00 bond pdb=" N HIS E 93 " pdb=" CA HIS E 93 " ideal model delta sigma weight residual 1.455 1.490 -0.034 1.21e-02 6.83e+03 8.09e+00 bond pdb=" N VAL D 256 " pdb=" CA VAL D 256 " ideal model delta sigma weight residual 1.461 1.494 -0.033 1.17e-02 7.31e+03 8.01e+00 bond pdb=" N VAL D 262 " pdb=" CA VAL D 262 " ideal model delta sigma weight residual 1.459 1.491 -0.032 1.17e-02 7.31e+03 7.66e+00 bond pdb=" N ILE C 198 " pdb=" CA ILE C 198 " ideal model delta sigma weight residual 1.461 1.493 -0.033 1.19e-02 7.06e+03 7.58e+00 ... (remaining 22684 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.02: 30457 2.02 - 4.05: 392 4.05 - 6.07: 48 6.07 - 8.09: 9 8.09 - 10.12: 3 Bond angle restraints: 30909 Sorted by residual: angle pdb=" CB ILE H 161 " pdb=" CG1 ILE H 161 " pdb=" CD1 ILE H 161 " ideal model delta sigma weight residual 113.80 122.52 -8.72 2.10e+00 2.27e-01 1.72e+01 angle pdb=" C VAL D 216 " pdb=" N LEU D 217 " pdb=" CA LEU D 217 " ideal model delta sigma weight residual 121.54 129.07 -7.53 1.91e+00 2.74e-01 1.55e+01 angle pdb=" CA ILE H 161 " pdb=" CB ILE H 161 " pdb=" CG1 ILE H 161 " ideal model delta sigma weight residual 110.40 116.75 -6.35 1.70e+00 3.46e-01 1.40e+01 angle pdb=" CA SER E 90 " pdb=" C SER E 90 " pdb=" N PRO E 91 " ideal model delta sigma weight residual 117.96 120.97 -3.01 8.10e-01 1.52e+00 1.38e+01 angle pdb=" CA ILE E 107 " pdb=" CB ILE E 107 " pdb=" CG1 ILE E 107 " ideal model delta sigma weight residual 110.40 116.71 -6.31 1.70e+00 3.46e-01 1.38e+01 ... (remaining 30904 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.71: 12717 31.71 - 63.43: 970 63.43 - 95.14: 32 95.14 - 126.85: 1 126.85 - 158.57: 2 Dihedral angle restraints: 13722 sinusoidal: 6046 harmonic: 7676 Sorted by residual: dihedral pdb=" C5' ADP E 500 " pdb=" O5' ADP E 500 " pdb=" PA ADP E 500 " pdb=" O2A ADP E 500 " ideal model delta sinusoidal sigma weight residual -60.00 98.57 -158.57 1 2.00e+01 2.50e-03 4.63e+01 dihedral pdb=" O2A ADP E 500 " pdb=" O3A ADP E 500 " pdb=" PA ADP E 500 " pdb=" PB ADP E 500 " ideal model delta sinusoidal sigma weight residual -60.00 72.96 -132.96 1 2.00e+01 2.50e-03 4.04e+01 dihedral pdb=" O1B ADP E 500 " pdb=" O3A ADP E 500 " pdb=" PB ADP E 500 " pdb=" PA ADP E 500 " ideal model delta sinusoidal sigma weight residual -60.00 64.39 -124.39 1 2.00e+01 2.50e-03 3.76e+01 ... (remaining 13719 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 2496 0.036 - 0.071: 766 0.071 - 0.107: 218 0.107 - 0.143: 82 0.143 - 0.178: 12 Chirality restraints: 3574 Sorted by residual: chirality pdb=" CA ILE F 468 " pdb=" N ILE F 468 " pdb=" C ILE F 468 " pdb=" CB ILE F 468 " both_signs ideal model delta sigma weight residual False 2.43 2.61 -0.18 2.00e-01 2.50e+01 7.94e-01 chirality pdb=" CA VAL E 88 " pdb=" N VAL E 88 " pdb=" C VAL E 88 " pdb=" CB VAL E 88 " both_signs ideal model delta sigma weight residual False 2.44 2.62 -0.17 2.00e-01 2.50e+01 7.59e-01 chirality pdb=" CB ILE E 211 " pdb=" CA ILE E 211 " pdb=" CG1 ILE E 211 " pdb=" CG2 ILE E 211 " both_signs ideal model delta sigma weight residual False 2.64 2.48 0.16 2.00e-01 2.50e+01 6.80e-01 ... (remaining 3571 not shown) Planarity restraints: 3695 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU D 217 " 0.016 2.00e-02 2.50e+03 3.18e-02 1.01e+01 pdb=" C LEU D 217 " -0.055 2.00e-02 2.50e+03 pdb=" O LEU D 217 " 0.021 2.00e-02 2.50e+03 pdb=" N GLU D 218 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY E 62 " 0.052 5.00e-02 4.00e+02 7.86e-02 9.88e+00 pdb=" N PRO E 63 " -0.136 5.00e-02 4.00e+02 pdb=" CA PRO E 63 " 0.041 5.00e-02 4.00e+02 pdb=" CD PRO E 63 " 0.043 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR E 97 " -0.042 5.00e-02 4.00e+02 6.44e-02 6.63e+00 pdb=" N PRO E 98 " 0.111 5.00e-02 4.00e+02 pdb=" CA PRO E 98 " -0.035 5.00e-02 4.00e+02 pdb=" CD PRO E 98 " -0.035 5.00e-02 4.00e+02 ... (remaining 3692 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.63: 254 2.63 - 3.20: 18985 3.20 - 3.77: 35787 3.77 - 4.33: 49329 4.33 - 4.90: 81329 Nonbonded interactions: 185684 Sorted by model distance: nonbonded pdb=" O2G AGS B 401 " pdb="MG MG B 402 " model vdw 2.068 2.170 nonbonded pdb="MG MG C 401 " pdb=" O2G AGS C 402 " model vdw 2.070 2.170 nonbonded pdb=" OG1 THR C 60 " pdb="MG MG C 401 " model vdw 2.075 2.170 nonbonded pdb=" OG1 THR B 56 " pdb="MG MG B 402 " model vdw 2.078 2.170 nonbonded pdb=" O3G AGS D 401 " pdb="MG MG D 402 " model vdw 2.098 2.170 ... (remaining 185679 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: 5.500 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.970 Check model and map are aligned: 0.180 Set scattering table: 0.210 Process input model: 60.880 Find NCS groups from input model: 0.670 Set up NCS constraints: 0.120 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:14.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 82.560 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8095 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 : 0.003 0.041 22689 Z= 0.160 Angle : 0.559 10.118 30909 Z= 0.316 Chirality : 0.041 0.178 3574 Planarity : 0.004 0.079 3695 Dihedral : 19.012 158.569 8718 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 2.37 % Allowed : 25.66 % Favored : 71.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.67 (0.17), residues: 2570 helix: 1.16 (0.15), residues: 1235 sheet: 0.25 (0.24), residues: 548 loop : -0.40 (0.22), residues: 787 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP E 259 HIS 0.006 0.001 HIS E 93 PHE 0.012 0.001 PHE H 152 TYR 0.025 0.001 TYR B 186 ARG 0.011 0.000 ARG D 230 Details of bonding type rmsd hydrogen bonds : bond 0.17236 ( 1209) hydrogen bonds : angle 6.91896 ( 3506) covalent geometry : bond 0.00271 (22689) covalent geometry : angle 0.55931 (30909) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5140 Ramachandran restraints generated. 2570 Oldfield, 0 Emsley, 2570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5140 Ramachandran restraints generated. 2570 Oldfield, 0 Emsley, 2570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 344 residues out of total 2368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 288 time to evaluate : 2.850 Fit side-chains revert: symmetry clash REVERT: A 284 ASN cc_start: 0.7204 (m-40) cc_final: 0.6977 (m110) REVERT: C 87 ASP cc_start: 0.7902 (t70) cc_final: 0.7647 (t0) REVERT: F 41 ARG cc_start: 0.5911 (OUTLIER) cc_final: 0.5591 (ptp-110) REVERT: F 470 ARG cc_start: 0.7572 (ptt90) cc_final: 0.7345 (ptt180) REVERT: G 151 ARG cc_start: 0.7635 (tpp80) cc_final: 0.7390 (mpp80) REVERT: G 202 PHE cc_start: 0.7272 (OUTLIER) cc_final: 0.6839 (m-80) REVERT: H 45 ASN cc_start: 0.7840 (t0) cc_final: 0.7613 (t0) REVERT: H 63 GLU cc_start: 0.6966 (pm20) cc_final: 0.6576 (pm20) REVERT: H 250 ASP cc_start: 0.7759 (p0) cc_final: 0.7555 (p0) REVERT: H 284 MET cc_start: 0.7030 (ttt) cc_final: 0.6811 (ttm) outliers start: 56 outliers final: 43 residues processed: 338 average time/residue: 1.1823 time to fit residues: 463.1046 Evaluate side-chains 306 residues out of total 2368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 261 time to evaluate : 2.457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 GLN Chi-restraints excluded: chain A residue 197 THR Chi-restraints excluded: chain A residue 313 SER Chi-restraints excluded: chain A residue 455 SER Chi-restraints excluded: chain A residue 483 GLU Chi-restraints excluded: chain A residue 536 VAL Chi-restraints excluded: chain B residue 135 SER Chi-restraints excluded: chain B residue 137 SER Chi-restraints excluded: chain B residue 148 ASN Chi-restraints excluded: chain B residue 167 SER Chi-restraints excluded: chain C residue 138 THR Chi-restraints excluded: chain C residue 268 SER Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 79 THR Chi-restraints excluded: chain D residue 86 ASP Chi-restraints excluded: chain D residue 96 ASN Chi-restraints excluded: chain D residue 173 VAL Chi-restraints excluded: chain D residue 254 THR Chi-restraints excluded: chain D residue 266 ASP Chi-restraints excluded: chain E residue 23 THR Chi-restraints excluded: chain E residue 93 HIS Chi-restraints excluded: chain E residue 297 ASN Chi-restraints excluded: chain E residue 352 CYS Chi-restraints excluded: chain F residue 41 ARG Chi-restraints excluded: chain F residue 81 THR Chi-restraints excluded: chain F residue 97 CYS Chi-restraints excluded: chain F residue 118 ASN Chi-restraints excluded: chain F residue 218 THR Chi-restraints excluded: chain F residue 409 ILE Chi-restraints excluded: chain F residue 414 ASP Chi-restraints excluded: chain F residue 419 SER Chi-restraints excluded: chain G residue 15 THR Chi-restraints excluded: chain G residue 82 LEU Chi-restraints excluded: chain G residue 89 ILE Chi-restraints excluded: chain G residue 130 VAL Chi-restraints excluded: chain G residue 173 ILE Chi-restraints excluded: chain G residue 202 PHE Chi-restraints excluded: chain H residue 109 ASP Chi-restraints excluded: chain H residue 117 THR Chi-restraints excluded: chain H residue 120 VAL Chi-restraints excluded: chain H residue 136 VAL Chi-restraints excluded: chain H residue 263 ILE Chi-restraints excluded: chain H residue 264 THR Chi-restraints excluded: chain H residue 322 ILE Chi-restraints excluded: chain H residue 369 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 221 optimal weight: 1.9990 chunk 198 optimal weight: 3.9990 chunk 110 optimal weight: 1.9990 chunk 67 optimal weight: 0.9980 chunk 133 optimal weight: 0.8980 chunk 106 optimal weight: 0.0070 chunk 205 optimal weight: 2.9990 chunk 79 optimal weight: 0.9990 chunk 124 optimal weight: 0.1980 chunk 152 optimal weight: 2.9990 chunk 237 optimal weight: 4.9990 overall best weight: 0.6200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 73 ASN ** A 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 409 ASN C 74 ASN ** C 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 292 ASN ** D 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 208 ASN H 233 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4060 r_free = 0.4060 target = 0.175844 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.139832 restraints weight = 24740.528| |-----------------------------------------------------------------------------| r_work (start): 0.3657 rms_B_bonded: 2.04 r_work: 0.3463 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.3463 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8162 moved from start: 0.0959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 22689 Z= 0.119 Angle : 0.519 9.378 30909 Z= 0.274 Chirality : 0.040 0.153 3574 Planarity : 0.004 0.058 3695 Dihedral : 16.309 172.420 3570 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.70 % Favored : 96.26 % Rotamer: Outliers : 4.44 % Allowed : 22.27 % Favored : 73.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.00 (0.17), residues: 2570 helix: 1.50 (0.15), residues: 1243 sheet: 0.28 (0.23), residues: 536 loop : -0.27 (0.23), residues: 791 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP F 69 HIS 0.005 0.001 HIS H 259 PHE 0.023 0.001 PHE G 40 TYR 0.015 0.001 TYR A 235 ARG 0.006 0.000 ARG D 230 Details of bonding type rmsd hydrogen bonds : bond 0.03952 ( 1209) hydrogen bonds : angle 4.89052 ( 3506) covalent geometry : bond 0.00263 (22689) covalent geometry : angle 0.51860 (30909) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5140 Ramachandran restraints generated. 2570 Oldfield, 0 Emsley, 2570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5140 Ramachandran restraints generated. 2570 Oldfield, 0 Emsley, 2570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 384 residues out of total 2368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 279 time to evaluate : 2.766 Fit side-chains REVERT: A 227 GLU cc_start: 0.8214 (mm-30) cc_final: 0.7982 (tt0) REVERT: A 354 ASN cc_start: 0.8413 (m-40) cc_final: 0.8201 (t0) REVERT: A 375 ASP cc_start: 0.7373 (OUTLIER) cc_final: 0.7144 (t0) REVERT: A 497 TYR cc_start: 0.5549 (OUTLIER) cc_final: 0.5267 (p90) REVERT: B 148 ASN cc_start: 0.7807 (OUTLIER) cc_final: 0.7467 (p0) REVERT: B 183 ASP cc_start: 0.7906 (t70) cc_final: 0.7349 (t0) REVERT: B 291 GLU cc_start: 0.7557 (OUTLIER) cc_final: 0.7188 (mp0) REVERT: C 94 ARG cc_start: 0.8365 (OUTLIER) cc_final: 0.7916 (mtp180) REVERT: C 167 GLN cc_start: 0.8842 (OUTLIER) cc_final: 0.8451 (pt0) REVERT: C 305 ASP cc_start: 0.7782 (m-30) cc_final: 0.7526 (m-30) REVERT: D 111 LYS cc_start: 0.8442 (OUTLIER) cc_final: 0.8016 (ttmt) REVERT: E 221 ARG cc_start: 0.7188 (mtp85) cc_final: 0.6915 (mtp-110) REVERT: F 199 LYS cc_start: 0.6621 (mptt) cc_final: 0.5722 (tptt) REVERT: F 224 MET cc_start: 0.6292 (OUTLIER) cc_final: 0.5729 (mmt) REVERT: F 232 MET cc_start: 0.8264 (OUTLIER) cc_final: 0.7921 (mpp) REVERT: F 470 ARG cc_start: 0.7636 (ptt90) cc_final: 0.7435 (ptt180) REVERT: G 159 LYS cc_start: 0.8246 (OUTLIER) cc_final: 0.7938 (ptmm) REVERT: H 55 ARG cc_start: 0.8830 (OUTLIER) cc_final: 0.8337 (mtm180) REVERT: H 284 MET cc_start: 0.7580 (ttt) cc_final: 0.7323 (ttm) REVERT: H 346 ASN cc_start: 0.4576 (OUTLIER) cc_final: 0.3018 (t0) REVERT: H 348 ASN cc_start: 0.7034 (p0) cc_final: 0.6527 (p0) outliers start: 105 outliers final: 37 residues processed: 352 average time/residue: 1.2198 time to fit residues: 496.4247 Evaluate side-chains 291 residues out of total 2368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 242 time to evaluate : 2.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 197 THR Chi-restraints excluded: chain A residue 375 ASP Chi-restraints excluded: chain A residue 497 TYR Chi-restraints excluded: chain A residue 536 VAL Chi-restraints excluded: chain B residue 148 ASN Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 291 GLU Chi-restraints excluded: chain C residue 94 ARG Chi-restraints excluded: chain C residue 122 MET Chi-restraints excluded: chain C residue 138 THR Chi-restraints excluded: chain C residue 167 GLN Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 79 THR Chi-restraints excluded: chain D residue 86 ASP Chi-restraints excluded: chain D residue 111 LYS Chi-restraints excluded: chain D residue 117 THR Chi-restraints excluded: chain D residue 123 LYS Chi-restraints excluded: chain D residue 173 VAL Chi-restraints excluded: chain D residue 178 ASP Chi-restraints excluded: chain D residue 274 LYS Chi-restraints excluded: chain E residue 90 SER Chi-restraints excluded: chain E residue 92 TYR Chi-restraints excluded: chain E residue 101 MET Chi-restraints excluded: chain E residue 164 ASN Chi-restraints excluded: chain E residue 181 ILE Chi-restraints excluded: chain F residue 81 THR Chi-restraints excluded: chain F residue 93 MET Chi-restraints excluded: chain F residue 224 MET Chi-restraints excluded: chain F residue 232 MET Chi-restraints excluded: chain F residue 280 GLU Chi-restraints excluded: chain F residue 409 ILE Chi-restraints excluded: chain F residue 437 SER Chi-restraints excluded: chain G residue 15 THR Chi-restraints excluded: chain G residue 125 PHE Chi-restraints excluded: chain G residue 159 LYS Chi-restraints excluded: chain G residue 173 ILE Chi-restraints excluded: chain G residue 190 ASN Chi-restraints excluded: chain G residue 196 SER Chi-restraints excluded: chain G residue 261 VAL Chi-restraints excluded: chain G residue 304 ILE Chi-restraints excluded: chain H residue 55 ARG Chi-restraints excluded: chain H residue 80 VAL Chi-restraints excluded: chain H residue 117 THR Chi-restraints excluded: chain H residue 258 VAL Chi-restraints excluded: chain H residue 261 LEU Chi-restraints excluded: chain H residue 264 THR Chi-restraints excluded: chain H residue 322 ILE Chi-restraints excluded: chain H residue 346 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 206 optimal weight: 4.9990 chunk 53 optimal weight: 2.9990 chunk 147 optimal weight: 5.9990 chunk 54 optimal weight: 5.9990 chunk 93 optimal weight: 4.9990 chunk 97 optimal weight: 7.9990 chunk 152 optimal weight: 2.9990 chunk 261 optimal weight: 5.9990 chunk 1 optimal weight: 0.0040 chunk 188 optimal weight: 4.9990 chunk 77 optimal weight: 2.9990 overall best weight: 2.8000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 73 ASN A 81 HIS A 203 GLN A 231 ASN B 148 ASN C 77 ASN ** C 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 184 HIS C 292 ASN E 19 ASN E 110 GLN E 141 ASN E 144 ASN E 227 ASN F 291 HIS ** H 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 100 HIS H 243 ASN H 286 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.164804 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.128080 restraints weight = 24617.713| |-----------------------------------------------------------------------------| r_work (start): 0.3529 rms_B_bonded: 1.80 r_work: 0.3335 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3187 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3187 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8426 moved from start: 0.1845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.066 22689 Z= 0.290 Angle : 0.665 9.896 30909 Z= 0.347 Chirality : 0.047 0.174 3574 Planarity : 0.005 0.067 3695 Dihedral : 16.440 143.254 3522 Min Nonbonded Distance : 1.916 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.47 % Favored : 95.49 % Rotamer: Outliers : 5.79 % Allowed : 21.39 % Favored : 72.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.55 (0.17), residues: 2570 helix: 1.08 (0.15), residues: 1239 sheet: 0.21 (0.22), residues: 542 loop : -0.49 (0.23), residues: 789 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP D 324 HIS 0.010 0.002 HIS B 232 PHE 0.016 0.002 PHE H 56 TYR 0.018 0.002 TYR A 175 ARG 0.013 0.001 ARG F 214 Details of bonding type rmsd hydrogen bonds : bond 0.05544 ( 1209) hydrogen bonds : angle 4.89320 ( 3506) covalent geometry : bond 0.00714 (22689) covalent geometry : angle 0.66504 (30909) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5140 Ramachandran restraints generated. 2570 Oldfield, 0 Emsley, 2570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5140 Ramachandran restraints generated. 2570 Oldfield, 0 Emsley, 2570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 396 residues out of total 2368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 137 poor density : 259 time to evaluate : 2.404 Fit side-chains REVERT: A 225 GLU cc_start: 0.8803 (OUTLIER) cc_final: 0.7867 (mt-10) REVERT: A 227 GLU cc_start: 0.8461 (mm-30) cc_final: 0.8019 (tt0) REVERT: A 288 LEU cc_start: 0.8022 (OUTLIER) cc_final: 0.7362 (mp) REVERT: B 48 SER cc_start: 0.8931 (OUTLIER) cc_final: 0.8446 (m) REVERT: B 100 LYS cc_start: 0.8899 (OUTLIER) cc_final: 0.8509 (tmtt) REVERT: B 148 ASN cc_start: 0.8082 (OUTLIER) cc_final: 0.7684 (p0) REVERT: B 281 LYS cc_start: 0.8026 (mtpt) cc_final: 0.7624 (mttm) REVERT: B 291 GLU cc_start: 0.8022 (OUTLIER) cc_final: 0.7512 (mp0) REVERT: C 94 ARG cc_start: 0.8619 (OUTLIER) cc_final: 0.8137 (mtp180) REVERT: C 106 ILE cc_start: 0.6627 (OUTLIER) cc_final: 0.6270 (pp) REVERT: D 279 ASP cc_start: 0.7881 (t70) cc_final: 0.7610 (t0) REVERT: E 34 ARG cc_start: 0.7586 (mmp-170) cc_final: 0.6687 (mmm-85) REVERT: E 256 LYS cc_start: 0.8210 (mtmm) cc_final: 0.8005 (mtpt) REVERT: F 224 MET cc_start: 0.6465 (OUTLIER) cc_final: 0.5899 (mmm) REVERT: F 232 MET cc_start: 0.8250 (OUTLIER) cc_final: 0.7170 (mpt) REVERT: F 265 MET cc_start: 0.7408 (OUTLIER) cc_final: 0.7141 (mmm) REVERT: F 470 ARG cc_start: 0.7669 (ptt90) cc_final: 0.7351 (ptt180) REVERT: G 10 LYS cc_start: 0.8414 (OUTLIER) cc_final: 0.8066 (mttm) REVERT: G 61 LEU cc_start: 0.8243 (OUTLIER) cc_final: 0.7917 (mp) REVERT: G 325 GLU cc_start: 0.6919 (pp20) cc_final: 0.6693 (pp20) REVERT: H 284 MET cc_start: 0.7830 (ttt) cc_final: 0.7279 (mtp) REVERT: H 346 ASN cc_start: 0.4793 (OUTLIER) cc_final: 0.3098 (m-40) REVERT: H 348 ASN cc_start: 0.7259 (p0) cc_final: 0.6783 (p0) outliers start: 137 outliers final: 71 residues processed: 363 average time/residue: 1.2798 time to fit residues: 532.7287 Evaluate side-chains 322 residues out of total 2368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 237 time to evaluate : 2.436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 GLU Chi-restraints excluded: chain A residue 104 ILE Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 162 GLN Chi-restraints excluded: chain A residue 197 THR Chi-restraints excluded: chain A residue 225 GLU Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 437 ASN Chi-restraints excluded: chain A residue 497 TYR Chi-restraints excluded: chain A residue 536 VAL Chi-restraints excluded: chain B residue 12 VAL Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 48 SER Chi-restraints excluded: chain B residue 100 LYS Chi-restraints excluded: chain B residue 148 ASN Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 246 GLU Chi-restraints excluded: chain B residue 291 GLU Chi-restraints excluded: chain B residue 297 MET Chi-restraints excluded: chain B residue 305 THR Chi-restraints excluded: chain C residue 76 SER Chi-restraints excluded: chain C residue 77 ASN Chi-restraints excluded: chain C residue 91 ASP Chi-restraints excluded: chain C residue 94 ARG Chi-restraints excluded: chain C residue 106 ILE Chi-restraints excluded: chain C residue 138 THR Chi-restraints excluded: chain C residue 258 THR Chi-restraints excluded: chain D residue 35 ASN Chi-restraints excluded: chain D residue 46 VAL Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 79 THR Chi-restraints excluded: chain D residue 86 ASP Chi-restraints excluded: chain D residue 117 THR Chi-restraints excluded: chain D residue 123 LYS Chi-restraints excluded: chain D residue 173 VAL Chi-restraints excluded: chain D residue 178 ASP Chi-restraints excluded: chain D residue 234 LEU Chi-restraints excluded: chain D residue 266 ASP Chi-restraints excluded: chain D residue 296 SER Chi-restraints excluded: chain D residue 316 THR Chi-restraints excluded: chain E residue 58 GLU Chi-restraints excluded: chain E residue 90 SER Chi-restraints excluded: chain E residue 92 TYR Chi-restraints excluded: chain E residue 101 MET Chi-restraints excluded: chain E residue 164 ASN Chi-restraints excluded: chain E residue 168 ILE Chi-restraints excluded: chain E residue 181 ILE Chi-restraints excluded: chain E residue 352 CYS Chi-restraints excluded: chain F residue 81 THR Chi-restraints excluded: chain F residue 93 MET Chi-restraints excluded: chain F residue 224 MET Chi-restraints excluded: chain F residue 225 ILE Chi-restraints excluded: chain F residue 232 MET Chi-restraints excluded: chain F residue 238 ILE Chi-restraints excluded: chain F residue 265 MET Chi-restraints excluded: chain F residue 280 GLU Chi-restraints excluded: chain F residue 281 LEU Chi-restraints excluded: chain F residue 409 ILE Chi-restraints excluded: chain F residue 414 ASP Chi-restraints excluded: chain F residue 437 SER Chi-restraints excluded: chain G residue 10 LYS Chi-restraints excluded: chain G residue 15 THR Chi-restraints excluded: chain G residue 61 LEU Chi-restraints excluded: chain G residue 82 LEU Chi-restraints excluded: chain G residue 125 PHE Chi-restraints excluded: chain G residue 173 ILE Chi-restraints excluded: chain G residue 190 ASN Chi-restraints excluded: chain G residue 196 SER Chi-restraints excluded: chain G residue 240 THR Chi-restraints excluded: chain G residue 261 VAL Chi-restraints excluded: chain G residue 266 SER Chi-restraints excluded: chain G residue 304 ILE Chi-restraints excluded: chain G residue 327 LEU Chi-restraints excluded: chain H residue 80 VAL Chi-restraints excluded: chain H residue 117 THR Chi-restraints excluded: chain H residue 120 VAL Chi-restraints excluded: chain H residue 250 ASP Chi-restraints excluded: chain H residue 258 VAL Chi-restraints excluded: chain H residue 261 LEU Chi-restraints excluded: chain H residue 263 ILE Chi-restraints excluded: chain H residue 264 THR Chi-restraints excluded: chain H residue 282 LEU Chi-restraints excluded: chain H residue 322 ILE Chi-restraints excluded: chain H residue 334 THR Chi-restraints excluded: chain H residue 346 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 51 optimal weight: 0.6980 chunk 193 optimal weight: 1.9990 chunk 47 optimal weight: 0.8980 chunk 57 optimal weight: 0.9980 chunk 194 optimal weight: 1.9990 chunk 231 optimal weight: 0.9980 chunk 125 optimal weight: 0.8980 chunk 17 optimal weight: 0.9980 chunk 78 optimal weight: 0.9980 chunk 238 optimal weight: 0.9990 chunk 137 optimal weight: 0.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 73 ASN A 231 ASN ** C 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 292 ASN E 227 ASN F 263 HIS ** H 100 HIS ** 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 = 0.4019 r_free = 0.4019 target = 0.171159 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.135999 restraints weight = 24774.839| |-----------------------------------------------------------------------------| r_work (start): 0.3634 rms_B_bonded: 1.73 r_work: 0.3442 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3296 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.3296 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8377 moved from start: 0.1844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 22689 Z= 0.133 Angle : 0.529 9.906 30909 Z= 0.281 Chirality : 0.041 0.144 3574 Planarity : 0.004 0.048 3695 Dihedral : 16.237 126.087 3522 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.81 % Favored : 96.15 % Rotamer: Outliers : 4.90 % Allowed : 22.53 % Favored : 72.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.80 (0.17), residues: 2570 helix: 1.33 (0.15), residues: 1243 sheet: 0.18 (0.22), residues: 548 loop : -0.36 (0.24), residues: 779 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 324 HIS 0.009 0.001 HIS E 292 PHE 0.021 0.001 PHE E 61 TYR 0.012 0.001 TYR A 235 ARG 0.009 0.000 ARG D 230 Details of bonding type rmsd hydrogen bonds : bond 0.03952 ( 1209) hydrogen bonds : angle 4.56300 ( 3506) covalent geometry : bond 0.00305 (22689) covalent geometry : angle 0.52917 (30909) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5140 Ramachandran restraints generated. 2570 Oldfield, 0 Emsley, 2570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5140 Ramachandran restraints generated. 2570 Oldfield, 0 Emsley, 2570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 374 residues out of total 2368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 258 time to evaluate : 2.656 Fit side-chains REVERT: A 225 GLU cc_start: 0.8659 (OUTLIER) cc_final: 0.7682 (mt-10) REVERT: A 227 GLU cc_start: 0.8425 (mm-30) cc_final: 0.7992 (tt0) REVERT: A 288 LEU cc_start: 0.8046 (OUTLIER) cc_final: 0.7472 (mp) REVERT: A 307 GLU cc_start: 0.7181 (mt-10) cc_final: 0.6926 (mt-10) REVERT: A 375 ASP cc_start: 0.7422 (OUTLIER) cc_final: 0.7088 (t0) REVERT: B 100 LYS cc_start: 0.8880 (OUTLIER) cc_final: 0.8495 (tmtt) REVERT: B 148 ASN cc_start: 0.8026 (OUTLIER) cc_final: 0.7703 (p0) REVERT: B 183 ASP cc_start: 0.8289 (t70) cc_final: 0.7591 (t0) REVERT: B 197 THR cc_start: 0.8854 (m) cc_final: 0.8562 (p) REVERT: B 291 GLU cc_start: 0.7864 (OUTLIER) cc_final: 0.7396 (mp0) REVERT: B 301 GLU cc_start: 0.8130 (OUTLIER) cc_final: 0.7755 (mt-10) REVERT: C 22 GLU cc_start: 0.8345 (OUTLIER) cc_final: 0.8056 (mm-30) REVERT: C 167 GLN cc_start: 0.9003 (OUTLIER) cc_final: 0.8754 (pt0) REVERT: C 199 GLU cc_start: 0.7815 (OUTLIER) cc_final: 0.7400 (tt0) REVERT: D 254 THR cc_start: 0.8181 (OUTLIER) cc_final: 0.7866 (t) REVERT: D 279 ASP cc_start: 0.7821 (t70) cc_final: 0.7556 (t0) REVERT: F 31 LYS cc_start: 0.7802 (ptmt) cc_final: 0.7457 (pmtt) REVERT: F 71 THR cc_start: 0.7871 (m) cc_final: 0.7516 (p) REVERT: F 88 LEU cc_start: 0.6395 (tp) cc_final: 0.6100 (tm) REVERT: F 224 MET cc_start: 0.6469 (OUTLIER) cc_final: 0.5833 (mmt) REVERT: F 232 MET cc_start: 0.8250 (OUTLIER) cc_final: 0.7160 (mpt) REVERT: F 265 MET cc_start: 0.7334 (OUTLIER) cc_final: 0.7094 (mmm) REVERT: F 470 ARG cc_start: 0.7645 (ptt90) cc_final: 0.7353 (ptt180) REVERT: G 10 LYS cc_start: 0.8405 (OUTLIER) cc_final: 0.7968 (mtpp) REVERT: G 61 LEU cc_start: 0.8166 (OUTLIER) cc_final: 0.7877 (mp) REVERT: G 159 LYS cc_start: 0.8486 (OUTLIER) cc_final: 0.8048 (ptmm) REVERT: H 55 ARG cc_start: 0.8851 (OUTLIER) cc_final: 0.8455 (mtm180) REVERT: H 284 MET cc_start: 0.7793 (ttt) cc_final: 0.7310 (mtp) REVERT: H 346 ASN cc_start: 0.4807 (OUTLIER) cc_final: 0.3237 (t0) REVERT: H 348 ASN cc_start: 0.7159 (p0) cc_final: 0.6587 (p0) outliers start: 116 outliers final: 56 residues processed: 341 average time/residue: 1.2493 time to fit residues: 490.0260 Evaluate side-chains 312 residues out of total 2368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 237 time to evaluate : 2.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 GLU Chi-restraints excluded: chain A residue 104 ILE Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 178 MET Chi-restraints excluded: chain A residue 197 THR Chi-restraints excluded: chain A residue 225 GLU Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 375 ASP Chi-restraints excluded: chain A residue 497 TYR Chi-restraints excluded: chain A residue 536 VAL Chi-restraints excluded: chain B residue 100 LYS Chi-restraints excluded: chain B residue 148 ASN Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 246 GLU Chi-restraints excluded: chain B residue 291 GLU Chi-restraints excluded: chain B residue 301 GLU Chi-restraints excluded: chain C residue 22 GLU Chi-restraints excluded: chain C residue 91 ASP Chi-restraints excluded: chain C residue 138 THR Chi-restraints excluded: chain C residue 167 GLN Chi-restraints excluded: chain C residue 199 GLU Chi-restraints excluded: chain C residue 245 LYS Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 79 THR Chi-restraints excluded: chain D residue 86 ASP Chi-restraints excluded: chain D residue 117 THR Chi-restraints excluded: chain D residue 123 LYS Chi-restraints excluded: chain D residue 173 VAL Chi-restraints excluded: chain D residue 178 ASP Chi-restraints excluded: chain D residue 254 THR Chi-restraints excluded: chain D residue 266 ASP Chi-restraints excluded: chain E residue 23 THR Chi-restraints excluded: chain E residue 58 GLU Chi-restraints excluded: chain E residue 90 SER Chi-restraints excluded: chain E residue 92 TYR Chi-restraints excluded: chain E residue 101 MET Chi-restraints excluded: chain E residue 181 ILE Chi-restraints excluded: chain E residue 232 VAL Chi-restraints excluded: chain E residue 297 ASN Chi-restraints excluded: chain F residue 81 THR Chi-restraints excluded: chain F residue 93 MET Chi-restraints excluded: chain F residue 99 SER Chi-restraints excluded: chain F residue 108 ASP Chi-restraints excluded: chain F residue 122 LYS Chi-restraints excluded: chain F residue 224 MET Chi-restraints excluded: chain F residue 225 ILE Chi-restraints excluded: chain F residue 232 MET Chi-restraints excluded: chain F residue 265 MET Chi-restraints excluded: chain F residue 280 GLU Chi-restraints excluded: chain F residue 281 LEU Chi-restraints excluded: chain F residue 409 ILE Chi-restraints excluded: chain F residue 414 ASP Chi-restraints excluded: chain F residue 437 SER Chi-restraints excluded: chain G residue 10 LYS Chi-restraints excluded: chain G residue 15 THR Chi-restraints excluded: chain G residue 61 LEU Chi-restraints excluded: chain G residue 125 PHE Chi-restraints excluded: chain G residue 159 LYS Chi-restraints excluded: chain G residue 190 ASN Chi-restraints excluded: chain G residue 196 SER Chi-restraints excluded: chain G residue 261 VAL Chi-restraints excluded: chain G residue 266 SER Chi-restraints excluded: chain G residue 304 ILE Chi-restraints excluded: chain G residue 327 LEU Chi-restraints excluded: chain H residue 55 ARG Chi-restraints excluded: chain H residue 80 VAL Chi-restraints excluded: chain H residue 117 THR Chi-restraints excluded: chain H residue 250 ASP Chi-restraints excluded: chain H residue 258 VAL Chi-restraints excluded: chain H residue 261 LEU Chi-restraints excluded: chain H residue 264 THR Chi-restraints excluded: chain H residue 322 ILE Chi-restraints excluded: chain H residue 334 THR Chi-restraints excluded: chain H residue 346 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 202 optimal weight: 2.9990 chunk 147 optimal weight: 9.9990 chunk 221 optimal weight: 9.9990 chunk 213 optimal weight: 1.9990 chunk 190 optimal weight: 5.9990 chunk 256 optimal weight: 0.7980 chunk 151 optimal weight: 6.9990 chunk 227 optimal weight: 4.9990 chunk 91 optimal weight: 0.5980 chunk 173 optimal weight: 4.9990 chunk 47 optimal weight: 4.9990 overall best weight: 2.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 73 ASN A 202 GLN A 231 ASN C 74 ASN C 77 ASN ** C 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 292 ASN E 227 ASN F 247 HIS ** H 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 355 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3940 r_free = 0.3940 target = 0.165003 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.128298 restraints weight = 24845.202| |-----------------------------------------------------------------------------| r_work (start): 0.3534 rms_B_bonded: 1.80 r_work: 0.3336 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3188 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3188 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8430 moved from start: 0.2144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 22689 Z= 0.241 Angle : 0.612 9.846 30909 Z= 0.319 Chirality : 0.045 0.166 3574 Planarity : 0.004 0.054 3695 Dihedral : 16.218 128.713 3520 Min Nonbonded Distance : 1.901 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.47 % Favored : 95.49 % Rotamer: Outliers : 5.66 % Allowed : 22.49 % Favored : 71.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.59 (0.17), residues: 2570 helix: 1.12 (0.15), residues: 1243 sheet: 0.12 (0.22), residues: 549 loop : -0.43 (0.24), residues: 778 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP D 324 HIS 0.011 0.002 HIS E 292 PHE 0.015 0.002 PHE A 201 TYR 0.017 0.002 TYR B 186 ARG 0.008 0.001 ARG D 230 Details of bonding type rmsd hydrogen bonds : bond 0.04891 ( 1209) hydrogen bonds : angle 4.67347 ( 3506) covalent geometry : bond 0.00591 (22689) covalent geometry : angle 0.61152 (30909) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5140 Ramachandran restraints generated. 2570 Oldfield, 0 Emsley, 2570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5140 Ramachandran restraints generated. 2570 Oldfield, 0 Emsley, 2570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 376 residues out of total 2368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 134 poor density : 242 time to evaluate : 2.614 Fit side-chains REVERT: A 225 GLU cc_start: 0.8816 (OUTLIER) cc_final: 0.7866 (mt-10) REVERT: A 288 LEU cc_start: 0.7986 (OUTLIER) cc_final: 0.7420 (mp) REVERT: A 296 LYS cc_start: 0.7769 (mptt) cc_final: 0.7505 (mtpt) REVERT: A 307 GLU cc_start: 0.7309 (mt-10) cc_final: 0.6955 (mt-10) REVERT: A 375 ASP cc_start: 0.7458 (OUTLIER) cc_final: 0.7090 (t0) REVERT: B 100 LYS cc_start: 0.8909 (OUTLIER) cc_final: 0.8523 (tmtt) REVERT: B 146 GLN cc_start: 0.8597 (OUTLIER) cc_final: 0.7596 (mm-40) REVERT: B 148 ASN cc_start: 0.8016 (OUTLIER) cc_final: 0.7668 (p0) REVERT: B 291 GLU cc_start: 0.7990 (OUTLIER) cc_final: 0.7485 (mp0) REVERT: B 301 GLU cc_start: 0.8232 (OUTLIER) cc_final: 0.7801 (mt-10) REVERT: D 279 ASP cc_start: 0.7834 (t70) cc_final: 0.7509 (t0) REVERT: E 96 ILE cc_start: 0.8982 (OUTLIER) cc_final: 0.8671 (pt) REVERT: F 100 LEU cc_start: 0.7295 (OUTLIER) cc_final: 0.6967 (mp) REVERT: F 224 MET cc_start: 0.6517 (OUTLIER) cc_final: 0.5940 (mmm) REVERT: G 10 LYS cc_start: 0.8413 (OUTLIER) cc_final: 0.7956 (mtpp) REVERT: G 61 LEU cc_start: 0.8252 (OUTLIER) cc_final: 0.7979 (mp) REVERT: H 55 ARG cc_start: 0.8928 (OUTLIER) cc_final: 0.8511 (mtm180) REVERT: H 160 ILE cc_start: 0.4571 (OUTLIER) cc_final: 0.4211 (mt) REVERT: H 284 MET cc_start: 0.7843 (ttt) cc_final: 0.7346 (mtp) REVERT: H 348 ASN cc_start: 0.7212 (p0) cc_final: 0.6860 (p0) outliers start: 134 outliers final: 67 residues processed: 345 average time/residue: 1.2336 time to fit residues: 489.9190 Evaluate side-chains 314 residues out of total 2368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 232 time to evaluate : 2.651 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 GLU Chi-restraints excluded: chain A residue 104 ILE Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 197 THR Chi-restraints excluded: chain A residue 225 GLU Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 375 ASP Chi-restraints excluded: chain A residue 497 TYR Chi-restraints excluded: chain A residue 536 VAL Chi-restraints excluded: chain B residue 12 VAL Chi-restraints excluded: chain B residue 38 LYS Chi-restraints excluded: chain B residue 48 SER Chi-restraints excluded: chain B residue 100 LYS Chi-restraints excluded: chain B residue 146 GLN Chi-restraints excluded: chain B residue 148 ASN Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 246 GLU Chi-restraints excluded: chain B residue 291 GLU Chi-restraints excluded: chain B residue 297 MET Chi-restraints excluded: chain B residue 301 GLU Chi-restraints excluded: chain C residue 138 THR Chi-restraints excluded: chain C residue 245 LYS Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 79 THR Chi-restraints excluded: chain D residue 86 ASP Chi-restraints excluded: chain D residue 117 THR Chi-restraints excluded: chain D residue 123 LYS Chi-restraints excluded: chain D residue 173 VAL Chi-restraints excluded: chain D residue 178 ASP Chi-restraints excluded: chain D residue 254 THR Chi-restraints excluded: chain D residue 266 ASP Chi-restraints excluded: chain D residue 296 SER Chi-restraints excluded: chain E residue 23 THR Chi-restraints excluded: chain E residue 58 GLU Chi-restraints excluded: chain E residue 90 SER Chi-restraints excluded: chain E residue 92 TYR Chi-restraints excluded: chain E residue 96 ILE Chi-restraints excluded: chain E residue 101 MET Chi-restraints excluded: chain E residue 168 ILE Chi-restraints excluded: chain E residue 181 ILE Chi-restraints excluded: chain E residue 232 VAL Chi-restraints excluded: chain E residue 297 ASN Chi-restraints excluded: chain E residue 315 THR Chi-restraints excluded: chain E residue 352 CYS Chi-restraints excluded: chain F residue 81 THR Chi-restraints excluded: chain F residue 93 MET Chi-restraints excluded: chain F residue 99 SER Chi-restraints excluded: chain F residue 100 LEU Chi-restraints excluded: chain F residue 122 LYS Chi-restraints excluded: chain F residue 224 MET Chi-restraints excluded: chain F residue 225 ILE Chi-restraints excluded: chain F residue 228 ILE Chi-restraints excluded: chain F residue 238 ILE Chi-restraints excluded: chain F residue 280 GLU Chi-restraints excluded: chain F residue 281 LEU Chi-restraints excluded: chain F residue 409 ILE Chi-restraints excluded: chain F residue 414 ASP Chi-restraints excluded: chain G residue 10 LYS Chi-restraints excluded: chain G residue 15 THR Chi-restraints excluded: chain G residue 61 LEU Chi-restraints excluded: chain G residue 82 LEU Chi-restraints excluded: chain G residue 125 PHE Chi-restraints excluded: chain G residue 130 VAL Chi-restraints excluded: chain G residue 196 SER Chi-restraints excluded: chain G residue 261 VAL Chi-restraints excluded: chain G residue 266 SER Chi-restraints excluded: chain G residue 271 SER Chi-restraints excluded: chain G residue 304 ILE Chi-restraints excluded: chain G residue 327 LEU Chi-restraints excluded: chain H residue 35 THR Chi-restraints excluded: chain H residue 55 ARG Chi-restraints excluded: chain H residue 80 VAL Chi-restraints excluded: chain H residue 117 THR Chi-restraints excluded: chain H residue 120 VAL Chi-restraints excluded: chain H residue 160 ILE Chi-restraints excluded: chain H residue 261 LEU Chi-restraints excluded: chain H residue 263 ILE Chi-restraints excluded: chain H residue 264 THR Chi-restraints excluded: chain H residue 277 LEU Chi-restraints excluded: chain H residue 282 LEU Chi-restraints excluded: chain H residue 322 ILE Chi-restraints excluded: chain H residue 350 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 78 optimal weight: 0.5980 chunk 208 optimal weight: 0.9980 chunk 255 optimal weight: 0.2980 chunk 164 optimal weight: 0.9990 chunk 154 optimal weight: 0.7980 chunk 227 optimal weight: 3.9990 chunk 187 optimal weight: 0.0010 chunk 152 optimal weight: 0.5980 chunk 112 optimal weight: 0.8980 chunk 14 optimal weight: 0.3980 chunk 58 optimal weight: 1.9990 overall best weight: 0.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 73 ASN C 74 ASN C 77 ASN ** C 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 292 ASN C 317 GLN E 227 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4033 r_free = 0.4033 target = 0.172526 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.137583 restraints weight = 24636.823| |-----------------------------------------------------------------------------| r_work (start): 0.3668 rms_B_bonded: 1.74 r_work: 0.3476 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3328 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.3328 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8345 moved from start: 0.2005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 22689 Z= 0.106 Angle : 0.504 9.399 30909 Z= 0.268 Chirality : 0.040 0.167 3574 Planarity : 0.004 0.046 3695 Dihedral : 15.988 123.777 3520 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.74 % Favored : 96.23 % Rotamer: Outliers : 4.18 % Allowed : 24.18 % Favored : 71.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.96 (0.17), residues: 2570 helix: 1.48 (0.15), residues: 1244 sheet: 0.23 (0.22), residues: 549 loop : -0.30 (0.24), residues: 777 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP E 259 HIS 0.007 0.001 HIS E 18 PHE 0.012 0.001 PHE A 201 TYR 0.013 0.001 TYR A 235 ARG 0.009 0.000 ARG D 230 Details of bonding type rmsd hydrogen bonds : bond 0.03403 ( 1209) hydrogen bonds : angle 4.34978 ( 3506) covalent geometry : bond 0.00227 (22689) covalent geometry : angle 0.50442 (30909) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5140 Ramachandran restraints generated. 2570 Oldfield, 0 Emsley, 2570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5140 Ramachandran restraints generated. 2570 Oldfield, 0 Emsley, 2570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 359 residues out of total 2368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 260 time to evaluate : 3.209 Fit side-chains REVERT: A 89 GLN cc_start: 0.8202 (OUTLIER) cc_final: 0.7807 (tt0) REVERT: A 250 MET cc_start: 0.8820 (OUTLIER) cc_final: 0.7683 (mmt) REVERT: A 288 LEU cc_start: 0.8021 (OUTLIER) cc_final: 0.7510 (mp) REVERT: A 296 LYS cc_start: 0.7749 (mptt) cc_final: 0.7468 (mtpt) REVERT: A 302 ASP cc_start: 0.8072 (m-30) cc_final: 0.7839 (m-30) REVERT: A 307 GLU cc_start: 0.7315 (mt-10) cc_final: 0.6939 (mt-10) REVERT: A 375 ASP cc_start: 0.7413 (OUTLIER) cc_final: 0.7060 (t0) REVERT: B 100 LYS cc_start: 0.8889 (OUTLIER) cc_final: 0.8508 (tmtt) REVERT: B 146 GLN cc_start: 0.8518 (OUTLIER) cc_final: 0.7559 (mm-40) REVERT: B 148 ASN cc_start: 0.7959 (OUTLIER) cc_final: 0.7668 (p0) REVERT: B 183 ASP cc_start: 0.8239 (t70) cc_final: 0.7559 (t0) REVERT: B 197 THR cc_start: 0.8783 (m) cc_final: 0.8478 (p) REVERT: B 291 GLU cc_start: 0.7828 (OUTLIER) cc_final: 0.7388 (mp0) REVERT: B 301 GLU cc_start: 0.8096 (OUTLIER) cc_final: 0.7770 (mt-10) REVERT: D 254 THR cc_start: 0.8106 (OUTLIER) cc_final: 0.7795 (t) REVERT: D 279 ASP cc_start: 0.7730 (t70) cc_final: 0.7458 (t0) REVERT: E 9 ARG cc_start: 0.8247 (tpt-90) cc_final: 0.7924 (tpt170) REVERT: E 163 LYS cc_start: 0.8622 (tttt) cc_final: 0.7998 (ttpt) REVERT: F 71 THR cc_start: 0.7943 (m) cc_final: 0.7666 (p) REVERT: F 224 MET cc_start: 0.6510 (OUTLIER) cc_final: 0.5873 (mmt) REVERT: G 10 LYS cc_start: 0.8366 (OUTLIER) cc_final: 0.7963 (mtpp) REVERT: G 61 LEU cc_start: 0.8146 (OUTLIER) cc_final: 0.7883 (mp) REVERT: G 159 LYS cc_start: 0.8476 (OUTLIER) cc_final: 0.8048 (ptmm) REVERT: H 284 MET cc_start: 0.7793 (ttt) cc_final: 0.7377 (mtp) REVERT: H 348 ASN cc_start: 0.7083 (p0) cc_final: 0.6695 (p0) outliers start: 99 outliers final: 47 residues processed: 336 average time/residue: 1.6896 time to fit residues: 658.0274 Evaluate side-chains 297 residues out of total 2368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 236 time to evaluate : 2.763 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 GLU Chi-restraints excluded: chain A residue 89 GLN Chi-restraints excluded: chain A residue 104 ILE Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 197 THR Chi-restraints excluded: chain A residue 250 MET Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 375 ASP Chi-restraints excluded: chain A residue 483 GLU Chi-restraints excluded: chain A residue 497 TYR Chi-restraints excluded: chain A residue 536 VAL Chi-restraints excluded: chain B residue 12 VAL Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 100 LYS Chi-restraints excluded: chain B residue 146 GLN Chi-restraints excluded: chain B residue 148 ASN Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 291 GLU Chi-restraints excluded: chain B residue 301 GLU Chi-restraints excluded: chain C residue 77 ASN Chi-restraints excluded: chain C residue 138 THR Chi-restraints excluded: chain D residue 46 VAL Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 79 THR Chi-restraints excluded: chain D residue 86 ASP Chi-restraints excluded: chain D residue 123 LYS Chi-restraints excluded: chain D residue 173 VAL Chi-restraints excluded: chain D residue 254 THR Chi-restraints excluded: chain D residue 266 ASP Chi-restraints excluded: chain E residue 58 GLU Chi-restraints excluded: chain E residue 90 SER Chi-restraints excluded: chain E residue 92 TYR Chi-restraints excluded: chain E residue 101 MET Chi-restraints excluded: chain E residue 181 ILE Chi-restraints excluded: chain E residue 204 ASP Chi-restraints excluded: chain E residue 232 VAL Chi-restraints excluded: chain E residue 352 CYS Chi-restraints excluded: chain F residue 81 THR Chi-restraints excluded: chain F residue 93 MET Chi-restraints excluded: chain F residue 99 SER Chi-restraints excluded: chain F residue 224 MET Chi-restraints excluded: chain F residue 225 ILE Chi-restraints excluded: chain F residue 238 ILE Chi-restraints excluded: chain F residue 279 VAL Chi-restraints excluded: chain F residue 409 ILE Chi-restraints excluded: chain F residue 414 ASP Chi-restraints excluded: chain G residue 10 LYS Chi-restraints excluded: chain G residue 15 THR Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain G residue 61 LEU Chi-restraints excluded: chain G residue 125 PHE Chi-restraints excluded: chain G residue 159 LYS Chi-restraints excluded: chain G residue 196 SER Chi-restraints excluded: chain G residue 304 ILE Chi-restraints excluded: chain G residue 327 LEU Chi-restraints excluded: chain H residue 80 VAL Chi-restraints excluded: chain H residue 117 THR Chi-restraints excluded: chain H residue 261 LEU Chi-restraints excluded: chain H residue 264 THR Chi-restraints excluded: chain H residue 277 LEU Chi-restraints excluded: chain H residue 334 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 58 optimal weight: 0.7980 chunk 49 optimal weight: 1.9990 chunk 125 optimal weight: 2.9990 chunk 73 optimal weight: 4.9990 chunk 141 optimal weight: 5.9990 chunk 7 optimal weight: 0.6980 chunk 158 optimal weight: 0.0010 chunk 2 optimal weight: 0.7980 chunk 46 optimal weight: 0.8980 chunk 45 optimal weight: 0.7980 chunk 47 optimal weight: 0.4980 overall best weight: 0.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 73 ASN B 145 ASN C 74 ASN ** C 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 167 GLN C 292 ASN E 227 ASN H 243 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4032 r_free = 0.4032 target = 0.172424 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.137390 restraints weight = 24795.699| |-----------------------------------------------------------------------------| r_work (start): 0.3665 rms_B_bonded: 1.75 r_work: 0.3475 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3329 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.3329 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8348 moved from start: 0.2024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 22689 Z= 0.112 Angle : 0.511 11.083 30909 Z= 0.270 Chirality : 0.040 0.162 3574 Planarity : 0.004 0.087 3695 Dihedral : 15.902 124.727 3518 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.81 % Favored : 96.15 % Rotamer: Outliers : 3.72 % Allowed : 24.64 % Favored : 71.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.08 (0.17), residues: 2570 helix: 1.56 (0.15), residues: 1246 sheet: 0.28 (0.22), residues: 548 loop : -0.21 (0.24), residues: 776 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 324 HIS 0.006 0.001 HIS E 18 PHE 0.012 0.001 PHE A 201 TYR 0.021 0.001 TYR B 186 ARG 0.011 0.000 ARG F 109 Details of bonding type rmsd hydrogen bonds : bond 0.03437 ( 1209) hydrogen bonds : angle 4.29038 ( 3506) covalent geometry : bond 0.00248 (22689) covalent geometry : angle 0.51106 (30909) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5140 Ramachandran restraints generated. 2570 Oldfield, 0 Emsley, 2570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5140 Ramachandran restraints generated. 2570 Oldfield, 0 Emsley, 2570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 341 residues out of total 2368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 253 time to evaluate : 2.575 Fit side-chains REVERT: A 250 MET cc_start: 0.8816 (OUTLIER) cc_final: 0.7662 (mmt) REVERT: A 288 LEU cc_start: 0.8000 (OUTLIER) cc_final: 0.7471 (mp) REVERT: A 296 LYS cc_start: 0.7786 (mptt) cc_final: 0.7500 (mtpt) REVERT: A 307 GLU cc_start: 0.7336 (OUTLIER) cc_final: 0.6965 (mt-10) REVERT: A 310 ASP cc_start: 0.8587 (t0) cc_final: 0.8371 (t70) REVERT: A 375 ASP cc_start: 0.7390 (OUTLIER) cc_final: 0.7022 (t0) REVERT: B 146 GLN cc_start: 0.8499 (OUTLIER) cc_final: 0.7550 (mm-40) REVERT: B 148 ASN cc_start: 0.8002 (OUTLIER) cc_final: 0.7698 (p0) REVERT: B 183 ASP cc_start: 0.8253 (t70) cc_final: 0.7577 (t0) REVERT: B 197 THR cc_start: 0.8782 (m) cc_final: 0.8466 (p) REVERT: B 291 GLU cc_start: 0.7834 (OUTLIER) cc_final: 0.7399 (mp0) REVERT: C 87 ASP cc_start: 0.8115 (t70) cc_final: 0.7855 (t0) REVERT: D 254 THR cc_start: 0.8097 (OUTLIER) cc_final: 0.7799 (t) REVERT: D 279 ASP cc_start: 0.7764 (t70) cc_final: 0.7497 (t0) REVERT: E 9 ARG cc_start: 0.8229 (tpt-90) cc_final: 0.7966 (tpt-90) REVERT: E 34 ARG cc_start: 0.7489 (mmp-170) cc_final: 0.6683 (mmm-85) REVERT: E 163 LYS cc_start: 0.8607 (tttt) cc_final: 0.7989 (ttpt) REVERT: E 256 LYS cc_start: 0.8162 (mtmm) cc_final: 0.7953 (mtpt) REVERT: F 71 THR cc_start: 0.7959 (m) cc_final: 0.7666 (p) REVERT: F 224 MET cc_start: 0.6516 (OUTLIER) cc_final: 0.5864 (mmt) REVERT: G 10 LYS cc_start: 0.8382 (OUTLIER) cc_final: 0.7987 (mtpp) REVERT: G 61 LEU cc_start: 0.8152 (OUTLIER) cc_final: 0.7883 (mp) REVERT: G 159 LYS cc_start: 0.8469 (OUTLIER) cc_final: 0.8045 (ptmm) REVERT: H 284 MET cc_start: 0.7786 (ttt) cc_final: 0.7399 (mtp) REVERT: H 348 ASN cc_start: 0.7094 (p0) cc_final: 0.6725 (p0) outliers start: 88 outliers final: 51 residues processed: 319 average time/residue: 1.2992 time to fit residues: 479.5249 Evaluate side-chains 307 residues out of total 2368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 244 time to evaluate : 2.506 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 GLU Chi-restraints excluded: chain A residue 104 ILE Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 197 THR Chi-restraints excluded: chain A residue 250 MET Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 307 GLU Chi-restraints excluded: chain A residue 375 ASP Chi-restraints excluded: chain A residue 483 GLU Chi-restraints excluded: chain A residue 497 TYR Chi-restraints excluded: chain A residue 536 VAL Chi-restraints excluded: chain B residue 12 VAL Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 146 GLN Chi-restraints excluded: chain B residue 148 ASN Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 291 GLU Chi-restraints excluded: chain B residue 297 MET Chi-restraints excluded: chain C residue 138 THR Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 79 THR Chi-restraints excluded: chain D residue 86 ASP Chi-restraints excluded: chain D residue 123 LYS Chi-restraints excluded: chain D residue 173 VAL Chi-restraints excluded: chain D residue 178 ASP Chi-restraints excluded: chain D residue 254 THR Chi-restraints excluded: chain D residue 266 ASP Chi-restraints excluded: chain D residue 296 SER Chi-restraints excluded: chain E residue 58 GLU Chi-restraints excluded: chain E residue 90 SER Chi-restraints excluded: chain E residue 92 TYR Chi-restraints excluded: chain E residue 101 MET Chi-restraints excluded: chain E residue 164 ASN Chi-restraints excluded: chain E residue 181 ILE Chi-restraints excluded: chain E residue 232 VAL Chi-restraints excluded: chain E residue 352 CYS Chi-restraints excluded: chain F residue 81 THR Chi-restraints excluded: chain F residue 93 MET Chi-restraints excluded: chain F residue 99 SER Chi-restraints excluded: chain F residue 224 MET Chi-restraints excluded: chain F residue 225 ILE Chi-restraints excluded: chain F residue 238 ILE Chi-restraints excluded: chain F residue 279 VAL Chi-restraints excluded: chain F residue 409 ILE Chi-restraints excluded: chain F residue 414 ASP Chi-restraints excluded: chain G residue 10 LYS Chi-restraints excluded: chain G residue 15 THR Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain G residue 61 LEU Chi-restraints excluded: chain G residue 125 PHE Chi-restraints excluded: chain G residue 159 LYS Chi-restraints excluded: chain G residue 196 SER Chi-restraints excluded: chain G residue 266 SER Chi-restraints excluded: chain G residue 304 ILE Chi-restraints excluded: chain G residue 327 LEU Chi-restraints excluded: chain H residue 80 VAL Chi-restraints excluded: chain H residue 117 THR Chi-restraints excluded: chain H residue 120 VAL Chi-restraints excluded: chain H residue 261 LEU Chi-restraints excluded: chain H residue 264 THR Chi-restraints excluded: chain H residue 277 LEU Chi-restraints excluded: chain H residue 282 LEU Chi-restraints excluded: chain H residue 334 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 71 optimal weight: 1.9990 chunk 136 optimal weight: 2.9990 chunk 11 optimal weight: 0.0470 chunk 235 optimal weight: 2.9990 chunk 52 optimal weight: 0.5980 chunk 92 optimal weight: 2.9990 chunk 27 optimal weight: 1.9990 chunk 128 optimal weight: 0.0070 chunk 76 optimal weight: 4.9990 chunk 135 optimal weight: 0.6980 chunk 147 optimal weight: 9.9990 overall best weight: 0.6698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 73 ASN C 77 ASN ** C 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 292 ASN E 208 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4032 r_free = 0.4032 target = 0.172520 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.136994 restraints weight = 24695.080| |-----------------------------------------------------------------------------| r_work (start): 0.3657 rms_B_bonded: 1.79 r_work: 0.3464 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3318 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.3318 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8355 moved from start: 0.2077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 22689 Z= 0.116 Angle : 0.514 11.256 30909 Z= 0.270 Chirality : 0.040 0.166 3574 Planarity : 0.004 0.068 3695 Dihedral : 15.807 128.921 3518 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.74 % Favored : 96.23 % Rotamer: Outliers : 3.72 % Allowed : 25.02 % Favored : 71.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.16 (0.17), residues: 2570 helix: 1.63 (0.15), residues: 1243 sheet: 0.34 (0.22), residues: 550 loop : -0.20 (0.24), residues: 777 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 324 HIS 0.005 0.001 HIS E 18 PHE 0.012 0.001 PHE A 201 TYR 0.011 0.001 TYR A 235 ARG 0.010 0.000 ARG D 230 Details of bonding type rmsd hydrogen bonds : bond 0.03429 ( 1209) hydrogen bonds : angle 4.23677 ( 3506) covalent geometry : bond 0.00261 (22689) covalent geometry : angle 0.51424 (30909) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5140 Ramachandran restraints generated. 2570 Oldfield, 0 Emsley, 2570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5140 Ramachandran restraints generated. 2570 Oldfield, 0 Emsley, 2570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 341 residues out of total 2368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 253 time to evaluate : 3.226 Fit side-chains REVERT: A 225 GLU cc_start: 0.8636 (OUTLIER) cc_final: 0.7637 (mt-10) REVERT: A 296 LYS cc_start: 0.7801 (mptt) cc_final: 0.7518 (mtpt) REVERT: A 307 GLU cc_start: 0.7362 (OUTLIER) cc_final: 0.6948 (mt-10) REVERT: A 375 ASP cc_start: 0.7392 (OUTLIER) cc_final: 0.7029 (t0) REVERT: B 146 GLN cc_start: 0.8505 (OUTLIER) cc_final: 0.7566 (mm-40) REVERT: B 148 ASN cc_start: 0.8011 (OUTLIER) cc_final: 0.7674 (p0) REVERT: B 183 ASP cc_start: 0.8252 (t70) cc_final: 0.7601 (t0) REVERT: B 197 THR cc_start: 0.8792 (m) cc_final: 0.8471 (p) REVERT: B 291 GLU cc_start: 0.7854 (OUTLIER) cc_final: 0.7416 (mp0) REVERT: C 87 ASP cc_start: 0.8132 (t70) cc_final: 0.7878 (t0) REVERT: D 111 LYS cc_start: 0.8677 (OUTLIER) cc_final: 0.8324 (ttmt) REVERT: D 196 ASN cc_start: 0.8523 (m-40) cc_final: 0.8287 (m110) REVERT: D 254 THR cc_start: 0.8102 (OUTLIER) cc_final: 0.7802 (t) REVERT: D 279 ASP cc_start: 0.7739 (t70) cc_final: 0.7466 (t0) REVERT: E 9 ARG cc_start: 0.8250 (tpt-90) cc_final: 0.8006 (tpt-90) REVERT: E 34 ARG cc_start: 0.7522 (mmp-170) cc_final: 0.6687 (mmm-85) REVERT: E 163 LYS cc_start: 0.8624 (tttt) cc_final: 0.8013 (ttpt) REVERT: E 256 LYS cc_start: 0.8138 (mtmm) cc_final: 0.7935 (mtpt) REVERT: F 71 THR cc_start: 0.7944 (m) cc_final: 0.7670 (p) REVERT: F 224 MET cc_start: 0.6493 (OUTLIER) cc_final: 0.5873 (mmt) REVERT: G 10 LYS cc_start: 0.8382 (OUTLIER) cc_final: 0.7986 (mtpp) REVERT: G 61 LEU cc_start: 0.8153 (OUTLIER) cc_final: 0.7870 (mp) REVERT: G 159 LYS cc_start: 0.8482 (OUTLIER) cc_final: 0.8063 (ptmm) REVERT: H 55 ARG cc_start: 0.8876 (mtm-85) cc_final: 0.8609 (mtm180) REVERT: H 284 MET cc_start: 0.7799 (ttt) cc_final: 0.7428 (mtp) REVERT: H 348 ASN cc_start: 0.7177 (p0) cc_final: 0.6871 (p0) outliers start: 88 outliers final: 53 residues processed: 317 average time/residue: 1.2733 time to fit residues: 465.3832 Evaluate side-chains 311 residues out of total 2368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 246 time to evaluate : 2.674 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 GLU Chi-restraints excluded: chain A residue 104 ILE Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 197 THR Chi-restraints excluded: chain A residue 225 GLU Chi-restraints excluded: chain A residue 307 GLU Chi-restraints excluded: chain A residue 375 ASP Chi-restraints excluded: chain A residue 497 TYR Chi-restraints excluded: chain A residue 536 VAL Chi-restraints excluded: chain B residue 12 VAL Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 146 GLN Chi-restraints excluded: chain B residue 148 ASN Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 291 GLU Chi-restraints excluded: chain B residue 297 MET Chi-restraints excluded: chain C residue 138 THR Chi-restraints excluded: chain D residue 46 VAL Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 79 THR Chi-restraints excluded: chain D residue 86 ASP Chi-restraints excluded: chain D residue 111 LYS Chi-restraints excluded: chain D residue 123 LYS Chi-restraints excluded: chain D residue 173 VAL Chi-restraints excluded: chain D residue 178 ASP Chi-restraints excluded: chain D residue 254 THR Chi-restraints excluded: chain D residue 266 ASP Chi-restraints excluded: chain E residue 23 THR Chi-restraints excluded: chain E residue 90 SER Chi-restraints excluded: chain E residue 92 TYR Chi-restraints excluded: chain E residue 101 MET Chi-restraints excluded: chain E residue 164 ASN Chi-restraints excluded: chain E residue 181 ILE Chi-restraints excluded: chain E residue 204 ASP Chi-restraints excluded: chain E residue 232 VAL Chi-restraints excluded: chain E residue 352 CYS Chi-restraints excluded: chain F residue 65 THR Chi-restraints excluded: chain F residue 93 MET Chi-restraints excluded: chain F residue 99 SER Chi-restraints excluded: chain F residue 224 MET Chi-restraints excluded: chain F residue 225 ILE Chi-restraints excluded: chain F residue 238 ILE Chi-restraints excluded: chain F residue 409 ILE Chi-restraints excluded: chain F residue 414 ASP Chi-restraints excluded: chain G residue 10 LYS Chi-restraints excluded: chain G residue 15 THR Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain G residue 61 LEU Chi-restraints excluded: chain G residue 125 PHE Chi-restraints excluded: chain G residue 130 VAL Chi-restraints excluded: chain G residue 153 SER Chi-restraints excluded: chain G residue 159 LYS Chi-restraints excluded: chain G residue 196 SER Chi-restraints excluded: chain G residue 202 PHE Chi-restraints excluded: chain G residue 266 SER Chi-restraints excluded: chain G residue 304 ILE Chi-restraints excluded: chain G residue 327 LEU Chi-restraints excluded: chain H residue 80 VAL Chi-restraints excluded: chain H residue 117 THR Chi-restraints excluded: chain H residue 120 VAL Chi-restraints excluded: chain H residue 261 LEU Chi-restraints excluded: chain H residue 263 ILE Chi-restraints excluded: chain H residue 264 THR Chi-restraints excluded: chain H residue 277 LEU Chi-restraints excluded: chain H residue 334 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 87 optimal weight: 0.8980 chunk 64 optimal weight: 0.9980 chunk 189 optimal weight: 4.9990 chunk 229 optimal weight: 5.9990 chunk 11 optimal weight: 4.9990 chunk 164 optimal weight: 1.9990 chunk 5 optimal weight: 0.6980 chunk 191 optimal weight: 3.9990 chunk 209 optimal weight: 1.9990 chunk 77 optimal weight: 0.9980 chunk 139 optimal weight: 0.0470 overall best weight: 0.7278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 77 ASN ** C 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 292 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4033 r_free = 0.4033 target = 0.172430 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.137187 restraints weight = 24680.595| |-----------------------------------------------------------------------------| r_work (start): 0.3657 rms_B_bonded: 1.76 r_work: 0.3467 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3327 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.3327 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8351 moved from start: 0.2113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 22689 Z= 0.119 Angle : 0.522 13.060 30909 Z= 0.273 Chirality : 0.040 0.159 3574 Planarity : 0.004 0.066 3695 Dihedral : 15.746 135.850 3517 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.85 % Favored : 96.11 % Rotamer: Outliers : 3.30 % Allowed : 25.74 % Favored : 70.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.19 (0.17), residues: 2570 helix: 1.65 (0.15), residues: 1243 sheet: 0.40 (0.22), residues: 546 loop : -0.20 (0.24), residues: 781 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 324 HIS 0.005 0.001 HIS E 18 PHE 0.012 0.001 PHE A 201 TYR 0.022 0.001 TYR B 186 ARG 0.008 0.000 ARG C 136 Details of bonding type rmsd hydrogen bonds : bond 0.03434 ( 1209) hydrogen bonds : angle 4.22678 ( 3506) covalent geometry : bond 0.00270 (22689) covalent geometry : angle 0.52236 (30909) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5140 Ramachandran restraints generated. 2570 Oldfield, 0 Emsley, 2570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5140 Ramachandran restraints generated. 2570 Oldfield, 0 Emsley, 2570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 329 residues out of total 2368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 251 time to evaluate : 2.704 Fit side-chains REVERT: A 225 GLU cc_start: 0.8612 (OUTLIER) cc_final: 0.7601 (mt-10) REVERT: A 296 LYS cc_start: 0.7840 (mptt) cc_final: 0.7555 (mtpt) REVERT: A 307 GLU cc_start: 0.7395 (OUTLIER) cc_final: 0.6965 (mt-10) REVERT: A 375 ASP cc_start: 0.7397 (OUTLIER) cc_final: 0.7038 (t0) REVERT: B 146 GLN cc_start: 0.8508 (OUTLIER) cc_final: 0.7572 (mm-40) REVERT: B 148 ASN cc_start: 0.8067 (OUTLIER) cc_final: 0.7741 (p0) REVERT: B 183 ASP cc_start: 0.8218 (t70) cc_final: 0.7628 (t0) REVERT: B 197 THR cc_start: 0.8812 (m) cc_final: 0.8497 (p) REVERT: B 291 GLU cc_start: 0.7805 (OUTLIER) cc_final: 0.7364 (mp0) REVERT: C 87 ASP cc_start: 0.8082 (t70) cc_final: 0.7834 (t0) REVERT: D 111 LYS cc_start: 0.8665 (OUTLIER) cc_final: 0.8313 (ttmt) REVERT: D 196 ASN cc_start: 0.8522 (m-40) cc_final: 0.8293 (m110) REVERT: D 254 THR cc_start: 0.8107 (OUTLIER) cc_final: 0.7827 (t) REVERT: D 279 ASP cc_start: 0.7711 (t70) cc_final: 0.7450 (t0) REVERT: E 9 ARG cc_start: 0.8261 (tpt-90) cc_final: 0.8029 (tpt-90) REVERT: E 34 ARG cc_start: 0.7436 (mmp-170) cc_final: 0.6674 (mmm-85) REVERT: E 163 LYS cc_start: 0.8634 (tttt) cc_final: 0.8036 (ttpt) REVERT: E 256 LYS cc_start: 0.8114 (mtmm) cc_final: 0.7906 (mtpt) REVERT: F 71 THR cc_start: 0.7935 (m) cc_final: 0.7679 (p) REVERT: F 224 MET cc_start: 0.6473 (OUTLIER) cc_final: 0.5838 (mmt) REVERT: G 10 LYS cc_start: 0.8405 (OUTLIER) cc_final: 0.8017 (mtpp) REVERT: G 61 LEU cc_start: 0.8126 (OUTLIER) cc_final: 0.7852 (mp) REVERT: G 159 LYS cc_start: 0.8481 (OUTLIER) cc_final: 0.8056 (ptmm) REVERT: H 55 ARG cc_start: 0.8888 (mtm-85) cc_final: 0.8614 (mtm180) REVERT: H 284 MET cc_start: 0.7829 (ttt) cc_final: 0.7421 (mtp) REVERT: H 348 ASN cc_start: 0.7178 (p0) cc_final: 0.6886 (p0) REVERT: H 362 MET cc_start: 0.8920 (OUTLIER) cc_final: 0.8598 (mtp) outliers start: 78 outliers final: 51 residues processed: 307 average time/residue: 1.2279 time to fit residues: 436.3513 Evaluate side-chains 310 residues out of total 2368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 246 time to evaluate : 2.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 GLU Chi-restraints excluded: chain A residue 104 ILE Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 197 THR Chi-restraints excluded: chain A residue 225 GLU Chi-restraints excluded: chain A residue 307 GLU Chi-restraints excluded: chain A residue 375 ASP Chi-restraints excluded: chain A residue 497 TYR Chi-restraints excluded: chain A residue 536 VAL Chi-restraints excluded: chain B residue 12 VAL Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 146 GLN Chi-restraints excluded: chain B residue 148 ASN Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 291 GLU Chi-restraints excluded: chain B residue 297 MET Chi-restraints excluded: chain C residue 91 ASP Chi-restraints excluded: chain C residue 138 THR Chi-restraints excluded: chain D residue 46 VAL Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 79 THR Chi-restraints excluded: chain D residue 86 ASP Chi-restraints excluded: chain D residue 111 LYS Chi-restraints excluded: chain D residue 123 LYS Chi-restraints excluded: chain D residue 173 VAL Chi-restraints excluded: chain D residue 178 ASP Chi-restraints excluded: chain D residue 254 THR Chi-restraints excluded: chain D residue 266 ASP Chi-restraints excluded: chain E residue 23 THR Chi-restraints excluded: chain E residue 90 SER Chi-restraints excluded: chain E residue 92 TYR Chi-restraints excluded: chain E residue 101 MET Chi-restraints excluded: chain E residue 164 ASN Chi-restraints excluded: chain E residue 181 ILE Chi-restraints excluded: chain E residue 204 ASP Chi-restraints excluded: chain E residue 232 VAL Chi-restraints excluded: chain E residue 352 CYS Chi-restraints excluded: chain F residue 65 THR Chi-restraints excluded: chain F residue 93 MET Chi-restraints excluded: chain F residue 99 SER Chi-restraints excluded: chain F residue 224 MET Chi-restraints excluded: chain F residue 225 ILE Chi-restraints excluded: chain F residue 238 ILE Chi-restraints excluded: chain F residue 409 ILE Chi-restraints excluded: chain G residue 10 LYS Chi-restraints excluded: chain G residue 15 THR Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain G residue 61 LEU Chi-restraints excluded: chain G residue 125 PHE Chi-restraints excluded: chain G residue 130 VAL Chi-restraints excluded: chain G residue 153 SER Chi-restraints excluded: chain G residue 159 LYS Chi-restraints excluded: chain G residue 266 SER Chi-restraints excluded: chain G residue 304 ILE Chi-restraints excluded: chain G residue 327 LEU Chi-restraints excluded: chain H residue 80 VAL Chi-restraints excluded: chain H residue 117 THR Chi-restraints excluded: chain H residue 120 VAL Chi-restraints excluded: chain H residue 261 LEU Chi-restraints excluded: chain H residue 263 ILE Chi-restraints excluded: chain H residue 264 THR Chi-restraints excluded: chain H residue 277 LEU Chi-restraints excluded: chain H residue 334 THR Chi-restraints excluded: chain H residue 362 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 102 optimal weight: 0.5980 chunk 160 optimal weight: 4.9990 chunk 148 optimal weight: 7.9990 chunk 11 optimal weight: 3.9990 chunk 5 optimal weight: 0.7980 chunk 161 optimal weight: 2.9990 chunk 8 optimal weight: 5.9990 chunk 38 optimal weight: 3.9990 chunk 47 optimal weight: 4.9990 chunk 138 optimal weight: 1.9990 chunk 112 optimal weight: 3.9990 overall best weight: 2.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 77 ASN ** C 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 292 ASN E 208 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.165925 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.129142 restraints weight = 24823.536| |-----------------------------------------------------------------------------| r_work (start): 0.3546 rms_B_bonded: 1.81 r_work: 0.3351 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3207 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3207 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8415 moved from start: 0.2333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 22689 Z= 0.219 Angle : 0.604 12.862 30909 Z= 0.314 Chirality : 0.044 0.166 3574 Planarity : 0.004 0.061 3695 Dihedral : 15.921 146.448 3517 Min Nonbonded Distance : 1.898 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.40 % Favored : 95.56 % Rotamer: Outliers : 3.04 % Allowed : 25.95 % Favored : 71.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.87 (0.17), residues: 2570 helix: 1.32 (0.15), residues: 1244 sheet: 0.36 (0.22), residues: 546 loop : -0.31 (0.24), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP C 256 HIS 0.008 0.001 HIS B 232 PHE 0.027 0.002 PHE G 154 TYR 0.013 0.002 TYR H 229 ARG 0.008 0.001 ARG C 136 Details of bonding type rmsd hydrogen bonds : bond 0.04533 ( 1209) hydrogen bonds : angle 4.47659 ( 3506) covalent geometry : bond 0.00534 (22689) covalent geometry : angle 0.60398 (30909) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5140 Ramachandran restraints generated. 2570 Oldfield, 0 Emsley, 2570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5140 Ramachandran restraints generated. 2570 Oldfield, 0 Emsley, 2570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 317 residues out of total 2368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 245 time to evaluate : 2.592 Fit side-chains REVERT: A 225 GLU cc_start: 0.8778 (OUTLIER) cc_final: 0.7795 (mt-10) REVERT: A 296 LYS cc_start: 0.7842 (mptt) cc_final: 0.7582 (mtpt) REVERT: A 307 GLU cc_start: 0.7449 (OUTLIER) cc_final: 0.6948 (mt-10) REVERT: A 375 ASP cc_start: 0.7435 (OUTLIER) cc_final: 0.7074 (t0) REVERT: B 146 GLN cc_start: 0.8620 (OUTLIER) cc_final: 0.7644 (mm-40) REVERT: B 148 ASN cc_start: 0.8036 (OUTLIER) cc_final: 0.7671 (p0) REVERT: B 183 ASP cc_start: 0.8370 (t70) cc_final: 0.7834 (t0) REVERT: B 291 GLU cc_start: 0.7960 (OUTLIER) cc_final: 0.7467 (mp0) REVERT: C 87 ASP cc_start: 0.8199 (t70) cc_final: 0.7743 (t0) REVERT: C 199 GLU cc_start: 0.7849 (tt0) cc_final: 0.7434 (tt0) REVERT: D 254 THR cc_start: 0.8123 (OUTLIER) cc_final: 0.7821 (t) REVERT: D 279 ASP cc_start: 0.7807 (t70) cc_final: 0.7489 (t0) REVERT: E 9 ARG cc_start: 0.8286 (tpt-90) cc_final: 0.7993 (tpt-90) REVERT: E 256 LYS cc_start: 0.8098 (mtmm) cc_final: 0.7879 (mtpt) REVERT: F 224 MET cc_start: 0.6539 (OUTLIER) cc_final: 0.5935 (mmm) REVERT: F 426 GLU cc_start: 0.6386 (mm-30) cc_final: 0.6035 (tp30) REVERT: G 10 LYS cc_start: 0.8418 (OUTLIER) cc_final: 0.7979 (mtpp) REVERT: G 61 LEU cc_start: 0.8219 (OUTLIER) cc_final: 0.7930 (mp) REVERT: G 122 GLU cc_start: 0.7855 (mm-30) cc_final: 0.7403 (mp0) REVERT: H 284 MET cc_start: 0.7848 (ttt) cc_final: 0.7371 (mtp) REVERT: H 348 ASN cc_start: 0.7182 (p0) cc_final: 0.6821 (p0) outliers start: 72 outliers final: 47 residues processed: 295 average time/residue: 1.3315 time to fit residues: 454.8641 Evaluate side-chains 300 residues out of total 2368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 243 time to evaluate : 2.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 GLU Chi-restraints excluded: chain A residue 104 ILE Chi-restraints excluded: chain A residue 197 THR Chi-restraints excluded: chain A residue 225 GLU Chi-restraints excluded: chain A residue 307 GLU Chi-restraints excluded: chain A residue 375 ASP Chi-restraints excluded: chain A residue 497 TYR Chi-restraints excluded: chain A residue 536 VAL Chi-restraints excluded: chain B residue 12 VAL Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 146 GLN Chi-restraints excluded: chain B residue 148 ASN Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 291 GLU Chi-restraints excluded: chain B residue 297 MET Chi-restraints excluded: chain C residue 91 ASP Chi-restraints excluded: chain C residue 138 THR Chi-restraints excluded: chain D residue 46 VAL Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 79 THR Chi-restraints excluded: chain D residue 86 ASP Chi-restraints excluded: chain D residue 123 LYS Chi-restraints excluded: chain D residue 173 VAL Chi-restraints excluded: chain D residue 178 ASP Chi-restraints excluded: chain D residue 254 THR Chi-restraints excluded: chain D residue 266 ASP Chi-restraints excluded: chain E residue 23 THR Chi-restraints excluded: chain E residue 90 SER Chi-restraints excluded: chain E residue 92 TYR Chi-restraints excluded: chain E residue 101 MET Chi-restraints excluded: chain E residue 181 ILE Chi-restraints excluded: chain E residue 232 VAL Chi-restraints excluded: chain E residue 352 CYS Chi-restraints excluded: chain F residue 65 THR Chi-restraints excluded: chain F residue 81 THR Chi-restraints excluded: chain F residue 99 SER Chi-restraints excluded: chain F residue 224 MET Chi-restraints excluded: chain F residue 225 ILE Chi-restraints excluded: chain F residue 238 ILE Chi-restraints excluded: chain F residue 409 ILE Chi-restraints excluded: chain G residue 10 LYS Chi-restraints excluded: chain G residue 15 THR Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain G residue 61 LEU Chi-restraints excluded: chain G residue 125 PHE Chi-restraints excluded: chain G residue 130 VAL Chi-restraints excluded: chain G residue 266 SER Chi-restraints excluded: chain G residue 304 ILE Chi-restraints excluded: chain G residue 327 LEU Chi-restraints excluded: chain H residue 80 VAL Chi-restraints excluded: chain H residue 117 THR Chi-restraints excluded: chain H residue 120 VAL Chi-restraints excluded: chain H residue 261 LEU Chi-restraints excluded: chain H residue 263 ILE Chi-restraints excluded: chain H residue 264 THR Chi-restraints excluded: chain H residue 277 LEU Chi-restraints excluded: chain H residue 334 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 257 optimal weight: 4.9990 chunk 243 optimal weight: 5.9990 chunk 105 optimal weight: 1.9990 chunk 200 optimal weight: 3.9990 chunk 124 optimal weight: 1.9990 chunk 68 optimal weight: 0.8980 chunk 12 optimal weight: 0.5980 chunk 249 optimal weight: 5.9990 chunk 248 optimal weight: 2.9990 chunk 67 optimal weight: 0.7980 chunk 179 optimal weight: 4.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 77 ASN ** C 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 292 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.167086 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.130898 restraints weight = 24497.033| |-----------------------------------------------------------------------------| r_work (start): 0.3569 rms_B_bonded: 1.78 r_work: 0.3385 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3241 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.3241 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8374 moved from start: 0.2325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 22689 Z= 0.159 Angle : 0.562 12.427 30909 Z= 0.293 Chirality : 0.042 0.168 3574 Planarity : 0.004 0.061 3695 Dihedral : 15.861 145.127 3517 Min Nonbonded Distance : 1.916 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.70 % Favored : 96.26 % Rotamer: Outliers : 2.83 % Allowed : 26.29 % Favored : 70.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.93 (0.17), residues: 2570 helix: 1.40 (0.15), residues: 1246 sheet: 0.36 (0.22), residues: 542 loop : -0.32 (0.24), residues: 782 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 324 HIS 0.006 0.001 HIS E 18 PHE 0.025 0.001 PHE G 154 TYR 0.021 0.001 TYR B 186 ARG 0.008 0.000 ARG D 230 Details of bonding type rmsd hydrogen bonds : bond 0.03978 ( 1209) hydrogen bonds : angle 4.39822 ( 3506) covalent geometry : bond 0.00379 (22689) covalent geometry : angle 0.56154 (30909) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 16072.82 seconds wall clock time: 280 minutes 39.00 seconds (16839.00 seconds total)