Starting phenix.real_space_refine on Wed Nov 20 13:47:03 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fs3_29412/11_2024/8fs3_29412.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fs3_29412/11_2024/8fs3_29412.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.93 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fs3_29412/11_2024/8fs3_29412.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fs3_29412/11_2024/8fs3_29412.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fs3_29412/11_2024/8fs3_29412.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fs3_29412/11_2024/8fs3_29412.cif" } resolution = 2.93 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= 0.032 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 40 5.49 5 Mg 4 5.21 5 S 114 5.16 5 C 13358 2.51 5 N 3643 2.21 5 O 4063 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 29 residue(s): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 21222 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 3564 Number of conformers: 1 Conformer: "" Number of residues, atoms: 437, 3564 Classifications: {'peptide': 437} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 17, 'TRANS': 419} 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: 2593 Number of conformers: 1 Conformer: "" Number of residues, atoms: 328, 2593 Classifications: {'peptide': 328} Link IDs: {'PTRANS': 12, 'TRANS': 315} 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: 2732 Number of conformers: 1 Conformer: "" Number of residues, atoms: 346, 2732 Classifications: {'peptide': 346} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 14, 'TRANS': 331} Chain breaks: 1 Chain: "F" Number of atoms: 2240 Number of conformers: 1 Conformer: "" Number of residues, atoms: 278, 2240 Classifications: {'peptide': 278} Link IDs: {'PTRANS': 9, 'TRANS': 268} Chain breaks: 7 Chain: "G" Number of atoms: 2257 Number of conformers: 1 Conformer: "" Number of residues, atoms: 285, 2257 Classifications: {'peptide': 285} Link IDs: {'PTRANS': 4, 'TRANS': 280} Chain breaks: 3 Chain: "H" Number of atoms: 2017 Number of conformers: 1 Conformer: "" Number of residues, atoms: 249, 2017 Classifications: {'peptide': 249} Link IDs: {'PTRANS': 8, 'TRANS': 240} Chain breaks: 6 Chain: "I" Number of atoms: 344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 344 Classifications: {'DNA': 17} Link IDs: {'rna3p': 16} Chain breaks: 1 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: 13.32, per 1000 atoms: 0.63 Number of scatterers: 21222 At special positions: 0 Unit cell: (111.78, 134.964, 137.448, 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 40 15.00 Mg 4 11.99 O 4063 8.00 N 3643 7.00 C 13358 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: 4.69 Conformation dependent library (CDL) restraints added in 2.8 seconds 5036 Ramachandran restraints generated. 2518 Oldfield, 0 Emsley, 2518 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4920 Finding SS restraints... Secondary structure from input PDB file: 120 helices and 14 sheets defined 53.5% alpha, 14.9% beta 10 base pairs and 18 stacking pairs defined. Time for finding SS restraints: 5.53 Creating SS restraints... Processing helix chain 'A' and resid 65 through 70 Processing helix chain 'A' and resid 74 through 78 removed outlier: 3.560A pdb=" N VAL A 78 " --> pdb=" O LEU A 75 " (cutoff:3.500A) Processing helix chain 'A' and resid 81 through 97 removed outlier: 3.665A pdb=" N ALA A 91 " --> pdb=" O ASP A 87 " (cutoff:3.500A) Processing helix chain 'A' and resid 114 through 126 removed outlier: 3.637A pdb=" N VAL A 118 " --> pdb=" O SER A 114 " (cutoff:3.500A) Processing helix chain 'A' and resid 126 through 131 removed outlier: 3.651A pdb=" N TYR A 130 " --> pdb=" O LEU A 126 " (cutoff:3.500A) 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 245 through 250 Processing helix chain 'A' and resid 251 through 256 Processing helix chain 'A' and resid 269 through 283 Processing helix chain 'A' and resid 284 through 291 Processing helix chain 'A' and resid 292 through 295 removed outlier: 4.043A pdb=" N ASN A 295 " --> pdb=" O ASN A 292 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 292 through 295' Processing helix chain 'A' and resid 296 through 308 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: 3.976A 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: 3.517A pdb=" N ALA A 397 " --> pdb=" O SER A 393 " (cutoff:3.500A) Processing helix chain 'A' and resid 413 through 432 removed outlier: 3.627A pdb=" N ASN A 417 " --> pdb=" O LEU A 413 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ILE A 431 " --> pdb=" O THR A 427 " (cutoff:3.500A) Processing helix chain 'A' and resid 445 through 470 removed outlier: 3.890A pdb=" N TYR A 469 " --> pdb=" O ASN A 465 " (cutoff:3.500A) 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 removed outlier: 3.515A pdb=" N ILE B 23 " --> pdb=" O LEU B 20 " (cutoff:3.500A) Processing helix chain 'B' and resid 26 through 40 Processing helix chain 'B' and resid 54 through 68 Processing helix chain 'B' and resid 69 through 72 removed outlier: 4.291A 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: 3.593A 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: 3.517A pdb=" N LYS B 149 " --> pdb=" O GLN B 146 " (cutoff:3.500A) Processing helix chain 'B' and resid 151 through 156 Processing helix chain 'B' and resid 167 through 183 Processing helix chain 'B' and resid 187 through 199 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 removed outlier: 3.549A pdb=" N ILE B 235 " --> pdb=" O PRO B 231 " (cutoff:3.500A) Processing helix chain 'B' and resid 244 through 257 Processing helix chain 'B' and resid 262 through 276 removed outlier: 3.518A pdb=" N ASN B 276 " --> pdb=" O ARG B 272 " (cutoff:3.500A) Processing helix chain 'B' and resid 281 through 301 Processing helix chain 'B' and resid 305 through 321 removed outlier: 3.688A pdb=" N LEU B 309 " --> pdb=" O THR B 305 " (cutoff:3.500A) Processing helix chain 'C' and resid 9 through 13 removed outlier: 3.540A pdb=" N ASN C 12 " --> pdb=" O SER C 9 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N LEU C 13 " --> pdb=" O LYS C 10 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 9 through 13' 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: 3.872A pdb=" N ILE C 97 " --> pdb=" O VAL C 93 " (cutoff:3.500A) removed outlier: 4.209A 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: 4.282A pdb=" N ARG C 132 " --> pdb=" O ASN C 128 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N VAL C 133 " --> pdb=" O ALA C 129 " (cutoff:3.500A) Processing helix chain 'C' and resid 149 through 153 removed outlier: 3.720A pdb=" N LYS C 152 " --> pdb=" O TYR C 149 " (cutoff:3.500A) Processing helix chain 'C' and resid 154 through 160 Processing helix chain 'C' and resid 170 through 186 removed outlier: 3.530A pdb=" N ILE C 174 " --> pdb=" O PRO C 170 " (cutoff:3.500A) Processing helix chain 'C' and resid 190 through 202 removed outlier: 3.705A pdb=" N ASN C 202 " --> pdb=" O ILE C 198 " (cutoff:3.500A) Processing helix chain 'C' and resid 204 through 219 removed outlier: 3.731A 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 253 Processing helix chain 'C' and resid 255 through 271 removed outlier: 4.011A pdb=" N LYS C 270 " --> pdb=" O VAL C 266 " (cutoff:3.500A) Processing helix chain 'C' and resid 273 through 287 removed outlier: 3.922A pdb=" N ASP C 287 " --> pdb=" O LYS C 283 " (cutoff:3.500A) Processing helix chain 'C' and resid 293 through 313 Processing helix chain 'C' and resid 315 through 331 Processing helix chain 'C' and resid 331 through 336 removed outlier: 4.189A pdb=" N THR C 335 " --> pdb=" O PHE C 331 " (cutoff:3.500A) Processing helix chain 'D' and resid 26 through 31 Processing helix chain 'D' and resid 42 through 55 removed outlier: 3.775A 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: 4.433A pdb=" N LYS D 89 " --> pdb=" O PRO D 85 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N SER D 90 " --> pdb=" O ASP D 86 " (cutoff:3.500A) Processing helix chain 'D' and resid 102 through 116 removed outlier: 3.840A pdb=" N VAL D 110 " --> pdb=" O VAL D 106 " (cutoff:3.500A) removed outlier: 4.388A 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 142 through 145 Processing helix chain 'D' and resid 146 through 160 removed outlier: 4.497A pdb=" N ARG D 155 " --> pdb=" O SER D 151 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N THR D 156 " --> pdb=" O ALA D 152 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N TYR D 160 " --> pdb=" O THR D 156 " (cutoff:3.500A) Processing helix chain 'D' and resid 172 through 176 Processing helix chain 'D' and resid 177 through 184 Processing helix chain 'D' and resid 193 through 208 removed outlier: 5.249A pdb=" N ASP D 199 " --> pdb=" O SER D 195 " (cutoff:3.500A) removed outlier: 5.417A pdb=" N ARG D 200 " --> pdb=" O ASN D 196 " (cutoff:3.500A) Processing helix chain 'D' and resid 218 through 224 Processing helix chain 'D' and resid 227 through 246 removed outlier: 3.699A pdb=" N GLY D 246 " --> pdb=" O ALA D 242 " (cutoff:3.500A) Processing helix chain 'D' and resid 252 through 260 Processing helix chain 'D' and resid 264 through 277 Processing helix chain 'D' and resid 279 through 293 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 removed outlier: 3.551A pdb=" N TYR E 8 " --> pdb=" O TRP E 4 " (cutoff:3.500A) Processing helix chain 'E' and resid 20 through 32 removed outlier: 4.637A 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 98 through 101 Processing helix chain 'E' and resid 102 through 103 No H-bonds generated for 'chain 'E' and resid 102 through 103' Processing helix chain 'E' and resid 104 through 119 removed outlier: 4.115A pdb=" N VAL E 108 " --> pdb=" O ASN E 104 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N LEU E 113 " --> pdb=" O ILE E 109 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N VAL E 116 " --> pdb=" O LEU E 112 " (cutoff:3.500A) Processing helix chain 'E' and resid 142 through 146 removed outlier: 3.531A pdb=" N LEU E 146 " --> pdb=" O ALA E 143 " (cutoff:3.500A) Processing helix chain 'E' and resid 149 through 161 removed outlier: 3.512A pdb=" N ALA E 153 " --> pdb=" O ASP E 149 " (cutoff:3.500A) removed outlier: 4.099A 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 210 Processing helix chain 'E' and resid 216 through 227 removed outlier: 3.506A pdb=" N LYS E 220 " --> pdb=" O LYS E 216 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ILE E 222 " --> pdb=" O ILE E 218 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ASN E 227 " --> pdb=" O ALA E 223 " (cutoff:3.500A) Processing helix chain 'E' and resid 229 through 243 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 308 Processing helix chain 'E' and resid 314 through 335 Processing helix chain 'E' and resid 337 through 354 removed outlier: 4.308A pdb=" N HIS E 341 " --> pdb=" O LYS E 337 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N ASP E 354 " --> pdb=" O MET E 350 " (cutoff:3.500A) Processing helix chain 'F' and resid 12 through 30 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 112 removed outlier: 3.609A pdb=" N LEU F 100 " --> pdb=" O ASN F 96 " (cutoff:3.500A) Processing helix chain 'F' and resid 213 through 219 removed outlier: 3.673A pdb=" N ARG F 219 " --> pdb=" O ALA F 215 " (cutoff:3.500A) Processing helix chain 'F' and resid 240 through 252 removed outlier: 4.550A pdb=" N SER F 244 " --> pdb=" O GLY F 240 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N ALA F 245 " --> pdb=" O GLU F 241 " (cutoff:3.500A) Processing helix chain 'F' and resid 253 through 256 removed outlier: 3.999A pdb=" N TYR F 256 " --> pdb=" O VAL F 253 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 253 through 256' Processing helix chain 'F' and resid 412 through 424 removed outlier: 3.614A pdb=" N ALA F 424 " --> pdb=" O LYS F 420 " (cutoff:3.500A) Processing helix chain 'G' and resid 17 through 28 removed outlier: 4.220A pdb=" N ILE G 21 " --> pdb=" O HIS G 17 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LEU G 28 " --> pdb=" O ALA G 24 " (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 174 Processing helix chain 'G' and resid 239 through 243 Processing helix chain 'G' and resid 245 through 252 removed outlier: 4.117A pdb=" N ILE G 251 " --> pdb=" O LYS G 247 " (cutoff:3.500A) Processing helix chain 'G' and resid 318 through 330 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: 3.902A 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: 5.920A pdb=" N THR A 149 " --> pdb=" O LEU A 185 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 109 through 114 removed outlier: 6.251A pdb=" N LYS B 109 " --> pdb=" O ARG B 139 " (cutoff:3.500A) removed outlier: 7.464A pdb=" N ALA B 141 " --> pdb=" O LYS B 109 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N VAL B 111 " --> pdb=" O ALA B 141 " (cutoff:3.500A) removed outlier: 7.338A pdb=" N ALA B 143 " --> pdb=" O VAL B 111 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N LEU B 113 " --> pdb=" O ALA B 143 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N GLY B 49 " --> pdb=" O CYS B 144 " (cutoff:3.500A) removed outlier: 5.819A pdb=" N ILE B 46 " --> pdb=" O LEU B 161 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N TYR B 163 " --> pdb=" O ILE B 46 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N SER B 48 " --> pdb=" O TYR B 163 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 79 through 82 removed outlier: 6.041A pdb=" N LEU C 50 " --> pdb=" O PHE C 164 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 92 through 95 removed outlier: 6.488A pdb=" N MET D 61 " --> pdb=" O LEU D 168 " (cutoff:3.500A) removed outlier: 8.020A pdb=" N CYS D 170 " --> pdb=" O MET D 61 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N PHE D 63 " --> pdb=" O CYS D 170 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 69 through 76 removed outlier: 3.707A pdb=" N HIS E 93 " --> pdb=" O SER E 90 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N LEU E 94 " --> pdb=" O ILE E 139 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N LEU E 39 " --> pdb=" O MET E 169 " (cutoff:3.500A) removed outlier: 8.045A pdb=" N CYS E 171 " --> pdb=" O LEU E 39 " (cutoff:3.500A) removed outlier: 5.898A pdb=" N LEU E 41 " --> pdb=" O CYS E 171 " (cutoff:3.500A) removed outlier: 6.009A pdb=" N LEU E 40 " --> pdb=" O ILE E 188 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'E' and resid 212 through 213 removed outlier: 6.789A pdb=" N GLN E 212 " --> pdb=" O LEU E 248 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'F' and resid 82 through 83 removed outlier: 3.720A pdb=" N GLU F 94 " --> pdb=" O LYS F 210 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ARG F 41 " --> pdb=" O ASN F 38 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N GLY F 462 " --> pdb=" O LEU F 444 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N SER F 437 " --> pdb=" O SER F 433 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N GLU F 427 " --> pdb=" O SER F 443 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N VAL F 428 " --> pdb=" O LEU F 235 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'F' and resid 408 through 411 removed outlier: 3.996A pdb=" N VAL F 267 " --> pdb=" O GLU F 280 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N GLU F 280 " --> pdb=" O VAL F 267 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ARG G 129 " --> pdb=" O GLU F 293 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N PHE G 121 " --> pdb=" O GLU G 128 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'G' and resid 80 through 85 removed outlier: 7.212A pdb=" N ASP G 36 " --> pdb=" O GLU G 51 " (cutoff:3.500A) removed outlier: 5.687A pdb=" N GLU G 51 " --> pdb=" O ASP G 36 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N VAL G 305 " --> pdb=" O LEU G 61 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N ILE G 304 " --> pdb=" O SER G 271 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N LEU G 270 " --> pdb=" O LYS G 254 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N LYS G 254 " --> pdb=" O LEU G 270 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N LYS G 216 " --> pdb=" O ILE G 157 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'G' and resid 233 through 238 removed outlier: 3.548A pdb=" N GLU G 177 " --> pdb=" O LYS G 197 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N PHE G 192 " --> pdb=" O LEU G 207 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N GLU H 139 " --> pdb=" O SER H 115 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N SER H 115 " --> pdb=" O GLU H 139 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N PHE H 116 " --> pdb=" O ILE H 7 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N PHE H 3 " --> pdb=" O VAL H 120 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'H' and resid 152 through 153 removed outlier: 7.021A pdb=" N ASP H 29 " --> pdb=" O MET H 44 " (cutoff:3.500A) removed outlier: 5.562A pdb=" N MET H 44 " --> pdb=" O ASP H 29 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ILE H 40 " --> pdb=" O THR H 33 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N CYS H 52 " --> pdb=" O SER H 43 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'H' and resid 295 through 297 Processing sheet with id=AB4, first strand: chain 'H' and resid 284 through 289 removed outlier: 3.590A pdb=" N GLU H 251 " --> pdb=" O PHE H 266 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'H' and resid 270 through 271 removed outlier: 3.605A pdb=" N ARG H 279 " --> pdb=" O VAL H 270 " (cutoff:3.500A) 1132 hydrogen bonds defined for protein. 3267 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 24 hydrogen bonds 48 hydrogen bond angles 0 basepair planarities 10 basepair parallelities 18 stacking parallelities Total time for adding SS restraints: 7.56 Time building geometry restraints manager: 5.62 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.36: 6925 1.36 - 1.50: 5618 1.50 - 1.65: 8916 1.65 - 1.80: 81 1.80 - 1.95: 89 Bond restraints: 21629 Sorted by residual: bond pdb=" N LYS A 498 " pdb=" CA LYS A 498 " ideal model delta sigma weight residual 1.456 1.498 -0.042 1.18e-02 7.18e+03 1.26e+01 bond pdb=" C LYS A 498 " pdb=" O LYS A 498 " ideal model delta sigma weight residual 1.236 1.277 -0.041 1.28e-02 6.10e+03 1.03e+01 bond pdb=" N ILE H 360 " pdb=" CA ILE H 360 " ideal model delta sigma weight residual 1.458 1.495 -0.037 1.17e-02 7.31e+03 1.00e+01 bond pdb=" N ILE F 432 " pdb=" CA ILE F 432 " ideal model delta sigma weight residual 1.458 1.492 -0.034 1.17e-02 7.31e+03 8.47e+00 bond pdb=" N TRP H 352 " pdb=" CA TRP H 352 " ideal model delta sigma weight residual 1.455 1.490 -0.035 1.21e-02 6.83e+03 8.41e+00 ... (remaining 21624 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.18: 28733 2.18 - 4.36: 543 4.36 - 6.54: 52 6.54 - 8.72: 4 8.72 - 10.90: 2 Bond angle restraints: 29334 Sorted by residual: angle pdb=" N GLU C 294 " pdb=" CA GLU C 294 " pdb=" C GLU C 294 " ideal model delta sigma weight residual 112.89 107.10 5.79 1.24e+00 6.50e-01 2.18e+01 angle pdb=" C PRO D 133 " pdb=" CA PRO D 133 " pdb=" CB PRO D 133 " ideal model delta sigma weight residual 112.89 107.58 5.31 1.31e+00 5.83e-01 1.64e+01 angle pdb=" C TYR A 497 " pdb=" N LYS A 498 " pdb=" CA LYS A 498 " ideal model delta sigma weight residual 122.73 116.23 6.50 1.61e+00 3.86e-01 1.63e+01 angle pdb=" N GLN A 283 " pdb=" CA GLN A 283 " pdb=" C GLN A 283 " ideal model delta sigma weight residual 113.17 108.18 4.99 1.26e+00 6.30e-01 1.57e+01 angle pdb=" N GLU B 182 " pdb=" CA GLU B 182 " pdb=" C GLU B 182 " ideal model delta sigma weight residual 113.72 108.86 4.86 1.30e+00 5.92e-01 1.40e+01 ... (remaining 29329 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.54: 12473 34.54 - 69.08: 671 69.08 - 103.62: 26 103.62 - 138.16: 2 138.16 - 172.69: 1 Dihedral angle restraints: 13173 sinusoidal: 5632 harmonic: 7541 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 300.00 127.31 172.69 1 2.00e+01 2.50e-03 4.78e+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 74.45 -134.45 1 2.00e+01 2.50e-03 4.08e+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 56.94 -116.95 1 2.00e+01 2.50e-03 3.49e+01 ... (remaining 13170 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.068: 2983 0.068 - 0.136: 394 0.136 - 0.204: 23 0.204 - 0.272: 2 0.272 - 0.340: 1 Chirality restraints: 3403 Sorted by residual: chirality pdb=" CB THR D 47 " pdb=" CA THR D 47 " pdb=" OG1 THR D 47 " pdb=" CG2 THR D 47 " both_signs ideal model delta sigma weight residual False 2.55 2.21 0.34 2.00e-01 2.50e+01 2.89e+00 chirality pdb=" CB ILE B 47 " pdb=" CA ILE B 47 " pdb=" CG1 ILE B 47 " pdb=" CG2 ILE B 47 " both_signs ideal model delta sigma weight residual False 2.64 2.41 0.24 2.00e-01 2.50e+01 1.43e+00 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 2.65 -0.22 2.00e-01 2.50e+01 1.19e+00 ... (remaining 3400 not shown) Planarity restraints: 3593 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE F 213 " 0.026 2.00e-02 2.50e+03 2.78e-02 1.35e+01 pdb=" CG PHE F 213 " -0.065 2.00e-02 2.50e+03 pdb=" CD1 PHE F 213 " 0.013 2.00e-02 2.50e+03 pdb=" CD2 PHE F 213 " 0.018 2.00e-02 2.50e+03 pdb=" CE1 PHE F 213 " 0.005 2.00e-02 2.50e+03 pdb=" CE2 PHE F 213 " -0.002 2.00e-02 2.50e+03 pdb=" CZ PHE F 213 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 294 " 0.020 2.00e-02 2.50e+03 2.30e-02 1.32e+01 pdb=" CG TRP A 294 " -0.059 2.00e-02 2.50e+03 pdb=" CD1 TRP A 294 " 0.035 2.00e-02 2.50e+03 pdb=" CD2 TRP A 294 " 0.003 2.00e-02 2.50e+03 pdb=" NE1 TRP A 294 " -0.011 2.00e-02 2.50e+03 pdb=" CE2 TRP A 294 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP A 294 " 0.005 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 294 " 0.003 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 294 " 0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP A 294 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS B 180 " -0.017 2.00e-02 2.50e+03 3.32e-02 1.10e+01 pdb=" C LYS B 180 " 0.057 2.00e-02 2.50e+03 pdb=" O LYS B 180 " -0.021 2.00e-02 2.50e+03 pdb=" N LEU B 181 " -0.019 2.00e-02 2.50e+03 ... (remaining 3590 not shown) Histogram of nonbonded interaction distances: 1.91 - 2.51: 154 2.51 - 3.11: 15292 3.11 - 3.70: 33162 3.70 - 4.30: 48382 4.30 - 4.90: 81164 Nonbonded interactions: 178154 Sorted by model distance: nonbonded pdb="MG MG A 601 " pdb=" O3A AGS A 602 " model vdw 1.912 2.170 nonbonded pdb="MG MG C 401 " pdb=" O2G AGS C 402 " model vdw 1.943 2.170 nonbonded pdb=" OG1 THR B 56 " pdb="MG MG B 402 " model vdw 1.965 2.170 nonbonded pdb=" O2G AGS B 401 " pdb="MG MG B 402 " model vdw 1.966 2.170 nonbonded pdb=" OG SER A 116 " pdb="MG MG A 601 " model vdw 1.983 2.170 ... (remaining 178149 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: 5.710 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.820 Check model and map are aligned: 0.140 Set scattering table: 0.210 Process input model: 49.910 Find NCS groups from input model: 0.490 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: 0.020 Load rotamer database and sin/cos tables:14.460 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 71.900 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7852 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 21629 Z= 0.263 Angle : 0.675 10.904 29334 Z= 0.397 Chirality : 0.045 0.340 3403 Planarity : 0.005 0.095 3593 Dihedral : 18.519 172.694 8253 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 11.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 4.30 % Allowed : 27.80 % Favored : 67.90 % 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: 0.21 (0.17), residues: 2518 helix: 0.91 (0.15), residues: 1238 sheet: -0.12 (0.24), residues: 516 loop : -0.76 (0.23), residues: 764 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.059 0.002 TRP A 294 HIS 0.014 0.001 HIS E 18 PHE 0.065 0.002 PHE F 213 TYR 0.026 0.002 TYR B 163 ARG 0.010 0.000 ARG C 136 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5036 Ramachandran restraints generated. 2518 Oldfield, 0 Emsley, 2518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5036 Ramachandran restraints generated. 2518 Oldfield, 0 Emsley, 2518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 380 residues out of total 2326 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 280 time to evaluate : 2.399 Fit side-chains revert: symmetry clash REVERT: A 273 LEU cc_start: 0.7523 (OUTLIER) cc_final: 0.7099 (mp) REVERT: C 136 ARG cc_start: 0.7588 (ttt90) cc_final: 0.7380 (ttt90) REVERT: F 436 GLU cc_start: 0.7501 (OUTLIER) cc_final: 0.7094 (tp30) REVERT: G 60 LEU cc_start: 0.7510 (OUTLIER) cc_final: 0.7066 (tp) outliers start: 100 outliers final: 78 residues processed: 363 average time/residue: 1.0487 time to fit residues: 446.1041 Evaluate side-chains 339 residues out of total 2326 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 258 time to evaluate : 2.536 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 PHE 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 204 LEU Chi-restraints excluded: chain A residue 266 ASN Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 325 SER Chi-restraints excluded: chain A residue 330 ILE Chi-restraints excluded: chain A residue 336 THR Chi-restraints excluded: chain A residue 351 HIS Chi-restraints excluded: chain A residue 457 LYS Chi-restraints excluded: chain A residue 466 VAL Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 482 LEU Chi-restraints excluded: chain A residue 536 VAL Chi-restraints excluded: chain B residue 48 SER Chi-restraints excluded: chain B residue 66 LEU Chi-restraints excluded: chain B residue 70 SER Chi-restraints excluded: chain B residue 114 ASP Chi-restraints excluded: chain B residue 120 THR Chi-restraints excluded: chain B residue 135 SER Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 222 ASP Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain B residue 243 SER Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 57 THR Chi-restraints excluded: chain C residue 85 SER Chi-restraints excluded: chain C residue 132 ARG Chi-restraints excluded: chain C residue 138 THR Chi-restraints excluded: chain C residue 154 THR Chi-restraints excluded: chain C residue 199 GLU Chi-restraints excluded: chain C residue 201 SER Chi-restraints excluded: chain C residue 218 THR Chi-restraints excluded: chain C residue 256 TRP Chi-restraints excluded: chain C residue 258 THR Chi-restraints excluded: chain D residue 28 VAL Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain D residue 79 THR Chi-restraints excluded: chain D residue 94 GLU Chi-restraints excluded: chain D residue 163 VAL Chi-restraints excluded: chain D residue 173 VAL Chi-restraints excluded: chain D residue 182 SER Chi-restraints excluded: chain D residue 239 SER Chi-restraints excluded: chain E residue 18 HIS Chi-restraints excluded: chain E residue 76 VAL Chi-restraints excluded: chain E residue 89 SER Chi-restraints excluded: chain E residue 108 VAL Chi-restraints excluded: chain E residue 167 LEU Chi-restraints excluded: chain E residue 170 VAL Chi-restraints excluded: chain E residue 194 SER Chi-restraints excluded: chain E residue 221 ARG Chi-restraints excluded: chain E residue 230 LEU Chi-restraints excluded: chain E residue 297 ASN Chi-restraints excluded: chain E residue 315 THR Chi-restraints excluded: chain E residue 326 SER Chi-restraints excluded: chain F residue 59 THR Chi-restraints excluded: chain F residue 207 VAL Chi-restraints excluded: chain F residue 225 ILE Chi-restraints excluded: chain F residue 286 ASN Chi-restraints excluded: chain F residue 405 THR Chi-restraints excluded: chain F residue 436 GLU Chi-restraints excluded: chain G residue 12 SER Chi-restraints excluded: chain G residue 21 ILE Chi-restraints excluded: chain G residue 35 ASP Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 60 LEU Chi-restraints excluded: chain G residue 73 ARG Chi-restraints excluded: chain G residue 77 GLU Chi-restraints excluded: chain G residue 89 ILE Chi-restraints excluded: chain G residue 104 VAL Chi-restraints excluded: chain G residue 130 VAL Chi-restraints excluded: chain G residue 173 ILE Chi-restraints excluded: chain G residue 190 ASN Chi-restraints excluded: chain G residue 245 ILE Chi-restraints excluded: chain H residue 50 THR Chi-restraints excluded: chain H residue 144 ILE Chi-restraints excluded: chain H residue 147 GLU Chi-restraints excluded: chain H residue 252 VAL Chi-restraints excluded: chain H residue 258 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 254 random chunks: chunk 214 optimal weight: 2.9990 chunk 192 optimal weight: 4.9990 chunk 106 optimal weight: 0.6980 chunk 65 optimal weight: 0.7980 chunk 129 optimal weight: 0.9990 chunk 102 optimal weight: 0.7980 chunk 199 optimal weight: 4.9990 chunk 77 optimal weight: 0.0570 chunk 121 optimal weight: 0.9990 chunk 148 optimal weight: 3.9990 chunk 230 optimal weight: 9.9990 overall best weight: 0.6700 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 81 HIS A 284 ASN B 102 HIS D 24 GLN D 207 GLN D 311 ASN E 104 ASN ** F 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 291 HIS H 45 ASN H 355 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7838 moved from start: 0.0887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 21629 Z= 0.204 Angle : 0.590 10.397 29334 Z= 0.309 Chirality : 0.042 0.162 3403 Planarity : 0.004 0.052 3593 Dihedral : 14.152 135.885 3256 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 5.42 % Allowed : 25.43 % Favored : 69.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.52 (0.17), residues: 2518 helix: 1.19 (0.15), residues: 1237 sheet: -0.06 (0.23), residues: 530 loop : -0.61 (0.24), residues: 751 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 294 HIS 0.009 0.001 HIS E 18 PHE 0.025 0.002 PHE H 240 TYR 0.025 0.001 TYR A 497 ARG 0.007 0.001 ARG C 136 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5036 Ramachandran restraints generated. 2518 Oldfield, 0 Emsley, 2518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5036 Ramachandran restraints generated. 2518 Oldfield, 0 Emsley, 2518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 416 residues out of total 2326 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 126 poor density : 290 time to evaluate : 2.384 Fit side-chains revert: symmetry clash REVERT: A 68 GLU cc_start: 0.7384 (OUTLIER) cc_final: 0.6569 (tm-30) REVERT: A 178 MET cc_start: 0.1941 (mmt) cc_final: 0.0568 (ttm) REVERT: A 256 MET cc_start: 0.6261 (mpt) cc_final: 0.6060 (mpm) REVERT: A 465 ASN cc_start: 0.6456 (t0) cc_final: 0.6190 (m-40) REVERT: C 81 GLU cc_start: 0.8754 (OUTLIER) cc_final: 0.8223 (tt0) REVERT: C 204 ASP cc_start: 0.8483 (OUTLIER) cc_final: 0.8017 (t0) REVERT: D 86 ASP cc_start: 0.7206 (OUTLIER) cc_final: 0.6906 (m-30) REVERT: D 148 ASP cc_start: 0.7881 (OUTLIER) cc_final: 0.7648 (p0) REVERT: D 175 ARG cc_start: 0.8617 (OUTLIER) cc_final: 0.7817 (mmt-90) REVERT: D 254 THR cc_start: 0.8411 (m) cc_final: 0.8146 (m) REVERT: E 8 TYR cc_start: 0.8636 (m-80) cc_final: 0.8351 (m-80) REVERT: E 52 ARG cc_start: 0.8802 (OUTLIER) cc_final: 0.5246 (mtt90) REVERT: E 119 MET cc_start: 0.7875 (ttp) cc_final: 0.7643 (ttp) REVERT: E 184 ARG cc_start: 0.8499 (OUTLIER) cc_final: 0.8235 (mtm180) REVERT: F 232 MET cc_start: 0.5959 (mpp) cc_final: 0.5759 (mpt) REVERT: F 265 MET cc_start: 0.7557 (OUTLIER) cc_final: 0.6916 (tmm) REVERT: F 436 GLU cc_start: 0.7278 (OUTLIER) cc_final: 0.6828 (tp30) REVERT: G 60 LEU cc_start: 0.7756 (OUTLIER) cc_final: 0.7363 (tp) REVERT: G 155 GLU cc_start: 0.7191 (tt0) cc_final: 0.6772 (pp20) REVERT: G 238 ASP cc_start: 0.7174 (t0) cc_final: 0.6818 (t0) REVERT: H 20 ILE cc_start: 0.6569 (mm) cc_final: 0.6161 (mt) outliers start: 126 outliers final: 47 residues processed: 381 average time/residue: 1.1567 time to fit residues: 511.1336 Evaluate side-chains 319 residues out of total 2326 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 261 time to evaluate : 2.435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 GLU Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 243 THR Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain A residue 330 ILE Chi-restraints excluded: chain A residue 403 CYS Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 536 VAL Chi-restraints excluded: chain B residue 66 LEU Chi-restraints excluded: chain B residue 114 ASP Chi-restraints excluded: chain B residue 119 MET Chi-restraints excluded: chain B residue 120 THR Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain C residue 10 LYS Chi-restraints excluded: chain C residue 81 GLU Chi-restraints excluded: chain C residue 132 ARG Chi-restraints excluded: chain C residue 154 THR Chi-restraints excluded: chain C residue 204 ASP 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 94 GLU Chi-restraints excluded: chain D residue 148 ASP Chi-restraints excluded: chain D residue 173 VAL Chi-restraints excluded: chain D residue 175 ARG Chi-restraints excluded: chain E residue 52 ARG Chi-restraints excluded: chain E residue 65 VAL Chi-restraints excluded: chain E residue 88 VAL Chi-restraints excluded: chain E residue 94 LEU Chi-restraints excluded: chain E residue 167 LEU Chi-restraints excluded: chain E residue 170 VAL Chi-restraints excluded: chain E residue 184 ARG Chi-restraints excluded: chain E residue 230 LEU Chi-restraints excluded: chain E residue 239 SER Chi-restraints excluded: chain E residue 298 ILE Chi-restraints excluded: chain E residue 315 THR Chi-restraints excluded: chain F residue 59 THR Chi-restraints excluded: chain F residue 79 LEU Chi-restraints excluded: chain F residue 119 MET Chi-restraints excluded: chain F residue 207 VAL Chi-restraints excluded: chain F residue 225 ILE Chi-restraints excluded: chain F residue 265 MET Chi-restraints excluded: chain F residue 267 VAL Chi-restraints excluded: chain F residue 286 ASN Chi-restraints excluded: chain F residue 407 GLU Chi-restraints excluded: chain F residue 436 GLU Chi-restraints excluded: chain F residue 440 PHE Chi-restraints excluded: chain G residue 35 ASP Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 60 LEU Chi-restraints excluded: chain H residue 117 THR Chi-restraints excluded: chain H residue 144 ILE Chi-restraints excluded: chain H residue 147 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 254 random chunks: chunk 128 optimal weight: 4.9990 chunk 71 optimal weight: 1.9990 chunk 191 optimal weight: 10.0000 chunk 157 optimal weight: 2.9990 chunk 63 optimal weight: 0.9980 chunk 231 optimal weight: 10.0000 chunk 249 optimal weight: 5.9990 chunk 205 optimal weight: 0.7980 chunk 229 optimal weight: 10.0000 chunk 78 optimal weight: 1.9990 chunk 185 optimal weight: 0.7980 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 298 GLN D 24 GLN D 207 GLN D 352 GLN ** E 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 104 ASN E 118 GLN F 291 HIS G 268 ASN H 97 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7885 moved from start: 0.1247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 21629 Z= 0.273 Angle : 0.599 10.064 29334 Z= 0.309 Chirality : 0.043 0.177 3403 Planarity : 0.004 0.055 3593 Dihedral : 13.646 128.803 3175 Min Nonbonded Distance : 1.855 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 6.63 % Allowed : 24.66 % Favored : 68.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.48 (0.17), residues: 2518 helix: 1.11 (0.15), residues: 1240 sheet: -0.03 (0.23), residues: 529 loop : -0.60 (0.24), residues: 749 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 294 HIS 0.012 0.001 HIS E 18 PHE 0.023 0.002 PHE H 152 TYR 0.018 0.002 TYR B 186 ARG 0.009 0.001 ARG C 136 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5036 Ramachandran restraints generated. 2518 Oldfield, 0 Emsley, 2518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5036 Ramachandran restraints generated. 2518 Oldfield, 0 Emsley, 2518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 437 residues out of total 2326 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 154 poor density : 283 time to evaluate : 2.395 Fit side-chains revert: symmetry clash REVERT: A 68 GLU cc_start: 0.7456 (OUTLIER) cc_final: 0.6523 (tm-30) REVERT: A 178 MET cc_start: 0.1798 (mmt) cc_final: 0.0264 (ttm) REVERT: A 465 ASN cc_start: 0.6630 (t0) cc_final: 0.6270 (m-40) REVERT: B 87 ASP cc_start: 0.7491 (OUTLIER) cc_final: 0.7218 (t0) REVERT: B 301 GLU cc_start: 0.7951 (OUTLIER) cc_final: 0.7553 (mt-10) REVERT: C 66 LEU cc_start: 0.8617 (OUTLIER) cc_final: 0.8135 (tp) REVERT: C 81 GLU cc_start: 0.8784 (OUTLIER) cc_final: 0.8304 (tt0) REVERT: C 204 ASP cc_start: 0.8604 (OUTLIER) cc_final: 0.8271 (m-30) REVERT: C 293 GLU cc_start: 0.7349 (OUTLIER) cc_final: 0.7069 (tt0) REVERT: D 80 LYS cc_start: 0.8137 (OUTLIER) cc_final: 0.7680 (ttpt) REVERT: D 86 ASP cc_start: 0.7235 (OUTLIER) cc_final: 0.6923 (m-30) REVERT: D 160 TYR cc_start: 0.8611 (m-80) cc_final: 0.8329 (m-80) REVERT: D 175 ARG cc_start: 0.8644 (OUTLIER) cc_final: 0.7925 (mmt-90) REVERT: D 190 LYS cc_start: 0.8520 (OUTLIER) cc_final: 0.7490 (mttp) REVERT: D 254 THR cc_start: 0.8425 (m) cc_final: 0.8153 (m) REVERT: E 8 TYR cc_start: 0.8698 (m-80) cc_final: 0.8387 (m-80) REVERT: E 119 MET cc_start: 0.7945 (ttp) cc_final: 0.7738 (ttp) REVERT: E 220 LYS cc_start: 0.7344 (mppt) cc_final: 0.6997 (mppt) REVERT: F 265 MET cc_start: 0.7495 (OUTLIER) cc_final: 0.6773 (tmm) REVERT: G 60 LEU cc_start: 0.7737 (OUTLIER) cc_final: 0.7247 (tp) REVERT: G 95 VAL cc_start: 0.3238 (OUTLIER) cc_final: 0.2958 (p) REVERT: G 155 GLU cc_start: 0.7274 (tt0) cc_final: 0.7067 (tt0) REVERT: G 218 GLN cc_start: 0.6719 (mt0) cc_final: 0.6134 (mm-40) REVERT: G 238 ASP cc_start: 0.7269 (t0) cc_final: 0.6787 (t0) REVERT: H 101 LEU cc_start: 0.7081 (OUTLIER) cc_final: 0.6840 (tt) outliers start: 154 outliers final: 77 residues processed: 396 average time/residue: 1.1278 time to fit residues: 519.6118 Evaluate side-chains 355 residues out of total 2326 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 263 time to evaluate : 2.493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 GLU Chi-restraints excluded: chain A residue 96 PHE Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 243 THR Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 254 ILE Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain A residue 330 ILE Chi-restraints excluded: chain A residue 336 THR Chi-restraints excluded: chain A residue 351 HIS Chi-restraints excluded: chain A residue 358 GLU Chi-restraints excluded: chain A residue 403 CYS Chi-restraints excluded: chain A residue 457 LYS Chi-restraints excluded: chain A residue 458 VAL Chi-restraints excluded: chain A residue 464 LEU Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 536 VAL Chi-restraints excluded: chain B residue 48 SER Chi-restraints excluded: chain B residue 66 LEU Chi-restraints excluded: chain B residue 87 ASP Chi-restraints excluded: chain B residue 114 ASP Chi-restraints excluded: chain B residue 119 MET Chi-restraints excluded: chain B residue 120 THR Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain B residue 301 GLU Chi-restraints excluded: chain C residue 10 LYS Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 66 LEU Chi-restraints excluded: chain C residue 71 TYR Chi-restraints excluded: chain C residue 81 GLU Chi-restraints excluded: chain C residue 86 ASP Chi-restraints excluded: chain C residue 132 ARG Chi-restraints excluded: chain C residue 138 THR Chi-restraints excluded: chain C residue 204 ASP Chi-restraints excluded: chain C residue 258 THR Chi-restraints excluded: chain C residue 268 SER Chi-restraints excluded: chain C residue 293 GLU Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 79 THR Chi-restraints excluded: chain D residue 80 LYS Chi-restraints excluded: chain D residue 86 ASP Chi-restraints excluded: chain D residue 94 GLU Chi-restraints excluded: chain D residue 148 ASP Chi-restraints excluded: chain D residue 163 VAL Chi-restraints excluded: chain D residue 173 VAL Chi-restraints excluded: chain D residue 175 ARG Chi-restraints excluded: chain D residue 190 LYS Chi-restraints excluded: chain D residue 247 ASP Chi-restraints excluded: chain D residue 259 LEU Chi-restraints excluded: chain D residue 269 ILE Chi-restraints excluded: chain D residue 277 SER Chi-restraints excluded: chain D residue 296 SER Chi-restraints excluded: chain E residue 65 VAL Chi-restraints excluded: chain E residue 76 VAL Chi-restraints excluded: chain E residue 88 VAL Chi-restraints excluded: chain E residue 89 SER Chi-restraints excluded: chain E residue 94 LEU Chi-restraints excluded: chain E residue 165 ILE Chi-restraints excluded: chain E residue 167 LEU Chi-restraints excluded: chain E residue 170 VAL Chi-restraints excluded: chain E residue 230 LEU Chi-restraints excluded: chain E residue 239 SER Chi-restraints excluded: chain E residue 298 ILE Chi-restraints excluded: chain E residue 315 THR Chi-restraints excluded: chain F residue 59 THR Chi-restraints excluded: chain F residue 79 LEU Chi-restraints excluded: chain F residue 88 LEU Chi-restraints excluded: chain F residue 207 VAL Chi-restraints excluded: chain F residue 225 ILE Chi-restraints excluded: chain F residue 262 ILE Chi-restraints excluded: chain F residue 265 MET Chi-restraints excluded: chain F residue 286 ASN Chi-restraints excluded: chain F residue 407 GLU Chi-restraints excluded: chain F residue 408 VAL Chi-restraints excluded: chain F residue 440 PHE Chi-restraints excluded: chain F residue 471 SER Chi-restraints excluded: chain G residue 21 ILE Chi-restraints excluded: chain G residue 28 LEU Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 60 LEU Chi-restraints excluded: chain G residue 95 VAL Chi-restraints excluded: chain G residue 226 THR Chi-restraints excluded: chain H residue 50 THR Chi-restraints excluded: chain H residue 101 LEU Chi-restraints excluded: chain H residue 117 THR Chi-restraints excluded: chain H residue 144 ILE Chi-restraints excluded: chain H residue 147 GLU Chi-restraints excluded: chain H residue 254 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 254 random chunks: chunk 228 optimal weight: 10.0000 chunk 173 optimal weight: 20.0000 chunk 119 optimal weight: 0.8980 chunk 25 optimal weight: 5.9990 chunk 110 optimal weight: 0.0010 chunk 155 optimal weight: 0.9990 chunk 231 optimal weight: 20.0000 chunk 245 optimal weight: 10.0000 chunk 121 optimal weight: 0.8980 chunk 219 optimal weight: 2.9990 chunk 66 optimal weight: 0.5980 overall best weight: 0.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 95 ASN D 24 GLN ** E 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 104 ASN F 291 HIS H 233 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7846 moved from start: 0.1469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 21629 Z= 0.187 Angle : 0.549 9.218 29334 Z= 0.285 Chirality : 0.041 0.145 3403 Planarity : 0.004 0.043 3593 Dihedral : 13.372 118.689 3169 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 5.68 % Allowed : 25.69 % Favored : 68.63 % 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: 0.68 (0.17), residues: 2518 helix: 1.31 (0.15), residues: 1240 sheet: 0.03 (0.23), residues: 528 loop : -0.52 (0.24), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 294 HIS 0.012 0.001 HIS E 18 PHE 0.025 0.001 PHE A 279 TYR 0.019 0.001 TYR B 186 ARG 0.010 0.000 ARG C 136 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5036 Ramachandran restraints generated. 2518 Oldfield, 0 Emsley, 2518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5036 Ramachandran restraints generated. 2518 Oldfield, 0 Emsley, 2518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 415 residues out of total 2326 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 132 poor density : 283 time to evaluate : 2.407 Fit side-chains revert: symmetry clash REVERT: A 68 GLU cc_start: 0.7462 (OUTLIER) cc_final: 0.6529 (tm-30) REVERT: A 163 MET cc_start: 0.6494 (OUTLIER) cc_final: 0.6078 (mtm) REVERT: A 178 MET cc_start: 0.1988 (mmt) cc_final: 0.0517 (ttm) REVERT: A 273 LEU cc_start: 0.7704 (OUTLIER) cc_final: 0.7295 (mp) REVERT: A 285 MET cc_start: 0.7480 (ttp) cc_final: 0.7144 (tpp) REVERT: A 288 LEU cc_start: 0.6754 (OUTLIER) cc_final: 0.6438 (mm) REVERT: A 465 ASN cc_start: 0.6661 (t0) cc_final: 0.6284 (m-40) REVERT: C 81 GLU cc_start: 0.8747 (OUTLIER) cc_final: 0.8207 (tt0) REVERT: C 204 ASP cc_start: 0.8483 (OUTLIER) cc_final: 0.8168 (m-30) REVERT: C 292 ASN cc_start: 0.8492 (t0) cc_final: 0.8072 (t0) REVERT: C 293 GLU cc_start: 0.7138 (tm-30) cc_final: 0.6936 (tt0) REVERT: D 86 ASP cc_start: 0.7191 (OUTLIER) cc_final: 0.6777 (m-30) REVERT: D 175 ARG cc_start: 0.8632 (OUTLIER) cc_final: 0.7919 (mmt-90) REVERT: D 190 LYS cc_start: 0.8502 (OUTLIER) cc_final: 0.6856 (mmtp) REVERT: D 254 THR cc_start: 0.8341 (m) cc_final: 0.8085 (m) REVERT: E 8 TYR cc_start: 0.8681 (m-80) cc_final: 0.8462 (m-80) REVERT: E 52 ARG cc_start: 0.8825 (OUTLIER) cc_final: 0.5324 (mtt90) REVERT: E 119 MET cc_start: 0.7949 (ttp) cc_final: 0.7738 (ttp) REVERT: E 184 ARG cc_start: 0.8498 (OUTLIER) cc_final: 0.8290 (mtm180) REVERT: F 436 GLU cc_start: 0.7193 (OUTLIER) cc_final: 0.6801 (tp30) REVERT: G 155 GLU cc_start: 0.7265 (tt0) cc_final: 0.6932 (pp20) REVERT: G 218 GLN cc_start: 0.6662 (mt0) cc_final: 0.6028 (mm-40) REVERT: G 238 ASP cc_start: 0.7170 (t0) cc_final: 0.6545 (t0) outliers start: 132 outliers final: 63 residues processed: 382 average time/residue: 1.1160 time to fit residues: 496.0377 Evaluate side-chains 335 residues out of total 2326 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 260 time to evaluate : 2.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 GLU Chi-restraints excluded: chain A residue 96 PHE Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 163 MET Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 266 ASN Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain A residue 330 ILE Chi-restraints excluded: chain A residue 351 HIS Chi-restraints excluded: chain A residue 358 GLU Chi-restraints excluded: chain A residue 403 CYS Chi-restraints excluded: chain A residue 464 LEU Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain B residue 48 SER Chi-restraints excluded: chain B residue 66 LEU Chi-restraints excluded: chain B residue 119 MET Chi-restraints excluded: chain B residue 120 THR Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain C residue 10 LYS Chi-restraints excluded: chain C residue 81 GLU Chi-restraints excluded: chain C residue 86 ASP Chi-restraints excluded: chain C residue 132 ARG Chi-restraints excluded: chain C residue 138 THR Chi-restraints excluded: chain C residue 169 LEU Chi-restraints excluded: chain C residue 204 ASP Chi-restraints excluded: chain C residue 220 ASP 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 88 MET Chi-restraints excluded: chain D residue 94 GLU Chi-restraints excluded: chain D residue 163 VAL Chi-restraints excluded: chain D residue 173 VAL Chi-restraints excluded: chain D residue 175 ARG Chi-restraints excluded: chain D residue 190 LYS Chi-restraints excluded: chain D residue 247 ASP Chi-restraints excluded: chain D residue 277 SER Chi-restraints excluded: chain D residue 334 ASN Chi-restraints excluded: chain E residue 52 ARG Chi-restraints excluded: chain E residue 65 VAL Chi-restraints excluded: chain E residue 88 VAL Chi-restraints excluded: chain E residue 94 LEU Chi-restraints excluded: chain E residue 167 LEU Chi-restraints excluded: chain E residue 170 VAL Chi-restraints excluded: chain E residue 184 ARG Chi-restraints excluded: chain E residue 230 LEU Chi-restraints excluded: chain E residue 298 ILE Chi-restraints excluded: chain E residue 350 MET Chi-restraints excluded: chain F residue 59 THR Chi-restraints excluded: chain F residue 88 LEU Chi-restraints excluded: chain F residue 207 VAL Chi-restraints excluded: chain F residue 225 ILE Chi-restraints excluded: chain F residue 262 ILE Chi-restraints excluded: chain F residue 286 ASN Chi-restraints excluded: chain F residue 407 GLU Chi-restraints excluded: chain F residue 408 VAL Chi-restraints excluded: chain F residue 436 GLU Chi-restraints excluded: chain F residue 440 PHE Chi-restraints excluded: chain F residue 471 SER Chi-restraints excluded: chain G residue 21 ILE Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 60 LEU Chi-restraints excluded: chain G residue 226 THR Chi-restraints excluded: chain H residue 50 THR Chi-restraints excluded: chain H residue 117 THR Chi-restraints excluded: chain H residue 136 VAL Chi-restraints excluded: chain H residue 144 ILE Chi-restraints excluded: chain H residue 147 GLU Chi-restraints excluded: chain H residue 254 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 254 random chunks: chunk 204 optimal weight: 3.9990 chunk 139 optimal weight: 0.5980 chunk 3 optimal weight: 1.9990 chunk 182 optimal weight: 0.8980 chunk 101 optimal weight: 0.8980 chunk 209 optimal weight: 2.9990 chunk 169 optimal weight: 1.9990 chunk 0 optimal weight: 4.9990 chunk 125 optimal weight: 2.9990 chunk 220 optimal weight: 1.9990 chunk 61 optimal weight: 2.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 8 GLN D 24 GLN E 18 HIS E 104 ASN F 291 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7886 moved from start: 0.1607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 21629 Z= 0.265 Angle : 0.588 10.607 29334 Z= 0.302 Chirality : 0.043 0.166 3403 Planarity : 0.004 0.044 3593 Dihedral : 13.324 118.790 3165 Min Nonbonded Distance : 1.852 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 6.24 % Allowed : 25.56 % Favored : 68.20 % 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: 0.64 (0.17), residues: 2518 helix: 1.24 (0.15), residues: 1240 sheet: -0.00 (0.23), residues: 540 loop : -0.48 (0.24), residues: 738 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 324 HIS 0.011 0.001 HIS E 18 PHE 0.025 0.002 PHE H 152 TYR 0.019 0.002 TYR B 186 ARG 0.008 0.000 ARG C 136 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5036 Ramachandran restraints generated. 2518 Oldfield, 0 Emsley, 2518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5036 Ramachandran restraints generated. 2518 Oldfield, 0 Emsley, 2518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 424 residues out of total 2326 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 145 poor density : 279 time to evaluate : 2.281 Fit side-chains revert: symmetry clash REVERT: A 68 GLU cc_start: 0.7474 (OUTLIER) cc_final: 0.6451 (tm-30) REVERT: A 163 MET cc_start: 0.6467 (OUTLIER) cc_final: 0.6044 (mtm) REVERT: A 256 MET cc_start: 0.6686 (mpm) cc_final: 0.6482 (mpm) REVERT: A 273 LEU cc_start: 0.7698 (OUTLIER) cc_final: 0.7292 (mp) REVERT: B 87 ASP cc_start: 0.7496 (OUTLIER) cc_final: 0.7225 (t0) REVERT: C 11 GLU cc_start: 0.7282 (OUTLIER) cc_final: 0.6879 (mp0) REVERT: C 66 LEU cc_start: 0.8641 (OUTLIER) cc_final: 0.8134 (tp) REVERT: C 204 ASP cc_start: 0.8582 (OUTLIER) cc_final: 0.8256 (m-30) REVERT: C 292 ASN cc_start: 0.8494 (t0) cc_final: 0.8022 (t0) REVERT: D 80 LYS cc_start: 0.8116 (OUTLIER) cc_final: 0.7675 (ttpt) REVERT: D 86 ASP cc_start: 0.7225 (OUTLIER) cc_final: 0.6899 (m-30) REVERT: D 175 ARG cc_start: 0.8650 (OUTLIER) cc_final: 0.7896 (mmt-90) REVERT: D 190 LYS cc_start: 0.8510 (OUTLIER) cc_final: 0.7591 (mttp) REVERT: D 254 THR cc_start: 0.8357 (m) cc_final: 0.8097 (m) REVERT: D 259 LEU cc_start: 0.8857 (OUTLIER) cc_final: 0.8653 (pt) REVERT: E 18 HIS cc_start: 0.8448 (OUTLIER) cc_final: 0.8003 (p-80) REVERT: E 52 ARG cc_start: 0.8825 (OUTLIER) cc_final: 0.5355 (mtt90) REVERT: E 119 MET cc_start: 0.7934 (ttp) cc_final: 0.7733 (ttp) REVERT: E 158 MET cc_start: 0.8850 (ptt) cc_final: 0.8647 (ptt) REVERT: E 184 ARG cc_start: 0.8520 (OUTLIER) cc_final: 0.8302 (mtm180) REVERT: E 220 LYS cc_start: 0.7378 (mppt) cc_final: 0.7067 (mppt) REVERT: F 233 TYR cc_start: 0.6569 (m-80) cc_final: 0.6196 (m-80) REVERT: G 218 GLN cc_start: 0.6774 (mt0) cc_final: 0.6114 (mm-40) REVERT: G 238 ASP cc_start: 0.7237 (t0) cc_final: 0.6645 (t0) REVERT: H 101 LEU cc_start: 0.7165 (OUTLIER) cc_final: 0.6930 (tt) outliers start: 145 outliers final: 70 residues processed: 387 average time/residue: 1.1479 time to fit residues: 515.0190 Evaluate side-chains 349 residues out of total 2326 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 263 time to evaluate : 2.541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 GLU Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 163 MET Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 243 THR Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 266 ASN Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain A residue 336 THR Chi-restraints excluded: chain A residue 351 HIS Chi-restraints excluded: chain A residue 358 GLU Chi-restraints excluded: chain A residue 403 CYS Chi-restraints excluded: chain A residue 457 LYS Chi-restraints excluded: chain A residue 458 VAL Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 482 LEU Chi-restraints excluded: chain A residue 536 VAL Chi-restraints excluded: chain B residue 48 SER Chi-restraints excluded: chain B residue 66 LEU Chi-restraints excluded: chain B residue 87 ASP Chi-restraints excluded: chain B residue 114 ASP Chi-restraints excluded: chain B residue 119 MET Chi-restraints excluded: chain B residue 120 THR Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 211 SER Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain C residue 11 GLU Chi-restraints excluded: chain C residue 66 LEU Chi-restraints excluded: chain C residue 132 ARG Chi-restraints excluded: chain C residue 138 THR Chi-restraints excluded: chain C residue 204 ASP Chi-restraints excluded: chain C residue 220 ASP Chi-restraints excluded: chain C residue 250 SER 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 80 LYS Chi-restraints excluded: chain D residue 86 ASP Chi-restraints excluded: chain D residue 94 GLU Chi-restraints excluded: chain D residue 163 VAL Chi-restraints excluded: chain D residue 173 VAL Chi-restraints excluded: chain D residue 175 ARG Chi-restraints excluded: chain D residue 190 LYS Chi-restraints excluded: chain D residue 247 ASP Chi-restraints excluded: chain D residue 259 LEU Chi-restraints excluded: chain D residue 277 SER Chi-restraints excluded: chain D residue 296 SER Chi-restraints excluded: chain D residue 334 ASN Chi-restraints excluded: chain E residue 18 HIS Chi-restraints excluded: chain E residue 52 ARG Chi-restraints excluded: chain E residue 65 VAL Chi-restraints excluded: chain E residue 88 VAL Chi-restraints excluded: chain E residue 89 SER Chi-restraints excluded: chain E residue 94 LEU Chi-restraints excluded: chain E residue 121 GLN Chi-restraints excluded: chain E residue 167 LEU Chi-restraints excluded: chain E residue 170 VAL Chi-restraints excluded: chain E residue 184 ARG Chi-restraints excluded: chain E residue 230 LEU Chi-restraints excluded: chain E residue 298 ILE Chi-restraints excluded: chain E residue 315 THR Chi-restraints excluded: chain E residue 350 MET Chi-restraints excluded: chain F residue 14 ASP Chi-restraints excluded: chain F residue 59 THR Chi-restraints excluded: chain F residue 207 VAL Chi-restraints excluded: chain F residue 225 ILE Chi-restraints excluded: chain F residue 262 ILE Chi-restraints excluded: chain F residue 286 ASN Chi-restraints excluded: chain F residue 407 GLU Chi-restraints excluded: chain F residue 408 VAL Chi-restraints excluded: chain F residue 440 PHE Chi-restraints excluded: chain F residue 471 SER Chi-restraints excluded: chain G residue 21 ILE Chi-restraints excluded: chain G residue 28 LEU Chi-restraints excluded: chain G residue 35 ASP Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 60 LEU Chi-restraints excluded: chain G residue 226 THR Chi-restraints excluded: chain H residue 101 LEU Chi-restraints excluded: chain H residue 117 THR Chi-restraints excluded: chain H residue 144 ILE Chi-restraints excluded: chain H residue 147 GLU Chi-restraints excluded: chain H residue 254 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 254 random chunks: chunk 82 optimal weight: 1.9990 chunk 221 optimal weight: 10.0000 chunk 48 optimal weight: 3.9990 chunk 144 optimal weight: 1.9990 chunk 60 optimal weight: 0.6980 chunk 245 optimal weight: 5.9990 chunk 204 optimal weight: 4.9990 chunk 113 optimal weight: 0.9990 chunk 20 optimal weight: 0.9980 chunk 81 optimal weight: 0.9980 chunk 129 optimal weight: 0.7980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 24 GLN D 207 GLN E 104 ASN F 291 HIS H 45 ASN H 53 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7866 moved from start: 0.1734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 21629 Z= 0.215 Angle : 0.564 11.742 29334 Z= 0.291 Chirality : 0.042 0.169 3403 Planarity : 0.004 0.042 3593 Dihedral : 13.219 116.094 3163 Min Nonbonded Distance : 1.905 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 5.51 % Allowed : 26.51 % Favored : 67.99 % 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: 0.71 (0.17), residues: 2518 helix: 1.28 (0.15), residues: 1248 sheet: 0.05 (0.23), residues: 539 loop : -0.45 (0.24), residues: 731 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 324 HIS 0.023 0.001 HIS E 18 PHE 0.027 0.001 PHE A 279 TYR 0.019 0.001 TYR B 186 ARG 0.009 0.000 ARG B 128 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5036 Ramachandran restraints generated. 2518 Oldfield, 0 Emsley, 2518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5036 Ramachandran restraints generated. 2518 Oldfield, 0 Emsley, 2518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 396 residues out of total 2326 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 128 poor density : 268 time to evaluate : 2.402 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 68 GLU cc_start: 0.7511 (OUTLIER) cc_final: 0.6496 (tm-30) REVERT: A 163 MET cc_start: 0.6473 (OUTLIER) cc_final: 0.6047 (mtm) REVERT: A 178 MET cc_start: 0.1935 (mmt) cc_final: 0.0382 (ttm) REVERT: A 273 LEU cc_start: 0.7699 (OUTLIER) cc_final: 0.7313 (mp) REVERT: B 87 ASP cc_start: 0.7473 (OUTLIER) cc_final: 0.7198 (t0) REVERT: C 81 GLU cc_start: 0.8763 (OUTLIER) cc_final: 0.8272 (tt0) REVERT: C 204 ASP cc_start: 0.8541 (OUTLIER) cc_final: 0.8219 (m-30) REVERT: C 292 ASN cc_start: 0.8468 (t0) cc_final: 0.7990 (t0) REVERT: D 80 LYS cc_start: 0.8097 (OUTLIER) cc_final: 0.7647 (ttpt) REVERT: D 86 ASP cc_start: 0.7210 (OUTLIER) cc_final: 0.6785 (m-30) REVERT: D 175 ARG cc_start: 0.8639 (OUTLIER) cc_final: 0.7891 (mmt-90) REVERT: D 190 LYS cc_start: 0.8495 (OUTLIER) cc_final: 0.7550 (mttp) REVERT: D 254 THR cc_start: 0.8361 (m) cc_final: 0.8075 (m) REVERT: E 47 THR cc_start: 0.8896 (t) cc_final: 0.8534 (p) REVERT: E 52 ARG cc_start: 0.8862 (OUTLIER) cc_final: 0.5439 (mtt90) REVERT: E 119 MET cc_start: 0.7921 (ttp) cc_final: 0.7709 (ttp) REVERT: E 184 ARG cc_start: 0.8460 (OUTLIER) cc_final: 0.8220 (mtm180) REVERT: F 233 TYR cc_start: 0.6662 (m-80) cc_final: 0.6343 (m-80) REVERT: G 218 GLN cc_start: 0.6796 (mt0) cc_final: 0.6114 (mm-40) REVERT: G 238 ASP cc_start: 0.7247 (t0) cc_final: 0.6614 (t0) outliers start: 128 outliers final: 80 residues processed: 365 average time/residue: 1.1224 time to fit residues: 477.2799 Evaluate side-chains 348 residues out of total 2326 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 256 time to evaluate : 2.724 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 GLU Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 163 MET Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 243 THR Chi-restraints excluded: chain A residue 251 ASN Chi-restraints excluded: chain A residue 254 ILE Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain A residue 330 ILE Chi-restraints excluded: chain A residue 336 THR Chi-restraints excluded: chain A residue 351 HIS Chi-restraints excluded: chain A residue 358 GLU Chi-restraints excluded: chain A residue 403 CYS Chi-restraints excluded: chain A residue 457 LYS Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 536 VAL Chi-restraints excluded: chain B residue 48 SER Chi-restraints excluded: chain B residue 66 LEU Chi-restraints excluded: chain B residue 82 ASP Chi-restraints excluded: chain B residue 87 ASP Chi-restraints excluded: chain B residue 119 MET Chi-restraints excluded: chain B residue 120 THR Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 211 SER Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain C residue 10 LYS Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 71 TYR Chi-restraints excluded: chain C residue 81 GLU Chi-restraints excluded: chain C residue 132 ARG Chi-restraints excluded: chain C residue 138 THR Chi-restraints excluded: chain C residue 169 LEU Chi-restraints excluded: chain C residue 204 ASP Chi-restraints excluded: chain C residue 220 ASP Chi-restraints excluded: chain C residue 250 SER Chi-restraints excluded: chain C residue 268 SER Chi-restraints excluded: chain C residue 293 GLU Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 79 THR Chi-restraints excluded: chain D residue 80 LYS Chi-restraints excluded: chain D residue 86 ASP Chi-restraints excluded: chain D residue 88 MET Chi-restraints excluded: chain D residue 94 GLU Chi-restraints excluded: chain D residue 155 ARG Chi-restraints excluded: chain D residue 163 VAL Chi-restraints excluded: chain D residue 173 VAL Chi-restraints excluded: chain D residue 175 ARG Chi-restraints excluded: chain D residue 190 LYS Chi-restraints excluded: chain D residue 193 ASP Chi-restraints excluded: chain D residue 239 SER Chi-restraints excluded: chain D residue 247 ASP Chi-restraints excluded: chain D residue 277 SER Chi-restraints excluded: chain D residue 334 ASN Chi-restraints excluded: chain E residue 52 ARG Chi-restraints excluded: chain E residue 65 VAL Chi-restraints excluded: chain E residue 88 VAL Chi-restraints excluded: chain E residue 93 HIS Chi-restraints excluded: chain E residue 94 LEU Chi-restraints excluded: chain E residue 121 GLN Chi-restraints excluded: chain E residue 165 ILE Chi-restraints excluded: chain E residue 167 LEU Chi-restraints excluded: chain E residue 170 VAL Chi-restraints excluded: chain E residue 184 ARG Chi-restraints excluded: chain E residue 230 LEU Chi-restraints excluded: chain E residue 298 ILE Chi-restraints excluded: chain E residue 315 THR Chi-restraints excluded: chain E residue 350 MET Chi-restraints excluded: chain F residue 14 ASP Chi-restraints excluded: chain F residue 59 THR Chi-restraints excluded: chain F residue 207 VAL Chi-restraints excluded: chain F residue 225 ILE Chi-restraints excluded: chain F residue 262 ILE Chi-restraints excluded: chain F residue 286 ASN Chi-restraints excluded: chain F residue 407 GLU Chi-restraints excluded: chain F residue 408 VAL Chi-restraints excluded: chain F residue 440 PHE Chi-restraints excluded: chain F residue 471 SER Chi-restraints excluded: chain G residue 28 LEU Chi-restraints excluded: chain G residue 35 ASP Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 60 LEU Chi-restraints excluded: chain G residue 77 GLU Chi-restraints excluded: chain G residue 226 THR Chi-restraints excluded: chain H residue 50 THR Chi-restraints excluded: chain H residue 117 THR Chi-restraints excluded: chain H residue 144 ILE Chi-restraints excluded: chain H residue 147 GLU Chi-restraints excluded: chain H residue 254 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 254 random chunks: chunk 236 optimal weight: 0.0970 chunk 27 optimal weight: 0.9980 chunk 140 optimal weight: 4.9990 chunk 179 optimal weight: 0.6980 chunk 139 optimal weight: 1.9990 chunk 206 optimal weight: 2.9990 chunk 137 optimal weight: 0.0370 chunk 244 optimal weight: 9.9990 chunk 153 optimal weight: 0.3980 chunk 149 optimal weight: 0.8980 chunk 113 optimal weight: 0.9980 overall best weight: 0.4256 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 104 ASN F 291 HIS H 45 ASN H 259 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7821 moved from start: 0.1889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 21629 Z= 0.163 Angle : 0.542 16.851 29334 Z= 0.277 Chirality : 0.040 0.142 3403 Planarity : 0.004 0.040 3593 Dihedral : 12.979 115.514 3163 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 4.73 % Allowed : 27.54 % Favored : 67.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2518 helix: 1.48 (0.15), residues: 1235 sheet: 0.16 (0.23), residues: 537 loop : -0.37 (0.24), residues: 746 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 294 HIS 0.008 0.001 HIS E 18 PHE 0.024 0.001 PHE H 332 TYR 0.020 0.001 TYR B 186 ARG 0.008 0.000 ARG C 136 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5036 Ramachandran restraints generated. 2518 Oldfield, 0 Emsley, 2518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5036 Ramachandran restraints generated. 2518 Oldfield, 0 Emsley, 2518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 400 residues out of total 2326 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 290 time to evaluate : 2.341 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 68 GLU cc_start: 0.7487 (OUTLIER) cc_final: 0.6467 (tm-30) REVERT: A 178 MET cc_start: 0.1730 (mmt) cc_final: 0.0407 (ttm) REVERT: A 273 LEU cc_start: 0.7633 (OUTLIER) cc_final: 0.7240 (mp) REVERT: A 285 MET cc_start: 0.7758 (OUTLIER) cc_final: 0.7377 (tpp) REVERT: A 288 LEU cc_start: 0.6627 (OUTLIER) cc_final: 0.6335 (mm) REVERT: A 291 LYS cc_start: 0.7354 (OUTLIER) cc_final: 0.7031 (ttmt) REVERT: A 294 TRP cc_start: 0.7286 (t-100) cc_final: 0.7084 (t-100) REVERT: C 136 ARG cc_start: 0.7530 (ttt90) cc_final: 0.7307 (ttt90) REVERT: C 204 ASP cc_start: 0.8449 (OUTLIER) cc_final: 0.8153 (m-30) REVERT: C 292 ASN cc_start: 0.8391 (t0) cc_final: 0.7939 (t0) REVERT: D 86 ASP cc_start: 0.7207 (OUTLIER) cc_final: 0.6771 (m-30) REVERT: D 175 ARG cc_start: 0.8612 (OUTLIER) cc_final: 0.7861 (mmt-90) REVERT: D 207 GLN cc_start: 0.7859 (OUTLIER) cc_final: 0.7600 (mp-120) REVERT: D 254 THR cc_start: 0.8340 (m) cc_final: 0.8120 (m) REVERT: E 47 THR cc_start: 0.8857 (t) cc_final: 0.8545 (p) REVERT: E 52 ARG cc_start: 0.8799 (OUTLIER) cc_final: 0.5300 (mtt90) REVERT: E 119 MET cc_start: 0.7917 (ttp) cc_final: 0.7689 (ttp) REVERT: E 156 ARG cc_start: 0.7669 (tpt170) cc_final: 0.7258 (tpt90) REVERT: E 315 THR cc_start: 0.8030 (OUTLIER) cc_final: 0.7819 (m) REVERT: G 21 ILE cc_start: 0.7574 (mp) cc_final: 0.7205 (mp) REVERT: G 218 GLN cc_start: 0.6814 (mt0) cc_final: 0.6071 (mm-40) REVERT: G 238 ASP cc_start: 0.7209 (t0) cc_final: 0.6526 (t0) REVERT: H 20 ILE cc_start: 0.6676 (mm) cc_final: 0.6246 (mt) REVERT: H 35 THR cc_start: 0.7185 (m) cc_final: 0.6699 (p) outliers start: 110 outliers final: 58 residues processed: 369 average time/residue: 1.1721 time to fit residues: 501.6163 Evaluate side-chains 333 residues out of total 2326 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 264 time to evaluate : 2.526 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 GLU Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 251 ASN Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 285 MET Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 291 LYS Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain A residue 351 HIS Chi-restraints excluded: chain A residue 358 GLU Chi-restraints excluded: chain A residue 403 CYS Chi-restraints excluded: chain A residue 464 LEU Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 535 VAL Chi-restraints excluded: chain A residue 536 VAL Chi-restraints excluded: chain B residue 48 SER Chi-restraints excluded: chain B residue 119 MET Chi-restraints excluded: chain B residue 120 THR Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 211 SER Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain C residue 10 LYS Chi-restraints excluded: chain C residue 71 TYR Chi-restraints excluded: chain C residue 86 ASP Chi-restraints excluded: chain C residue 132 ARG Chi-restraints excluded: chain C residue 138 THR Chi-restraints excluded: chain C residue 204 ASP Chi-restraints excluded: chain C residue 220 ASP 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 94 GLU Chi-restraints excluded: chain D residue 155 ARG Chi-restraints excluded: chain D residue 173 VAL Chi-restraints excluded: chain D residue 175 ARG Chi-restraints excluded: chain D residue 207 GLN Chi-restraints excluded: chain D residue 239 SER Chi-restraints excluded: chain D residue 269 ILE Chi-restraints excluded: chain E residue 52 ARG Chi-restraints excluded: chain E residue 88 VAL Chi-restraints excluded: chain E residue 93 HIS Chi-restraints excluded: chain E residue 94 LEU Chi-restraints excluded: chain E residue 121 GLN Chi-restraints excluded: chain E residue 170 VAL Chi-restraints excluded: chain E residue 230 LEU Chi-restraints excluded: chain E residue 298 ILE Chi-restraints excluded: chain E residue 315 THR Chi-restraints excluded: chain E residue 350 MET Chi-restraints excluded: chain F residue 14 ASP Chi-restraints excluded: chain F residue 34 ILE Chi-restraints excluded: chain F residue 59 THR Chi-restraints excluded: chain F residue 207 VAL Chi-restraints excluded: chain F residue 225 ILE Chi-restraints excluded: chain F residue 286 ASN Chi-restraints excluded: chain F residue 407 GLU Chi-restraints excluded: chain F residue 408 VAL Chi-restraints excluded: chain F residue 440 PHE Chi-restraints excluded: chain F residue 471 SER Chi-restraints excluded: chain G residue 28 LEU Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 60 LEU Chi-restraints excluded: chain G residue 77 GLU Chi-restraints excluded: chain H residue 50 THR Chi-restraints excluded: chain H residue 117 THR Chi-restraints excluded: chain H residue 144 ILE Chi-restraints excluded: chain H residue 147 GLU Chi-restraints excluded: chain H residue 254 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 254 random chunks: chunk 151 optimal weight: 6.9990 chunk 97 optimal weight: 0.9980 chunk 146 optimal weight: 7.9990 chunk 73 optimal weight: 3.9990 chunk 48 optimal weight: 4.9990 chunk 47 optimal weight: 3.9990 chunk 155 optimal weight: 0.9990 chunk 166 optimal weight: 2.9990 chunk 121 optimal weight: 1.9990 chunk 22 optimal weight: 7.9990 chunk 192 optimal weight: 4.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 207 GLN E 18 HIS E 104 ASN E 292 HIS F 291 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7926 moved from start: 0.1970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.056 21629 Z= 0.402 Angle : 0.667 15.440 29334 Z= 0.340 Chirality : 0.046 0.188 3403 Planarity : 0.005 0.058 3593 Dihedral : 13.227 117.624 3159 Min Nonbonded Distance : 1.796 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.81 % Favored : 95.19 % Rotamer: Outliers : 5.03 % Allowed : 27.45 % Favored : 67.51 % 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: 0.47 (0.17), residues: 2518 helix: 1.06 (0.15), residues: 1245 sheet: -0.03 (0.22), residues: 541 loop : -0.52 (0.24), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP D 324 HIS 0.010 0.001 HIS B 232 PHE 0.031 0.002 PHE A 279 TYR 0.019 0.002 TYR B 186 ARG 0.008 0.001 ARG B 128 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5036 Ramachandran restraints generated. 2518 Oldfield, 0 Emsley, 2518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5036 Ramachandran restraints generated. 2518 Oldfield, 0 Emsley, 2518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 391 residues out of total 2326 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 274 time to evaluate : 2.545 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 68 GLU cc_start: 0.7544 (OUTLIER) cc_final: 0.6437 (tm-30) REVERT: A 119 ILE cc_start: 0.8075 (mm) cc_final: 0.7803 (mp) REVERT: A 163 MET cc_start: 0.6465 (OUTLIER) cc_final: 0.5735 (mtm) REVERT: A 196 ASP cc_start: 0.7757 (OUTLIER) cc_final: 0.7217 (t0) REVERT: A 273 LEU cc_start: 0.7679 (OUTLIER) cc_final: 0.7277 (mp) REVERT: B 87 ASP cc_start: 0.7472 (OUTLIER) cc_final: 0.7220 (t0) REVERT: C 66 LEU cc_start: 0.8625 (OUTLIER) cc_final: 0.8133 (tp) REVERT: C 136 ARG cc_start: 0.7681 (ttt90) cc_final: 0.7476 (ttt90) REVERT: C 204 ASP cc_start: 0.8734 (OUTLIER) cc_final: 0.8405 (m-30) REVERT: D 80 LYS cc_start: 0.8171 (OUTLIER) cc_final: 0.7700 (ttpt) REVERT: D 86 ASP cc_start: 0.7225 (OUTLIER) cc_final: 0.6866 (m-30) REVERT: D 190 LYS cc_start: 0.8537 (OUTLIER) cc_final: 0.7645 (mttp) REVERT: D 254 THR cc_start: 0.8475 (m) cc_final: 0.8152 (m) REVERT: E 119 MET cc_start: 0.7931 (ttp) cc_final: 0.7692 (ttp) REVERT: E 158 MET cc_start: 0.8827 (ptt) cc_final: 0.8618 (ptt) REVERT: E 220 LYS cc_start: 0.7481 (mppt) cc_final: 0.7135 (mppt) REVERT: G 21 ILE cc_start: 0.7625 (mp) cc_final: 0.7257 (mp) REVERT: G 60 LEU cc_start: 0.7707 (OUTLIER) cc_final: 0.7111 (tp) REVERT: G 155 GLU cc_start: 0.7701 (OUTLIER) cc_final: 0.7364 (pp20) REVERT: G 218 GLN cc_start: 0.6817 (mt0) cc_final: 0.6116 (mm-40) REVERT: H 101 LEU cc_start: 0.7279 (OUTLIER) cc_final: 0.7055 (tt) outliers start: 117 outliers final: 64 residues processed: 361 average time/residue: 1.1560 time to fit residues: 483.8521 Evaluate side-chains 339 residues out of total 2326 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 262 time to evaluate : 2.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 GLU Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 163 MET Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 196 ASP Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 243 THR Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 280 ILE Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain A residue 330 ILE Chi-restraints excluded: chain A residue 358 GLU Chi-restraints excluded: chain A residue 403 CYS Chi-restraints excluded: chain A residue 457 LYS Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 536 VAL Chi-restraints excluded: chain B residue 48 SER Chi-restraints excluded: chain B residue 82 ASP Chi-restraints excluded: chain B residue 87 ASP Chi-restraints excluded: chain B residue 119 MET Chi-restraints excluded: chain B residue 120 THR Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 211 SER Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain C residue 66 LEU Chi-restraints excluded: chain C residue 132 ARG Chi-restraints excluded: chain C residue 138 THR Chi-restraints excluded: chain C residue 204 ASP Chi-restraints excluded: chain C residue 220 ASP Chi-restraints excluded: chain C residue 293 GLU Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 79 THR Chi-restraints excluded: chain D residue 80 LYS Chi-restraints excluded: chain D residue 86 ASP Chi-restraints excluded: chain D residue 94 GLU Chi-restraints excluded: chain D residue 155 ARG Chi-restraints excluded: chain D residue 163 VAL Chi-restraints excluded: chain D residue 173 VAL Chi-restraints excluded: chain D residue 190 LYS Chi-restraints excluded: chain D residue 247 ASP Chi-restraints excluded: chain D residue 277 SER Chi-restraints excluded: chain E residue 65 VAL Chi-restraints excluded: chain E residue 88 VAL Chi-restraints excluded: chain E residue 94 LEU Chi-restraints excluded: chain E residue 121 GLN Chi-restraints excluded: chain E residue 165 ILE Chi-restraints excluded: chain E residue 167 LEU Chi-restraints excluded: chain E residue 170 VAL Chi-restraints excluded: chain E residue 230 LEU Chi-restraints excluded: chain E residue 298 ILE Chi-restraints excluded: chain E residue 315 THR Chi-restraints excluded: chain E residue 350 MET Chi-restraints excluded: chain F residue 34 ILE Chi-restraints excluded: chain F residue 59 THR Chi-restraints excluded: chain F residue 207 VAL Chi-restraints excluded: chain F residue 225 ILE Chi-restraints excluded: chain F residue 286 ASN Chi-restraints excluded: chain F residue 408 VAL Chi-restraints excluded: chain F residue 440 PHE Chi-restraints excluded: chain F residue 471 SER Chi-restraints excluded: chain G residue 28 LEU Chi-restraints excluded: chain G residue 35 ASP Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 60 LEU Chi-restraints excluded: chain G residue 62 LEU Chi-restraints excluded: chain G residue 77 GLU Chi-restraints excluded: chain G residue 155 GLU Chi-restraints excluded: chain G residue 226 THR Chi-restraints excluded: chain H residue 50 THR Chi-restraints excluded: chain H residue 101 LEU Chi-restraints excluded: chain H residue 117 THR Chi-restraints excluded: chain H residue 144 ILE Chi-restraints excluded: chain H residue 147 GLU Chi-restraints excluded: chain H residue 254 LEU Chi-restraints excluded: chain H residue 261 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 254 random chunks: chunk 222 optimal weight: 2.9990 chunk 234 optimal weight: 0.6980 chunk 213 optimal weight: 4.9990 chunk 228 optimal weight: 10.0000 chunk 137 optimal weight: 0.5980 chunk 99 optimal weight: 0.5980 chunk 179 optimal weight: 0.5980 chunk 70 optimal weight: 0.9990 chunk 206 optimal weight: 5.9990 chunk 215 optimal weight: 0.9980 chunk 227 optimal weight: 1.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 298 GLN ** B 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 146 GLN E 104 ASN F 291 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7864 moved from start: 0.2006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 21629 Z= 0.204 Angle : 0.582 13.284 29334 Z= 0.298 Chirality : 0.042 0.163 3403 Planarity : 0.004 0.040 3593 Dihedral : 13.072 116.934 3159 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 4.09 % Allowed : 28.49 % Favored : 67.43 % 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: 0.71 (0.17), residues: 2518 helix: 1.26 (0.15), residues: 1248 sheet: 0.11 (0.23), residues: 537 loop : -0.44 (0.24), residues: 733 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 294 HIS 0.006 0.001 HIS E 18 PHE 0.024 0.001 PHE H 152 TYR 0.023 0.001 TYR C 71 ARG 0.009 0.000 ARG F 20 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5036 Ramachandran restraints generated. 2518 Oldfield, 0 Emsley, 2518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5036 Ramachandran restraints generated. 2518 Oldfield, 0 Emsley, 2518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 363 residues out of total 2326 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 268 time to evaluate : 1.802 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 68 GLU cc_start: 0.7522 (OUTLIER) cc_final: 0.6412 (tm-30) REVERT: A 163 MET cc_start: 0.6468 (OUTLIER) cc_final: 0.6043 (mtm) REVERT: A 273 LEU cc_start: 0.7653 (OUTLIER) cc_final: 0.7297 (mp) REVERT: C 11 GLU cc_start: 0.7301 (OUTLIER) cc_final: 0.6903 (mp0) REVERT: C 136 ARG cc_start: 0.7615 (ttt90) cc_final: 0.7359 (ttt90) REVERT: C 204 ASP cc_start: 0.8494 (OUTLIER) cc_final: 0.8187 (m-30) REVERT: D 86 ASP cc_start: 0.7227 (OUTLIER) cc_final: 0.6772 (m-30) REVERT: D 254 THR cc_start: 0.8389 (m) cc_final: 0.8083 (m) REVERT: E 47 THR cc_start: 0.8886 (t) cc_final: 0.8537 (p) REVERT: E 52 ARG cc_start: 0.8823 (OUTLIER) cc_final: 0.5309 (mtt90) REVERT: E 119 MET cc_start: 0.7886 (ttp) cc_final: 0.7644 (ttp) REVERT: G 21 ILE cc_start: 0.7536 (mp) cc_final: 0.7179 (mp) REVERT: G 155 GLU cc_start: 0.7621 (OUTLIER) cc_final: 0.7334 (pp20) REVERT: G 218 GLN cc_start: 0.6850 (mt0) cc_final: 0.6172 (mm-40) REVERT: G 323 GLU cc_start: 0.6751 (tp30) cc_final: 0.6212 (mt-10) REVERT: H 35 THR cc_start: 0.7243 (m) cc_final: 0.6808 (p) outliers start: 95 outliers final: 61 residues processed: 341 average time/residue: 0.8389 time to fit residues: 332.1889 Evaluate side-chains 326 residues out of total 2326 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 257 time to evaluate : 1.444 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 GLU Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 163 MET Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain A residue 330 ILE Chi-restraints excluded: chain A residue 358 GLU Chi-restraints excluded: chain A residue 403 CYS Chi-restraints excluded: chain A residue 457 LYS Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 536 VAL Chi-restraints excluded: chain B residue 48 SER Chi-restraints excluded: chain B residue 119 MET Chi-restraints excluded: chain B residue 120 THR Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 211 SER Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain C residue 11 GLU Chi-restraints excluded: chain C residue 71 TYR Chi-restraints excluded: chain C residue 132 ARG Chi-restraints excluded: chain C residue 138 THR Chi-restraints excluded: chain C residue 204 ASP Chi-restraints excluded: chain C residue 220 ASP Chi-restraints excluded: chain C residue 268 SER Chi-restraints excluded: chain C residue 293 GLU 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 94 GLU Chi-restraints excluded: chain D residue 155 ARG Chi-restraints excluded: chain D residue 173 VAL Chi-restraints excluded: chain D residue 277 SER Chi-restraints excluded: chain D residue 296 SER Chi-restraints excluded: chain E residue 52 ARG Chi-restraints excluded: chain E residue 65 VAL Chi-restraints excluded: chain E residue 88 VAL Chi-restraints excluded: chain E residue 93 HIS Chi-restraints excluded: chain E residue 94 LEU Chi-restraints excluded: chain E residue 121 GLN Chi-restraints excluded: chain E residue 167 LEU Chi-restraints excluded: chain E residue 170 VAL Chi-restraints excluded: chain E residue 230 LEU Chi-restraints excluded: chain E residue 298 ILE Chi-restraints excluded: chain E residue 315 THR Chi-restraints excluded: chain E residue 350 MET Chi-restraints excluded: chain F residue 34 ILE Chi-restraints excluded: chain F residue 59 THR Chi-restraints excluded: chain F residue 207 VAL Chi-restraints excluded: chain F residue 225 ILE Chi-restraints excluded: chain F residue 286 ASN Chi-restraints excluded: chain F residue 407 GLU Chi-restraints excluded: chain F residue 408 VAL Chi-restraints excluded: chain F residue 440 PHE Chi-restraints excluded: chain F residue 471 SER Chi-restraints excluded: chain G residue 28 LEU Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 60 LEU Chi-restraints excluded: chain G residue 77 GLU Chi-restraints excluded: chain G residue 155 GLU Chi-restraints excluded: chain G residue 226 THR Chi-restraints excluded: chain H residue 33 THR Chi-restraints excluded: chain H residue 50 THR Chi-restraints excluded: chain H residue 117 THR Chi-restraints excluded: chain H residue 144 ILE Chi-restraints excluded: chain H residue 147 GLU Chi-restraints excluded: chain H residue 254 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 254 random chunks: chunk 149 optimal weight: 0.9990 chunk 241 optimal weight: 10.0000 chunk 147 optimal weight: 8.9990 chunk 114 optimal weight: 2.9990 chunk 167 optimal weight: 0.9980 chunk 253 optimal weight: 4.9990 chunk 232 optimal weight: 6.9990 chunk 201 optimal weight: 5.9990 chunk 20 optimal weight: 0.0570 chunk 155 optimal weight: 0.2980 chunk 123 optimal weight: 0.5980 overall best weight: 0.5900 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 298 GLN A 411 ASN ** B 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 146 GLN E 104 ASN F 291 HIS ** F 434 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7842 moved from start: 0.2127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 21629 Z= 0.185 Angle : 0.571 12.752 29334 Z= 0.292 Chirality : 0.041 0.162 3403 Planarity : 0.004 0.042 3593 Dihedral : 12.881 112.020 3159 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 3.53 % Allowed : 29.43 % Favored : 67.04 % 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: 0.85 (0.17), residues: 2518 helix: 1.35 (0.15), residues: 1247 sheet: 0.20 (0.23), residues: 537 loop : -0.36 (0.24), residues: 734 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 294 HIS 0.007 0.001 HIS E 18 PHE 0.031 0.001 PHE A 279 TYR 0.022 0.001 TYR C 71 ARG 0.008 0.000 ARG C 136 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5036 Ramachandran restraints generated. 2518 Oldfield, 0 Emsley, 2518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5036 Ramachandran restraints generated. 2518 Oldfield, 0 Emsley, 2518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 344 residues out of total 2326 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 262 time to evaluate : 2.394 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 68 GLU cc_start: 0.7509 (OUTLIER) cc_final: 0.6391 (tm-30) REVERT: A 178 MET cc_start: 0.1758 (mmt) cc_final: 0.0325 (ttm) REVERT: A 273 LEU cc_start: 0.7620 (OUTLIER) cc_final: 0.7286 (mp) REVERT: B 149 LYS cc_start: 0.8641 (mmtm) cc_final: 0.8381 (mmmm) REVERT: C 136 ARG cc_start: 0.7594 (ttt90) cc_final: 0.7362 (ttt90) REVERT: C 204 ASP cc_start: 0.8486 (OUTLIER) cc_final: 0.8169 (m-30) REVERT: C 292 ASN cc_start: 0.8329 (t0) cc_final: 0.7886 (t0) REVERT: D 86 ASP cc_start: 0.7249 (OUTLIER) cc_final: 0.6827 (m-30) REVERT: D 254 THR cc_start: 0.8351 (m) cc_final: 0.8074 (m) REVERT: E 47 THR cc_start: 0.8859 (t) cc_final: 0.8579 (p) REVERT: E 52 ARG cc_start: 0.8803 (OUTLIER) cc_final: 0.5283 (mtt90) REVERT: G 21 ILE cc_start: 0.7502 (mp) cc_final: 0.7167 (mp) REVERT: G 60 LEU cc_start: 0.7645 (OUTLIER) cc_final: 0.7136 (tp) REVERT: G 155 GLU cc_start: 0.7637 (OUTLIER) cc_final: 0.7360 (pp20) REVERT: G 218 GLN cc_start: 0.6865 (mt0) cc_final: 0.6184 (mm-40) REVERT: G 323 GLU cc_start: 0.6694 (tp30) cc_final: 0.6251 (mt-10) REVERT: H 35 THR cc_start: 0.7231 (m) cc_final: 0.6822 (p) REVERT: H 371 LEU cc_start: 0.7803 (mt) cc_final: 0.7590 (mm) outliers start: 82 outliers final: 55 residues processed: 327 average time/residue: 1.0776 time to fit residues: 408.3480 Evaluate side-chains 319 residues out of total 2326 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 257 time to evaluate : 2.067 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 GLU Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain A residue 330 ILE Chi-restraints excluded: chain A residue 358 GLU Chi-restraints excluded: chain A residue 403 CYS Chi-restraints excluded: chain A residue 457 LYS Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 536 VAL Chi-restraints excluded: chain B residue 48 SER Chi-restraints excluded: chain B residue 119 MET Chi-restraints excluded: chain B residue 120 THR Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 211 SER Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain C residue 71 TYR Chi-restraints excluded: chain C residue 86 ASP Chi-restraints excluded: chain C residue 132 ARG Chi-restraints excluded: chain C residue 138 THR Chi-restraints excluded: chain C residue 204 ASP Chi-restraints excluded: chain C residue 293 GLU 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 94 GLU Chi-restraints excluded: chain D residue 155 ARG Chi-restraints excluded: chain D residue 173 VAL Chi-restraints excluded: chain E residue 52 ARG Chi-restraints excluded: chain E residue 65 VAL Chi-restraints excluded: chain E residue 88 VAL Chi-restraints excluded: chain E residue 93 HIS Chi-restraints excluded: chain E residue 94 LEU Chi-restraints excluded: chain E residue 121 GLN Chi-restraints excluded: chain E residue 167 LEU Chi-restraints excluded: chain E residue 170 VAL Chi-restraints excluded: chain E residue 208 ASN Chi-restraints excluded: chain E residue 230 LEU Chi-restraints excluded: chain E residue 298 ILE Chi-restraints excluded: chain E residue 350 MET Chi-restraints excluded: chain F residue 34 ILE Chi-restraints excluded: chain F residue 59 THR Chi-restraints excluded: chain F residue 207 VAL Chi-restraints excluded: chain F residue 225 ILE Chi-restraints excluded: chain F residue 286 ASN Chi-restraints excluded: chain F residue 407 GLU Chi-restraints excluded: chain F residue 408 VAL Chi-restraints excluded: chain F residue 440 PHE Chi-restraints excluded: chain F residue 471 SER Chi-restraints excluded: chain G residue 28 LEU Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 60 LEU Chi-restraints excluded: chain G residue 155 GLU Chi-restraints excluded: chain G residue 226 THR Chi-restraints excluded: chain H residue 33 THR Chi-restraints excluded: chain H residue 50 THR Chi-restraints excluded: chain H residue 117 THR Chi-restraints excluded: chain H residue 144 ILE Chi-restraints excluded: chain H residue 147 GLU Chi-restraints excluded: chain H residue 254 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 254 random chunks: chunk 160 optimal weight: 2.9990 chunk 214 optimal weight: 1.9990 chunk 61 optimal weight: 1.9990 chunk 185 optimal weight: 0.0370 chunk 29 optimal weight: 4.9990 chunk 55 optimal weight: 2.9990 chunk 201 optimal weight: 6.9990 chunk 84 optimal weight: 2.9990 chunk 207 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 37 optimal weight: 0.9990 overall best weight: 1.4066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 298 GLN A 411 ASN ** B 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 146 GLN E 104 ASN F 291 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4279 r_free = 0.4279 target = 0.200288 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.150420 restraints weight = 23782.872| |-----------------------------------------------------------------------------| r_work (start): 0.3748 rms_B_bonded: 2.06 r_work: 0.3515 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3379 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3379 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8005 moved from start: 0.2155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 21629 Z= 0.283 Angle : 0.617 13.352 29334 Z= 0.316 Chirality : 0.043 0.173 3403 Planarity : 0.004 0.051 3593 Dihedral : 12.984 110.650 3159 Min Nonbonded Distance : 1.842 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 3.74 % Allowed : 29.39 % Favored : 66.87 % 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: 0.66 (0.17), residues: 2518 helix: 1.19 (0.15), residues: 1249 sheet: 0.11 (0.22), residues: 538 loop : -0.44 (0.24), residues: 731 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP A 294 HIS 0.010 0.001 HIS E 18 PHE 0.028 0.002 PHE H 332 TYR 0.023 0.002 TYR A 497 ARG 0.017 0.001 ARG F 20 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7981.90 seconds wall clock time: 320 minutes 41.86 seconds (19241.86 seconds total)