Starting phenix.real_space_refine on Wed May 21 07:16:02 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6l31_0816/05_2025/6l31_0816.cif Found real_map, /net/cci-nas-00/data/ceres_data/6l31_0816/05_2025/6l31_0816.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.18 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6l31_0816/05_2025/6l31_0816.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6l31_0816/05_2025/6l31_0816.map" model { file = "/net/cci-nas-00/data/ceres_data/6l31_0816/05_2025/6l31_0816.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6l31_0816/05_2025/6l31_0816.cif" } resolution = 4.18 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= 0.005 sd= 1.105 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: 4 Type Number sf(0) Gaussians S 126 5.16 5 C 13247 2.51 5 N 3516 2.21 5 O 4016 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 26 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 20905 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 3477 Number of conformers: 1 Conformer: "" Number of residues, atoms: 444, 3477 Classifications: {'peptide': 444} Link IDs: {'CIS': 1, 'PTRANS': 30, 'TRANS': 412} Chain: "B" Number of atoms: 3497 Number of conformers: 1 Conformer: "" Number of residues, atoms: 447, 3497 Classifications: {'peptide': 447} Link IDs: {'CIS': 1, 'PTRANS': 30, 'TRANS': 415} Chain: "C" Number of atoms: 3497 Number of conformers: 1 Conformer: "" Number of residues, atoms: 447, 3497 Classifications: {'peptide': 447} Link IDs: {'PTRANS': 30, 'TRANS': 416} Chain: "D" Number of atoms: 3485 Number of conformers: 1 Conformer: "" Number of residues, atoms: 445, 3485 Classifications: {'peptide': 445} Link IDs: {'PTRANS': 30, 'TRANS': 414} Chain: "E" Number of atoms: 3472 Number of conformers: 1 Conformer: "" Number of residues, atoms: 443, 3472 Classifications: {'peptide': 443} Link IDs: {'PTRANS': 30, 'TRANS': 412} Chain: "F" Number of atoms: 3477 Number of conformers: 1 Conformer: "" Number of residues, atoms: 444, 3477 Classifications: {'peptide': 444} Link IDs: {'PTRANS': 30, 'TRANS': 413} Time building chain proxies: 12.46, per 1000 atoms: 0.60 Number of scatterers: 20905 At special positions: 0 Unit cell: (221.76, 154.56, 108.64, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 126 16.00 O 4016 8.00 N 3516 7.00 C 13247 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 423 " - pdb=" SG CYS B 171 " distance=2.04 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: 4.47 Conformation dependent library (CDL) restraints added in 2.7 seconds 5316 Ramachandran restraints generated. 2658 Oldfield, 0 Emsley, 2658 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4908 Finding SS restraints... Secondary structure from input PDB file: 47 helices and 45 sheets defined 12.4% alpha, 21.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.16 Creating SS restraints... Processing helix chain 'A' and resid 217 through 223 Processing helix chain 'A' and resid 229 through 236 removed outlier: 3.920A pdb=" N ASP A 236 " --> pdb=" O GLN A 232 " (cutoff:3.500A) Processing helix chain 'A' and resid 379 through 388 removed outlier: 3.779A pdb=" N TYR A 385 " --> pdb=" O GLU A 381 " (cutoff:3.500A) Processing helix chain 'A' and resid 390 through 395 removed outlier: 4.068A pdb=" N LEU A 394 " --> pdb=" O ASN A 390 " (cutoff:3.500A) Processing helix chain 'A' and resid 411 through 415 removed outlier: 3.837A pdb=" N TYR A 415 " --> pdb=" O THR A 412 " (cutoff:3.500A) Processing helix chain 'A' and resid 434 through 439 removed outlier: 3.992A pdb=" N ASN A 438 " --> pdb=" O PRO A 435 " (cutoff:3.500A) Processing helix chain 'A' and resid 447 through 450 removed outlier: 4.122A pdb=" N PHE A 450 " --> pdb=" O LYS A 447 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 447 through 450' Processing helix chain 'A' and resid 457 through 468 removed outlier: 4.114A pdb=" N ARG A 461 " --> pdb=" O TYR A 457 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N LYS A 462 " --> pdb=" O PRO A 458 " (cutoff:3.500A) Processing helix chain 'B' and resid 22 through 26 removed outlier: 3.843A pdb=" N ALA B 25 " --> pdb=" O ALA B 22 " (cutoff:3.500A) Processing helix chain 'B' and resid 217 through 221 Processing helix chain 'B' and resid 230 through 236 Processing helix chain 'B' and resid 268 through 272 removed outlier: 3.592A pdb=" N LEU B 271 " --> pdb=" O PRO B 268 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ILE B 272 " --> pdb=" O ASP B 269 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 268 through 272' Processing helix chain 'B' and resid 276 through 281 removed outlier: 3.591A pdb=" N THR B 280 " --> pdb=" O GLY B 277 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N SER B 281 " --> pdb=" O ASN B 278 " (cutoff:3.500A) Processing helix chain 'B' and resid 320 through 322 No H-bonds generated for 'chain 'B' and resid 320 through 322' Processing helix chain 'B' and resid 381 through 390 removed outlier: 4.036A pdb=" N TYR B 385 " --> pdb=" O GLU B 381 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N ILE B 386 " --> pdb=" O VAL B 382 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ASN B 390 " --> pdb=" O ILE B 386 " (cutoff:3.500A) Processing helix chain 'B' and resid 390 through 397 removed outlier: 4.701A pdb=" N LEU B 394 " --> pdb=" O ASN B 390 " (cutoff:3.500A) Processing helix chain 'B' and resid 434 through 438 removed outlier: 4.142A pdb=" N LYS B 437 " --> pdb=" O ASP B 434 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N ASN B 438 " --> pdb=" O PRO B 435 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 434 through 438' Processing helix chain 'B' and resid 453 through 457 removed outlier: 4.256A pdb=" N GLN B 456 " --> pdb=" O GLU B 453 " (cutoff:3.500A) Processing helix chain 'B' and resid 460 through 468 Processing helix chain 'C' and resid 22 through 26 removed outlier: 4.167A pdb=" N ALA C 25 " --> pdb=" O ALA C 22 " (cutoff:3.500A) Processing helix chain 'C' and resid 205 through 210 Processing helix chain 'C' and resid 217 through 222 removed outlier: 3.635A pdb=" N CYS C 221 " --> pdb=" O PRO C 217 " (cutoff:3.500A) Processing helix chain 'C' and resid 229 through 235 removed outlier: 3.525A pdb=" N MET C 233 " --> pdb=" O ASP C 229 " (cutoff:3.500A) Processing helix chain 'C' and resid 379 through 390 removed outlier: 3.847A pdb=" N HIS C 387 " --> pdb=" O MET C 383 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N THR C 388 " --> pdb=" O ALA C 384 " (cutoff:3.500A) Processing helix chain 'C' and resid 392 through 397 removed outlier: 4.132A pdb=" N ASP C 396 " --> pdb=" O SER C 392 " (cutoff:3.500A) Processing helix chain 'C' and resid 457 through 468 removed outlier: 4.129A pdb=" N ARG C 461 " --> pdb=" O TYR C 457 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N LYS C 462 " --> pdb=" O PRO C 458 " (cutoff:3.500A) Processing helix chain 'D' and resid 205 through 210 Processing helix chain 'D' and resid 229 through 234 Processing helix chain 'D' and resid 276 through 280 removed outlier: 4.076A pdb=" N THR D 280 " --> pdb=" O GLY D 277 " (cutoff:3.500A) Processing helix chain 'D' and resid 297 through 301 removed outlier: 3.768A pdb=" N GLN D 301 " --> pdb=" O SER D 298 " (cutoff:3.500A) Processing helix chain 'D' and resid 379 through 390 removed outlier: 3.797A pdb=" N HIS D 387 " --> pdb=" O MET D 383 " (cutoff:3.500A) Processing helix chain 'D' and resid 391 through 394 removed outlier: 4.012A pdb=" N LEU D 394 " --> pdb=" O PRO D 391 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 391 through 394' Processing helix chain 'D' and resid 420 through 424 removed outlier: 3.855A pdb=" N CYS D 423 " --> pdb=" O ALA D 420 " (cutoff:3.500A) Processing helix chain 'D' and resid 453 through 457 removed outlier: 4.261A pdb=" N GLN D 456 " --> pdb=" O GLU D 453 " (cutoff:3.500A) Processing helix chain 'D' and resid 461 through 468 removed outlier: 3.778A pdb=" N LEU D 465 " --> pdb=" O ARG D 461 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N GLN D 466 " --> pdb=" O LYS D 462 " (cutoff:3.500A) Processing helix chain 'E' and resid 217 through 222 removed outlier: 4.633A pdb=" N GLY E 222 " --> pdb=" O ILE E 218 " (cutoff:3.500A) Processing helix chain 'E' and resid 229 through 234 Processing helix chain 'E' and resid 276 through 281 Processing helix chain 'E' and resid 379 through 390 removed outlier: 3.877A pdb=" N HIS E 387 " --> pdb=" O MET E 383 " (cutoff:3.500A) Processing helix chain 'E' and resid 392 through 396 Processing helix chain 'E' and resid 457 through 468 removed outlier: 3.550A pdb=" N GLN E 466 " --> pdb=" O LYS E 462 " (cutoff:3.500A) Processing helix chain 'F' and resid 205 through 210 Processing helix chain 'F' and resid 217 through 221 Processing helix chain 'F' and resid 230 through 236 Processing helix chain 'F' and resid 276 through 281 removed outlier: 3.624A pdb=" N SER F 281 " --> pdb=" O ASN F 278 " (cutoff:3.500A) Processing helix chain 'F' and resid 379 through 390 removed outlier: 3.527A pdb=" N MET F 389 " --> pdb=" O TYR F 385 " (cutoff:3.500A) Processing helix chain 'F' and resid 457 through 467 removed outlier: 3.525A pdb=" N LYS F 462 " --> pdb=" O PRO F 458 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N LEU F 465 " --> pdb=" O ARG F 461 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLN F 466 " --> pdb=" O LYS F 462 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 33 through 34 removed outlier: 6.664A pdb=" N ILE A 370 " --> pdb=" O THR A 100 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LEU A 102 " --> pdb=" O TYR A 307 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N TYR A 307 " --> pdb=" O LEU A 102 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 247 through 250 removed outlier: 7.706A pdb=" N VAL A 444 " --> pdb=" O VAL A 69 " (cutoff:3.500A) removed outlier: 5.988A pdb=" N LYS A 71 " --> pdb=" O VAL A 444 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 161 through 166 removed outlier: 3.993A pdb=" N GLY A 166 " --> pdb=" O GLU A 185 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N GLU A 185 " --> pdb=" O GLY A 166 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 338 through 340 removed outlier: 3.664A pdb=" N MET A 338 " --> pdb=" O ARG A 360 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N ARG A 360 " --> pdb=" O MET A 338 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 33 through 37 removed outlier: 3.673A pdb=" N PHE B 371 " --> pdb=" O TYR B 34 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N ALA B 36 " --> pdb=" O PHE B 369 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N PHE B 369 " --> pdb=" O ALA B 36 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N GLN B 368 " --> pdb=" O LEU B 102 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N LEU B 102 " --> pdb=" O GLN B 368 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N ILE B 370 " --> pdb=" O THR B 100 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N LEU B 102 " --> pdb=" O TYR B 307 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N TYR B 307 " --> pdb=" O LEU B 102 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 44 through 45 Processing sheet with id=AA7, first strand: chain 'B' and resid 51 through 52 Processing sheet with id=AA8, first strand: chain 'B' and resid 151 through 156 removed outlier: 3.578A pdb=" N LEU B 325 " --> pdb=" O VAL B 72 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 111 through 112 removed outlier: 6.264A pdb=" N GLY B 111 " --> pdb=" O SER B 335 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'B' and resid 115 through 120 removed outlier: 5.005A pdb=" N GLY B 116 " --> pdb=" O MET B 145 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N MET B 145 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 5.088A pdb=" N VAL B 143 " --> pdb=" O PRO B 118 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 161 through 167 Processing sheet with id=AB3, first strand: chain 'B' and resid 196 through 197 removed outlier: 5.917A pdb=" N MET B 196 " --> pdb=" O LYS B 226 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'B' and resid 252 through 257 removed outlier: 5.172A pdb=" N ALA B 253 " --> pdb=" O SER B 292 " (cutoff:3.500A) removed outlier: 5.814A pdb=" N SER B 292 " --> pdb=" O ALA B 253 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N HIS B 255 " --> pdb=" O THR B 290 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 296 through 297 removed outlier: 3.804A pdb=" N PHE C 252 " --> pdb=" O SER C 292 " (cutoff:3.500A) removed outlier: 6.163A pdb=" N THR C 290 " --> pdb=" O ARG C 254 " (cutoff:3.500A) removed outlier: 4.656A pdb=" N PHE C 256 " --> pdb=" O VAL C 288 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N VAL C 288 " --> pdb=" O PHE C 256 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 296 through 297 removed outlier: 4.033A pdb=" N LEU C 246 " --> pdb=" O CYS C 153 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N CYS C 153 " --> pdb=" O LEU C 246 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N GLN C 250 " --> pdb=" O GLN C 149 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N GLN C 149 " --> pdb=" O GLN C 250 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N GLY C 156 " --> pdb=" O PHE C 326 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N PHE C 326 " --> pdb=" O GLY C 156 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N VAL C 69 " --> pdb=" O TRP C 442 " (cutoff:3.500A) removed outlier: 8.058A pdb=" N VAL C 444 " --> pdb=" O VAL C 69 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N LYS C 71 " --> pdb=" O VAL C 444 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 341 through 343 Processing sheet with id=AB8, first strand: chain 'C' and resid 28 through 36 removed outlier: 8.456A pdb=" N THR C 28 " --> pdb=" O THR C 377 " (cutoff:3.500A) removed outlier: 8.287A pdb=" N THR C 377 " --> pdb=" O THR C 28 " (cutoff:3.500A) removed outlier: 6.994A pdb=" N THR C 30 " --> pdb=" O SER C 375 " (cutoff:3.500A) removed outlier: 7.944A pdb=" N SER C 375 " --> pdb=" O THR C 30 " (cutoff:3.500A) removed outlier: 5.166A pdb=" N ILE C 32 " --> pdb=" O LEU C 373 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N ILE C 370 " --> pdb=" O THR C 100 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ARG C 94 " --> pdb=" O ILE C 376 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N LEU C 102 " --> pdb=" O TYR C 307 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N TYR C 307 " --> pdb=" O LEU C 102 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 104 through 105 Processing sheet with id=AC1, first strand: chain 'C' and resid 115 through 121 removed outlier: 3.556A pdb=" N SER C 115 " --> pdb=" O MET C 145 " (cutoff:3.500A) removed outlier: 5.131A pdb=" N VAL C 141 " --> pdb=" O PHE C 119 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 161 through 167 Processing sheet with id=AC3, first strand: chain 'C' and resid 337 through 343 Processing sheet with id=AC4, first strand: chain 'D' and resid 28 through 37 removed outlier: 6.856A pdb=" N THR D 30 " --> pdb=" O SER D 375 " (cutoff:3.500A) removed outlier: 7.821A pdb=" N SER D 375 " --> pdb=" O THR D 30 " (cutoff:3.500A) removed outlier: 4.778A pdb=" N ILE D 32 " --> pdb=" O LEU D 373 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N PHE D 371 " --> pdb=" O TYR D 34 " (cutoff:3.500A) removed outlier: 7.218A pdb=" N GLN D 368 " --> pdb=" O LEU D 102 " (cutoff:3.500A) removed outlier: 4.852A pdb=" N LEU D 102 " --> pdb=" O GLN D 368 " (cutoff:3.500A) removed outlier: 7.454A pdb=" N ILE D 370 " --> pdb=" O THR D 100 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 42 through 45 removed outlier: 4.112A pdb=" N ALA D 43 " --> pdb=" O GLU D 363 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N TYR D 358 " --> pdb=" O LEU D 340 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N LEU D 340 " --> pdb=" O TYR D 358 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 42 through 45 removed outlier: 4.112A pdb=" N ALA D 43 " --> pdb=" O GLU D 363 " (cutoff:3.500A) removed outlier: 5.957A pdb=" N TYR D 355 " --> pdb=" O GLU E 262 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'D' and resid 72 through 73 removed outlier: 3.592A pdb=" N GLN D 149 " --> pdb=" O GLN D 250 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLN D 250 " --> pdb=" O GLN D 149 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LEU D 246 " --> pdb=" O CYS D 153 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N VAL D 155 " --> pdb=" O PHE D 244 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N PHE D 244 " --> pdb=" O VAL D 155 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'D' and resid 115 through 120 removed outlier: 4.825A pdb=" N GLY D 116 " --> pdb=" O MET D 145 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N MET D 145 " --> pdb=" O GLY D 116 " (cutoff:3.500A) removed outlier: 5.190A pdb=" N VAL D 143 " --> pdb=" O PRO D 118 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'D' and resid 184 through 190 Processing sheet with id=AD1, first strand: chain 'D' and resid 252 through 257 removed outlier: 5.043A pdb=" N ALA D 253 " --> pdb=" O SER D 292 " (cutoff:3.500A) removed outlier: 5.945A pdb=" N SER D 292 " --> pdb=" O ALA D 253 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N HIS D 255 " --> pdb=" O THR D 290 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'E' and resid 35 through 37 removed outlier: 6.569A pdb=" N ASP E 366 " --> pdb=" O VAL E 104 " (cutoff:3.500A) removed outlier: 5.342A pdb=" N VAL E 104 " --> pdb=" O ASP E 366 " (cutoff:3.500A) removed outlier: 7.220A pdb=" N GLN E 368 " --> pdb=" O LEU E 102 " (cutoff:3.500A) removed outlier: 4.793A pdb=" N LEU E 102 " --> pdb=" O GLN E 368 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N ILE E 370 " --> pdb=" O THR E 100 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'E' and resid 44 through 45 Processing sheet with id=AD4, first strand: chain 'E' and resid 51 through 52 removed outlier: 3.515A pdb=" N ILE E 51 " --> pdb=" O VAL E 59 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N VAL E 59 " --> pdb=" O ILE E 51 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD4 Processing sheet with id=AD5, first strand: chain 'E' and resid 244 through 247 removed outlier: 4.542A pdb=" N PHE E 244 " --> pdb=" O VAL E 155 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N VAL E 155 " --> pdb=" O PHE E 244 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N LEU E 246 " --> pdb=" O CYS E 153 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N LEU E 325 " --> pdb=" O VAL E 72 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N VAL E 72 " --> pdb=" O LEU E 325 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N TRP E 442 " --> pdb=" O VAL E 69 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N LYS E 71 " --> pdb=" O TRP E 442 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'E' and resid 117 through 120 removed outlier: 4.929A pdb=" N VAL E 141 " --> pdb=" O PHE E 119 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'E' and resid 161 through 167 Processing sheet with id=AD8, first strand: chain 'E' and resid 252 through 253 Processing sheet with id=AD9, first strand: chain 'F' and resid 338 through 343 removed outlier: 3.837A pdb=" N MET F 338 " --> pdb=" O ARG F 360 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N ARG F 360 " --> pdb=" O MET F 338 " (cutoff:3.500A) removed outlier: 6.064A pdb=" N GLN F 372 " --> pdb=" O CYS F 99 " (cutoff:3.500A) removed outlier: 4.975A pdb=" N CYS F 99 " --> pdb=" O GLN F 372 " (cutoff:3.500A) removed outlier: 5.349A pdb=" N CYS F 374 " --> pdb=" O TRP F 97 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N TRP F 97 " --> pdb=" O CYS F 374 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N LEU F 102 " --> pdb=" O TYR F 307 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'F' and resid 28 through 33 removed outlier: 3.522A pdb=" N THR F 30 " --> pdb=" O LEU F 373 " (cutoff:3.500A) removed outlier: 5.327A pdb=" N LEU F 373 " --> pdb=" O THR F 30 " (cutoff:3.500A) removed outlier: 7.985A pdb=" N ILE F 32 " --> pdb=" O PHE F 371 " (cutoff:3.500A) removed outlier: 8.386A pdb=" N PHE F 371 " --> pdb=" O ILE F 32 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N PHE F 369 " --> pdb=" O ALA F 36 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N ALA F 36 " --> pdb=" O PHE F 369 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'F' and resid 41 through 45 removed outlier: 4.060A pdb=" N ALA F 43 " --> pdb=" O GLU F 363 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'F' and resid 51 through 52 removed outlier: 3.658A pdb=" N VAL F 59 " --> pdb=" O ILE F 51 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'F' and resid 324 through 327 removed outlier: 6.747A pdb=" N LYS F 71 " --> pdb=" O VAL F 444 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'F' and resid 111 through 112 removed outlier: 7.036A pdb=" N GLY F 111 " --> pdb=" O SER F 335 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE5 Processing sheet with id=AE6, first strand: chain 'F' and resid 115 through 117 removed outlier: 4.305A pdb=" N SER F 115 " --> pdb=" O MET F 145 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'F' and resid 149 through 152 removed outlier: 3.561A pdb=" N GLN F 250 " --> pdb=" O GLN F 149 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'F' and resid 161 through 167 Processing sheet with id=AE9, first strand: chain 'F' and resid 252 through 257 removed outlier: 6.831A pdb=" N THR F 290 " --> pdb=" O ARG F 254 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N PHE F 256 " --> pdb=" O VAL F 288 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N VAL F 288 " --> pdb=" O PHE F 256 " (cutoff:3.500A) 342 hydrogen bonds defined for protein. 870 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.03 Time building geometry restraints manager: 5.32 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 6670 1.34 - 1.46: 5142 1.46 - 1.59: 9457 1.59 - 1.71: 2 1.71 - 1.83: 186 Bond restraints: 21457 Sorted by residual: bond pdb=" CA ARG B 414 " pdb=" C ARG B 414 " ideal model delta sigma weight residual 1.524 1.606 -0.081 1.28e-02 6.10e+03 4.05e+01 bond pdb=" C LYS A 226 " pdb=" N TYR A 227 " ideal model delta sigma weight residual 1.329 1.261 0.068 1.21e-02 6.83e+03 3.12e+01 bond pdb=" CA GLN B 417 " pdb=" C GLN B 417 " ideal model delta sigma weight residual 1.523 1.597 -0.075 1.45e-02 4.76e+03 2.65e+01 bond pdb=" C THR A 427 " pdb=" N PRO A 428 " ideal model delta sigma weight residual 1.331 1.386 -0.054 1.21e-02 6.83e+03 2.03e+01 bond pdb=" C PRO C 404 " pdb=" N PRO C 405 " ideal model delta sigma weight residual 1.329 1.377 -0.048 1.20e-02 6.94e+03 1.62e+01 ... (remaining 21452 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.52: 28885 4.52 - 9.03: 263 9.03 - 13.55: 36 13.55 - 18.06: 3 18.06 - 22.58: 3 Bond angle restraints: 29190 Sorted by residual: angle pdb=" N VAL A 27 " pdb=" CA VAL A 27 " pdb=" C VAL A 27 " ideal model delta sigma weight residual 111.62 123.71 -12.09 7.90e-01 1.60e+00 2.34e+02 angle pdb=" N LYS C 169 " pdb=" CA LYS C 169 " pdb=" C LYS C 169 " ideal model delta sigma weight residual 109.24 131.50 -22.26 1.63e+00 3.76e-01 1.86e+02 angle pdb=" N SER B 418 " pdb=" CA SER B 418 " pdb=" CB SER B 418 " ideal model delta sigma weight residual 110.49 133.07 -22.58 1.69e+00 3.50e-01 1.79e+02 angle pdb=" CA GLN B 417 " pdb=" C GLN B 417 " pdb=" N SER B 418 " ideal model delta sigma weight residual 117.74 102.17 15.57 1.58e+00 4.01e-01 9.72e+01 angle pdb=" CA GLN B 417 " pdb=" C GLN B 417 " pdb=" O GLN B 417 " ideal model delta sigma weight residual 120.12 130.16 -10.04 1.15e+00 7.56e-01 7.62e+01 ... (remaining 29185 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.27: 10984 17.27 - 34.54: 1412 34.54 - 51.81: 271 51.81 - 69.08: 63 69.08 - 86.34: 25 Dihedral angle restraints: 12755 sinusoidal: 5057 harmonic: 7698 Sorted by residual: dihedral pdb=" CA THR C 422 " pdb=" C THR C 422 " pdb=" N CYS C 423 " pdb=" CA CYS C 423 " ideal model delta harmonic sigma weight residual -180.00 -121.53 -58.47 0 5.00e+00 4.00e-02 1.37e+02 dihedral pdb=" CA VAL A 267 " pdb=" C VAL A 267 " pdb=" N PRO A 268 " pdb=" CA PRO A 268 " ideal model delta harmonic sigma weight residual -180.00 -127.74 -52.26 0 5.00e+00 4.00e-02 1.09e+02 dihedral pdb=" N SER B 418 " pdb=" C SER B 418 " pdb=" CA SER B 418 " pdb=" CB SER B 418 " ideal model delta harmonic sigma weight residual 122.80 146.72 -23.92 0 2.50e+00 1.60e-01 9.16e+01 ... (remaining 12752 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.170: 3066 0.170 - 0.340: 70 0.340 - 0.510: 8 0.510 - 0.680: 1 0.680 - 0.850: 1 Chirality restraints: 3146 Sorted by residual: chirality pdb=" CA SER B 418 " pdb=" N SER B 418 " pdb=" C SER B 418 " pdb=" CB SER B 418 " both_signs ideal model delta sigma weight residual False 2.51 1.66 0.85 2.00e-01 2.50e+01 1.81e+01 chirality pdb=" CA LYS C 169 " pdb=" N LYS C 169 " pdb=" C LYS C 169 " pdb=" CB LYS C 169 " both_signs ideal model delta sigma weight residual False 2.51 1.93 0.58 2.00e-01 2.50e+01 8.51e+00 chirality pdb=" CA THR B 412 " pdb=" N THR B 412 " pdb=" C THR B 412 " pdb=" CB THR B 412 " both_signs ideal model delta sigma weight residual False 2.53 2.04 0.48 2.00e-01 2.50e+01 5.80e+00 ... (remaining 3143 not shown) Planarity restraints: 3837 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO E 403 " -0.081 5.00e-02 4.00e+02 1.22e-01 2.38e+01 pdb=" N PRO E 404 " 0.211 5.00e-02 4.00e+02 pdb=" CA PRO E 404 " -0.065 5.00e-02 4.00e+02 pdb=" CD PRO E 404 " -0.065 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS F 425 " -0.063 5.00e-02 4.00e+02 9.59e-02 1.47e+01 pdb=" N PRO F 426 " 0.166 5.00e-02 4.00e+02 pdb=" CA PRO F 426 " -0.048 5.00e-02 4.00e+02 pdb=" CD PRO F 426 " -0.055 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL D 216 " -0.061 5.00e-02 4.00e+02 9.16e-02 1.34e+01 pdb=" N PRO D 217 " 0.158 5.00e-02 4.00e+02 pdb=" CA PRO D 217 " -0.048 5.00e-02 4.00e+02 pdb=" CD PRO D 217 " -0.050 5.00e-02 4.00e+02 ... (remaining 3834 not shown) Histogram of nonbonded interaction distances: 1.74 - 2.37: 115 2.37 - 3.00: 11184 3.00 - 3.64: 34263 3.64 - 4.27: 47258 4.27 - 4.90: 72669 Nonbonded interactions: 165489 Sorted by model distance: nonbonded pdb=" O VAL A 27 " pdb=" O SER A 375 " model vdw 1.738 3.040 nonbonded pdb=" O TYR A 26 " pdb=" CD1 ILE A 376 " model vdw 1.940 3.460 nonbonded pdb=" NE2 GLN B 419 " pdb=" N ILE B 421 " model vdw 1.941 3.200 nonbonded pdb=" O THR B 422 " pdb=" SG CYS B 423 " model vdw 1.990 3.400 nonbonded pdb=" CB ARG B 414 " pdb=" NE2 GLN B 424 " model vdw 1.998 3.520 ... (remaining 165484 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 26 through 468) selection = (chain 'B' and resid 26 through 468) selection = (chain 'C' and resid 26 through 468) selection = (chain 'D' and resid 26 through 468) selection = chain 'E' selection = (chain 'F' and resid 26 through 468) } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.230 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: 0.690 Check model and map are aligned: 0.140 Set scattering table: 0.180 Process input model: 43.620 Find NCS groups from input model: 1.190 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.220 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7314 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 : 0.007 0.108 21458 Z= 0.363 Angle : 1.259 22.581 29192 Z= 0.718 Chirality : 0.072 0.850 3146 Planarity : 0.009 0.122 3837 Dihedral : 16.233 86.344 7844 Min Nonbonded Distance : 1.738 Molprobity Statistics. All-atom Clashscore : 16.77 Ramachandran Plot: Outliers : 0.34 % Allowed : 11.66 % Favored : 88.00 % Rotamer: Outliers : 2.27 % Allowed : 14.62 % Favored : 83.11 % Cbeta Deviations : 0.29 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.04 % Twisted Proline : 2.78 % Twisted General : 0.36 % 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: -4.45 (0.13), residues: 2658 helix: -4.27 (0.17), residues: 197 sheet: -2.23 (0.19), residues: 593 loop : -3.29 (0.12), residues: 1868 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.003 TRP F 97 HIS 0.016 0.003 HIS A 35 PHE 0.043 0.003 PHE A 369 TYR 0.031 0.003 TYR C 67 ARG 0.011 0.001 ARG E 106 Details of bonding type rmsd hydrogen bonds : bond 0.31864 ( 337) hydrogen bonds : angle 11.94436 ( 870) SS BOND : bond 0.00478 ( 1) SS BOND : angle 0.64104 ( 2) covalent geometry : bond 0.00699 (21457) covalent geometry : angle 1.25887 (29190) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5316 Ramachandran restraints generated. 2658 Oldfield, 0 Emsley, 2658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5316 Ramachandran restraints generated. 2658 Oldfield, 0 Emsley, 2658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 738 residues out of total 2333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 685 time to evaluate : 2.304 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 121 ASN cc_start: 0.6633 (m110) cc_final: 0.5240 (m110) REVERT: A 195 ASP cc_start: 0.8012 (t70) cc_final: 0.7697 (t0) REVERT: A 210 GLN cc_start: 0.4474 (mt0) cc_final: 0.4206 (mt0) REVERT: A 250 GLN cc_start: 0.7435 (mm-40) cc_final: 0.7177 (mm-40) REVERT: A 255 HIS cc_start: 0.8514 (m90) cc_final: 0.8191 (m-70) REVERT: A 257 PHE cc_start: 0.9036 (t80) cc_final: 0.8458 (t80) REVERT: A 288 VAL cc_start: 0.8580 (m) cc_final: 0.8195 (m) REVERT: A 302 LEU cc_start: 0.9215 (mm) cc_final: 0.8775 (mm) REVERT: A 303 PHE cc_start: 0.8612 (m-10) cc_final: 0.8394 (m-80) REVERT: A 305 LYS cc_start: 0.9428 (mmtm) cc_final: 0.9178 (mppt) REVERT: A 364 GLU cc_start: 0.8481 (tt0) cc_final: 0.8263 (tt0) REVERT: A 371 PHE cc_start: 0.8702 (m-80) cc_final: 0.8267 (m-80) REVERT: A 389 MET cc_start: 0.9060 (ttt) cc_final: 0.8462 (tmm) REVERT: A 450 PHE cc_start: 0.8819 (m-10) cc_final: 0.8533 (m-10) REVERT: B 26 TYR cc_start: 0.8140 (m-80) cc_final: 0.7625 (m-80) REVERT: B 61 LYS cc_start: 0.8177 (tttt) cc_final: 0.7806 (ttpt) REVERT: B 74 LEU cc_start: 0.9126 (tp) cc_final: 0.8749 (tp) REVERT: B 151 GLN cc_start: 0.9176 (mt0) cc_final: 0.8920 (mt0) REVERT: B 206 PHE cc_start: 0.9301 (m-80) cc_final: 0.9085 (m-80) REVERT: B 210 GLN cc_start: 0.9519 (mp10) cc_final: 0.9035 (mp10) REVERT: B 211 THR cc_start: 0.8888 (p) cc_final: 0.8501 (p) REVERT: B 236 ASP cc_start: 0.8965 (t0) cc_final: 0.8748 (t70) REVERT: B 262 GLU cc_start: 0.7918 (mt-10) cc_final: 0.7128 (mt-10) REVERT: B 273 ILE cc_start: 0.9328 (mm) cc_final: 0.9100 (mm) REVERT: B 301 GLN cc_start: 0.9144 (mp-120) cc_final: 0.8715 (mp10) REVERT: B 302 LEU cc_start: 0.8896 (pp) cc_final: 0.8588 (pp) REVERT: B 305 LYS cc_start: 0.9351 (mtpt) cc_final: 0.8990 (mtpt) REVERT: B 338 MET cc_start: 0.8437 (mpp) cc_final: 0.8193 (mpp) REVERT: B 355 TYR cc_start: 0.7177 (m-80) cc_final: 0.6793 (m-10) REVERT: B 359 MET cc_start: 0.8261 (mmm) cc_final: 0.7802 (mmm) REVERT: B 389 MET cc_start: 0.8764 (ppp) cc_final: 0.8555 (ppp) REVERT: B 449 LYS cc_start: 0.8844 (mmtp) cc_final: 0.8484 (mtpt) REVERT: B 461 ARG cc_start: 0.9298 (ttp-170) cc_final: 0.8631 (mtm-85) REVERT: B 462 LYS cc_start: 0.9187 (mtpt) cc_final: 0.8895 (mmtt) REVERT: C 53 ARG cc_start: 0.7013 (mmt-90) cc_final: 0.6732 (tpt-90) REVERT: C 108 GLN cc_start: 0.8824 (mm-40) cc_final: 0.8356 (mm-40) REVERT: C 171 CYS cc_start: 0.4719 (OUTLIER) cc_final: 0.4389 (t) REVERT: C 201 PHE cc_start: 0.8438 (m-10) cc_final: 0.7813 (m-80) REVERT: C 232 GLN cc_start: 0.8666 (mt0) cc_final: 0.8351 (mm-40) REVERT: C 302 LEU cc_start: 0.9527 (mm) cc_final: 0.9325 (mm) REVERT: C 305 LYS cc_start: 0.8950 (mppt) cc_final: 0.8621 (mppt) REVERT: C 310 GLN cc_start: 0.8998 (tm-30) cc_final: 0.8638 (tm-30) REVERT: C 395 GLU cc_start: 0.9140 (tm-30) cc_final: 0.8874 (tm-30) REVERT: C 415 TYR cc_start: -0.0971 (OUTLIER) cc_final: -0.1259 (t80) REVERT: D 69 VAL cc_start: 0.8504 (t) cc_final: 0.8294 (t) REVERT: D 117 HIS cc_start: 0.8596 (t-90) cc_final: 0.7960 (t-90) REVERT: D 120 LEU cc_start: 0.8500 (mt) cc_final: 0.8091 (mt) REVERT: D 121 ASN cc_start: 0.7466 (t0) cc_final: 0.7049 (t0) REVERT: D 147 TYR cc_start: 0.8507 (m-80) cc_final: 0.8243 (m-80) REVERT: D 165 TRP cc_start: 0.8466 (m-90) cc_final: 0.7886 (m100) REVERT: D 187 ILE cc_start: 0.9410 (mt) cc_final: 0.9015 (mt) REVERT: D 193 ASP cc_start: 0.7590 (t0) cc_final: 0.7091 (t0) REVERT: D 206 PHE cc_start: 0.8267 (m-80) cc_final: 0.7939 (m-80) REVERT: D 219 ASP cc_start: 0.9263 (p0) cc_final: 0.9045 (p0) REVERT: D 226 LYS cc_start: 0.8092 (mtpt) cc_final: 0.7769 (mtpp) REVERT: D 233 MET cc_start: 0.8808 (mmp) cc_final: 0.8590 (mmm) REVERT: D 355 TYR cc_start: 0.7904 (m-80) cc_final: 0.7689 (m-80) REVERT: D 361 HIS cc_start: 0.7015 (t-90) cc_final: 0.6588 (t70) REVERT: D 364 GLU cc_start: 0.8770 (tm-30) cc_final: 0.8566 (tm-30) REVERT: D 397 TRP cc_start: 0.8843 (m-90) cc_final: 0.8614 (m100) REVERT: D 449 LYS cc_start: 0.7830 (mmtp) cc_final: 0.7499 (mmmt) REVERT: E 41 LEU cc_start: 0.8249 (tt) cc_final: 0.7835 (tt) REVERT: E 120 LEU cc_start: 0.8984 (mt) cc_final: 0.8341 (mt) REVERT: E 184 LEU cc_start: 0.9132 (tp) cc_final: 0.8767 (tp) REVERT: E 226 LYS cc_start: 0.8581 (mmtt) cc_final: 0.8256 (mmtm) REVERT: E 232 GLN cc_start: 0.8461 (mt0) cc_final: 0.7735 (tp-100) REVERT: E 233 MET cc_start: 0.9576 (mtm) cc_final: 0.9003 (mtt) REVERT: E 256 PHE cc_start: 0.9186 (m-80) cc_final: 0.8874 (m-10) REVERT: E 257 PHE cc_start: 0.8583 (m-80) cc_final: 0.8290 (m-80) REVERT: E 265 GLU cc_start: 0.8422 (mt-10) cc_final: 0.8198 (mt-10) REVERT: E 324 GLN cc_start: 0.8839 (mt0) cc_final: 0.8594 (mt0) REVERT: E 352 ASN cc_start: 0.9379 (p0) cc_final: 0.9171 (p0) REVERT: E 374 CYS cc_start: 0.9331 (m) cc_final: 0.8902 (p) REVERT: E 397 TRP cc_start: 0.6823 (m100) cc_final: 0.6118 (m100) REVERT: F 65 TYR cc_start: 0.9121 (m-80) cc_final: 0.8782 (m-10) REVERT: F 103 GLU cc_start: 0.8068 (tp30) cc_final: 0.7576 (tp30) REVERT: F 106 ARG cc_start: 0.8392 (mmm160) cc_final: 0.8163 (tpp80) REVERT: F 125 ASP cc_start: 0.9035 (p0) cc_final: 0.8661 (p0) REVERT: F 149 GLN cc_start: 0.8145 (pt0) cc_final: 0.7573 (pm20) REVERT: F 150 THR cc_start: 0.9453 (m) cc_final: 0.8327 (m) REVERT: F 165 TRP cc_start: 0.8931 (m100) cc_final: 0.8332 (m100) REVERT: F 170 GLN cc_start: 0.8345 (OUTLIER) cc_final: 0.7795 (tm-30) REVERT: F 184 LEU cc_start: 0.8144 (tp) cc_final: 0.7870 (tp) REVERT: F 186 LEU cc_start: 0.8813 (tp) cc_final: 0.8393 (tp) REVERT: F 196 MET cc_start: 0.7829 (mmm) cc_final: 0.7082 (mmm) REVERT: F 204 MET cc_start: 0.8533 (mpp) cc_final: 0.8329 (mpp) REVERT: F 210 GLN cc_start: 0.9423 (tp40) cc_final: 0.9122 (mm110) REVERT: F 219 ASP cc_start: 0.9286 (m-30) cc_final: 0.9018 (m-30) REVERT: F 249 GLU cc_start: 0.8748 (mp0) cc_final: 0.8522 (mp0) REVERT: F 251 MET cc_start: 0.8743 (tmm) cc_final: 0.8534 (tpp) REVERT: F 273 ILE cc_start: 0.8042 (mm) cc_final: 0.7593 (mm) REVERT: F 334 ARG cc_start: 0.9215 (mtt90) cc_final: 0.8551 (mtp85) REVERT: F 357 GLU cc_start: 0.8530 (tm-30) cc_final: 0.8218 (tm-30) REVERT: F 360 ARG cc_start: 0.7286 (mtt180) cc_final: 0.7058 (mtt180) REVERT: F 373 LEU cc_start: 0.9056 (mm) cc_final: 0.8774 (mm) REVERT: F 414 ARG cc_start: 0.7517 (mmp-170) cc_final: 0.6615 (mpt-90) REVERT: F 445 ASN cc_start: 0.8799 (t0) cc_final: 0.8578 (p0) outliers start: 53 outliers final: 19 residues processed: 729 average time/residue: 0.3152 time to fit residues: 349.7761 Evaluate side-chains 568 residues out of total 2333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 546 time to evaluate : 2.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 222 optimal weight: 8.9990 chunk 200 optimal weight: 10.0000 chunk 111 optimal weight: 4.9990 chunk 68 optimal weight: 2.9990 chunk 134 optimal weight: 6.9990 chunk 106 optimal weight: 2.9990 chunk 206 optimal weight: 20.0000 chunk 80 optimal weight: 0.5980 chunk 125 optimal weight: 0.0050 chunk 154 optimal weight: 2.9990 chunk 239 optimal weight: 3.9990 overall best weight: 1.9200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 258 ASN A 289 ASN ** A 323 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 337 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 361 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 372 GLN ** A 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 55 ASN ** B 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 192 GLN B 212 ASN B 255 HIS B 419 GLN C 78 ASN C 139 ASN ** C 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 212 ASN ** C 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 323 ASN C 387 HIS D 139 ASN D 151 GLN D 258 ASN D 352 ASN ** E 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 78 ASN E 139 ASN E 212 ASN ** E 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 337 ASN ** F 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 139 ASN ** F 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 289 ASN F 301 GLN F 315 HIS F 316 ASN F 337 ASN F 361 HIS F 387 HIS Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4049 r_free = 0.4049 target = 0.136102 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.109153 restraints weight = 60529.581| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.113077 restraints weight = 34857.135| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.115814 restraints weight = 23390.855| |-----------------------------------------------------------------------------| r_work (final): 0.3773 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7150 moved from start: 0.2518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 21458 Z= 0.160 Angle : 0.778 12.154 29192 Z= 0.401 Chirality : 0.050 0.276 3146 Planarity : 0.007 0.107 3837 Dihedral : 7.103 44.761 2886 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 14.09 Ramachandran Plot: Outliers : 0.11 % Allowed : 9.52 % Favored : 90.37 % Rotamer: Outliers : 0.17 % Allowed : 5.79 % Favored : 94.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.08 % Twisted Proline : 2.22 % Twisted General : 0.20 % 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: -3.86 (0.14), residues: 2658 helix: -3.13 (0.24), residues: 239 sheet: -1.95 (0.19), residues: 636 loop : -2.89 (0.13), residues: 1783 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP D 165 HIS 0.008 0.001 HIS B 35 PHE 0.031 0.002 PHE A 88 TYR 0.024 0.002 TYR E 230 ARG 0.011 0.001 ARG E 40 Details of bonding type rmsd hydrogen bonds : bond 0.05001 ( 337) hydrogen bonds : angle 8.45850 ( 870) SS BOND : bond 0.00108 ( 1) SS BOND : angle 0.40168 ( 2) covalent geometry : bond 0.00338 (21457) covalent geometry : angle 0.77787 (29190) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5316 Ramachandran restraints generated. 2658 Oldfield, 0 Emsley, 2658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5316 Ramachandran restraints generated. 2658 Oldfield, 0 Emsley, 2658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 720 residues out of total 2333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 716 time to evaluate : 2.115 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 ASN cc_start: 0.9163 (m110) cc_final: 0.8943 (m110) REVERT: A 223 THR cc_start: 0.8429 (t) cc_final: 0.8121 (t) REVERT: A 369 PHE cc_start: 0.8769 (m-80) cc_final: 0.8511 (m-80) REVERT: A 371 PHE cc_start: 0.8565 (m-80) cc_final: 0.7939 (m-80) REVERT: A 389 MET cc_start: 0.8857 (ttt) cc_final: 0.8049 (ppp) REVERT: A 449 LYS cc_start: 0.9095 (mmtm) cc_final: 0.8519 (mptt) REVERT: A 450 PHE cc_start: 0.8914 (m-10) cc_final: 0.8647 (m-10) REVERT: B 26 TYR cc_start: 0.8240 (m-80) cc_final: 0.7917 (m-80) REVERT: B 74 LEU cc_start: 0.9140 (tp) cc_final: 0.8762 (tp) REVERT: B 145 MET cc_start: 0.8644 (mpp) cc_final: 0.8396 (mmt) REVERT: B 151 GLN cc_start: 0.9157 (mt0) cc_final: 0.8794 (mt0) REVERT: B 210 GLN cc_start: 0.9355 (mp10) cc_final: 0.8998 (mp10) REVERT: B 219 ASP cc_start: 0.9208 (p0) cc_final: 0.8959 (p0) REVERT: B 220 ILE cc_start: 0.9691 (pt) cc_final: 0.9446 (pt) REVERT: B 236 ASP cc_start: 0.8558 (t0) cc_final: 0.8311 (t70) REVERT: B 246 LEU cc_start: 0.9413 (mt) cc_final: 0.9131 (mt) REVERT: B 247 ARG cc_start: 0.8407 (mpp-170) cc_final: 0.8012 (mmm-85) REVERT: B 251 MET cc_start: 0.8709 (tmm) cc_final: 0.8489 (tpp) REVERT: B 273 ILE cc_start: 0.9404 (mm) cc_final: 0.9170 (mm) REVERT: B 301 GLN cc_start: 0.9170 (mp-120) cc_final: 0.8612 (mp10) REVERT: B 302 LEU cc_start: 0.9020 (pp) cc_final: 0.8585 (pp) REVERT: B 305 LYS cc_start: 0.9463 (mtpt) cc_final: 0.9018 (mtmt) REVERT: B 307 TYR cc_start: 0.8244 (m-80) cc_final: 0.8018 (m-10) REVERT: B 461 ARG cc_start: 0.9169 (ttp-170) cc_final: 0.8754 (ptp-110) REVERT: C 51 ILE cc_start: 0.8353 (tt) cc_final: 0.8075 (tt) REVERT: C 53 ARG cc_start: 0.7012 (mmt-90) cc_final: 0.6726 (ttt-90) REVERT: C 108 GLN cc_start: 0.8610 (mm-40) cc_final: 0.7928 (mm-40) REVERT: C 154 MET cc_start: 0.8805 (mmp) cc_final: 0.8461 (mmp) REVERT: C 201 PHE cc_start: 0.8532 (m-10) cc_final: 0.7710 (m-80) REVERT: C 204 MET cc_start: 0.8327 (ptp) cc_final: 0.8098 (pmm) REVERT: C 246 LEU cc_start: 0.9369 (mp) cc_final: 0.9099 (mp) REVERT: C 310 GLN cc_start: 0.8848 (tm-30) cc_final: 0.8482 (tm-30) REVERT: C 359 MET cc_start: 0.8488 (mmm) cc_final: 0.8089 (mmt) REVERT: C 395 GLU cc_start: 0.9033 (tm-30) cc_final: 0.8787 (tm-30) REVERT: C 457 TYR cc_start: 0.9316 (m-80) cc_final: 0.9026 (m-80) REVERT: D 117 HIS cc_start: 0.8627 (t-90) cc_final: 0.7682 (t-90) REVERT: D 120 LEU cc_start: 0.8500 (mt) cc_final: 0.7872 (mt) REVERT: D 147 TYR cc_start: 0.8076 (m-80) cc_final: 0.7783 (m-80) REVERT: D 193 ASP cc_start: 0.7160 (t0) cc_final: 0.6807 (t0) REVERT: D 197 VAL cc_start: 0.8431 (t) cc_final: 0.8146 (m) REVERT: D 206 PHE cc_start: 0.8166 (m-80) cc_final: 0.7782 (m-80) REVERT: D 233 MET cc_start: 0.8851 (mmp) cc_final: 0.8629 (mmm) REVERT: D 339 THR cc_start: 0.7378 (p) cc_final: 0.6549 (p) REVERT: D 355 TYR cc_start: 0.7959 (m-80) cc_final: 0.7681 (m-80) REVERT: D 397 TRP cc_start: 0.8841 (m-90) cc_final: 0.8575 (m100) REVERT: D 445 ASN cc_start: 0.9106 (t0) cc_final: 0.8897 (t0) REVERT: D 449 LYS cc_start: 0.7777 (mmtp) cc_final: 0.7431 (mmmt) REVERT: E 41 LEU cc_start: 0.8543 (tt) cc_final: 0.7896 (tt) REVERT: E 66 GLN cc_start: 0.6638 (mt0) cc_final: 0.6180 (mt0) REVERT: E 120 LEU cc_start: 0.8655 (mt) cc_final: 0.8058 (mt) REVERT: E 196 MET cc_start: 0.8755 (mpp) cc_final: 0.8482 (mpp) REVERT: E 232 GLN cc_start: 0.8249 (mt0) cc_final: 0.7668 (tp-100) REVERT: E 233 MET cc_start: 0.9302 (mtm) cc_final: 0.8848 (mtm) REVERT: E 303 PHE cc_start: 0.9043 (m-80) cc_final: 0.8831 (m-80) REVERT: E 326 PHE cc_start: 0.9057 (m-80) cc_final: 0.8356 (m-80) REVERT: E 350 TYR cc_start: 0.6890 (t80) cc_final: 0.6657 (t80) REVERT: E 371 PHE cc_start: 0.9527 (m-80) cc_final: 0.9253 (m-80) REVERT: E 397 TRP cc_start: 0.6295 (m100) cc_final: 0.6069 (m100) REVERT: E 411 ASP cc_start: 0.8132 (t0) cc_final: 0.7837 (t70) REVERT: E 450 PHE cc_start: 0.8474 (m-80) cc_final: 0.8131 (m-80) REVERT: F 65 TYR cc_start: 0.9138 (m-80) cc_final: 0.8820 (m-10) REVERT: F 103 GLU cc_start: 0.7700 (tp30) cc_final: 0.7299 (tp30) REVERT: F 125 ASP cc_start: 0.9179 (p0) cc_final: 0.8847 (p0) REVERT: F 148 LYS cc_start: 0.9083 (ptmm) cc_final: 0.8431 (ptmm) REVERT: F 149 GLN cc_start: 0.8779 (pt0) cc_final: 0.8404 (pt0) REVERT: F 150 THR cc_start: 0.9508 (m) cc_final: 0.8334 (m) REVERT: F 151 GLN cc_start: 0.8166 (tt0) cc_final: 0.7335 (tt0) REVERT: F 165 TRP cc_start: 0.8923 (m100) cc_final: 0.8272 (m100) REVERT: F 185 GLU cc_start: 0.8133 (tp30) cc_final: 0.7861 (mt-10) REVERT: F 196 MET cc_start: 0.7612 (mmm) cc_final: 0.6731 (mmm) REVERT: F 216 VAL cc_start: 0.7322 (m) cc_final: 0.7117 (m) REVERT: F 230 TYR cc_start: 0.8880 (m-80) cc_final: 0.8573 (m-80) REVERT: F 249 GLU cc_start: 0.8662 (mp0) cc_final: 0.8263 (mp0) REVERT: F 273 ILE cc_start: 0.8210 (mm) cc_final: 0.7768 (mm) REVERT: F 302 LEU cc_start: 0.9019 (mt) cc_final: 0.8138 (mt) REVERT: F 315 HIS cc_start: 0.8097 (m-70) cc_final: 0.7443 (m90) REVERT: F 334 ARG cc_start: 0.9020 (mtt90) cc_final: 0.8757 (mtt-85) REVERT: F 357 GLU cc_start: 0.8130 (tm-30) cc_final: 0.7803 (tm-30) REVERT: F 359 MET cc_start: 0.8442 (tpp) cc_final: 0.7927 (tpp) outliers start: 4 outliers final: 1 residues processed: 719 average time/residue: 0.3303 time to fit residues: 356.9506 Evaluate side-chains 567 residues out of total 2333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 566 time to evaluate : 2.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 123 optimal weight: 9.9990 chunk 42 optimal weight: 20.0000 chunk 158 optimal weight: 5.9990 chunk 119 optimal weight: 7.9990 chunk 183 optimal weight: 20.0000 chunk 157 optimal weight: 30.0000 chunk 43 optimal weight: 7.9990 chunk 122 optimal weight: 8.9990 chunk 8 optimal weight: 20.0000 chunk 168 optimal weight: 20.0000 chunk 29 optimal weight: 6.9990 overall best weight: 7.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 192 GLN A 255 HIS ** A 323 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 337 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 361 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 212 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 255 HIS C 387 HIS ** D 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 164 HIS D 255 HIS E 212 ASN E 313 GLN ** F 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 149 GLN ** F 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 301 GLN F 317 ASN F 337 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.130933 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.104889 restraints weight = 63970.216| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.108495 restraints weight = 37798.601| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.111055 restraints weight = 25759.249| |-----------------------------------------------------------------------------| r_work (final): 0.3740 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7328 moved from start: 0.3138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.084 21458 Z= 0.210 Angle : 0.774 11.731 29192 Z= 0.401 Chirality : 0.049 0.305 3146 Planarity : 0.007 0.109 3837 Dihedral : 6.920 41.730 2886 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 19.25 Ramachandran Plot: Outliers : 0.08 % Allowed : 11.06 % Favored : 88.86 % Rotamer: Outliers : 0.09 % Allowed : 6.47 % Favored : 93.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.08 % Twisted Proline : 2.22 % Twisted General : 0.16 % 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: -3.59 (0.15), residues: 2658 helix: -2.63 (0.27), residues: 231 sheet: -1.82 (0.19), residues: 617 loop : -2.73 (0.13), residues: 1810 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP F 308 HIS 0.011 0.002 HIS F 35 PHE 0.031 0.002 PHE A 369 TYR 0.028 0.002 TYR B 365 ARG 0.008 0.001 ARG D 68 Details of bonding type rmsd hydrogen bonds : bond 0.04616 ( 337) hydrogen bonds : angle 8.06149 ( 870) SS BOND : bond 0.00241 ( 1) SS BOND : angle 0.30066 ( 2) covalent geometry : bond 0.00451 (21457) covalent geometry : angle 0.77410 (29190) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5316 Ramachandran restraints generated. 2658 Oldfield, 0 Emsley, 2658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5316 Ramachandran restraints generated. 2658 Oldfield, 0 Emsley, 2658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 658 residues out of total 2333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 656 time to evaluate : 2.206 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 TYR cc_start: 0.8393 (m-80) cc_final: 0.8167 (m-80) REVERT: A 165 TRP cc_start: 0.8831 (m100) cc_final: 0.8552 (m100) REVERT: A 195 ASP cc_start: 0.8545 (t0) cc_final: 0.7946 (t0) REVERT: A 196 MET cc_start: 0.7932 (mtp) cc_final: 0.7316 (mtp) REVERT: A 223 THR cc_start: 0.8574 (t) cc_final: 0.8321 (t) REVERT: A 247 ARG cc_start: 0.8089 (ptt180) cc_final: 0.7518 (ptp-170) REVERT: A 257 PHE cc_start: 0.8603 (t80) cc_final: 0.8060 (t80) REVERT: A 288 VAL cc_start: 0.8973 (m) cc_final: 0.8630 (m) REVERT: A 366 ASP cc_start: 0.7803 (t0) cc_final: 0.6769 (t70) REVERT: A 371 PHE cc_start: 0.8392 (m-80) cc_final: 0.7744 (m-80) REVERT: A 381 GLU cc_start: 0.9143 (mp0) cc_final: 0.8871 (mp0) REVERT: A 389 MET cc_start: 0.8980 (ttt) cc_final: 0.8362 (tmm) REVERT: B 26 TYR cc_start: 0.8400 (m-80) cc_final: 0.7980 (m-80) REVERT: B 65 TYR cc_start: 0.8902 (m-80) cc_final: 0.8672 (m-80) REVERT: B 151 GLN cc_start: 0.8791 (mt0) cc_final: 0.8583 (mt0) REVERT: B 187 ILE cc_start: 0.8903 (mp) cc_final: 0.7382 (mp) REVERT: B 210 GLN cc_start: 0.9269 (mp10) cc_final: 0.8831 (mp10) REVERT: B 211 THR cc_start: 0.9136 (p) cc_final: 0.8898 (p) REVERT: B 220 ILE cc_start: 0.9698 (pt) cc_final: 0.9436 (pt) REVERT: B 236 ASP cc_start: 0.8616 (t0) cc_final: 0.8371 (t70) REVERT: B 246 LEU cc_start: 0.9369 (mt) cc_final: 0.9115 (mt) REVERT: B 254 ARG cc_start: 0.9126 (ttt-90) cc_final: 0.8506 (ttt-90) REVERT: B 273 ILE cc_start: 0.9432 (mm) cc_final: 0.9230 (mm) REVERT: B 298 SER cc_start: 0.8986 (p) cc_final: 0.8657 (p) REVERT: B 301 GLN cc_start: 0.9092 (mp-120) cc_final: 0.8434 (mp10) REVERT: B 302 LEU cc_start: 0.8955 (pp) cc_final: 0.8537 (pp) REVERT: B 305 LYS cc_start: 0.9449 (mtpt) cc_final: 0.9055 (mtpt) REVERT: B 307 TYR cc_start: 0.8331 (m-80) cc_final: 0.7695 (m-10) REVERT: B 357 GLU cc_start: 0.8641 (mp0) cc_final: 0.8314 (mp0) REVERT: B 461 ARG cc_start: 0.9011 (ttp-110) cc_final: 0.8547 (mtm-85) REVERT: C 51 ILE cc_start: 0.8536 (tt) cc_final: 0.8213 (tp) REVERT: C 53 ARG cc_start: 0.7060 (mmt-90) cc_final: 0.6691 (ttt-90) REVERT: C 108 GLN cc_start: 0.8695 (tp-100) cc_final: 0.8294 (mm-40) REVERT: C 201 PHE cc_start: 0.8386 (m-10) cc_final: 0.7860 (m-80) REVERT: C 204 MET cc_start: 0.8171 (ptp) cc_final: 0.7755 (ptp) REVERT: C 310 GLN cc_start: 0.8778 (tm-30) cc_final: 0.8413 (tm-30) REVERT: C 383 MET cc_start: 0.8668 (mmt) cc_final: 0.8198 (mmt) REVERT: C 386 ILE cc_start: 0.9642 (pt) cc_final: 0.9412 (pt) REVERT: C 395 GLU cc_start: 0.9118 (tm-30) cc_final: 0.8827 (tm-30) REVERT: D 63 SER cc_start: 0.9365 (t) cc_final: 0.8843 (p) REVERT: D 69 VAL cc_start: 0.8264 (t) cc_final: 0.7998 (t) REVERT: D 117 HIS cc_start: 0.8430 (t-90) cc_final: 0.7704 (t-170) REVERT: D 120 LEU cc_start: 0.8404 (mt) cc_final: 0.7831 (mt) REVERT: D 145 MET cc_start: 0.9060 (ppp) cc_final: 0.8781 (ppp) REVERT: D 197 VAL cc_start: 0.8472 (t) cc_final: 0.8200 (m) REVERT: D 198 ASP cc_start: 0.7357 (t0) cc_final: 0.7053 (t0) REVERT: D 206 PHE cc_start: 0.8102 (m-80) cc_final: 0.7828 (m-80) REVERT: D 219 ASP cc_start: 0.9178 (p0) cc_final: 0.8887 (p0) REVERT: D 303 PHE cc_start: 0.8843 (m-80) cc_final: 0.8544 (m-80) REVERT: D 326 PHE cc_start: 0.8165 (m-80) cc_final: 0.7928 (m-10) REVERT: D 355 TYR cc_start: 0.8037 (m-80) cc_final: 0.7666 (m-80) REVERT: D 361 HIS cc_start: 0.6189 (t70) cc_final: 0.5711 (t70) REVERT: D 397 TRP cc_start: 0.8764 (m-90) cc_final: 0.8455 (m100) REVERT: D 449 LYS cc_start: 0.7872 (mmtp) cc_final: 0.7498 (mmmt) REVERT: D 459 LEU cc_start: 0.8931 (OUTLIER) cc_final: 0.8645 (pp) REVERT: E 66 GLN cc_start: 0.7201 (mt0) cc_final: 0.5883 (mt0) REVERT: E 120 LEU cc_start: 0.8563 (mt) cc_final: 0.8082 (mt) REVERT: E 146 ASP cc_start: 0.8945 (p0) cc_final: 0.8622 (p0) REVERT: E 196 MET cc_start: 0.8858 (mpp) cc_final: 0.8291 (mmt) REVERT: E 232 GLN cc_start: 0.8365 (mt0) cc_final: 0.8143 (mt0) REVERT: E 233 MET cc_start: 0.9183 (mtm) cc_final: 0.8726 (mtt) REVERT: E 257 PHE cc_start: 0.8583 (m-10) cc_final: 0.8259 (m-80) REVERT: E 326 PHE cc_start: 0.9019 (m-80) cc_final: 0.8325 (m-80) REVERT: E 352 ASN cc_start: 0.9040 (p0) cc_final: 0.8795 (p0) REVERT: E 371 PHE cc_start: 0.9561 (m-80) cc_final: 0.9321 (m-80) REVERT: E 389 MET cc_start: 0.9065 (mmp) cc_final: 0.8859 (mmm) REVERT: E 411 ASP cc_start: 0.8005 (t0) cc_final: 0.7734 (t70) REVERT: E 450 PHE cc_start: 0.8345 (m-80) cc_final: 0.8083 (m-80) REVERT: E 457 TYR cc_start: 0.8826 (m-80) cc_final: 0.8343 (m-80) REVERT: F 103 GLU cc_start: 0.7631 (tp30) cc_final: 0.7188 (tp30) REVERT: F 148 LYS cc_start: 0.8959 (ptmm) cc_final: 0.8333 (ptmm) REVERT: F 149 GLN cc_start: 0.8890 (pt0) cc_final: 0.8523 (pt0) REVERT: F 150 THR cc_start: 0.9372 (m) cc_final: 0.7925 (m) REVERT: F 151 GLN cc_start: 0.8265 (tt0) cc_final: 0.6881 (tt0) REVERT: F 185 GLU cc_start: 0.7973 (tp30) cc_final: 0.7078 (mt-10) REVERT: F 196 MET cc_start: 0.7592 (mmm) cc_final: 0.6955 (mmm) REVERT: F 204 MET cc_start: 0.8459 (mpp) cc_final: 0.7856 (mpp) REVERT: F 215 ASP cc_start: 0.8333 (m-30) cc_final: 0.8058 (m-30) REVERT: F 230 TYR cc_start: 0.8787 (m-80) cc_final: 0.8570 (m-80) REVERT: F 249 GLU cc_start: 0.8564 (mp0) cc_final: 0.8263 (mp0) REVERT: F 273 ILE cc_start: 0.8231 (mm) cc_final: 0.7796 (mm) REVERT: F 302 LEU cc_start: 0.8807 (mt) cc_final: 0.7977 (mt) REVERT: F 315 HIS cc_start: 0.8009 (m-70) cc_final: 0.7442 (m90) REVERT: F 338 MET cc_start: 0.8196 (mpp) cc_final: 0.7962 (ptp) REVERT: F 355 TYR cc_start: 0.8853 (m-80) cc_final: 0.8273 (m-80) REVERT: F 356 LYS cc_start: 0.9338 (mmpt) cc_final: 0.9041 (mmtt) REVERT: F 373 LEU cc_start: 0.8840 (mm) cc_final: 0.8556 (mm) outliers start: 2 outliers final: 1 residues processed: 656 average time/residue: 0.3137 time to fit residues: 315.1891 Evaluate side-chains 526 residues out of total 2333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 524 time to evaluate : 2.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 173 optimal weight: 6.9990 chunk 186 optimal weight: 8.9990 chunk 17 optimal weight: 10.0000 chunk 20 optimal weight: 4.9990 chunk 153 optimal weight: 30.0000 chunk 175 optimal weight: 6.9990 chunk 58 optimal weight: 30.0000 chunk 145 optimal weight: 3.9990 chunk 68 optimal weight: 0.7980 chunk 246 optimal weight: 2.9990 chunk 26 optimal weight: 20.0000 overall best weight: 3.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 66 GLN A 192 GLN A 210 GLN A 323 ASN ** A 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 78 ASN ** B 212 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 372 GLN ** E 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 212 ASN F 149 GLN ** F 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 301 GLN F 337 ASN ** F 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4032 r_free = 0.4032 target = 0.134470 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.107691 restraints weight = 63240.041| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.111412 restraints weight = 37572.391| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.114040 restraints weight = 25720.029| |-----------------------------------------------------------------------------| r_work (final): 0.3782 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7260 moved from start: 0.3605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 21458 Z= 0.148 Angle : 0.730 11.913 29192 Z= 0.368 Chirality : 0.049 0.346 3146 Planarity : 0.006 0.104 3837 Dihedral : 6.493 39.464 2886 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 16.96 Ramachandran Plot: Outliers : 0.04 % Allowed : 9.97 % Favored : 89.99 % Rotamer: Outliers : 0.09 % Allowed : 4.07 % Favored : 95.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.08 % Twisted Proline : 1.11 % Twisted General : 0.08 % 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: -3.44 (0.15), residues: 2658 helix: -2.35 (0.29), residues: 228 sheet: -1.68 (0.20), residues: 603 loop : -2.67 (0.13), residues: 1827 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP C 308 HIS 0.008 0.001 HIS C 35 PHE 0.029 0.002 PHE C 33 TYR 0.028 0.002 TYR C 365 ARG 0.009 0.001 ARG A 334 Details of bonding type rmsd hydrogen bonds : bond 0.03836 ( 337) hydrogen bonds : angle 7.51846 ( 870) SS BOND : bond 0.00132 ( 1) SS BOND : angle 0.24580 ( 2) covalent geometry : bond 0.00328 (21457) covalent geometry : angle 0.73008 (29190) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5316 Ramachandran restraints generated. 2658 Oldfield, 0 Emsley, 2658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5316 Ramachandran restraints generated. 2658 Oldfield, 0 Emsley, 2658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 668 residues out of total 2333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 666 time to evaluate : 2.305 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 165 TRP cc_start: 0.8818 (m100) cc_final: 0.8603 (m100) REVERT: A 223 THR cc_start: 0.8559 (t) cc_final: 0.8243 (t) REVERT: A 247 ARG cc_start: 0.8161 (ptt180) cc_final: 0.7554 (ptp-170) REVERT: A 257 PHE cc_start: 0.8693 (t80) cc_final: 0.8166 (t80) REVERT: A 288 VAL cc_start: 0.8958 (OUTLIER) cc_final: 0.8699 (m) REVERT: A 366 ASP cc_start: 0.7358 (t0) cc_final: 0.6951 (t0) REVERT: A 368 GLN cc_start: 0.8833 (mt0) cc_final: 0.8523 (mt0) REVERT: A 371 PHE cc_start: 0.8247 (m-80) cc_final: 0.7397 (m-80) REVERT: A 381 GLU cc_start: 0.9183 (mp0) cc_final: 0.8951 (mp0) REVERT: A 389 MET cc_start: 0.8908 (ttt) cc_final: 0.8341 (tmm) REVERT: B 26 TYR cc_start: 0.8343 (m-80) cc_final: 0.7949 (m-80) REVERT: B 65 TYR cc_start: 0.8819 (m-80) cc_final: 0.8584 (m-80) REVERT: B 67 TYR cc_start: 0.8079 (m-80) cc_final: 0.7473 (m-80) REVERT: B 74 LEU cc_start: 0.8978 (tp) cc_final: 0.8626 (tp) REVERT: B 210 GLN cc_start: 0.9318 (mp10) cc_final: 0.8949 (mp10) REVERT: B 220 ILE cc_start: 0.9717 (pt) cc_final: 0.9482 (pt) REVERT: B 236 ASP cc_start: 0.8533 (t0) cc_final: 0.8328 (t70) REVERT: B 246 LEU cc_start: 0.9164 (mt) cc_final: 0.8823 (mt) REVERT: B 273 ILE cc_start: 0.9436 (mm) cc_final: 0.9221 (mm) REVERT: B 301 GLN cc_start: 0.9033 (mp-120) cc_final: 0.8469 (mp10) REVERT: B 328 THR cc_start: 0.8970 (m) cc_final: 0.8178 (p) REVERT: B 364 GLU cc_start: 0.8659 (pp20) cc_final: 0.8350 (tp30) REVERT: C 53 ARG cc_start: 0.7017 (mmt-90) cc_final: 0.6758 (ttt-90) REVERT: C 108 GLN cc_start: 0.8697 (tp-100) cc_final: 0.8238 (mm-40) REVERT: C 154 MET cc_start: 0.8777 (mmp) cc_final: 0.8475 (mmp) REVERT: C 204 MET cc_start: 0.8072 (ptp) cc_final: 0.7552 (ptp) REVERT: C 310 GLN cc_start: 0.8711 (tm-30) cc_final: 0.8383 (tm-30) REVERT: C 359 MET cc_start: 0.8240 (mmt) cc_final: 0.7979 (mmt) REVERT: C 383 MET cc_start: 0.8681 (mmt) cc_final: 0.8168 (mmt) REVERT: C 395 GLU cc_start: 0.9178 (tm-30) cc_final: 0.8855 (tm-30) REVERT: D 48 TYR cc_start: 0.7831 (m-80) cc_final: 0.7081 (m-80) REVERT: D 63 SER cc_start: 0.9350 (t) cc_final: 0.8904 (p) REVERT: D 70 PHE cc_start: 0.9104 (m-80) cc_final: 0.8782 (m-80) REVERT: D 117 HIS cc_start: 0.8428 (t-90) cc_final: 0.7602 (t-170) REVERT: D 120 LEU cc_start: 0.8571 (mt) cc_final: 0.8066 (mt) REVERT: D 149 GLN cc_start: 0.8568 (tm-30) cc_final: 0.8276 (tm-30) REVERT: D 206 PHE cc_start: 0.8207 (m-80) cc_final: 0.7792 (m-80) REVERT: D 233 MET cc_start: 0.8825 (mmp) cc_final: 0.8591 (mmm) REVERT: D 326 PHE cc_start: 0.8202 (m-80) cc_final: 0.7857 (m-10) REVERT: D 355 TYR cc_start: 0.7998 (m-80) cc_final: 0.7677 (m-80) REVERT: D 361 HIS cc_start: 0.5976 (t70) cc_final: 0.5616 (t70) REVERT: D 397 TRP cc_start: 0.8737 (m-90) cc_final: 0.8408 (m100) REVERT: D 449 LYS cc_start: 0.7850 (mmtp) cc_final: 0.7372 (mmmt) REVERT: E 41 LEU cc_start: 0.8051 (tt) cc_final: 0.7363 (tt) REVERT: E 66 GLN cc_start: 0.7199 (mt0) cc_final: 0.5891 (mt0) REVERT: E 120 LEU cc_start: 0.8481 (mt) cc_final: 0.7943 (mt) REVERT: E 146 ASP cc_start: 0.8944 (p0) cc_final: 0.8680 (p0) REVERT: E 153 CYS cc_start: 0.8536 (t) cc_final: 0.8319 (t) REVERT: E 196 MET cc_start: 0.8952 (mpp) cc_final: 0.8411 (mmt) REVERT: E 232 GLN cc_start: 0.8341 (mt0) cc_final: 0.8031 (mt0) REVERT: E 233 MET cc_start: 0.9133 (mtm) cc_final: 0.8824 (mtm) REVERT: E 244 PHE cc_start: 0.8209 (t80) cc_final: 0.8002 (t80) REVERT: E 251 MET cc_start: 0.7934 (tmm) cc_final: 0.7656 (tmm) REVERT: E 257 PHE cc_start: 0.8556 (m-10) cc_final: 0.8276 (m-80) REVERT: E 303 PHE cc_start: 0.8958 (m-80) cc_final: 0.8121 (m-80) REVERT: E 326 PHE cc_start: 0.9015 (m-80) cc_final: 0.8356 (m-80) REVERT: E 338 MET cc_start: 0.9156 (mpp) cc_final: 0.8936 (mpp) REVERT: E 352 ASN cc_start: 0.9080 (p0) cc_final: 0.8858 (p0) REVERT: E 364 GLU cc_start: 0.8156 (tp30) cc_final: 0.7675 (tp30) REVERT: E 411 ASP cc_start: 0.8000 (t0) cc_final: 0.7741 (t70) REVERT: E 457 TYR cc_start: 0.8791 (m-80) cc_final: 0.8233 (m-10) REVERT: E 461 ARG cc_start: 0.9015 (ptp90) cc_final: 0.8806 (ptt-90) REVERT: F 103 GLU cc_start: 0.7792 (tp30) cc_final: 0.7212 (tp30) REVERT: F 145 MET cc_start: 0.8885 (tpt) cc_final: 0.8563 (tpt) REVERT: F 148 LYS cc_start: 0.8937 (ptmm) cc_final: 0.8412 (ptmm) REVERT: F 149 GLN cc_start: 0.8843 (pt0) cc_final: 0.8501 (pt0) REVERT: F 150 THR cc_start: 0.9441 (m) cc_final: 0.8113 (m) REVERT: F 165 TRP cc_start: 0.8857 (m100) cc_final: 0.8054 (m100) REVERT: F 185 GLU cc_start: 0.7982 (tp30) cc_final: 0.7661 (mt-10) REVERT: F 196 MET cc_start: 0.7518 (mmm) cc_final: 0.6843 (mmm) REVERT: F 204 MET cc_start: 0.8418 (mpp) cc_final: 0.7762 (mpp) REVERT: F 216 VAL cc_start: 0.7578 (m) cc_final: 0.7369 (m) REVERT: F 249 GLU cc_start: 0.8600 (mp0) cc_final: 0.8263 (mp0) REVERT: F 273 ILE cc_start: 0.8311 (mm) cc_final: 0.7921 (mm) REVERT: F 315 HIS cc_start: 0.7968 (m-70) cc_final: 0.7444 (m90) REVERT: F 334 ARG cc_start: 0.8764 (mtt180) cc_final: 0.8522 (mtt180) REVERT: F 356 LYS cc_start: 0.9161 (mmpt) cc_final: 0.8827 (mppt) REVERT: F 357 GLU cc_start: 0.8066 (tm-30) cc_final: 0.7540 (tm-30) REVERT: F 360 ARG cc_start: 0.6820 (mtt180) cc_final: 0.6007 (mtt180) outliers start: 2 outliers final: 1 residues processed: 667 average time/residue: 0.3164 time to fit residues: 320.6249 Evaluate side-chains 555 residues out of total 2333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 553 time to evaluate : 2.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 236 optimal weight: 30.0000 chunk 101 optimal weight: 0.5980 chunk 149 optimal weight: 9.9990 chunk 44 optimal weight: 6.9990 chunk 234 optimal weight: 8.9990 chunk 174 optimal weight: 8.9990 chunk 20 optimal weight: 10.0000 chunk 102 optimal weight: 10.0000 chunk 180 optimal weight: 3.9990 chunk 204 optimal weight: 10.0000 chunk 32 optimal weight: 40.0000 overall best weight: 5.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 372 GLN ** B 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 212 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 387 HIS ** D 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 149 GLN ** F 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 255 HIS F 301 GLN F 337 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.132757 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.106036 restraints weight = 63895.756| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.109639 restraints weight = 38226.600| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.112220 restraints weight = 26341.718| |-----------------------------------------------------------------------------| r_work (final): 0.3759 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7302 moved from start: 0.3887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 21458 Z= 0.172 Angle : 0.735 11.534 29192 Z= 0.373 Chirality : 0.048 0.342 3146 Planarity : 0.006 0.105 3837 Dihedral : 6.440 38.374 2886 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 17.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.02 % Favored : 88.98 % Rotamer: Outliers : 0.04 % Allowed : 3.64 % Favored : 96.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.08 % Twisted Proline : 1.67 % Twisted General : 0.12 % 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: -3.34 (0.15), residues: 2658 helix: -2.04 (0.30), residues: 228 sheet: -1.59 (0.20), residues: 620 loop : -2.65 (0.13), residues: 1810 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP F 308 HIS 0.009 0.002 HIS C 35 PHE 0.035 0.002 PHE A 88 TYR 0.026 0.002 TYR C 365 ARG 0.007 0.001 ARG F 259 Details of bonding type rmsd hydrogen bonds : bond 0.03777 ( 337) hydrogen bonds : angle 7.41162 ( 870) SS BOND : bond 0.00197 ( 1) SS BOND : angle 0.21220 ( 2) covalent geometry : bond 0.00377 (21457) covalent geometry : angle 0.73483 (29190) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5316 Ramachandran restraints generated. 2658 Oldfield, 0 Emsley, 2658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5316 Ramachandran restraints generated. 2658 Oldfield, 0 Emsley, 2658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 657 residues out of total 2333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 656 time to evaluate : 2.160 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 TYR cc_start: 0.8352 (m-80) cc_final: 0.7947 (m-80) REVERT: A 66 GLN cc_start: 0.8926 (mm110) cc_final: 0.8725 (mm110) REVERT: A 74 LEU cc_start: 0.8681 (tp) cc_final: 0.8427 (tp) REVERT: A 165 TRP cc_start: 0.8882 (m100) cc_final: 0.8645 (m100) REVERT: A 246 LEU cc_start: 0.9374 (mt) cc_final: 0.9174 (mt) REVERT: A 247 ARG cc_start: 0.8190 (ptt180) cc_final: 0.7672 (ptt180) REVERT: A 257 PHE cc_start: 0.8844 (t80) cc_final: 0.8491 (t80) REVERT: A 288 VAL cc_start: 0.9120 (m) cc_final: 0.8886 (m) REVERT: A 368 GLN cc_start: 0.8840 (mt0) cc_final: 0.8403 (mt0) REVERT: A 371 PHE cc_start: 0.8298 (m-80) cc_final: 0.7535 (m-80) REVERT: A 381 GLU cc_start: 0.9153 (mp0) cc_final: 0.8902 (mp0) REVERT: A 389 MET cc_start: 0.8975 (ttt) cc_final: 0.8383 (tmm) REVERT: B 26 TYR cc_start: 0.8364 (m-80) cc_final: 0.7942 (m-80) REVERT: B 32 ILE cc_start: 0.9179 (mp) cc_final: 0.8942 (mp) REVERT: B 65 TYR cc_start: 0.8946 (m-80) cc_final: 0.8741 (m-80) REVERT: B 67 TYR cc_start: 0.8033 (m-80) cc_final: 0.7468 (m-80) REVERT: B 74 LEU cc_start: 0.8981 (tp) cc_final: 0.8604 (tp) REVERT: B 210 GLN cc_start: 0.9338 (mp10) cc_final: 0.8978 (mp10) REVERT: B 220 ILE cc_start: 0.9700 (pt) cc_final: 0.9443 (pt) REVERT: B 236 ASP cc_start: 0.8572 (t0) cc_final: 0.8346 (t70) REVERT: B 246 LEU cc_start: 0.9151 (mt) cc_final: 0.8873 (mt) REVERT: B 251 MET cc_start: 0.8312 (tmm) cc_final: 0.7826 (tmm) REVERT: B 254 ARG cc_start: 0.9101 (ttt-90) cc_final: 0.8628 (ttt90) REVERT: B 298 SER cc_start: 0.9026 (p) cc_final: 0.8779 (p) REVERT: B 301 GLN cc_start: 0.9146 (mp-120) cc_final: 0.8551 (mp10) REVERT: B 302 LEU cc_start: 0.9061 (pp) cc_final: 0.8683 (pp) REVERT: B 305 LYS cc_start: 0.9561 (mtmt) cc_final: 0.9200 (mtpt) REVERT: B 307 TYR cc_start: 0.8367 (m-10) cc_final: 0.7921 (m-10) REVERT: B 373 LEU cc_start: 0.8928 (mm) cc_final: 0.8709 (mm) REVERT: B 421 ILE cc_start: 0.7459 (mp) cc_final: 0.7248 (mm) REVERT: C 53 ARG cc_start: 0.7106 (mmt-90) cc_final: 0.6694 (ttt-90) REVERT: C 65 TYR cc_start: 0.9348 (m-80) cc_final: 0.9065 (m-10) REVERT: C 108 GLN cc_start: 0.8619 (tp-100) cc_final: 0.8177 (mm-40) REVERT: C 201 PHE cc_start: 0.8361 (m-10) cc_final: 0.7784 (m-80) REVERT: C 204 MET cc_start: 0.8055 (ptp) cc_final: 0.7606 (ptp) REVERT: C 310 GLN cc_start: 0.8756 (tm-30) cc_final: 0.8425 (tm-30) REVERT: C 359 MET cc_start: 0.8256 (mmt) cc_final: 0.7873 (mmt) REVERT: C 372 GLN cc_start: 0.7982 (tt0) cc_final: 0.7560 (tt0) REVERT: C 383 MET cc_start: 0.8719 (mmt) cc_final: 0.8217 (mmt) REVERT: C 386 ILE cc_start: 0.9544 (pt) cc_final: 0.9294 (pt) REVERT: C 395 GLU cc_start: 0.9199 (tm-30) cc_final: 0.8879 (tm-30) REVERT: D 63 SER cc_start: 0.9380 (t) cc_final: 0.9028 (p) REVERT: D 70 PHE cc_start: 0.9090 (m-80) cc_final: 0.8823 (m-80) REVERT: D 106 ARG cc_start: 0.8098 (mmm-85) cc_final: 0.7755 (mmm-85) REVERT: D 117 HIS cc_start: 0.8383 (t-90) cc_final: 0.7609 (t-170) REVERT: D 120 LEU cc_start: 0.8542 (mt) cc_final: 0.8014 (mt) REVERT: D 149 GLN cc_start: 0.8532 (tm-30) cc_final: 0.8229 (tm-30) REVERT: D 184 LEU cc_start: 0.8138 (tp) cc_final: 0.7911 (tp) REVERT: D 206 PHE cc_start: 0.8185 (m-80) cc_final: 0.7688 (m-80) REVERT: D 219 ASP cc_start: 0.9350 (p0) cc_final: 0.9104 (p0) REVERT: D 355 TYR cc_start: 0.8042 (m-80) cc_final: 0.7640 (m-80) REVERT: D 361 HIS cc_start: 0.6137 (t70) cc_final: 0.5898 (t70) REVERT: D 364 GLU cc_start: 0.8629 (tm-30) cc_final: 0.8222 (tm-30) REVERT: D 397 TRP cc_start: 0.8801 (m-90) cc_final: 0.8331 (m100) REVERT: D 449 LYS cc_start: 0.8087 (mmtp) cc_final: 0.7661 (mmmt) REVERT: E 41 LEU cc_start: 0.8057 (tt) cc_final: 0.7421 (tt) REVERT: E 66 GLN cc_start: 0.7286 (mt0) cc_final: 0.6468 (mt0) REVERT: E 120 LEU cc_start: 0.8599 (mt) cc_final: 0.8027 (mt) REVERT: E 146 ASP cc_start: 0.8869 (p0) cc_final: 0.8651 (p0) REVERT: E 196 MET cc_start: 0.8865 (mpp) cc_final: 0.8311 (mpp) REVERT: E 225 CYS cc_start: 0.8684 (m) cc_final: 0.8447 (m) REVERT: E 233 MET cc_start: 0.9210 (mtm) cc_final: 0.8721 (mtt) REVERT: E 249 GLU cc_start: 0.9108 (mp0) cc_final: 0.8368 (mp0) REVERT: E 257 PHE cc_start: 0.8485 (m-10) cc_final: 0.8257 (m-80) REVERT: E 326 PHE cc_start: 0.9023 (m-80) cc_final: 0.8362 (m-80) REVERT: E 338 MET cc_start: 0.9063 (mpp) cc_final: 0.8521 (mpp) REVERT: E 364 GLU cc_start: 0.8293 (tp30) cc_final: 0.7928 (tp30) REVERT: E 397 TRP cc_start: 0.7609 (m100) cc_final: 0.7309 (m100) REVERT: E 411 ASP cc_start: 0.8024 (t0) cc_final: 0.7777 (t70) REVERT: E 457 TYR cc_start: 0.8778 (m-80) cc_final: 0.8415 (m-10) REVERT: E 461 ARG cc_start: 0.9012 (ptp90) cc_final: 0.8697 (mtt180) REVERT: F 71 LYS cc_start: 0.7824 (tptm) cc_final: 0.7493 (tptp) REVERT: F 103 GLU cc_start: 0.7725 (tp30) cc_final: 0.7252 (tp30) REVERT: F 149 GLN cc_start: 0.8873 (pt0) cc_final: 0.8435 (pt0) REVERT: F 150 THR cc_start: 0.9457 (m) cc_final: 0.8291 (m) REVERT: F 165 TRP cc_start: 0.8875 (m100) cc_final: 0.8099 (m100) REVERT: F 186 LEU cc_start: 0.8851 (tp) cc_final: 0.8566 (tp) REVERT: F 192 GLN cc_start: 0.8998 (mt0) cc_final: 0.8629 (mm-40) REVERT: F 193 ASP cc_start: 0.9014 (t0) cc_final: 0.8790 (t0) REVERT: F 196 MET cc_start: 0.7372 (mmm) cc_final: 0.6759 (mmm) REVERT: F 204 MET cc_start: 0.8425 (mpp) cc_final: 0.7743 (mpp) REVERT: F 216 VAL cc_start: 0.7635 (m) cc_final: 0.7432 (m) REVERT: F 237 PRO cc_start: 0.9236 (Cg_endo) cc_final: 0.9017 (Cg_exo) REVERT: F 249 GLU cc_start: 0.8525 (mp0) cc_final: 0.8138 (mp0) REVERT: F 273 ILE cc_start: 0.8378 (mm) cc_final: 0.7998 (mm) REVERT: F 315 HIS cc_start: 0.7912 (m-70) cc_final: 0.7268 (m-70) REVERT: F 334 ARG cc_start: 0.8796 (mtt180) cc_final: 0.8534 (mtt180) REVERT: F 360 ARG cc_start: 0.6328 (mtt180) cc_final: 0.5445 (mtt180) REVERT: F 449 LYS cc_start: 0.9227 (mmtp) cc_final: 0.8977 (mtmt) outliers start: 1 outliers final: 1 residues processed: 656 average time/residue: 0.3151 time to fit residues: 315.8110 Evaluate side-chains 540 residues out of total 2333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 539 time to evaluate : 2.197 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 33 optimal weight: 7.9990 chunk 29 optimal weight: 10.0000 chunk 172 optimal weight: 7.9990 chunk 253 optimal weight: 5.9990 chunk 213 optimal weight: 6.9990 chunk 211 optimal weight: 30.0000 chunk 234 optimal weight: 6.9990 chunk 142 optimal weight: 30.0000 chunk 101 optimal weight: 0.8980 chunk 260 optimal weight: 6.9990 chunk 247 optimal weight: 20.0000 overall best weight: 5.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 192 GLN ** A 323 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 466 GLN ** B 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 212 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 456 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 232 GLN F 149 GLN ** F 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 210 GLN F 301 GLN F 337 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4014 r_free = 0.4014 target = 0.133103 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.106408 restraints weight = 63573.030| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.110063 restraints weight = 38070.561| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.112634 restraints weight = 26214.039| |-----------------------------------------------------------------------------| r_work (final): 0.3764 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7295 moved from start: 0.4137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 21458 Z= 0.163 Angle : 0.718 11.099 29192 Z= 0.362 Chirality : 0.048 0.284 3146 Planarity : 0.006 0.104 3837 Dihedral : 6.247 37.078 2886 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 18.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.84 % Favored : 89.16 % Rotamer: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.08 % Twisted Proline : 0.56 % Twisted General : 0.08 % 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: -3.29 (0.15), residues: 2658 helix: -2.02 (0.30), residues: 235 sheet: -1.60 (0.20), residues: 621 loop : -2.59 (0.13), residues: 1802 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP C 308 HIS 0.008 0.002 HIS F 35 PHE 0.055 0.002 PHE D 257 TYR 0.017 0.002 TYR D 65 ARG 0.007 0.001 ARG E 334 Details of bonding type rmsd hydrogen bonds : bond 0.03426 ( 337) hydrogen bonds : angle 7.21564 ( 870) SS BOND : bond 0.00199 ( 1) SS BOND : angle 0.20649 ( 2) covalent geometry : bond 0.00361 (21457) covalent geometry : angle 0.71835 (29190) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5316 Ramachandran restraints generated. 2658 Oldfield, 0 Emsley, 2658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5316 Ramachandran restraints generated. 2658 Oldfield, 0 Emsley, 2658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 654 residues out of total 2333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 654 time to evaluate : 2.358 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 TYR cc_start: 0.8340 (m-80) cc_final: 0.8040 (m-80) REVERT: A 165 TRP cc_start: 0.8873 (m100) cc_final: 0.8411 (m100) REVERT: A 257 PHE cc_start: 0.8868 (t80) cc_final: 0.8507 (t80) REVERT: A 288 VAL cc_start: 0.9047 (m) cc_final: 0.8764 (m) REVERT: A 371 PHE cc_start: 0.8283 (m-80) cc_final: 0.7458 (m-80) REVERT: A 381 GLU cc_start: 0.9171 (mp0) cc_final: 0.8896 (mp0) REVERT: A 389 MET cc_start: 0.8943 (ttt) cc_final: 0.8332 (tmm) REVERT: A 412 THR cc_start: 0.9328 (t) cc_final: 0.8966 (t) REVERT: B 26 TYR cc_start: 0.8276 (m-80) cc_final: 0.7895 (m-80) REVERT: B 32 ILE cc_start: 0.9241 (mp) cc_final: 0.9016 (mp) REVERT: B 67 TYR cc_start: 0.8127 (m-80) cc_final: 0.7536 (m-80) REVERT: B 74 LEU cc_start: 0.8945 (tp) cc_final: 0.8558 (tp) REVERT: B 206 PHE cc_start: 0.8939 (m-10) cc_final: 0.8687 (m-10) REVERT: B 210 GLN cc_start: 0.9330 (mp10) cc_final: 0.8865 (mp10) REVERT: B 220 ILE cc_start: 0.9700 (pt) cc_final: 0.9454 (pt) REVERT: B 223 THR cc_start: 0.9322 (t) cc_final: 0.9117 (t) REVERT: B 233 MET cc_start: 0.8713 (mmt) cc_final: 0.7998 (mmt) REVERT: B 298 SER cc_start: 0.9006 (p) cc_final: 0.8751 (p) REVERT: B 301 GLN cc_start: 0.9114 (mp-120) cc_final: 0.8493 (mp10) REVERT: B 302 LEU cc_start: 0.9064 (pp) cc_final: 0.8732 (pp) REVERT: B 305 LYS cc_start: 0.9516 (mtmt) cc_final: 0.9151 (mtpt) REVERT: C 53 ARG cc_start: 0.7104 (mmt-90) cc_final: 0.6683 (ttt-90) REVERT: C 68 ARG cc_start: 0.9011 (mmt180) cc_final: 0.8686 (mmt-90) REVERT: C 74 LEU cc_start: 0.8774 (tp) cc_final: 0.8290 (tp) REVERT: C 108 GLN cc_start: 0.8609 (tp-100) cc_final: 0.8103 (mm-40) REVERT: C 154 MET cc_start: 0.8847 (mmp) cc_final: 0.8598 (mmm) REVERT: C 201 PHE cc_start: 0.8369 (m-10) cc_final: 0.7784 (m-80) REVERT: C 204 MET cc_start: 0.8048 (ptp) cc_final: 0.7607 (ptp) REVERT: C 307 TYR cc_start: 0.8980 (m-10) cc_final: 0.8764 (m-10) REVERT: C 310 GLN cc_start: 0.8688 (tm-30) cc_final: 0.8358 (tm-30) REVERT: C 323 ASN cc_start: 0.6781 (m110) cc_final: 0.6559 (m110) REVERT: C 359 MET cc_start: 0.8112 (mmt) cc_final: 0.7912 (mmt) REVERT: C 372 GLN cc_start: 0.7923 (tt0) cc_final: 0.7366 (pp30) REVERT: C 383 MET cc_start: 0.8730 (mmt) cc_final: 0.8212 (mmt) REVERT: C 386 ILE cc_start: 0.9498 (pt) cc_final: 0.9271 (pt) REVERT: C 395 GLU cc_start: 0.9189 (tm-30) cc_final: 0.8856 (tm-30) REVERT: C 438 ASN cc_start: 0.9169 (m110) cc_final: 0.8925 (m110) REVERT: D 48 TYR cc_start: 0.7995 (m-80) cc_final: 0.7489 (m-80) REVERT: D 63 SER cc_start: 0.9385 (t) cc_final: 0.8991 (p) REVERT: D 70 PHE cc_start: 0.9088 (m-80) cc_final: 0.8861 (m-80) REVERT: D 106 ARG cc_start: 0.7876 (mmm-85) cc_final: 0.7523 (mmm-85) REVERT: D 117 HIS cc_start: 0.8366 (t-90) cc_final: 0.7577 (t-170) REVERT: D 120 LEU cc_start: 0.8473 (mt) cc_final: 0.7957 (mt) REVERT: D 145 MET cc_start: 0.8880 (ppp) cc_final: 0.8296 (tmm) REVERT: D 149 GLN cc_start: 0.8558 (tm-30) cc_final: 0.8300 (tm-30) REVERT: D 184 LEU cc_start: 0.8172 (tp) cc_final: 0.7908 (tp) REVERT: D 206 PHE cc_start: 0.8139 (m-80) cc_final: 0.7589 (m-80) REVERT: D 355 TYR cc_start: 0.7965 (m-80) cc_final: 0.7559 (m-80) REVERT: D 361 HIS cc_start: 0.6172 (t70) cc_final: 0.5797 (t70) REVERT: D 364 GLU cc_start: 0.8796 (tm-30) cc_final: 0.8365 (tm-30) REVERT: D 397 TRP cc_start: 0.8826 (m-90) cc_final: 0.8343 (m100) REVERT: D 445 ASN cc_start: 0.9160 (t0) cc_final: 0.8938 (t0) REVERT: D 449 LYS cc_start: 0.8037 (mmtp) cc_final: 0.7599 (mmmt) REVERT: E 66 GLN cc_start: 0.7292 (mt0) cc_final: 0.6011 (mt0) REVERT: E 120 LEU cc_start: 0.8632 (mt) cc_final: 0.8060 (mt) REVERT: E 184 LEU cc_start: 0.8923 (mm) cc_final: 0.8709 (tp) REVERT: E 196 MET cc_start: 0.8972 (mpp) cc_final: 0.8403 (mmt) REVERT: E 232 GLN cc_start: 0.8490 (mt0) cc_final: 0.8283 (tt0) REVERT: E 249 GLU cc_start: 0.9032 (mp0) cc_final: 0.8409 (mp0) REVERT: E 326 PHE cc_start: 0.9034 (m-80) cc_final: 0.8296 (m-80) REVERT: E 352 ASN cc_start: 0.9202 (p0) cc_final: 0.8990 (p0) REVERT: E 374 CYS cc_start: 0.8922 (m) cc_final: 0.8715 (p) REVERT: E 411 ASP cc_start: 0.8067 (t0) cc_final: 0.7862 (t70) REVERT: E 457 TYR cc_start: 0.8730 (m-80) cc_final: 0.8162 (m-10) REVERT: E 461 ARG cc_start: 0.8987 (ptp90) cc_final: 0.8744 (ptt-90) REVERT: F 65 TYR cc_start: 0.9183 (m-10) cc_final: 0.8926 (m-80) REVERT: F 103 GLU cc_start: 0.7657 (tp30) cc_final: 0.7209 (tp30) REVERT: F 148 LYS cc_start: 0.8997 (ptmm) cc_final: 0.8429 (ptmm) REVERT: F 149 GLN cc_start: 0.8931 (pt0) cc_final: 0.8426 (pt0) REVERT: F 150 THR cc_start: 0.9456 (m) cc_final: 0.8013 (m) REVERT: F 165 TRP cc_start: 0.8901 (m100) cc_final: 0.8093 (m100) REVERT: F 192 GLN cc_start: 0.9001 (mt0) cc_final: 0.8662 (mt0) REVERT: F 193 ASP cc_start: 0.8966 (t0) cc_final: 0.8766 (t0) REVERT: F 196 MET cc_start: 0.7454 (mmm) cc_final: 0.6847 (mmm) REVERT: F 204 MET cc_start: 0.8403 (mpp) cc_final: 0.7732 (mpp) REVERT: F 216 VAL cc_start: 0.7688 (m) cc_final: 0.7486 (m) REVERT: F 237 PRO cc_start: 0.9230 (Cg_endo) cc_final: 0.8804 (Cg_exo) REVERT: F 249 GLU cc_start: 0.8468 (mp0) cc_final: 0.7995 (mp0) REVERT: F 273 ILE cc_start: 0.8420 (mm) cc_final: 0.8071 (mm) REVERT: F 285 SER cc_start: 0.9202 (t) cc_final: 0.8934 (t) REVERT: F 315 HIS cc_start: 0.7894 (m-70) cc_final: 0.7339 (m90) REVERT: F 360 ARG cc_start: 0.6876 (mtt180) cc_final: 0.6153 (mtt180) REVERT: F 397 TRP cc_start: 0.7614 (m-10) cc_final: 0.6662 (m-90) outliers start: 0 outliers final: 0 residues processed: 654 average time/residue: 0.3129 time to fit residues: 314.8911 Evaluate side-chains 543 residues out of total 2333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 543 time to evaluate : 2.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 226 optimal weight: 30.0000 chunk 120 optimal weight: 0.9990 chunk 255 optimal weight: 40.0000 chunk 75 optimal weight: 7.9990 chunk 180 optimal weight: 7.9990 chunk 64 optimal weight: 8.9990 chunk 68 optimal weight: 10.0000 chunk 108 optimal weight: 6.9990 chunk 199 optimal weight: 20.0000 chunk 260 optimal weight: 7.9990 chunk 157 optimal weight: 40.0000 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 139 ASN A 142 ASN A 192 GLN ** A 323 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 372 GLN A 466 GLN ** B 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 212 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 31 ASN ** C 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 387 HIS ** C 456 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 149 GLN ** F 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 337 ASN ** F 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.132109 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.105382 restraints weight = 63202.957| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.108985 restraints weight = 37872.854| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.111507 restraints weight = 26155.021| |-----------------------------------------------------------------------------| r_work (final): 0.3752 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7308 moved from start: 0.4325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 21458 Z= 0.177 Angle : 0.746 13.148 29192 Z= 0.374 Chirality : 0.048 0.231 3146 Planarity : 0.006 0.104 3837 Dihedral : 6.265 35.658 2886 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 19.15 Ramachandran Plot: Outliers : 0.04 % Allowed : 11.66 % Favored : 88.30 % Rotamer: Outliers : 0.04 % Allowed : 2.44 % Favored : 97.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.08 % Twisted Proline : 0.56 % Twisted General : 0.08 % 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: -3.34 (0.15), residues: 2658 helix: -2.06 (0.29), residues: 237 sheet: -1.66 (0.20), residues: 600 loop : -2.60 (0.13), residues: 1821 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP F 308 HIS 0.010 0.002 HIS C 35 PHE 0.028 0.002 PHE A 88 TYR 0.022 0.002 TYR E 307 ARG 0.006 0.001 ARG F 259 Details of bonding type rmsd hydrogen bonds : bond 0.03507 ( 337) hydrogen bonds : angle 7.20611 ( 870) SS BOND : bond 0.00187 ( 1) SS BOND : angle 0.26180 ( 2) covalent geometry : bond 0.00390 (21457) covalent geometry : angle 0.74611 (29190) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5316 Ramachandran restraints generated. 2658 Oldfield, 0 Emsley, 2658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5316 Ramachandran restraints generated. 2658 Oldfield, 0 Emsley, 2658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 634 residues out of total 2333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 633 time to evaluate : 2.186 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 TYR cc_start: 0.8373 (m-80) cc_final: 0.7962 (m-80) REVERT: A 165 TRP cc_start: 0.8867 (m100) cc_final: 0.8436 (m100) REVERT: A 195 ASP cc_start: 0.8042 (t70) cc_final: 0.7430 (t70) REVERT: A 257 PHE cc_start: 0.8932 (t80) cc_final: 0.8684 (t80) REVERT: A 288 VAL cc_start: 0.9147 (m) cc_final: 0.8946 (m) REVERT: A 371 PHE cc_start: 0.8340 (m-80) cc_final: 0.7540 (m-80) REVERT: A 381 GLU cc_start: 0.9179 (mp0) cc_final: 0.8914 (mp0) REVERT: A 389 MET cc_start: 0.8944 (ttt) cc_final: 0.8363 (tmm) REVERT: A 412 THR cc_start: 0.9310 (t) cc_final: 0.8921 (t) REVERT: B 26 TYR cc_start: 0.8265 (m-80) cc_final: 0.7868 (m-80) REVERT: B 32 ILE cc_start: 0.9140 (mp) cc_final: 0.8900 (mp) REVERT: B 67 TYR cc_start: 0.8212 (m-80) cc_final: 0.7679 (m-80) REVERT: B 68 ARG cc_start: 0.8761 (mmp-170) cc_final: 0.8007 (mmp-170) REVERT: B 74 LEU cc_start: 0.9052 (tp) cc_final: 0.8675 (tp) REVERT: B 186 LEU cc_start: 0.8688 (pp) cc_final: 0.7906 (pp) REVERT: B 204 MET cc_start: 0.9077 (mpp) cc_final: 0.8803 (mpp) REVERT: B 206 PHE cc_start: 0.9260 (m-10) cc_final: 0.9024 (m-80) REVERT: B 210 GLN cc_start: 0.9354 (mp10) cc_final: 0.9023 (mp10) REVERT: B 220 ILE cc_start: 0.9699 (pt) cc_final: 0.9434 (pt) REVERT: B 223 THR cc_start: 0.9372 (t) cc_final: 0.9099 (p) REVERT: B 233 MET cc_start: 0.8647 (mmt) cc_final: 0.7931 (mmt) REVERT: B 236 ASP cc_start: 0.8528 (t0) cc_final: 0.8196 (t70) REVERT: B 298 SER cc_start: 0.9021 (p) cc_final: 0.8718 (p) REVERT: B 301 GLN cc_start: 0.9123 (mp-120) cc_final: 0.8532 (mp10) REVERT: B 302 LEU cc_start: 0.9147 (pp) cc_final: 0.8829 (pp) REVERT: B 305 LYS cc_start: 0.9538 (mtmt) cc_final: 0.9179 (mtpt) REVERT: B 355 TYR cc_start: 0.7230 (m-80) cc_final: 0.6851 (m-80) REVERT: C 33 PHE cc_start: 0.8045 (m-10) cc_final: 0.7731 (m-80) REVERT: C 53 ARG cc_start: 0.7188 (mmt-90) cc_final: 0.6780 (ttt-90) REVERT: C 74 LEU cc_start: 0.8844 (tp) cc_final: 0.8332 (tp) REVERT: C 108 GLN cc_start: 0.8529 (tp-100) cc_final: 0.7983 (mm-40) REVERT: C 150 THR cc_start: 0.8345 (m) cc_final: 0.7989 (m) REVERT: C 204 MET cc_start: 0.8075 (ptp) cc_final: 0.7558 (ptp) REVERT: C 310 GLN cc_start: 0.8763 (tm-30) cc_final: 0.8427 (tm-30) REVERT: C 323 ASN cc_start: 0.6911 (m110) cc_final: 0.6632 (m110) REVERT: C 333 THR cc_start: 0.9494 (p) cc_final: 0.9022 (p) REVERT: C 357 GLU cc_start: 0.9096 (mm-30) cc_final: 0.8871 (mm-30) REVERT: C 383 MET cc_start: 0.8749 (mmt) cc_final: 0.8228 (mmt) REVERT: C 386 ILE cc_start: 0.9494 (pt) cc_final: 0.9248 (pt) REVERT: C 395 GLU cc_start: 0.9177 (tm-30) cc_final: 0.8857 (tm-30) REVERT: C 438 ASN cc_start: 0.9176 (m110) cc_final: 0.8928 (m-40) REVERT: D 63 SER cc_start: 0.9376 (t) cc_final: 0.8999 (p) REVERT: D 70 PHE cc_start: 0.9068 (m-80) cc_final: 0.8866 (m-80) REVERT: D 117 HIS cc_start: 0.8329 (t-90) cc_final: 0.7615 (t-170) REVERT: D 120 LEU cc_start: 0.8344 (mt) cc_final: 0.7752 (pp) REVERT: D 145 MET cc_start: 0.8921 (ppp) cc_final: 0.8467 (tmm) REVERT: D 149 GLN cc_start: 0.8488 (tm-30) cc_final: 0.8243 (tm-30) REVERT: D 184 LEU cc_start: 0.8171 (tp) cc_final: 0.7901 (tp) REVERT: D 197 VAL cc_start: 0.8237 (t) cc_final: 0.7800 (m) REVERT: D 204 MET cc_start: 0.8115 (mpp) cc_final: 0.7899 (mpp) REVERT: D 206 PHE cc_start: 0.8167 (m-80) cc_final: 0.7662 (m-80) REVERT: D 355 TYR cc_start: 0.7906 (m-80) cc_final: 0.7522 (m-80) REVERT: D 361 HIS cc_start: 0.6109 (t70) cc_final: 0.5866 (t70) REVERT: D 364 GLU cc_start: 0.8805 (tm-30) cc_final: 0.8601 (tm-30) REVERT: D 449 LYS cc_start: 0.8029 (mmtp) cc_final: 0.7605 (mmmt) REVERT: E 41 LEU cc_start: 0.8118 (tt) cc_final: 0.7424 (tt) REVERT: E 66 GLN cc_start: 0.7317 (mt0) cc_final: 0.6028 (mt0) REVERT: E 120 LEU cc_start: 0.8856 (mt) cc_final: 0.8071 (mt) REVERT: E 196 MET cc_start: 0.8885 (mpp) cc_final: 0.8277 (mmt) REVERT: E 225 CYS cc_start: 0.8712 (m) cc_final: 0.8470 (m) REVERT: E 232 GLN cc_start: 0.8440 (mt0) cc_final: 0.8169 (mt0) REVERT: E 249 GLU cc_start: 0.9104 (mp0) cc_final: 0.8444 (mp0) REVERT: E 257 PHE cc_start: 0.8276 (m-80) cc_final: 0.8070 (m-80) REVERT: E 359 MET cc_start: 0.8587 (mmm) cc_final: 0.8209 (mmm) REVERT: E 364 GLU cc_start: 0.8226 (tp30) cc_final: 0.7763 (tp30) REVERT: E 411 ASP cc_start: 0.8053 (t0) cc_final: 0.7820 (t70) REVERT: E 457 TYR cc_start: 0.8730 (m-80) cc_final: 0.8177 (m-10) REVERT: E 461 ARG cc_start: 0.8990 (ptp90) cc_final: 0.8646 (ptp90) REVERT: F 65 TYR cc_start: 0.9132 (m-10) cc_final: 0.8878 (m-10) REVERT: F 103 GLU cc_start: 0.7488 (tp30) cc_final: 0.7020 (tp30) REVERT: F 149 GLN cc_start: 0.8874 (pt0) cc_final: 0.8197 (pt0) REVERT: F 150 THR cc_start: 0.9439 (m) cc_final: 0.8162 (m) REVERT: F 165 TRP cc_start: 0.8941 (m100) cc_final: 0.8032 (m100) REVERT: F 193 ASP cc_start: 0.8965 (t0) cc_final: 0.8732 (t0) REVERT: F 196 MET cc_start: 0.7385 (mmm) cc_final: 0.6822 (mmm) REVERT: F 204 MET cc_start: 0.8454 (mpp) cc_final: 0.7748 (mpp) REVERT: F 216 VAL cc_start: 0.7740 (m) cc_final: 0.7528 (m) REVERT: F 237 PRO cc_start: 0.9225 (Cg_endo) cc_final: 0.8818 (Cg_exo) REVERT: F 249 GLU cc_start: 0.8548 (mp0) cc_final: 0.8271 (mp0) REVERT: F 273 ILE cc_start: 0.8458 (mm) cc_final: 0.8116 (mm) REVERT: F 315 HIS cc_start: 0.7906 (m-70) cc_final: 0.7361 (m90) REVERT: F 357 GLU cc_start: 0.8094 (tm-30) cc_final: 0.7649 (tm-30) REVERT: F 360 ARG cc_start: 0.6849 (mtt180) cc_final: 0.6039 (mtt180) REVERT: F 397 TRP cc_start: 0.7789 (m-10) cc_final: 0.7347 (m-10) outliers start: 1 outliers final: 1 residues processed: 633 average time/residue: 0.3002 time to fit residues: 294.8382 Evaluate side-chains 531 residues out of total 2333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 530 time to evaluate : 2.460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 14 optimal weight: 10.0000 chunk 187 optimal weight: 50.0000 chunk 126 optimal weight: 50.0000 chunk 239 optimal weight: 0.1980 chunk 249 optimal weight: 9.9990 chunk 49 optimal weight: 0.6980 chunk 43 optimal weight: 9.9990 chunk 154 optimal weight: 20.0000 chunk 116 optimal weight: 8.9990 chunk 80 optimal weight: 7.9990 chunk 9 optimal weight: 20.0000 overall best weight: 5.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 192 GLN ** A 323 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 212 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 456 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 121 ASN ** E 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 337 ASN ** F 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.132827 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.106237 restraints weight = 64132.679| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.109843 restraints weight = 38455.629| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.112379 restraints weight = 26592.522| |-----------------------------------------------------------------------------| r_work (final): 0.3761 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7296 moved from start: 0.4529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 21458 Z= 0.162 Angle : 0.733 12.534 29192 Z= 0.369 Chirality : 0.048 0.259 3146 Planarity : 0.006 0.103 3837 Dihedral : 6.147 35.635 2886 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 18.08 Ramachandran Plot: Outliers : 0.04 % Allowed : 10.84 % Favored : 89.13 % Rotamer: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.08 % Twisted Proline : 0.56 % Twisted General : 0.04 % 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: -3.22 (0.15), residues: 2658 helix: -1.90 (0.29), residues: 237 sheet: -1.56 (0.20), residues: 605 loop : -2.54 (0.14), residues: 1816 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.002 TRP C 308 HIS 0.012 0.002 HIS F 35 PHE 0.036 0.002 PHE D 257 TYR 0.030 0.002 TYR F 457 ARG 0.005 0.001 ARG E 334 Details of bonding type rmsd hydrogen bonds : bond 0.03438 ( 337) hydrogen bonds : angle 7.10458 ( 870) SS BOND : bond 0.00157 ( 1) SS BOND : angle 0.27172 ( 2) covalent geometry : bond 0.00362 (21457) covalent geometry : angle 0.73273 (29190) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5316 Ramachandran restraints generated. 2658 Oldfield, 0 Emsley, 2658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5316 Ramachandran restraints generated. 2658 Oldfield, 0 Emsley, 2658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 648 residues out of total 2333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 648 time to evaluate : 2.187 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 TYR cc_start: 0.8348 (m-80) cc_final: 0.8048 (m-80) REVERT: A 97 TRP cc_start: 0.8022 (m100) cc_final: 0.7801 (m100) REVERT: A 165 TRP cc_start: 0.8868 (m100) cc_final: 0.8464 (m100) REVERT: A 247 ARG cc_start: 0.8502 (ptt180) cc_final: 0.8055 (ptp-170) REVERT: A 257 PHE cc_start: 0.8889 (t80) cc_final: 0.8655 (t80) REVERT: A 288 VAL cc_start: 0.9138 (m) cc_final: 0.8924 (m) REVERT: A 371 PHE cc_start: 0.8345 (m-80) cc_final: 0.7524 (m-80) REVERT: A 389 MET cc_start: 0.8878 (ttt) cc_final: 0.8369 (tmm) REVERT: A 412 THR cc_start: 0.9300 (t) cc_final: 0.8953 (t) REVERT: B 26 TYR cc_start: 0.8339 (m-80) cc_final: 0.7922 (m-80) REVERT: B 32 ILE cc_start: 0.9257 (mp) cc_final: 0.9027 (mp) REVERT: B 61 LYS cc_start: 0.8194 (tttt) cc_final: 0.7792 (ttpt) REVERT: B 67 TYR cc_start: 0.8188 (m-80) cc_final: 0.7731 (m-80) REVERT: B 68 ARG cc_start: 0.8750 (mmp-170) cc_final: 0.7963 (mmp-170) REVERT: B 74 LEU cc_start: 0.8969 (tp) cc_final: 0.8566 (tp) REVERT: B 149 GLN cc_start: 0.7783 (mp10) cc_final: 0.7570 (mp10) REVERT: B 186 LEU cc_start: 0.8653 (pp) cc_final: 0.7766 (pp) REVERT: B 204 MET cc_start: 0.9178 (mpp) cc_final: 0.8901 (mpp) REVERT: B 206 PHE cc_start: 0.9226 (m-10) cc_final: 0.8998 (m-80) REVERT: B 210 GLN cc_start: 0.9329 (mp10) cc_final: 0.9020 (mp10) REVERT: B 211 THR cc_start: 0.8994 (p) cc_final: 0.8642 (p) REVERT: B 219 ASP cc_start: 0.9081 (p0) cc_final: 0.8852 (p0) REVERT: B 220 ILE cc_start: 0.9695 (pt) cc_final: 0.9424 (pt) REVERT: B 233 MET cc_start: 0.8647 (mmt) cc_final: 0.7859 (mmt) REVERT: B 236 ASP cc_start: 0.8535 (t0) cc_final: 0.8203 (t70) REVERT: B 250 GLN cc_start: 0.8263 (tp40) cc_final: 0.7896 (tp40) REVERT: B 298 SER cc_start: 0.9032 (p) cc_final: 0.8728 (p) REVERT: B 301 GLN cc_start: 0.9104 (mp-120) cc_final: 0.8508 (mp10) REVERT: B 302 LEU cc_start: 0.9126 (pp) cc_final: 0.8797 (pp) REVERT: B 305 LYS cc_start: 0.9542 (mtmt) cc_final: 0.9183 (mtpt) REVERT: B 355 TYR cc_start: 0.7233 (m-80) cc_final: 0.6787 (m-80) REVERT: C 53 ARG cc_start: 0.7215 (mmt-90) cc_final: 0.6839 (ttt-90) REVERT: C 74 LEU cc_start: 0.8903 (tp) cc_final: 0.8366 (tp) REVERT: C 108 GLN cc_start: 0.8510 (tp-100) cc_final: 0.8055 (mm-40) REVERT: C 154 MET cc_start: 0.8868 (mmp) cc_final: 0.8616 (mmm) REVERT: C 201 PHE cc_start: 0.8472 (m-10) cc_final: 0.7809 (m-10) REVERT: C 204 MET cc_start: 0.8015 (ptp) cc_final: 0.7541 (ptp) REVERT: C 310 GLN cc_start: 0.8710 (tm-30) cc_final: 0.8393 (tm-30) REVERT: C 323 ASN cc_start: 0.6977 (m110) cc_final: 0.6513 (m110) REVERT: C 359 MET cc_start: 0.7787 (mmt) cc_final: 0.7513 (mmt) REVERT: C 383 MET cc_start: 0.8784 (mmt) cc_final: 0.8235 (mmt) REVERT: C 386 ILE cc_start: 0.9483 (pt) cc_final: 0.9263 (pt) REVERT: C 395 GLU cc_start: 0.9185 (tm-30) cc_final: 0.8882 (tm-30) REVERT: C 438 ASN cc_start: 0.9172 (m110) cc_final: 0.8934 (m110) REVERT: D 63 SER cc_start: 0.9367 (t) cc_final: 0.8971 (p) REVERT: D 117 HIS cc_start: 0.8377 (t-90) cc_final: 0.7653 (t-170) REVERT: D 120 LEU cc_start: 0.8320 (mt) cc_final: 0.7702 (pp) REVERT: D 184 LEU cc_start: 0.8184 (tp) cc_final: 0.7925 (tp) REVERT: D 197 VAL cc_start: 0.8240 (t) cc_final: 0.7822 (m) REVERT: D 326 PHE cc_start: 0.8040 (m-80) cc_final: 0.7759 (m-10) REVERT: D 355 TYR cc_start: 0.7912 (m-80) cc_final: 0.7568 (m-80) REVERT: D 361 HIS cc_start: 0.6281 (t70) cc_final: 0.5870 (t70) REVERT: D 364 GLU cc_start: 0.8838 (tm-30) cc_final: 0.8558 (tm-30) REVERT: D 397 TRP cc_start: 0.8697 (m-90) cc_final: 0.8264 (m100) REVERT: D 449 LYS cc_start: 0.8020 (mmtp) cc_final: 0.7590 (mmmt) REVERT: E 41 LEU cc_start: 0.8171 (tt) cc_final: 0.7399 (tt) REVERT: E 62 VAL cc_start: 0.8810 (t) cc_final: 0.8416 (t) REVERT: E 66 GLN cc_start: 0.6876 (mt0) cc_final: 0.6122 (mt0) REVERT: E 120 LEU cc_start: 0.8752 (mt) cc_final: 0.8139 (mt) REVERT: E 196 MET cc_start: 0.8926 (mpp) cc_final: 0.8422 (mpp) REVERT: E 225 CYS cc_start: 0.8649 (m) cc_final: 0.8429 (m) REVERT: E 232 GLN cc_start: 0.8428 (mt0) cc_final: 0.8208 (tt0) REVERT: E 233 MET cc_start: 0.9284 (ptp) cc_final: 0.9008 (ptp) REVERT: E 249 GLU cc_start: 0.8902 (mp0) cc_final: 0.8391 (mp0) REVERT: E 290 THR cc_start: 0.8473 (m) cc_final: 0.8081 (m) REVERT: E 359 MET cc_start: 0.8523 (mmm) cc_final: 0.8283 (mmm) REVERT: E 364 GLU cc_start: 0.8135 (tp30) cc_final: 0.7745 (tp30) REVERT: E 397 TRP cc_start: 0.7543 (m100) cc_final: 0.7293 (m100) REVERT: E 411 ASP cc_start: 0.8074 (t0) cc_final: 0.7855 (t70) REVERT: E 457 TYR cc_start: 0.8705 (m-80) cc_final: 0.8090 (m-80) REVERT: E 461 ARG cc_start: 0.8991 (ptp90) cc_final: 0.8706 (ptt-90) REVERT: F 65 TYR cc_start: 0.9140 (m-10) cc_final: 0.8874 (m-10) REVERT: F 103 GLU cc_start: 0.7431 (tp30) cc_final: 0.6939 (tp30) REVERT: F 149 GLN cc_start: 0.8755 (pt0) cc_final: 0.8423 (pt0) REVERT: F 165 TRP cc_start: 0.8936 (m100) cc_final: 0.8280 (m100) REVERT: F 192 GLN cc_start: 0.8947 (mt0) cc_final: 0.8673 (mt0) REVERT: F 193 ASP cc_start: 0.9009 (t0) cc_final: 0.8781 (t0) REVERT: F 196 MET cc_start: 0.7390 (mmm) cc_final: 0.6805 (mmm) REVERT: F 204 MET cc_start: 0.8445 (mpp) cc_final: 0.8175 (mpp) REVERT: F 237 PRO cc_start: 0.9218 (Cg_endo) cc_final: 0.8794 (Cg_exo) REVERT: F 273 ILE cc_start: 0.8511 (mm) cc_final: 0.8170 (mm) REVERT: F 315 HIS cc_start: 0.7876 (m-70) cc_final: 0.7347 (m90) REVERT: F 355 TYR cc_start: 0.8602 (m-80) cc_final: 0.8039 (m-80) REVERT: F 359 MET cc_start: 0.8247 (tpp) cc_final: 0.7733 (mmm) REVERT: F 397 TRP cc_start: 0.7814 (m-10) cc_final: 0.7389 (m-10) outliers start: 0 outliers final: 0 residues processed: 648 average time/residue: 0.3107 time to fit residues: 309.1492 Evaluate side-chains 543 residues out of total 2333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 543 time to evaluate : 2.143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 53.4267 > 50: distance: 6 - 8: 12.117 distance: 8 - 9: 10.224 distance: 9 - 10: 23.984 distance: 9 - 12: 11.955 distance: 10 - 11: 35.416 distance: 10 - 16: 12.837 distance: 12 - 13: 22.175 distance: 13 - 14: 19.736 distance: 13 - 15: 17.161 distance: 16 - 17: 11.210 distance: 17 - 18: 12.455 distance: 17 - 20: 10.020 distance: 18 - 19: 17.377 distance: 18 - 22: 19.899 distance: 20 - 21: 47.466 distance: 22 - 23: 13.138 distance: 22 - 28: 13.619 distance: 23 - 24: 8.671 distance: 23 - 26: 18.393 distance: 24 - 25: 18.044 distance: 24 - 29: 10.395 distance: 26 - 27: 9.820 distance: 27 - 28: 24.235 distance: 29 - 30: 12.922 distance: 29 - 35: 11.902 distance: 30 - 31: 18.513 distance: 30 - 33: 6.928 distance: 31 - 32: 15.887 distance: 31 - 36: 24.477 distance: 33 - 34: 15.203 distance: 34 - 35: 18.229 distance: 36 - 37: 6.243 distance: 36 - 42: 19.392 distance: 37 - 38: 13.602 distance: 37 - 40: 14.002 distance: 38 - 39: 13.039 distance: 38 - 43: 10.882 distance: 40 - 41: 17.009 distance: 41 - 42: 21.251 distance: 43 - 44: 18.820 distance: 44 - 45: 9.231 distance: 44 - 47: 8.318 distance: 45 - 46: 13.070 distance: 45 - 51: 21.509 distance: 47 - 48: 5.618 distance: 48 - 49: 10.015 distance: 48 - 50: 15.724 distance: 51 - 52: 30.998 distance: 52 - 53: 16.387 distance: 53 - 54: 21.584 distance: 53 - 55: 15.861 distance: 55 - 56: 16.991 distance: 56 - 57: 23.828 distance: 56 - 59: 11.293 distance: 57 - 58: 35.446 distance: 57 - 62: 16.898 distance: 59 - 60: 25.615 distance: 59 - 61: 39.786 distance: 62 - 63: 17.408 distance: 63 - 64: 10.754 distance: 63 - 66: 19.611 distance: 64 - 65: 49.584 distance: 64 - 70: 18.914 distance: 66 - 67: 28.113 distance: 67 - 68: 17.055 distance: 67 - 69: 44.854 distance: 70 - 71: 37.268 distance: 71 - 72: 21.897 distance: 71 - 74: 15.885 distance: 72 - 73: 21.734 distance: 72 - 79: 17.018 distance: 74 - 75: 17.363 distance: 75 - 76: 11.308 distance: 76 - 77: 14.911 distance: 76 - 78: 13.405