Starting phenix.real_space_refine on Sun Feb 18 05:01:44 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6l31_0816/02_2024/6l31_0816.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6l31_0816/02_2024/6l31_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6l31_0816/02_2024/6l31_0816.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6l31_0816/02_2024/6l31_0816.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6l31_0816/02_2024/6l31_0816.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6l31_0816/02_2024/6l31_0816.pdb" } 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 Residue "A GLU 103": "OE1" <-> "OE2" Residue "A GLU 299": "OE1" <-> "OE2" Residue "A GLU 357": "OE1" <-> "OE2" Residue "A GLU 429": "OE1" <-> "OE2" Residue "B TYR 26": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 249": "OE1" <-> "OE2" Residue "B ARG 414": "NH1" <-> "NH2" Residue "B GLU 443": "OE1" <-> "OE2" Residue "C ARG 414": "NH1" <-> "NH2" Residue "C TYR 415": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 40": "NH1" <-> "NH2" Residue "D PHE 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 247": "NH1" <-> "NH2" Residue "D GLU 249": "OE1" <-> "OE2" Residue "D GLU 262": "OE1" <-> "OE2" Residue "D GLU 429": "OE1" <-> "OE2" Residue "D GLU 453": "OE1" <-> "OE2" Residue "E GLU 249": "OE1" <-> "OE2" Residue "E GLU 395": "OE1" <-> "OE2" Residue "E GLU 410": "OE1" <-> "OE2" Residue "F GLU 127": "OE1" <-> "OE2" Residue "F GLU 163": "OE1" <-> "OE2" Residue "F GLU 249": "OE1" <-> "OE2" Residue "F GLU 363": "OE1" <-> "OE2" Residue "F GLU 381": "OE1" <-> "OE2" Residue "F GLU 410": "OE1" <-> "OE2" Time to flip residues: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/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: 10.66, per 1000 atoms: 0.51 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 - 3.50 Amino acid : False - 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: 7.43 Conformation dependent library (CDL) restraints added in 3.9 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: 2.03 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: 5.78 Time building geometry restraints manager: 8.09 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: 98.19 - 105.58: 672 105.58 - 112.97: 10929 112.97 - 120.37: 8527 120.37 - 127.76: 8818 127.76 - 135.15: 244 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 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: 3.920 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: 16.930 Check model and map are aligned: 0.330 Set scattering table: 0.180 Process input model: 52.740 Find NCS groups from input model: 1.590 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 78.570 ------------------------------------------------------------------------------- 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 21457 Z= 0.465 Angle : 1.259 22.581 29190 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 *********************** 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 fitting. rotamer outliers: 53 poor density : 685 time to evaluate : 2.404 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: 0.3430 time to fit residues: 386.4008 Evaluate side-chains 568 residues out of total 2333 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 546 time to evaluate : 2.316 ------------------------------------------------------------------------------- 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: 20.0000 chunk 200 optimal weight: 5.9990 chunk 111 optimal weight: 20.0000 chunk 68 optimal weight: 0.8980 chunk 134 optimal weight: 7.9990 chunk 106 optimal weight: 0.9990 chunk 206 optimal weight: 20.0000 chunk 80 optimal weight: 7.9990 chunk 125 optimal weight: 0.9990 chunk 154 optimal weight: 8.9990 chunk 239 optimal weight: 0.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 93 GLN ** A 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 250 GLN A 289 ASN A 313 GLN ** 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 55 ASN B 212 ASN ** B 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 372 GLN B 419 GLN C 78 ASN C 139 ASN ** C 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 212 ASN ** C 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 323 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 387 HIS C 419 GLN D 108 GLN D 139 ASN D 151 GLN ** D 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 352 ASN ** D 466 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 139 ASN E 212 ASN E 337 ASN ** E 417 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 139 ASN F 149 GLN ** F 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 289 ASN F 301 GLN F 316 ASN F 317 ASN F 337 ASN ** F 361 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 387 HIS Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7180 moved from start: 0.2305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.081 21457 Z= 0.215 Angle : 0.759 12.568 29190 Z= 0.389 Chirality : 0.049 0.283 3146 Planarity : 0.007 0.108 3837 Dihedral : 7.178 45.276 2886 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 19.03 Ramachandran Plot: Outliers : 0.15 % Allowed : 9.41 % Favored : 90.44 % Rotamer: Outliers : 0.26 % Allowed : 5.49 % Favored : 94.26 % 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: -3.86 (0.14), residues: 2658 helix: -3.19 (0.24), residues: 235 sheet: -1.87 (0.19), residues: 597 loop : -2.92 (0.13), residues: 1826 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP D 165 HIS 0.008 0.001 HIS B 35 PHE 0.031 0.002 PHE A 88 TYR 0.023 0.002 TYR E 230 ARG 0.012 0.001 ARG E 40 *********************** 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 708 residues out of total 2333 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 702 time to evaluate : 2.317 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: A 34 TYR cc_start: 0.8372 (m-80) cc_final: 0.8160 (m-80) REVERT: A 93 GLN cc_start: 0.6254 (OUTLIER) cc_final: 0.5973 (mm-40) REVERT: A 223 THR cc_start: 0.8134 (t) cc_final: 0.7843 (t) REVERT: A 366 ASP cc_start: 0.7926 (t0) cc_final: 0.7041 (t0) REVERT: A 369 PHE cc_start: 0.8788 (m-80) cc_final: 0.8562 (m-80) REVERT: A 371 PHE cc_start: 0.8594 (m-80) cc_final: 0.8007 (m-80) REVERT: A 389 MET cc_start: 0.8835 (ttt) cc_final: 0.8073 (ppp) REVERT: A 449 LYS cc_start: 0.9085 (mmtm) cc_final: 0.8595 (mptt) REVERT: A 450 PHE cc_start: 0.8727 (m-10) cc_final: 0.8450 (m-10) REVERT: B 26 TYR cc_start: 0.8168 (m-80) cc_final: 0.7868 (m-80) REVERT: B 74 LEU cc_start: 0.9069 (tp) cc_final: 0.8702 (tp) REVERT: B 151 GLN cc_start: 0.9108 (mt0) cc_final: 0.8858 (mt0) REVERT: B 210 GLN cc_start: 0.9279 (mp10) cc_final: 0.8892 (mp10) REVERT: B 219 ASP cc_start: 0.9197 (p0) cc_final: 0.8910 (p0) REVERT: B 220 ILE cc_start: 0.9695 (pt) cc_final: 0.9420 (pt) REVERT: B 246 LEU cc_start: 0.9445 (mt) cc_final: 0.9219 (mt) REVERT: B 301 GLN cc_start: 0.9071 (mp-120) cc_final: 0.8722 (mp10) REVERT: B 302 LEU cc_start: 0.8812 (pp) cc_final: 0.8529 (pp) REVERT: B 305 LYS cc_start: 0.9387 (mtpt) cc_final: 0.9035 (mtpt) REVERT: B 357 GLU cc_start: 0.8787 (mm-30) cc_final: 0.8561 (mp0) REVERT: B 374 CYS cc_start: 0.8857 (m) cc_final: 0.8582 (m) REVERT: B 461 ARG cc_start: 0.9220 (ttp-170) cc_final: 0.8480 (mtm110) REVERT: C 49 PHE cc_start: 0.8658 (t80) cc_final: 0.8193 (t80) REVERT: C 51 ILE cc_start: 0.8489 (tt) cc_final: 0.8209 (tt) REVERT: C 53 ARG cc_start: 0.7073 (mmt-90) cc_final: 0.6763 (ttt-90) REVERT: C 108 GLN cc_start: 0.8542 (mm-40) cc_final: 0.8012 (mm-40) REVERT: C 201 PHE cc_start: 0.8526 (m-10) cc_final: 0.7863 (m-80) REVERT: C 232 GLN cc_start: 0.8614 (mt0) cc_final: 0.8363 (mm-40) REVERT: C 233 MET cc_start: 0.9108 (mtt) cc_final: 0.8866 (mmt) REVERT: C 310 GLN cc_start: 0.8935 (tm-30) cc_final: 0.8589 (tm-30) REVERT: C 319 ILE cc_start: 0.8852 (mp) cc_final: 0.8650 (mp) REVERT: C 359 MET cc_start: 0.8309 (mmm) cc_final: 0.8086 (mmt) REVERT: C 395 GLU cc_start: 0.9035 (tm-30) cc_final: 0.8786 (tm-30) REVERT: C 457 TYR cc_start: 0.9267 (m-80) cc_final: 0.8676 (m-80) REVERT: C 463 PHE cc_start: 0.8817 (t80) cc_final: 0.8597 (t80) REVERT: D 120 LEU cc_start: 0.8497 (mt) cc_final: 0.8163 (mt) REVERT: D 193 ASP cc_start: 0.7048 (t0) cc_final: 0.6694 (t0) REVERT: D 206 PHE cc_start: 0.8143 (m-80) cc_final: 0.7786 (m-80) REVERT: D 219 ASP cc_start: 0.9139 (p0) cc_final: 0.8903 (p0) REVERT: D 257 PHE cc_start: 0.7804 (m-10) cc_final: 0.7517 (m-10) REVERT: D 339 THR cc_start: 0.7447 (p) cc_final: 0.7023 (p) REVERT: D 355 TYR cc_start: 0.7911 (m-80) cc_final: 0.7668 (m-80) REVERT: D 361 HIS cc_start: 0.6990 (t-90) cc_final: 0.6641 (t-170) REVERT: D 397 TRP cc_start: 0.8852 (m-90) cc_final: 0.8621 (m100) REVERT: D 449 LYS cc_start: 0.7812 (mmtp) cc_final: 0.7455 (mmmt) REVERT: E 41 LEU cc_start: 0.8363 (tt) cc_final: 0.7627 (tt) REVERT: E 66 GLN cc_start: 0.6176 (mt0) cc_final: 0.5197 (mt0) REVERT: E 120 LEU cc_start: 0.8781 (mt) cc_final: 0.8329 (mt) REVERT: E 196 MET cc_start: 0.8804 (mpp) cc_final: 0.8376 (mmt) REVERT: E 232 GLN cc_start: 0.8194 (mt0) cc_final: 0.7605 (tp-100) REVERT: E 233 MET cc_start: 0.9389 (mtm) cc_final: 0.8861 (mtm) REVERT: E 254 ARG cc_start: 0.9050 (mtp85) cc_final: 0.8621 (ttm-80) REVERT: E 303 PHE cc_start: 0.9007 (m-80) cc_final: 0.8460 (m-80) REVERT: E 326 PHE cc_start: 0.8967 (m-80) cc_final: 0.8306 (m-80) REVERT: E 371 PHE cc_start: 0.9538 (m-80) cc_final: 0.9327 (m-80) REVERT: E 397 TRP cc_start: 0.6326 (m100) cc_final: 0.6122 (m100) REVERT: E 411 ASP cc_start: 0.8044 (t0) cc_final: 0.7778 (t70) REVERT: E 450 PHE cc_start: 0.8301 (m-80) cc_final: 0.8092 (m-80) REVERT: F 65 TYR cc_start: 0.9115 (m-80) cc_final: 0.8773 (m-10) REVERT: F 103 GLU cc_start: 0.7793 (tp30) cc_final: 0.7396 (tp30) REVERT: F 106 ARG cc_start: 0.8337 (mmm160) cc_final: 0.8100 (mmm-85) REVERT: F 125 ASP cc_start: 0.9119 (p0) cc_final: 0.8755 (p0) REVERT: F 148 LYS cc_start: 0.8750 (ptmm) cc_final: 0.8467 (ptmm) REVERT: F 151 GLN cc_start: 0.8084 (tt0) cc_final: 0.7327 (tt0) REVERT: F 165 TRP cc_start: 0.8914 (m100) cc_final: 0.8168 (m100) REVERT: F 185 GLU cc_start: 0.8191 (tp30) cc_final: 0.7878 (mt-10) REVERT: F 196 MET cc_start: 0.7876 (mmm) cc_final: 0.7197 (mmm) REVERT: F 204 MET cc_start: 0.8309 (mpp) cc_final: 0.7721 (mpp) REVERT: F 230 TYR cc_start: 0.8683 (m-80) cc_final: 0.8320 (m-80) REVERT: F 273 ILE cc_start: 0.8103 (mm) cc_final: 0.7693 (mm) REVERT: F 302 LEU cc_start: 0.8997 (mt) cc_final: 0.8185 (mt) REVERT: F 315 HIS cc_start: 0.7642 (m90) cc_final: 0.7024 (m90) REVERT: F 334 ARG cc_start: 0.9127 (mtt90) cc_final: 0.8739 (mtt-85) REVERT: F 338 MET cc_start: 0.8258 (mpp) cc_final: 0.8030 (ptp) REVERT: F 357 GLU cc_start: 0.8265 (tm-30) cc_final: 0.7964 (tm-30) REVERT: F 359 MET cc_start: 0.8249 (tpp) cc_final: 0.7822 (tpp) REVERT: F 450 PHE cc_start: 0.8790 (m-80) cc_final: 0.8416 (m-80) outliers start: 6 outliers final: 1 residues processed: 707 average time/residue: 0.3355 time to fit residues: 354.8015 Evaluate side-chains 555 residues out of total 2333 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 553 time to evaluate : 2.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 133 optimal weight: 6.9990 chunk 74 optimal weight: 20.0000 chunk 199 optimal weight: 8.9990 chunk 163 optimal weight: 20.0000 chunk 66 optimal weight: 7.9990 chunk 240 optimal weight: 20.0000 chunk 259 optimal weight: 4.9990 chunk 213 optimal weight: 4.9990 chunk 238 optimal weight: 6.9990 chunk 81 optimal weight: 20.0000 chunk 192 optimal weight: 30.0000 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 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 212 ASN A 255 HIS A 258 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** ** B 212 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 372 GLN ** C 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 255 HIS C 258 ASN ** C 323 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 387 HIS C 417 GLN D 255 HIS ** D 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 466 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 212 ASN E 255 HIS E 258 ASN E 313 GLN ** E 417 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 149 GLN ** F 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 212 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 255 HIS F 301 GLN F 337 ASN ** F 361 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7227 moved from start: 0.2978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 21457 Z= 0.264 Angle : 0.752 11.737 29190 Z= 0.387 Chirality : 0.048 0.315 3146 Planarity : 0.007 0.109 3837 Dihedral : 6.862 42.230 2886 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 22.85 Ramachandran Plot: Outliers : 0.11 % Allowed : 11.17 % Favored : 88.71 % Rotamer: Outliers : 0.13 % Allowed : 6.34 % Favored : 93.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.08 % Twisted Proline : 2.22 % 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: -3.59 (0.15), residues: 2658 helix: -2.65 (0.27), residues: 236 sheet: -1.81 (0.19), residues: 618 loop : -2.73 (0.13), residues: 1804 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP F 308 HIS 0.013 0.002 HIS C 255 PHE 0.025 0.002 PHE A 369 TYR 0.024 0.002 TYR B 365 ARG 0.009 0.001 ARG A 334 *********************** 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 fitting. rotamer outliers: 3 poor density : 655 time to evaluate : 2.349 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: A 34 TYR cc_start: 0.8505 (m-80) cc_final: 0.8236 (m-80) REVERT: A 148 LYS cc_start: 0.8364 (ptpt) cc_final: 0.7974 (ptpp) REVERT: A 195 ASP cc_start: 0.8094 (t70) cc_final: 0.7178 (t0) REVERT: A 196 MET cc_start: 0.8039 (mtp) cc_final: 0.7390 (mtp) REVERT: A 223 THR cc_start: 0.8165 (t) cc_final: 0.7912 (t) REVERT: A 257 PHE cc_start: 0.8511 (t80) cc_final: 0.7943 (t80) REVERT: A 288 VAL cc_start: 0.9005 (m) cc_final: 0.8648 (m) REVERT: A 366 ASP cc_start: 0.7860 (t0) cc_final: 0.7180 (t0) REVERT: A 371 PHE cc_start: 0.8500 (m-80) cc_final: 0.7812 (m-80) REVERT: A 381 GLU cc_start: 0.9183 (mp0) cc_final: 0.8944 (mp0) REVERT: A 389 MET cc_start: 0.8933 (ttt) cc_final: 0.8520 (tmm) REVERT: B 26 TYR cc_start: 0.8381 (m-80) cc_final: 0.7922 (m-80) REVERT: B 74 LEU cc_start: 0.9041 (tp) cc_final: 0.8684 (tp) REVERT: B 126 VAL cc_start: 0.9012 (p) cc_final: 0.8781 (p) REVERT: B 210 GLN cc_start: 0.9174 (mp10) cc_final: 0.8904 (mp10) REVERT: B 211 THR cc_start: 0.8977 (p) cc_final: 0.8582 (p) REVERT: B 220 ILE cc_start: 0.9729 (pt) cc_final: 0.9467 (pt) REVERT: B 236 ASP cc_start: 0.8596 (t70) cc_final: 0.8214 (t70) REVERT: B 262 GLU cc_start: 0.7396 (mt-10) cc_final: 0.6760 (mt-10) REVERT: B 301 GLN cc_start: 0.8954 (mp-120) cc_final: 0.8597 (mp10) REVERT: B 302 LEU cc_start: 0.8763 (pp) cc_final: 0.8473 (pp) REVERT: B 305 LYS cc_start: 0.9359 (mtpt) cc_final: 0.8968 (mtmt) REVERT: B 461 ARG cc_start: 0.9038 (ttp-110) cc_final: 0.8571 (mtm110) REVERT: C 53 ARG cc_start: 0.7168 (mmt-90) cc_final: 0.6802 (ttt-90) REVERT: C 66 GLN cc_start: 0.8449 (mt0) cc_final: 0.7888 (mt0) REVERT: C 68 ARG cc_start: 0.8585 (mmt-90) cc_final: 0.8291 (mmt-90) REVERT: C 108 GLN cc_start: 0.8476 (mm-40) cc_final: 0.7988 (mm-40) REVERT: C 154 MET cc_start: 0.8832 (mmp) cc_final: 0.8627 (mmm) REVERT: C 232 GLN cc_start: 0.8717 (mt0) cc_final: 0.8419 (mm-40) REVERT: C 310 GLN cc_start: 0.8878 (tm-30) cc_final: 0.8508 (tm-30) REVERT: C 383 MET cc_start: 0.8740 (mmt) cc_final: 0.8288 (mmt) REVERT: C 385 TYR cc_start: 0.8600 (t80) cc_final: 0.8236 (t80) REVERT: C 386 ILE cc_start: 0.9626 (pt) cc_final: 0.9349 (pt) REVERT: C 395 GLU cc_start: 0.9109 (tm-30) cc_final: 0.8865 (tm-30) REVERT: C 457 TYR cc_start: 0.9309 (m-80) cc_final: 0.8730 (m-80) REVERT: C 461 ARG cc_start: 0.8849 (ptp90) cc_final: 0.8612 (ptp90) REVERT: D 63 SER cc_start: 0.9289 (t) cc_final: 0.8684 (p) REVERT: D 117 HIS cc_start: 0.8491 (t-90) cc_final: 0.7799 (t-170) REVERT: D 120 LEU cc_start: 0.8479 (mt) cc_final: 0.8118 (pp) REVERT: D 206 PHE cc_start: 0.8157 (m-80) cc_final: 0.7891 (m-80) REVERT: D 226 LYS cc_start: 0.7895 (mtpt) cc_final: 0.7545 (mtpp) REVERT: D 303 PHE cc_start: 0.8842 (m-80) cc_final: 0.8566 (m-80) REVERT: D 326 PHE cc_start: 0.8130 (m-80) cc_final: 0.7845 (m-10) REVERT: D 355 TYR cc_start: 0.8040 (m-80) cc_final: 0.7682 (m-80) REVERT: D 361 HIS cc_start: 0.6729 (t-90) cc_final: 0.6316 (t70) REVERT: D 397 TRP cc_start: 0.8853 (m-90) cc_final: 0.8614 (m100) REVERT: D 449 LYS cc_start: 0.7788 (mmtp) cc_final: 0.7462 (mmmt) REVERT: D 459 LEU cc_start: 0.8944 (OUTLIER) cc_final: 0.8588 (pp) REVERT: E 41 LEU cc_start: 0.7806 (tt) cc_final: 0.7585 (tt) REVERT: E 66 GLN cc_start: 0.6220 (mt0) cc_final: 0.5816 (mt0) REVERT: E 120 LEU cc_start: 0.8949 (mt) cc_final: 0.8304 (mt) REVERT: E 146 ASP cc_start: 0.8918 (p0) cc_final: 0.8585 (p0) REVERT: E 150 THR cc_start: 0.8937 (m) cc_final: 0.8626 (m) REVERT: E 196 MET cc_start: 0.8703 (mpp) cc_final: 0.8380 (mpp) REVERT: E 232 GLN cc_start: 0.8306 (mt0) cc_final: 0.8096 (mt0) REVERT: E 233 MET cc_start: 0.9385 (mtm) cc_final: 0.8808 (mtt) REVERT: E 249 GLU cc_start: 0.9176 (mp0) cc_final: 0.8849 (mp0) REVERT: E 254 ARG cc_start: 0.9081 (mtp85) cc_final: 0.8813 (ttm-80) REVERT: E 257 PHE cc_start: 0.8832 (m-10) cc_final: 0.8571 (m-80) REVERT: E 296 VAL cc_start: 0.9446 (p) cc_final: 0.8982 (p) REVERT: E 326 PHE cc_start: 0.8954 (m-80) cc_final: 0.8265 (m-80) REVERT: E 352 ASN cc_start: 0.9130 (p0) cc_final: 0.8884 (p0) REVERT: E 411 ASP cc_start: 0.7902 (t0) cc_final: 0.7671 (t70) REVERT: E 450 PHE cc_start: 0.8320 (m-80) cc_final: 0.8097 (m-80) REVERT: E 461 ARG cc_start: 0.8993 (ptp90) cc_final: 0.8572 (ptp90) REVERT: F 103 GLU cc_start: 0.7610 (tp30) cc_final: 0.7224 (tp30) REVERT: F 106 ARG cc_start: 0.8338 (mmm160) cc_final: 0.8066 (mmm-85) REVERT: F 125 ASP cc_start: 0.9068 (p0) cc_final: 0.8725 (p0) REVERT: F 149 GLN cc_start: 0.8424 (pt0) cc_final: 0.7984 (pt0) REVERT: F 150 THR cc_start: 0.9314 (m) cc_final: 0.8021 (m) REVERT: F 151 GLN cc_start: 0.8110 (tt0) cc_final: 0.6744 (tt0) REVERT: F 165 TRP cc_start: 0.8902 (m100) cc_final: 0.8330 (m100) REVERT: F 185 GLU cc_start: 0.8205 (tp30) cc_final: 0.7786 (mt-10) REVERT: F 196 MET cc_start: 0.8031 (mmm) cc_final: 0.7376 (mmm) REVERT: F 204 MET cc_start: 0.8483 (mpp) cc_final: 0.8140 (mpp) REVERT: F 230 TYR cc_start: 0.8775 (m-80) cc_final: 0.8486 (m-80) REVERT: F 249 GLU cc_start: 0.8639 (mp0) cc_final: 0.8322 (mp0) REVERT: F 273 ILE cc_start: 0.8189 (mm) cc_final: 0.7808 (mm) REVERT: F 302 LEU cc_start: 0.8926 (mt) cc_final: 0.8068 (mt) REVERT: F 334 ARG cc_start: 0.9160 (mtt90) cc_final: 0.8586 (mtt90) REVERT: F 356 LYS cc_start: 0.9270 (mmpt) cc_final: 0.9066 (mmmt) REVERT: F 359 MET cc_start: 0.8208 (tpp) cc_final: 0.7787 (tpp) outliers start: 3 outliers final: 1 residues processed: 655 average time/residue: 0.3125 time to fit residues: 313.5908 Evaluate side-chains 521 residues out of total 2333 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 519 time to evaluate : 2.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 237 optimal weight: 40.0000 chunk 180 optimal weight: 6.9990 chunk 124 optimal weight: 20.0000 chunk 26 optimal weight: 20.0000 chunk 114 optimal weight: 20.0000 chunk 161 optimal weight: 0.8980 chunk 241 optimal weight: 20.0000 chunk 255 optimal weight: 6.9990 chunk 125 optimal weight: 7.9990 chunk 228 optimal weight: 20.0000 chunk 68 optimal weight: 0.0370 overall best weight: 4.5864 ------------------------------------------------------------------------------- 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 66 GLN ** A 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 323 ASN ** A 337 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 361 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 406 ASN ** B 212 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 372 GLN ** C 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 323 ASN D 258 ASN ** D 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 466 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 212 ASN ** E 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 372 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 417 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 212 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 301 GLN F 337 ASN F 361 HIS ** F 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7195 moved from start: 0.3431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 21457 Z= 0.225 Angle : 0.723 12.051 29190 Z= 0.366 Chirality : 0.048 0.341 3146 Planarity : 0.006 0.105 3837 Dihedral : 6.506 39.090 2886 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 21.93 Ramachandran Plot: Outliers : 0.08 % Allowed : 10.05 % Favored : 89.88 % Rotamer: Outliers : 0.09 % Allowed : 4.63 % Favored : 95.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.08 % Twisted Proline : 1.11 % 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: -3.43 (0.15), residues: 2658 helix: -2.39 (0.28), residues: 230 sheet: -1.64 (0.20), residues: 586 loop : -2.66 (0.13), residues: 1842 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP F 308 HIS 0.008 0.001 HIS F 35 PHE 0.035 0.002 PHE A 88 TYR 0.030 0.002 TYR C 365 ARG 0.005 0.001 ARG A 334 *********************** 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 660 residues out of total 2333 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 658 time to evaluate : 2.311 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: A 34 TYR cc_start: 0.8422 (m-80) cc_final: 0.8113 (m-80) REVERT: A 148 LYS cc_start: 0.8245 (ptpt) cc_final: 0.7953 (ptpp) REVERT: A 247 ARG cc_start: 0.8162 (ptt180) cc_final: 0.7492 (ptp-170) REVERT: A 257 PHE cc_start: 0.8661 (t80) cc_final: 0.8073 (t80) REVERT: A 288 VAL cc_start: 0.8975 (OUTLIER) cc_final: 0.8675 (m) REVERT: A 334 ARG cc_start: 0.9226 (mtt90) cc_final: 0.8548 (mpp80) REVERT: A 366 ASP cc_start: 0.7786 (t0) cc_final: 0.7256 (t0) REVERT: A 368 GLN cc_start: 0.8828 (mt0) cc_final: 0.8523 (mt0) REVERT: A 371 PHE cc_start: 0.8358 (m-80) cc_final: 0.7470 (m-80) REVERT: A 381 GLU cc_start: 0.9161 (mp0) cc_final: 0.8948 (mp0) REVERT: A 389 MET cc_start: 0.8863 (ttt) cc_final: 0.8458 (tmm) REVERT: B 26 TYR cc_start: 0.8292 (m-80) cc_final: 0.7883 (m-80) REVERT: B 68 ARG cc_start: 0.8877 (mmp-170) cc_final: 0.8573 (mmp-170) REVERT: B 74 LEU cc_start: 0.8988 (tp) cc_final: 0.8622 (tp) REVERT: B 210 GLN cc_start: 0.9263 (mp10) cc_final: 0.8871 (mp10) REVERT: B 211 THR cc_start: 0.8888 (p) cc_final: 0.8516 (p) REVERT: B 219 ASP cc_start: 0.9019 (p0) cc_final: 0.8813 (p0) REVERT: B 220 ILE cc_start: 0.9776 (pt) cc_final: 0.9530 (pt) REVERT: B 236 ASP cc_start: 0.8535 (t70) cc_final: 0.8276 (t70) REVERT: B 251 MET cc_start: 0.8978 (tpt) cc_final: 0.8577 (tpt) REVERT: B 262 GLU cc_start: 0.7438 (mt-10) cc_final: 0.6708 (mt-10) REVERT: B 301 GLN cc_start: 0.9005 (mp-120) cc_final: 0.8495 (mp10) REVERT: B 302 LEU cc_start: 0.8902 (pp) cc_final: 0.8643 (pp) REVERT: B 328 THR cc_start: 0.9118 (m) cc_final: 0.8290 (p) REVERT: C 51 ILE cc_start: 0.8469 (tt) cc_final: 0.8254 (tt) REVERT: C 53 ARG cc_start: 0.7124 (mmt-90) cc_final: 0.6755 (ttt-90) REVERT: C 65 TYR cc_start: 0.9491 (m-80) cc_final: 0.9228 (m-10) REVERT: C 66 GLN cc_start: 0.8392 (mt0) cc_final: 0.7779 (mt0) REVERT: C 68 ARG cc_start: 0.8726 (mmt-90) cc_final: 0.8480 (mmt-90) REVERT: C 108 GLN cc_start: 0.8395 (mm-40) cc_final: 0.7860 (mm-40) REVERT: C 204 MET cc_start: 0.7420 (pmm) cc_final: 0.6355 (pmm) REVERT: C 232 GLN cc_start: 0.8766 (mt0) cc_final: 0.8479 (mm-40) REVERT: C 310 GLN cc_start: 0.8879 (tm-30) cc_final: 0.8515 (tm-30) REVERT: C 359 MET cc_start: 0.8377 (mmt) cc_final: 0.7899 (mmt) REVERT: C 383 MET cc_start: 0.8738 (mmt) cc_final: 0.8262 (mmt) REVERT: C 385 TYR cc_start: 0.8657 (t80) cc_final: 0.8338 (t80) REVERT: C 386 ILE cc_start: 0.9569 (pt) cc_final: 0.9315 (pt) REVERT: C 395 GLU cc_start: 0.9135 (tm-30) cc_final: 0.8860 (tm-30) REVERT: C 425 LYS cc_start: 0.7991 (pttm) cc_final: 0.7706 (mmtt) REVERT: D 48 TYR cc_start: 0.7826 (m-80) cc_final: 0.7246 (m-80) REVERT: D 63 SER cc_start: 0.9321 (t) cc_final: 0.8718 (p) REVERT: D 70 PHE cc_start: 0.8968 (m-80) cc_final: 0.8718 (m-80) REVERT: D 117 HIS cc_start: 0.8521 (t-90) cc_final: 0.7858 (t-170) REVERT: D 120 LEU cc_start: 0.8492 (mt) cc_final: 0.8031 (pp) REVERT: D 184 LEU cc_start: 0.8046 (tp) cc_final: 0.7781 (tp) REVERT: D 197 VAL cc_start: 0.8494 (t) cc_final: 0.8184 (m) REVERT: D 204 MET cc_start: 0.8311 (mpp) cc_final: 0.8022 (mpp) REVERT: D 206 PHE cc_start: 0.8028 (m-80) cc_final: 0.7809 (m-80) REVERT: D 219 ASP cc_start: 0.9260 (p0) cc_final: 0.9039 (p0) REVERT: D 233 MET cc_start: 0.8853 (mmp) cc_final: 0.8639 (mmm) REVERT: D 303 PHE cc_start: 0.8817 (m-80) cc_final: 0.8553 (m-80) REVERT: D 355 TYR cc_start: 0.7843 (m-80) cc_final: 0.7514 (m-80) REVERT: D 361 HIS cc_start: 0.6739 (t-90) cc_final: 0.6441 (t70) REVERT: D 397 TRP cc_start: 0.8858 (m-90) cc_final: 0.8586 (m100) REVERT: D 449 LYS cc_start: 0.7781 (mmtp) cc_final: 0.7437 (mmmt) REVERT: E 41 LEU cc_start: 0.7842 (tt) cc_final: 0.7182 (tt) REVERT: E 66 GLN cc_start: 0.6333 (mt0) cc_final: 0.5903 (mt0) REVERT: E 120 LEU cc_start: 0.8580 (mt) cc_final: 0.8095 (mt) REVERT: E 146 ASP cc_start: 0.9032 (p0) cc_final: 0.8750 (p0) REVERT: E 185 GLU cc_start: 0.8412 (mt-10) cc_final: 0.7895 (mp0) REVERT: E 196 MET cc_start: 0.8723 (mpp) cc_final: 0.8390 (mpp) REVERT: E 204 MET cc_start: 0.8175 (mmp) cc_final: 0.7684 (mmm) REVERT: E 232 GLN cc_start: 0.8421 (mt0) cc_final: 0.8134 (mt0) REVERT: E 233 MET cc_start: 0.9376 (mtm) cc_final: 0.9003 (mtm) REVERT: E 257 PHE cc_start: 0.8900 (m-10) cc_final: 0.8605 (m-80) REVERT: E 296 VAL cc_start: 0.9223 (p) cc_final: 0.8921 (p) REVERT: E 326 PHE cc_start: 0.8931 (m-80) cc_final: 0.8243 (m-80) REVERT: E 338 MET cc_start: 0.9059 (mpp) cc_final: 0.8819 (mpp) REVERT: E 352 ASN cc_start: 0.9094 (p0) cc_final: 0.8885 (p0) REVERT: E 364 GLU cc_start: 0.8458 (tp30) cc_final: 0.8142 (tp30) REVERT: E 389 MET cc_start: 0.9089 (mmp) cc_final: 0.8888 (mmm) REVERT: E 411 ASP cc_start: 0.7960 (t0) cc_final: 0.7721 (t70) REVERT: E 450 PHE cc_start: 0.8341 (m-80) cc_final: 0.7857 (m-80) REVERT: F 103 GLU cc_start: 0.7693 (tp30) cc_final: 0.7178 (tp30) REVERT: F 106 ARG cc_start: 0.8256 (mmm160) cc_final: 0.7844 (mmm-85) REVERT: F 149 GLN cc_start: 0.8789 (pt0) cc_final: 0.8414 (pt0) REVERT: F 150 THR cc_start: 0.9323 (m) cc_final: 0.7980 (m) REVERT: F 151 GLN cc_start: 0.8071 (tt0) cc_final: 0.6597 (tt0) REVERT: F 165 TRP cc_start: 0.8895 (m100) cc_final: 0.8375 (m100) REVERT: F 185 GLU cc_start: 0.8127 (tp30) cc_final: 0.7711 (mt-10) REVERT: F 196 MET cc_start: 0.8126 (mmm) cc_final: 0.7532 (mmm) REVERT: F 204 MET cc_start: 0.8464 (mpp) cc_final: 0.8221 (mpp) REVERT: F 230 TYR cc_start: 0.8737 (m-80) cc_final: 0.8488 (m-80) REVERT: F 249 GLU cc_start: 0.8819 (mp0) cc_final: 0.8327 (mp0) REVERT: F 250 GLN cc_start: 0.9190 (mm110) cc_final: 0.8926 (mm110) REVERT: F 273 ILE cc_start: 0.8168 (mm) cc_final: 0.7827 (mm) REVERT: F 302 LEU cc_start: 0.8883 (mt) cc_final: 0.7992 (mt) REVERT: F 334 ARG cc_start: 0.9108 (mtt90) cc_final: 0.8642 (mmt90) REVERT: F 356 LYS cc_start: 0.9279 (mmpt) cc_final: 0.9020 (mmmt) REVERT: F 360 ARG cc_start: 0.7198 (mtt180) cc_final: 0.6498 (mtt180) outliers start: 2 outliers final: 1 residues processed: 659 average time/residue: 0.3199 time to fit residues: 321.1007 Evaluate side-chains 531 residues out of total 2333 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 529 time to evaluate : 2.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 212 optimal weight: 30.0000 chunk 144 optimal weight: 8.9990 chunk 3 optimal weight: 30.0000 chunk 190 optimal weight: 30.0000 chunk 105 optimal weight: 30.0000 chunk 217 optimal weight: 5.9990 chunk 176 optimal weight: 6.9990 chunk 0 optimal weight: 20.0000 chunk 130 optimal weight: 10.0000 chunk 229 optimal weight: 20.0000 chunk 64 optimal weight: 8.9990 overall best weight: 8.1992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 192 GLN ** A 210 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** B 372 GLN ** C 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 387 HIS ** D 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 466 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 212 ASN ** E 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 372 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 417 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 210 GLN ** F 212 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 301 GLN F 317 ASN F 337 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7263 moved from start: 0.3744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.076 21457 Z= 0.305 Angle : 0.788 11.586 29190 Z= 0.400 Chirality : 0.049 0.327 3146 Planarity : 0.006 0.107 3837 Dihedral : 6.695 37.219 2886 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 28.13 Ramachandran Plot: Outliers : 0.11 % Allowed : 12.19 % Favored : 87.70 % Rotamer: Outliers : 0.04 % Allowed : 4.63 % Favored : 95.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.08 % Twisted Proline : 1.11 % 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: -3.49 (0.15), residues: 2658 helix: -2.27 (0.29), residues: 223 sheet: -1.73 (0.20), residues: 601 loop : -2.71 (0.13), residues: 1834 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP C 308 HIS 0.012 0.003 HIS B 35 PHE 0.030 0.002 PHE A 88 TYR 0.023 0.002 TYR E 457 ARG 0.012 0.001 ARG A 106 *********************** 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 633 residues out of total 2333 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 632 time to evaluate : 2.631 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: A 34 TYR cc_start: 0.8582 (m-80) cc_final: 0.8173 (m-80) REVERT: A 48 TYR cc_start: 0.7433 (m-80) cc_final: 0.6884 (m-80) REVERT: A 103 GLU cc_start: 0.7884 (tp30) cc_final: 0.7442 (tp30) REVERT: A 165 TRP cc_start: 0.8920 (m100) cc_final: 0.8421 (m100) REVERT: A 250 GLN cc_start: 0.8348 (mp-120) cc_final: 0.8034 (mp-120) REVERT: A 257 PHE cc_start: 0.8974 (t80) cc_final: 0.8510 (t80) REVERT: A 288 VAL cc_start: 0.9090 (m) cc_final: 0.8799 (m) REVERT: A 366 ASP cc_start: 0.8053 (t0) cc_final: 0.7475 (t0) REVERT: A 368 GLN cc_start: 0.8901 (mt0) cc_final: 0.8435 (mt0) REVERT: A 371 PHE cc_start: 0.8513 (m-80) cc_final: 0.7762 (m-80) REVERT: A 381 GLU cc_start: 0.9149 (mp0) cc_final: 0.8912 (mp0) REVERT: A 389 MET cc_start: 0.8892 (ttt) cc_final: 0.8529 (tmm) REVERT: B 26 TYR cc_start: 0.8337 (m-80) cc_final: 0.7883 (m-80) REVERT: B 68 ARG cc_start: 0.8901 (mmp-170) cc_final: 0.8583 (mmp-170) REVERT: B 74 LEU cc_start: 0.9094 (tp) cc_final: 0.8723 (tp) REVERT: B 210 GLN cc_start: 0.9301 (mp10) cc_final: 0.8931 (mp10) REVERT: B 219 ASP cc_start: 0.9053 (p0) cc_final: 0.8821 (p0) REVERT: B 220 ILE cc_start: 0.9771 (pt) cc_final: 0.9533 (pt) REVERT: B 233 MET cc_start: 0.9174 (mmt) cc_final: 0.8700 (mmt) REVERT: B 236 ASP cc_start: 0.8638 (t70) cc_final: 0.8435 (t70) REVERT: B 246 LEU cc_start: 0.9474 (mt) cc_final: 0.9221 (mt) REVERT: B 251 MET cc_start: 0.8961 (tpt) cc_final: 0.8545 (tpt) REVERT: B 301 GLN cc_start: 0.9013 (mp-120) cc_final: 0.8503 (mp10) REVERT: B 302 LEU cc_start: 0.9064 (pp) cc_final: 0.8755 (pp) REVERT: B 355 TYR cc_start: 0.7215 (m-80) cc_final: 0.6831 (m-80) REVERT: B 461 ARG cc_start: 0.9117 (ttp-110) cc_final: 0.8601 (mtm110) REVERT: C 53 ARG cc_start: 0.7185 (mmt-90) cc_final: 0.6787 (ttt-90) REVERT: C 108 GLN cc_start: 0.8384 (mm-40) cc_final: 0.7875 (mm-40) REVERT: C 204 MET cc_start: 0.7783 (pmm) cc_final: 0.6610 (pmm) REVERT: C 232 GLN cc_start: 0.8833 (mt0) cc_final: 0.8498 (mm-40) REVERT: C 310 GLN cc_start: 0.8841 (tm-30) cc_final: 0.8525 (tm-30) REVERT: C 359 MET cc_start: 0.8446 (mmt) cc_final: 0.7986 (mmt) REVERT: C 383 MET cc_start: 0.8758 (mmt) cc_final: 0.8270 (mmt) REVERT: C 385 TYR cc_start: 0.8664 (t80) cc_final: 0.8344 (t80) REVERT: C 386 ILE cc_start: 0.9620 (pt) cc_final: 0.9415 (pt) REVERT: C 395 GLU cc_start: 0.9134 (tm-30) cc_final: 0.8841 (tm-30) REVERT: C 457 TYR cc_start: 0.9296 (m-80) cc_final: 0.8937 (m-80) REVERT: C 461 ARG cc_start: 0.8801 (ptp90) cc_final: 0.8530 (ptp90) REVERT: D 70 PHE cc_start: 0.8956 (m-80) cc_final: 0.8712 (m-80) REVERT: D 117 HIS cc_start: 0.8564 (t-90) cc_final: 0.7821 (t-170) REVERT: D 120 LEU cc_start: 0.8423 (mt) cc_final: 0.7922 (mt) REVERT: D 184 LEU cc_start: 0.7930 (tp) cc_final: 0.7677 (tp) REVERT: D 197 VAL cc_start: 0.8442 (t) cc_final: 0.8164 (m) REVERT: D 198 ASP cc_start: 0.6894 (t0) cc_final: 0.6450 (t0) REVERT: D 204 MET cc_start: 0.8303 (mpp) cc_final: 0.8045 (mpp) REVERT: D 219 ASP cc_start: 0.9303 (p0) cc_final: 0.9072 (p0) REVERT: D 326 PHE cc_start: 0.8086 (m-80) cc_final: 0.7839 (m-10) REVERT: D 355 TYR cc_start: 0.7649 (m-80) cc_final: 0.7398 (m-80) REVERT: D 361 HIS cc_start: 0.6845 (t-90) cc_final: 0.6538 (t70) REVERT: D 449 LYS cc_start: 0.7831 (mmtp) cc_final: 0.7537 (mmmt) REVERT: E 41 LEU cc_start: 0.7887 (tt) cc_final: 0.7247 (tt) REVERT: E 66 GLN cc_start: 0.6464 (mt0) cc_final: 0.5977 (mt0) REVERT: E 120 LEU cc_start: 0.8769 (mt) cc_final: 0.8207 (mt) REVERT: E 146 ASP cc_start: 0.8965 (p0) cc_final: 0.8652 (p0) REVERT: E 161 LEU cc_start: 0.9372 (mm) cc_final: 0.9165 (mm) REVERT: E 185 GLU cc_start: 0.8302 (mt-10) cc_final: 0.7944 (mp0) REVERT: E 196 MET cc_start: 0.8659 (mpp) cc_final: 0.8346 (mpp) REVERT: E 225 CYS cc_start: 0.8709 (m) cc_final: 0.8504 (m) REVERT: E 233 MET cc_start: 0.9418 (mtm) cc_final: 0.8840 (mtt) REVERT: E 257 PHE cc_start: 0.8894 (m-10) cc_final: 0.8664 (m-80) REVERT: E 290 THR cc_start: 0.8653 (m) cc_final: 0.8321 (m) REVERT: E 296 VAL cc_start: 0.9174 (p) cc_final: 0.8949 (p) REVERT: E 338 MET cc_start: 0.8972 (mpp) cc_final: 0.8750 (mpp) REVERT: E 365 TYR cc_start: 0.9262 (m-80) cc_final: 0.9005 (m-80) REVERT: E 397 TRP cc_start: 0.7774 (m100) cc_final: 0.7539 (m100) REVERT: E 452 SER cc_start: 0.9089 (m) cc_final: 0.8794 (t) REVERT: F 71 LYS cc_start: 0.8141 (tmtt) cc_final: 0.7843 (tptp) REVERT: F 103 GLU cc_start: 0.7546 (tp30) cc_final: 0.7187 (tp30) REVERT: F 106 ARG cc_start: 0.8425 (mmm160) cc_final: 0.8168 (mmm-85) REVERT: F 149 GLN cc_start: 0.8818 (pt0) cc_final: 0.8427 (pt0) REVERT: F 151 GLN cc_start: 0.8275 (tt0) cc_final: 0.6955 (tt0) REVERT: F 185 GLU cc_start: 0.8150 (tp30) cc_final: 0.7219 (mt-10) REVERT: F 186 LEU cc_start: 0.8930 (tp) cc_final: 0.8691 (tp) REVERT: F 192 GLN cc_start: 0.8910 (mt0) cc_final: 0.8602 (mm-40) REVERT: F 196 MET cc_start: 0.7816 (mmm) cc_final: 0.7540 (mmm) REVERT: F 204 MET cc_start: 0.8439 (mpp) cc_final: 0.7991 (mpp) REVERT: F 219 ASP cc_start: 0.9046 (m-30) cc_final: 0.8325 (t0) REVERT: F 230 TYR cc_start: 0.8625 (m-80) cc_final: 0.8385 (m-80) REVERT: F 249 GLU cc_start: 0.8747 (mp0) cc_final: 0.8483 (mp0) REVERT: F 273 ILE cc_start: 0.8244 (mm) cc_final: 0.7874 (mm) REVERT: F 302 LEU cc_start: 0.8905 (mt) cc_final: 0.7929 (mt) REVERT: F 334 ARG cc_start: 0.9209 (mtt90) cc_final: 0.8709 (mmt90) REVERT: F 356 LYS cc_start: 0.9288 (mmpt) cc_final: 0.9009 (mmtt) REVERT: F 357 GLU cc_start: 0.8548 (tm-30) cc_final: 0.8328 (tm-30) REVERT: F 369 PHE cc_start: 0.9101 (m-80) cc_final: 0.8752 (m-10) REVERT: F 397 TRP cc_start: 0.7460 (m-10) cc_final: 0.7086 (m-10) REVERT: F 444 VAL cc_start: 0.9528 (m) cc_final: 0.9319 (m) outliers start: 1 outliers final: 1 residues processed: 632 average time/residue: 0.3193 time to fit residues: 310.8853 Evaluate side-chains 516 residues out of total 2333 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 515 time to evaluate : 2.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 85 optimal weight: 7.9990 chunk 229 optimal weight: 7.9990 chunk 50 optimal weight: 2.9990 chunk 149 optimal weight: 9.9990 chunk 62 optimal weight: 6.9990 chunk 255 optimal weight: 6.9990 chunk 212 optimal weight: 40.0000 chunk 118 optimal weight: 6.9990 chunk 21 optimal weight: 5.9990 chunk 84 optimal weight: 0.3980 chunk 134 optimal weight: 10.0000 overall best weight: 4.6788 ------------------------------------------------------------------------------- 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 210 GLN ** A 323 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 151 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** B 372 GLN ** C 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 466 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 212 ASN ** E 372 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 417 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 212 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 301 GLN F 317 ASN F 337 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7199 moved from start: 0.4006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 21457 Z= 0.220 Angle : 0.715 10.931 29190 Z= 0.357 Chirality : 0.048 0.294 3146 Planarity : 0.006 0.104 3837 Dihedral : 6.316 36.115 2886 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 22.76 Ramachandran Plot: Outliers : 0.04 % Allowed : 10.35 % Favored : 89.62 % Rotamer: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.08 % Twisted Proline : 0.56 % 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: -3.36 (0.15), residues: 2658 helix: -2.18 (0.29), residues: 229 sheet: -1.64 (0.20), residues: 588 loop : -2.61 (0.13), residues: 1841 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP C 308 HIS 0.009 0.002 HIS A 35 PHE 0.042 0.002 PHE D 257 TYR 0.023 0.002 TYR B 147 ARG 0.006 0.000 ARG F 461 *********************** 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 641 residues out of total 2333 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 641 time to evaluate : 2.337 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: A 34 TYR cc_start: 0.8422 (m-80) cc_final: 0.8012 (m-80) REVERT: A 48 TYR cc_start: 0.7326 (m-80) cc_final: 0.6779 (m-80) REVERT: A 103 GLU cc_start: 0.7737 (tp30) cc_final: 0.7524 (tp30) REVERT: A 165 TRP cc_start: 0.8903 (m100) cc_final: 0.8414 (m100) REVERT: A 195 ASP cc_start: 0.8705 (t0) cc_final: 0.7914 (t70) REVERT: A 247 ARG cc_start: 0.8263 (ptt180) cc_final: 0.7710 (ptt180) REVERT: A 257 PHE cc_start: 0.8963 (t80) cc_final: 0.8512 (t80) REVERT: A 288 VAL cc_start: 0.9088 (m) cc_final: 0.8715 (m) REVERT: A 360 ARG cc_start: 0.9146 (mmp80) cc_final: 0.8917 (mmm160) REVERT: A 366 ASP cc_start: 0.8022 (t0) cc_final: 0.7573 (t0) REVERT: A 368 GLN cc_start: 0.8877 (mt0) cc_final: 0.8453 (mt0) REVERT: A 371 PHE cc_start: 0.8461 (m-80) cc_final: 0.7527 (m-80) REVERT: A 381 GLU cc_start: 0.9156 (mp0) cc_final: 0.8913 (mp0) REVERT: A 389 MET cc_start: 0.8903 (ttt) cc_final: 0.8557 (tmm) REVERT: A 412 THR cc_start: 0.9276 (t) cc_final: 0.9012 (t) REVERT: B 26 TYR cc_start: 0.8311 (m-80) cc_final: 0.7864 (m-80) REVERT: B 32 ILE cc_start: 0.9293 (mp) cc_final: 0.9079 (mp) REVERT: B 68 ARG cc_start: 0.8932 (mmp-170) cc_final: 0.8184 (mmp-170) REVERT: B 74 LEU cc_start: 0.9151 (tp) cc_final: 0.8756 (tp) REVERT: B 210 GLN cc_start: 0.9338 (mp10) cc_final: 0.8837 (mp10) REVERT: B 219 ASP cc_start: 0.9126 (p0) cc_final: 0.8879 (p0) REVERT: B 220 ILE cc_start: 0.9768 (pt) cc_final: 0.9520 (pt) REVERT: B 233 MET cc_start: 0.9146 (mmt) cc_final: 0.8667 (mmt) REVERT: B 246 LEU cc_start: 0.9510 (mt) cc_final: 0.9278 (mt) REVERT: B 251 MET cc_start: 0.8889 (tpt) cc_final: 0.8477 (tpt) REVERT: B 302 LEU cc_start: 0.8945 (pp) cc_final: 0.8098 (pp) REVERT: B 305 LYS cc_start: 0.9315 (mttt) cc_final: 0.9025 (mtpt) REVERT: B 328 THR cc_start: 0.9138 (m) cc_final: 0.8342 (p) REVERT: B 461 ARG cc_start: 0.9069 (ttp-110) cc_final: 0.8823 (mtm-85) REVERT: C 53 ARG cc_start: 0.7163 (mmt-90) cc_final: 0.6845 (ttt180) REVERT: C 108 GLN cc_start: 0.8592 (mm-40) cc_final: 0.8173 (mm-40) REVERT: C 150 THR cc_start: 0.8414 (m) cc_final: 0.7508 (m) REVERT: C 201 PHE cc_start: 0.8159 (m-10) cc_final: 0.7731 (m-10) REVERT: C 204 MET cc_start: 0.7761 (pmm) cc_final: 0.6959 (pmm) REVERT: C 310 GLN cc_start: 0.8783 (tm-30) cc_final: 0.8436 (tm-30) REVERT: C 359 MET cc_start: 0.8418 (mmt) cc_final: 0.7916 (mmt) REVERT: C 383 MET cc_start: 0.8764 (mmt) cc_final: 0.8249 (mmt) REVERT: C 395 GLU cc_start: 0.9141 (tm-30) cc_final: 0.8852 (tm-30) REVERT: C 457 TYR cc_start: 0.9184 (m-80) cc_final: 0.8880 (m-80) REVERT: D 48 TYR cc_start: 0.7846 (m-80) cc_final: 0.7334 (m-80) REVERT: D 70 PHE cc_start: 0.8950 (m-80) cc_final: 0.8673 (m-80) REVERT: D 94 ARG cc_start: 0.4963 (mpp-170) cc_final: 0.4588 (mpp80) REVERT: D 117 HIS cc_start: 0.8549 (t-90) cc_final: 0.7886 (t-170) REVERT: D 120 LEU cc_start: 0.8364 (mt) cc_final: 0.7947 (mt) REVERT: D 197 VAL cc_start: 0.8448 (t) cc_final: 0.8161 (m) REVERT: D 204 MET cc_start: 0.8455 (mpp) cc_final: 0.8048 (mpp) REVERT: D 209 LEU cc_start: 0.9426 (mt) cc_final: 0.9169 (mt) REVERT: D 233 MET cc_start: 0.8825 (mmp) cc_final: 0.8595 (mmm) REVERT: D 326 PHE cc_start: 0.8051 (m-80) cc_final: 0.7772 (m-10) REVERT: D 355 TYR cc_start: 0.7647 (m-80) cc_final: 0.7358 (m-80) REVERT: D 361 HIS cc_start: 0.6734 (t-90) cc_final: 0.6464 (t70) REVERT: D 397 TRP cc_start: 0.8861 (m-90) cc_final: 0.8510 (m100) REVERT: D 449 LYS cc_start: 0.7874 (mmtp) cc_final: 0.7496 (mmmt) REVERT: E 41 LEU cc_start: 0.7216 (tt) cc_final: 0.6711 (tt) REVERT: E 66 GLN cc_start: 0.6353 (mt0) cc_final: 0.5297 (mt0) REVERT: E 120 LEU cc_start: 0.8708 (mt) cc_final: 0.8127 (mt) REVERT: E 146 ASP cc_start: 0.8950 (p0) cc_final: 0.8610 (p0) REVERT: E 150 THR cc_start: 0.9109 (m) cc_final: 0.8739 (m) REVERT: E 185 GLU cc_start: 0.8412 (mt-10) cc_final: 0.7999 (mp0) REVERT: E 196 MET cc_start: 0.8777 (mpp) cc_final: 0.8294 (mmt) REVERT: E 204 MET cc_start: 0.8147 (mmp) cc_final: 0.7884 (mmp) REVERT: E 257 PHE cc_start: 0.8902 (m-10) cc_final: 0.8664 (m-80) REVERT: E 290 THR cc_start: 0.8519 (m) cc_final: 0.8217 (m) REVERT: E 296 VAL cc_start: 0.9385 (p) cc_final: 0.9080 (p) REVERT: E 303 PHE cc_start: 0.9047 (m-80) cc_final: 0.8352 (m-80) REVERT: E 326 PHE cc_start: 0.8898 (m-80) cc_final: 0.8220 (m-80) REVERT: E 364 GLU cc_start: 0.7671 (mm-30) cc_final: 0.6787 (mm-30) REVERT: E 450 PHE cc_start: 0.8303 (m-80) cc_final: 0.7798 (m-80) REVERT: F 102 LEU cc_start: 0.8933 (mp) cc_final: 0.8722 (mp) REVERT: F 103 GLU cc_start: 0.7741 (tp30) cc_final: 0.6866 (tp30) REVERT: F 149 GLN cc_start: 0.8817 (pt0) cc_final: 0.8467 (pt0) REVERT: F 150 THR cc_start: 0.9394 (m) cc_final: 0.8093 (m) REVERT: F 151 GLN cc_start: 0.8120 (tt0) cc_final: 0.6676 (tt0) REVERT: F 165 TRP cc_start: 0.8866 (m100) cc_final: 0.8441 (m100) REVERT: F 185 GLU cc_start: 0.8121 (tp30) cc_final: 0.7822 (mp0) REVERT: F 186 LEU cc_start: 0.8958 (tp) cc_final: 0.8674 (tp) REVERT: F 192 GLN cc_start: 0.8850 (mt0) cc_final: 0.8561 (mt0) REVERT: F 196 MET cc_start: 0.7877 (mmm) cc_final: 0.7297 (mmm) REVERT: F 204 MET cc_start: 0.8539 (mpp) cc_final: 0.8266 (mpp) REVERT: F 230 TYR cc_start: 0.8594 (m-80) cc_final: 0.8290 (m-80) REVERT: F 249 GLU cc_start: 0.8544 (mp0) cc_final: 0.8203 (mp0) REVERT: F 250 GLN cc_start: 0.9272 (mm-40) cc_final: 0.9053 (mm-40) REVERT: F 273 ILE cc_start: 0.8273 (mm) cc_final: 0.7946 (mm) REVERT: F 302 LEU cc_start: 0.8939 (mt) cc_final: 0.7977 (mt) REVERT: F 315 HIS cc_start: 0.7482 (m90) cc_final: 0.6990 (m90) REVERT: F 334 ARG cc_start: 0.9170 (mtt90) cc_final: 0.8824 (mmt90) REVERT: F 368 GLN cc_start: 0.9004 (mp-120) cc_final: 0.8186 (mp10) REVERT: F 371 PHE cc_start: 0.7938 (m-80) cc_final: 0.7592 (m-80) REVERT: F 397 TRP cc_start: 0.7546 (m-10) cc_final: 0.7155 (m-10) outliers start: 0 outliers final: 0 residues processed: 641 average time/residue: 0.3214 time to fit residues: 316.0018 Evaluate side-chains 535 residues out of total 2333 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 535 time to evaluate : 2.564 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 246 optimal weight: 40.0000 chunk 28 optimal weight: 10.0000 chunk 145 optimal weight: 7.9990 chunk 186 optimal weight: 1.9990 chunk 144 optimal weight: 6.9990 chunk 215 optimal weight: 0.4980 chunk 142 optimal weight: 30.0000 chunk 254 optimal weight: 8.9990 chunk 159 optimal weight: 0.9980 chunk 155 optimal weight: 5.9990 chunk 117 optimal weight: 20.0000 overall best weight: 3.2986 ------------------------------------------------------------------------------- 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 66 GLN A 142 ASN A 192 GLN A 210 GLN ** A 323 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 212 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 372 GLN C 387 HIS D 210 GLN ** D 466 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 212 ASN ** E 417 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 212 ASN ** 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7171 moved from start: 0.4261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 21457 Z= 0.198 Angle : 0.707 11.379 29190 Z= 0.349 Chirality : 0.047 0.233 3146 Planarity : 0.006 0.104 3837 Dihedral : 6.023 35.233 2886 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 21.42 Ramachandran Plot: Outliers : 0.04 % Allowed : 10.53 % Favored : 89.43 % Rotamer: Outliers : 0.04 % Allowed : 2.19 % Favored : 97.77 % 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: -3.23 (0.15), residues: 2658 helix: -2.17 (0.29), residues: 237 sheet: -1.37 (0.20), residues: 594 loop : -2.58 (0.13), residues: 1827 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.001 TRP C 308 HIS 0.008 0.001 HIS A 35 PHE 0.024 0.002 PHE C 463 TYR 0.021 0.001 TYR F 365 ARG 0.009 0.000 ARG F 461 *********************** 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 650 residues out of total 2333 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 649 time to evaluate : 2.444 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: A 34 TYR cc_start: 0.8379 (m-80) cc_final: 0.7958 (m-80) REVERT: A 48 TYR cc_start: 0.7312 (m-80) cc_final: 0.6708 (m-80) REVERT: A 165 TRP cc_start: 0.8928 (m100) cc_final: 0.8410 (m100) REVERT: A 204 MET cc_start: 0.4773 (pmm) cc_final: 0.4318 (pmm) REVERT: A 250 GLN cc_start: 0.8275 (mp-120) cc_final: 0.8065 (mp-120) REVERT: A 257 PHE cc_start: 0.8942 (t80) cc_final: 0.8610 (t80) REVERT: A 288 VAL cc_start: 0.9137 (m) cc_final: 0.8877 (m) REVERT: A 366 ASP cc_start: 0.7981 (t0) cc_final: 0.7576 (t0) REVERT: A 368 GLN cc_start: 0.8809 (mt0) cc_final: 0.8360 (mt0) REVERT: A 371 PHE cc_start: 0.8361 (m-80) cc_final: 0.7452 (m-80) REVERT: A 381 GLU cc_start: 0.9168 (mp0) cc_final: 0.8929 (mp0) REVERT: A 389 MET cc_start: 0.8840 (ttt) cc_final: 0.8528 (tmm) REVERT: A 412 THR cc_start: 0.9271 (t) cc_final: 0.9027 (t) REVERT: B 26 TYR cc_start: 0.8226 (m-80) cc_final: 0.7795 (m-80) REVERT: B 68 ARG cc_start: 0.8796 (mmp-170) cc_final: 0.8013 (mmp-170) REVERT: B 74 LEU cc_start: 0.9153 (tp) cc_final: 0.8796 (tp) REVERT: B 164 HIS cc_start: 0.9169 (p90) cc_final: 0.8740 (p90) REVERT: B 210 GLN cc_start: 0.9343 (mp10) cc_final: 0.8865 (mp10) REVERT: B 211 THR cc_start: 0.8928 (p) cc_final: 0.8633 (p) REVERT: B 219 ASP cc_start: 0.9114 (p0) cc_final: 0.8893 (p0) REVERT: B 220 ILE cc_start: 0.9756 (pt) cc_final: 0.9519 (pt) REVERT: B 233 MET cc_start: 0.9125 (mmt) cc_final: 0.8650 (mmt) REVERT: B 236 ASP cc_start: 0.8469 (t0) cc_final: 0.8247 (t0) REVERT: B 251 MET cc_start: 0.8832 (tpt) cc_final: 0.8427 (tpt) REVERT: B 301 GLN cc_start: 0.8988 (mp-120) cc_final: 0.8407 (mp10) REVERT: B 302 LEU cc_start: 0.9063 (pp) cc_final: 0.8717 (pp) REVERT: B 328 THR cc_start: 0.9127 (m) cc_final: 0.8426 (p) REVERT: B 461 ARG cc_start: 0.9081 (ttp-110) cc_final: 0.8672 (ptp-110) REVERT: C 53 ARG cc_start: 0.7164 (mmt-90) cc_final: 0.6771 (ttt-90) REVERT: C 66 GLN cc_start: 0.8442 (mt0) cc_final: 0.7698 (mt0) REVERT: C 150 THR cc_start: 0.8388 (m) cc_final: 0.7225 (m) REVERT: C 154 MET cc_start: 0.8848 (mmp) cc_final: 0.8630 (mmm) REVERT: C 201 PHE cc_start: 0.8202 (m-10) cc_final: 0.7773 (m-10) REVERT: C 204 MET cc_start: 0.7915 (pmm) cc_final: 0.7428 (pmm) REVERT: C 307 TYR cc_start: 0.8678 (m-80) cc_final: 0.8475 (m-10) REVERT: C 310 GLN cc_start: 0.8740 (tm-30) cc_final: 0.8406 (tm-30) REVERT: C 359 MET cc_start: 0.8483 (mmt) cc_final: 0.7698 (mmm) REVERT: C 383 MET cc_start: 0.8773 (mmt) cc_final: 0.8260 (mmt) REVERT: C 386 ILE cc_start: 0.9514 (pt) cc_final: 0.9240 (pt) REVERT: C 395 GLU cc_start: 0.9158 (tm-30) cc_final: 0.8856 (tm-30) REVERT: C 457 TYR cc_start: 0.9217 (m-80) cc_final: 0.8887 (m-80) REVERT: D 94 ARG cc_start: 0.4853 (mpp-170) cc_final: 0.4167 (mpp80) REVERT: D 117 HIS cc_start: 0.8598 (t-90) cc_final: 0.7880 (t-170) REVERT: D 120 LEU cc_start: 0.8378 (mt) cc_final: 0.7817 (mt) REVERT: D 197 VAL cc_start: 0.8461 (t) cc_final: 0.8154 (m) REVERT: D 204 MET cc_start: 0.8449 (mpp) cc_final: 0.8151 (mpp) REVERT: D 206 PHE cc_start: 0.7963 (m-80) cc_final: 0.7744 (m-80) REVERT: D 233 MET cc_start: 0.8818 (mmp) cc_final: 0.8609 (mmm) REVERT: D 326 PHE cc_start: 0.8048 (m-80) cc_final: 0.7768 (m-10) REVERT: D 355 TYR cc_start: 0.7630 (m-80) cc_final: 0.7237 (m-80) REVERT: D 364 GLU cc_start: 0.8351 (tm-30) cc_final: 0.7826 (tm-30) REVERT: D 397 TRP cc_start: 0.8845 (m-90) cc_final: 0.8477 (m100) REVERT: D 449 LYS cc_start: 0.7925 (mmtp) cc_final: 0.7590 (mmmt) REVERT: E 41 LEU cc_start: 0.7368 (tt) cc_final: 0.6822 (tt) REVERT: E 66 GLN cc_start: 0.6308 (mt0) cc_final: 0.5840 (mt0) REVERT: E 103 GLU cc_start: 0.8955 (tp30) cc_final: 0.8659 (tp30) REVERT: E 120 LEU cc_start: 0.8778 (mt) cc_final: 0.8154 (mt) REVERT: E 146 ASP cc_start: 0.8910 (p0) cc_final: 0.8502 (p0) REVERT: E 196 MET cc_start: 0.8812 (mpp) cc_final: 0.8476 (mpp) REVERT: E 233 MET cc_start: 0.9288 (ptp) cc_final: 0.9087 (ptp) REVERT: E 254 ARG cc_start: 0.8887 (mtp85) cc_final: 0.8599 (ptp-170) REVERT: E 257 PHE cc_start: 0.8876 (m-10) cc_final: 0.8623 (m-80) REVERT: E 290 THR cc_start: 0.8456 (m) cc_final: 0.8111 (m) REVERT: E 303 PHE cc_start: 0.8929 (m-80) cc_final: 0.8144 (m-80) REVERT: E 326 PHE cc_start: 0.8887 (m-80) cc_final: 0.8201 (m-80) REVERT: E 364 GLU cc_start: 0.7282 (mm-30) cc_final: 0.6711 (mm-30) REVERT: E 450 PHE cc_start: 0.8169 (m-80) cc_final: 0.7727 (m-80) REVERT: F 65 TYR cc_start: 0.9101 (m-10) cc_final: 0.8846 (m-80) REVERT: F 103 GLU cc_start: 0.7471 (tp30) cc_final: 0.6616 (tp30) REVERT: F 149 GLN cc_start: 0.8770 (pt0) cc_final: 0.8434 (pt0) REVERT: F 150 THR cc_start: 0.9420 (m) cc_final: 0.8101 (m) REVERT: F 151 GLN cc_start: 0.8040 (tt0) cc_final: 0.6657 (tt0) REVERT: F 165 TRP cc_start: 0.8870 (m100) cc_final: 0.8389 (m100) REVERT: F 185 GLU cc_start: 0.8100 (tp30) cc_final: 0.7642 (mt-10) REVERT: F 192 GLN cc_start: 0.8839 (mt0) cc_final: 0.8541 (mt0) REVERT: F 196 MET cc_start: 0.7886 (mmm) cc_final: 0.7305 (mmm) REVERT: F 204 MET cc_start: 0.8570 (mpp) cc_final: 0.8329 (mpp) REVERT: F 215 ASP cc_start: 0.8527 (m-30) cc_final: 0.8014 (m-30) REVERT: F 230 TYR cc_start: 0.8585 (m-80) cc_final: 0.8287 (m-80) REVERT: F 249 GLU cc_start: 0.8472 (mp0) cc_final: 0.8165 (mp0) REVERT: F 273 ILE cc_start: 0.8319 (mm) cc_final: 0.7992 (mm) REVERT: F 302 LEU cc_start: 0.8961 (mt) cc_final: 0.7956 (mt) REVERT: F 334 ARG cc_start: 0.9176 (mtt90) cc_final: 0.8694 (mmt90) REVERT: F 365 TYR cc_start: 0.8934 (m-80) cc_final: 0.8654 (m-80) REVERT: F 368 GLN cc_start: 0.9159 (mp-120) cc_final: 0.7869 (mp-120) REVERT: F 397 TRP cc_start: 0.7636 (m-10) cc_final: 0.7224 (m-10) REVERT: F 444 VAL cc_start: 0.9595 (m) cc_final: 0.9328 (m) outliers start: 1 outliers final: 1 residues processed: 649 average time/residue: 0.3194 time to fit residues: 320.4871 Evaluate side-chains 542 residues out of total 2333 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 541 time to evaluate : 2.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 157 optimal weight: 30.0000 chunk 101 optimal weight: 4.9990 chunk 151 optimal weight: 1.9990 chunk 76 optimal weight: 50.0000 chunk 49 optimal weight: 3.9990 chunk 161 optimal weight: 20.0000 chunk 173 optimal weight: 4.9990 chunk 125 optimal weight: 20.0000 chunk 23 optimal weight: 5.9990 chunk 200 optimal weight: 20.0000 chunk 231 optimal weight: 9.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- 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 139 ASN A 210 GLN ** A 323 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 212 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 372 GLN D 210 GLN ** D 466 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 212 ASN ** E 417 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 212 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 301 GLN F 317 ASN F 337 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7180 moved from start: 0.4488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 21457 Z= 0.212 Angle : 0.704 11.459 29190 Z= 0.350 Chirality : 0.047 0.234 3146 Planarity : 0.005 0.103 3837 Dihedral : 5.941 35.376 2886 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 22.51 Ramachandran Plot: Outliers : 0.04 % Allowed : 10.87 % Favored : 89.09 % Rotamer: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.08 % Twisted Proline : 0.56 % 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: -3.17 (0.15), residues: 2658 helix: -2.07 (0.29), residues: 245 sheet: -1.42 (0.20), residues: 569 loop : -2.51 (0.14), residues: 1844 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP F 308 HIS 0.013 0.002 HIS D 361 PHE 0.037 0.002 PHE D 257 TYR 0.019 0.001 TYR B 147 ARG 0.011 0.001 ARG C 106 *********************** 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 634 residues out of total 2333 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 634 time to evaluate : 2.603 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 33 PHE cc_start: 0.9452 (m-80) cc_final: 0.9019 (m-80) REVERT: A 48 TYR cc_start: 0.7353 (m-80) cc_final: 0.6869 (m-80) REVERT: A 103 GLU cc_start: 0.8163 (tp30) cc_final: 0.7939 (tp30) REVERT: A 165 TRP cc_start: 0.8973 (m100) cc_final: 0.8474 (m100) REVERT: A 204 MET cc_start: 0.5002 (pmm) cc_final: 0.4460 (pmm) REVERT: A 257 PHE cc_start: 0.8993 (t80) cc_final: 0.8671 (t80) REVERT: A 288 VAL cc_start: 0.9159 (m) cc_final: 0.8890 (m) REVERT: A 360 ARG cc_start: 0.9168 (mmp80) cc_final: 0.8885 (mmm160) REVERT: A 364 GLU cc_start: 0.7800 (pt0) cc_final: 0.7410 (pm20) REVERT: A 366 ASP cc_start: 0.8111 (t0) cc_final: 0.7705 (t0) REVERT: A 368 GLN cc_start: 0.8830 (mt0) cc_final: 0.8389 (mt0) REVERT: A 371 PHE cc_start: 0.8416 (m-80) cc_final: 0.7574 (m-80) REVERT: A 381 GLU cc_start: 0.9146 (mp0) cc_final: 0.8905 (mp0) REVERT: A 389 MET cc_start: 0.8768 (ttt) cc_final: 0.8516 (tmm) REVERT: A 395 GLU cc_start: 0.8491 (pt0) cc_final: 0.8231 (pp20) REVERT: A 412 THR cc_start: 0.9270 (t) cc_final: 0.9051 (t) REVERT: B 26 TYR cc_start: 0.8202 (m-80) cc_final: 0.7774 (m-80) REVERT: B 68 ARG cc_start: 0.8821 (mmp-170) cc_final: 0.8060 (mmp-170) REVERT: B 74 LEU cc_start: 0.9160 (tp) cc_final: 0.8749 (tp) REVERT: B 210 GLN cc_start: 0.9333 (mp10) cc_final: 0.8830 (mp10) REVERT: B 211 THR cc_start: 0.8987 (p) cc_final: 0.8667 (p) REVERT: B 220 ILE cc_start: 0.9758 (pt) cc_final: 0.9509 (pt) REVERT: B 236 ASP cc_start: 0.8514 (t0) cc_final: 0.8280 (t0) REVERT: B 251 MET cc_start: 0.8723 (tpt) cc_final: 0.8398 (tpt) REVERT: B 301 GLN cc_start: 0.9011 (mp-120) cc_final: 0.8366 (mp10) REVERT: B 302 LEU cc_start: 0.9153 (pp) cc_final: 0.8702 (pp) REVERT: B 305 LYS cc_start: 0.9510 (mtmt) cc_final: 0.9169 (mtmt) REVERT: B 328 THR cc_start: 0.9095 (m) cc_final: 0.8269 (p) REVERT: B 357 GLU cc_start: 0.8294 (mp0) cc_final: 0.8066 (mp0) REVERT: B 461 ARG cc_start: 0.9077 (ttp-110) cc_final: 0.8686 (ptp-110) REVERT: C 51 ILE cc_start: 0.8458 (tt) cc_final: 0.8243 (tt) REVERT: C 53 ARG cc_start: 0.7177 (mmt-90) cc_final: 0.6780 (ttt-90) REVERT: C 66 GLN cc_start: 0.8505 (mt0) cc_final: 0.7729 (mt0) REVERT: C 68 ARG cc_start: 0.8753 (mmt-90) cc_final: 0.8494 (mmt-90) REVERT: C 108 GLN cc_start: 0.8627 (tp-100) cc_final: 0.8223 (tp40) REVERT: C 154 MET cc_start: 0.8816 (mmp) cc_final: 0.8576 (mmm) REVERT: C 201 PHE cc_start: 0.8229 (m-10) cc_final: 0.7859 (m-10) REVERT: C 204 MET cc_start: 0.7825 (pmm) cc_final: 0.7239 (pmm) REVERT: C 310 GLN cc_start: 0.8720 (tm-30) cc_final: 0.8395 (tm-30) REVERT: C 359 MET cc_start: 0.8409 (mmt) cc_final: 0.7690 (mmm) REVERT: C 383 MET cc_start: 0.8782 (mmt) cc_final: 0.8268 (mmt) REVERT: C 386 ILE cc_start: 0.9505 (pt) cc_final: 0.9250 (pt) REVERT: C 395 GLU cc_start: 0.9160 (tm-30) cc_final: 0.8855 (tm-30) REVERT: C 457 TYR cc_start: 0.9179 (m-80) cc_final: 0.8888 (m-80) REVERT: D 94 ARG cc_start: 0.4477 (mpp-170) cc_final: 0.3891 (mpp80) REVERT: D 117 HIS cc_start: 0.8513 (t-90) cc_final: 0.8009 (t-90) REVERT: D 120 LEU cc_start: 0.8516 (mt) cc_final: 0.7825 (pp) REVERT: D 197 VAL cc_start: 0.8460 (t) cc_final: 0.8169 (m) REVERT: D 204 MET cc_start: 0.8361 (mpp) cc_final: 0.8070 (mpp) REVERT: D 355 TYR cc_start: 0.7633 (m-80) cc_final: 0.7220 (m-80) REVERT: D 361 HIS cc_start: 0.6673 (t70) cc_final: 0.6197 (t70) REVERT: D 364 GLU cc_start: 0.8487 (tm-30) cc_final: 0.8225 (tm-30) REVERT: D 397 TRP cc_start: 0.8843 (m-90) cc_final: 0.8375 (m100) REVERT: D 449 LYS cc_start: 0.7914 (mmtp) cc_final: 0.7590 (mmmt) REVERT: E 41 LEU cc_start: 0.7096 (tt) cc_final: 0.6650 (tt) REVERT: E 66 GLN cc_start: 0.6185 (mt0) cc_final: 0.5709 (mt0) REVERT: E 120 LEU cc_start: 0.8795 (mt) cc_final: 0.8205 (mt) REVERT: E 146 ASP cc_start: 0.8998 (p0) cc_final: 0.8669 (p0) REVERT: E 196 MET cc_start: 0.8786 (mpp) cc_final: 0.8440 (mpp) REVERT: E 232 GLN cc_start: 0.9234 (tt0) cc_final: 0.8677 (mt0) REVERT: E 254 ARG cc_start: 0.8853 (mtp85) cc_final: 0.8537 (ptp-170) REVERT: E 257 PHE cc_start: 0.8884 (m-10) cc_final: 0.8623 (m-80) REVERT: E 290 THR cc_start: 0.8425 (m) cc_final: 0.8061 (m) REVERT: E 303 PHE cc_start: 0.8920 (m-80) cc_final: 0.8175 (m-80) REVERT: E 326 PHE cc_start: 0.8834 (m-80) cc_final: 0.8182 (m-80) REVERT: E 364 GLU cc_start: 0.7543 (mm-30) cc_final: 0.6437 (mm-30) REVERT: E 450 PHE cc_start: 0.8079 (m-80) cc_final: 0.7637 (m-80) REVERT: E 461 ARG cc_start: 0.8998 (ptp90) cc_final: 0.8763 (mtm-85) REVERT: F 65 TYR cc_start: 0.9134 (m-10) cc_final: 0.8868 (m-80) REVERT: F 103 GLU cc_start: 0.7439 (tp30) cc_final: 0.7021 (tp30) REVERT: F 149 GLN cc_start: 0.8725 (pt0) cc_final: 0.8395 (pt0) REVERT: F 151 GLN cc_start: 0.8059 (tt0) cc_final: 0.6719 (tt0) REVERT: F 165 TRP cc_start: 0.8874 (m100) cc_final: 0.8373 (m100) REVERT: F 185 GLU cc_start: 0.8094 (tp30) cc_final: 0.7770 (mp0) REVERT: F 196 MET cc_start: 0.7816 (mmm) cc_final: 0.7287 (mmm) REVERT: F 204 MET cc_start: 0.8600 (mpp) cc_final: 0.8321 (mpp) REVERT: F 230 TYR cc_start: 0.8608 (m-80) cc_final: 0.8321 (m-80) REVERT: F 246 LEU cc_start: 0.9439 (pt) cc_final: 0.9168 (pp) REVERT: F 248 LYS cc_start: 0.9342 (ttmt) cc_final: 0.9117 (mttt) REVERT: F 249 GLU cc_start: 0.8561 (mp0) cc_final: 0.8321 (mp0) REVERT: F 273 ILE cc_start: 0.8336 (mm) cc_final: 0.8005 (mm) REVERT: F 285 SER cc_start: 0.9405 (t) cc_final: 0.9056 (t) REVERT: F 302 LEU cc_start: 0.8935 (mt) cc_final: 0.7681 (mt) REVERT: F 334 ARG cc_start: 0.9174 (mtt90) cc_final: 0.8668 (mmt90) REVERT: F 357 GLU cc_start: 0.8344 (tm-30) cc_final: 0.7851 (tm-30) REVERT: F 397 TRP cc_start: 0.7646 (m-10) cc_final: 0.7220 (m-10) outliers start: 0 outliers final: 0 residues processed: 634 average time/residue: 0.3388 time to fit residues: 334.6671 Evaluate side-chains 532 residues out of total 2333 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 532 time to evaluate : 2.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 243 optimal weight: 30.0000 chunk 222 optimal weight: 5.9990 chunk 237 optimal weight: 9.9990 chunk 142 optimal weight: 0.9980 chunk 103 optimal weight: 6.9990 chunk 186 optimal weight: 3.9990 chunk 72 optimal weight: 0.9990 chunk 214 optimal weight: 0.8980 chunk 224 optimal weight: 0.9980 chunk 236 optimal weight: 20.0000 chunk 155 optimal weight: 7.9990 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 HIS ** A 164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 210 GLN ** A 323 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 212 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 372 GLN ** C 323 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 387 HIS D 210 GLN ** D 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 466 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 417 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 210 GLN F 212 ASN F 301 GLN F 317 ASN F 337 ASN ** F 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7121 moved from start: 0.4702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 21457 Z= 0.176 Angle : 0.706 12.148 29190 Z= 0.346 Chirality : 0.048 0.308 3146 Planarity : 0.006 0.102 3837 Dihedral : 5.684 34.986 2886 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 19.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.22 % Favored : 90.78 % Rotamer: Outliers : 0.04 % Allowed : 0.73 % Favored : 99.23 % 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: -3.03 (0.15), residues: 2658 helix: -1.98 (0.30), residues: 239 sheet: -1.36 (0.20), residues: 590 loop : -2.39 (0.14), residues: 1829 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 97 HIS 0.008 0.001 HIS D 361 PHE 0.033 0.002 PHE D 257 TYR 0.015 0.001 TYR F 365 ARG 0.007 0.000 ARG D 106 *********************** REFINEMENT MACRO_CYCLE 9 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 645 residues out of total 2333 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 644 time to evaluate : 2.555 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: A 34 TYR cc_start: 0.8241 (m-80) cc_final: 0.7925 (m-80) REVERT: A 48 TYR cc_start: 0.7471 (m-80) cc_final: 0.6936 (m-80) REVERT: A 97 TRP cc_start: 0.7924 (m100) cc_final: 0.7306 (m100) REVERT: A 165 TRP cc_start: 0.8940 (m100) cc_final: 0.8459 (m100) REVERT: A 204 MET cc_start: 0.4576 (pmm) cc_final: 0.4136 (pmm) REVERT: A 233 MET cc_start: 0.8380 (mmt) cc_final: 0.7482 (mmm) REVERT: A 250 GLN cc_start: 0.8277 (mp-120) cc_final: 0.8007 (mp-120) REVERT: A 257 PHE cc_start: 0.8997 (t80) cc_final: 0.8715 (t80) REVERT: A 328 THR cc_start: 0.8510 (m) cc_final: 0.8030 (m) REVERT: A 360 ARG cc_start: 0.9112 (mmp80) cc_final: 0.8855 (mmm160) REVERT: A 364 GLU cc_start: 0.7659 (pt0) cc_final: 0.7266 (pm20) REVERT: A 369 PHE cc_start: 0.8926 (m-80) cc_final: 0.8564 (m-80) REVERT: A 371 PHE cc_start: 0.7952 (m-80) cc_final: 0.7277 (m-80) REVERT: A 381 GLU cc_start: 0.9111 (mp0) cc_final: 0.8858 (mp0) REVERT: A 389 MET cc_start: 0.8703 (ttt) cc_final: 0.8407 (tmm) REVERT: A 449 LYS cc_start: 0.8823 (mptt) cc_final: 0.8562 (mmtm) REVERT: B 26 TYR cc_start: 0.8238 (m-80) cc_final: 0.7841 (m-80) REVERT: B 68 ARG cc_start: 0.8777 (mmp-170) cc_final: 0.8052 (mmp-170) REVERT: B 74 LEU cc_start: 0.9173 (tp) cc_final: 0.8826 (tp) REVERT: B 145 MET cc_start: 0.9051 (mpp) cc_final: 0.8629 (mpp) REVERT: B 161 LEU cc_start: 0.8585 (tp) cc_final: 0.8326 (tp) REVERT: B 164 HIS cc_start: 0.9200 (p90) cc_final: 0.8823 (p-80) REVERT: B 208 ASP cc_start: 0.9403 (t0) cc_final: 0.9021 (p0) REVERT: B 209 LEU cc_start: 0.9503 (mm) cc_final: 0.8954 (mm) REVERT: B 210 GLN cc_start: 0.9324 (mp10) cc_final: 0.8845 (mp10) REVERT: B 211 THR cc_start: 0.9016 (p) cc_final: 0.8771 (p) REVERT: B 220 ILE cc_start: 0.9755 (pt) cc_final: 0.9537 (pt) REVERT: B 236 ASP cc_start: 0.8371 (t0) cc_final: 0.8131 (t0) REVERT: B 251 MET cc_start: 0.8564 (tpt) cc_final: 0.8248 (tpt) REVERT: B 262 GLU cc_start: 0.6725 (tt0) cc_final: 0.6229 (tt0) REVERT: B 301 GLN cc_start: 0.8951 (mp-120) cc_final: 0.8318 (mp10) REVERT: B 302 LEU cc_start: 0.9058 (pp) cc_final: 0.8561 (pp) REVERT: B 305 LYS cc_start: 0.9505 (mtmt) cc_final: 0.9134 (mtmt) REVERT: B 328 THR cc_start: 0.9180 (m) cc_final: 0.8518 (p) REVERT: B 357 GLU cc_start: 0.8353 (mp0) cc_final: 0.8094 (mp0) REVERT: C 53 ARG cc_start: 0.7211 (mmt-90) cc_final: 0.6884 (ttt-90) REVERT: C 66 GLN cc_start: 0.8412 (mt0) cc_final: 0.7635 (mt0) REVERT: C 108 GLN cc_start: 0.8594 (tp-100) cc_final: 0.8018 (tp40) REVERT: C 150 THR cc_start: 0.7932 (m) cc_final: 0.6991 (m) REVERT: C 154 MET cc_start: 0.8739 (mmp) cc_final: 0.8476 (mmm) REVERT: C 201 PHE cc_start: 0.8318 (m-10) cc_final: 0.7993 (m-10) REVERT: C 204 MET cc_start: 0.7872 (pmm) cc_final: 0.7380 (pmm) REVERT: C 310 GLN cc_start: 0.8678 (tm-30) cc_final: 0.8359 (tm-30) REVERT: C 359 MET cc_start: 0.8341 (mmt) cc_final: 0.7861 (mmt) REVERT: C 383 MET cc_start: 0.8811 (mmt) cc_final: 0.8270 (mmt) REVERT: C 456 GLN cc_start: 0.9406 (tm-30) cc_final: 0.9001 (pm20) REVERT: C 457 TYR cc_start: 0.9217 (m-80) cc_final: 0.8965 (m-80) REVERT: D 40 ARG cc_start: 0.8447 (ptt180) cc_final: 0.7999 (ptp-170) REVERT: D 117 HIS cc_start: 0.8452 (t-90) cc_final: 0.7967 (t-90) REVERT: D 120 LEU cc_start: 0.8573 (mt) cc_final: 0.7925 (pp) REVERT: D 197 VAL cc_start: 0.8371 (t) cc_final: 0.8043 (m) REVERT: D 303 PHE cc_start: 0.8667 (m-80) cc_final: 0.8446 (m-80) REVERT: D 355 TYR cc_start: 0.7662 (m-80) cc_final: 0.7178 (m-80) REVERT: D 361 HIS cc_start: 0.6558 (t70) cc_final: 0.5833 (t70) REVERT: D 364 GLU cc_start: 0.8481 (tm-30) cc_final: 0.8272 (tm-30) REVERT: D 397 TRP cc_start: 0.8768 (m-90) cc_final: 0.8418 (m100) REVERT: D 449 LYS cc_start: 0.7931 (mmtp) cc_final: 0.7557 (mmmt) REVERT: E 41 LEU cc_start: 0.7381 (tt) cc_final: 0.6920 (tt) REVERT: E 66 GLN cc_start: 0.6134 (mt0) cc_final: 0.5641 (mt0) REVERT: E 120 LEU cc_start: 0.8887 (mt) cc_final: 0.8118 (mt) REVERT: E 185 GLU cc_start: 0.8486 (mt-10) cc_final: 0.8263 (mp0) REVERT: E 196 MET cc_start: 0.8798 (mpp) cc_final: 0.8477 (mpp) REVERT: E 232 GLN cc_start: 0.9099 (tt0) cc_final: 0.8457 (mt0) REVERT: E 233 MET cc_start: 0.9446 (ptp) cc_final: 0.8998 (ptp) REVERT: E 303 PHE cc_start: 0.8917 (m-80) cc_final: 0.8167 (m-80) REVERT: E 326 PHE cc_start: 0.8822 (m-80) cc_final: 0.8223 (m-80) REVERT: E 364 GLU cc_start: 0.7433 (mm-30) cc_final: 0.6452 (mm-30) REVERT: E 365 TYR cc_start: 0.8179 (m-80) cc_final: 0.7965 (m-10) REVERT: E 450 PHE cc_start: 0.8004 (m-80) cc_final: 0.7576 (m-80) REVERT: E 461 ARG cc_start: 0.8967 (ptp90) cc_final: 0.8677 (ptt-90) REVERT: F 65 TYR cc_start: 0.9115 (m-10) cc_final: 0.8555 (m-10) REVERT: F 82 LEU cc_start: 0.8208 (mt) cc_final: 0.7984 (mt) REVERT: F 103 GLU cc_start: 0.7534 (tp30) cc_final: 0.7139 (tp30) REVERT: F 149 GLN cc_start: 0.8745 (pt0) cc_final: 0.8470 (pt0) REVERT: F 150 THR cc_start: 0.9461 (m) cc_final: 0.8079 (m) REVERT: F 151 GLN cc_start: 0.8011 (tt0) cc_final: 0.6919 (tt0) REVERT: F 165 TRP cc_start: 0.8864 (m100) cc_final: 0.8345 (m100) REVERT: F 185 GLU cc_start: 0.8088 (tp30) cc_final: 0.7756 (mp0) REVERT: F 192 GLN cc_start: 0.8790 (mt0) cc_final: 0.8523 (mt0) REVERT: F 196 MET cc_start: 0.7692 (mmm) cc_final: 0.7151 (mmm) REVERT: F 204 MET cc_start: 0.8556 (mpp) cc_final: 0.8342 (mpp) REVERT: F 230 TYR cc_start: 0.8589 (m-80) cc_final: 0.8309 (m-80) REVERT: F 248 LYS cc_start: 0.9335 (ttmt) cc_final: 0.9097 (mttt) REVERT: F 249 GLU cc_start: 0.8641 (mp0) cc_final: 0.8173 (mp0) REVERT: F 273 ILE cc_start: 0.8340 (mm) cc_final: 0.8025 (mm) REVERT: F 285 SER cc_start: 0.9339 (t) cc_final: 0.9092 (t) REVERT: F 302 LEU cc_start: 0.8991 (mt) cc_final: 0.7917 (mt) REVERT: F 334 ARG cc_start: 0.9155 (mtt90) cc_final: 0.8601 (mmt90) REVERT: F 356 LYS cc_start: 0.9042 (mmmt) cc_final: 0.8559 (mmtt) REVERT: F 357 GLU cc_start: 0.8331 (tm-30) cc_final: 0.7698 (tm-30) REVERT: F 360 ARG cc_start: 0.7065 (mtt180) cc_final: 0.6412 (mtt180) REVERT: F 397 TRP cc_start: 0.7697 (m-10) cc_final: 0.7418 (m-10) outliers start: 1 outliers final: 1 residues processed: 644 average time/residue: 0.3150 time to fit residues: 310.3069 Evaluate side-chains 547 residues out of total 2333 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 546 time to evaluate : 2.427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 250 optimal weight: 10.0000 chunk 153 optimal weight: 7.9990 chunk 118 optimal weight: 7.9990 chunk 174 optimal weight: 30.0000 chunk 263 optimal weight: 5.9990 chunk 242 optimal weight: 20.0000 chunk 209 optimal weight: 40.0000 chunk 21 optimal weight: 0.0370 chunk 161 optimal weight: 20.0000 chunk 128 optimal weight: 7.9990 chunk 166 optimal weight: 6.9990 overall best weight: 5.8066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 192 GLN ** A 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 323 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 151 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** B 372 GLN C 31 ASN ** C 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 323 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 466 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 212 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 323 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 417 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 301 GLN F 337 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7191 moved from start: 0.4814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 21457 Z= 0.244 Angle : 0.728 11.559 29190 Z= 0.364 Chirality : 0.048 0.263 3146 Planarity : 0.006 0.103 3837 Dihedral : 5.889 35.016 2886 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 24.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.51 % Favored : 88.49 % Rotamer: Outliers : 0.00 % Allowed : 0.64 % Favored : 99.36 % 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: -3.08 (0.15), residues: 2658 helix: -1.96 (0.29), residues: 239 sheet: -1.33 (0.20), residues: 581 loop : -2.46 (0.14), residues: 1838 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP F 308 HIS 0.008 0.002 HIS D 361 PHE 0.031 0.002 PHE E 252 TYR 0.022 0.002 TYR F 365 ARG 0.010 0.001 ARG E 254 ********************** REFINEMENT MACRO_CYCLE 10 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 626 residues out of total 2333 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 626 time to evaluate : 2.650 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: 0.8386 (m-80) cc_final: 0.8089 (m-80) REVERT: A 48 TYR cc_start: 0.7572 (m-80) cc_final: 0.7168 (m-80) REVERT: A 97 TRP cc_start: 0.8053 (m100) cc_final: 0.7591 (m100) REVERT: A 103 GLU cc_start: 0.8187 (tp30) cc_final: 0.7871 (tp30) REVERT: A 151 GLN cc_start: 0.8554 (mm-40) cc_final: 0.8279 (mm-40) REVERT: A 165 TRP cc_start: 0.8972 (m100) cc_final: 0.8463 (m100) REVERT: A 204 MET cc_start: 0.4582 (pmm) cc_final: 0.4017 (pmm) REVERT: A 257 PHE cc_start: 0.9031 (t80) cc_final: 0.8771 (t80) REVERT: A 332 THR cc_start: 0.8797 (p) cc_final: 0.8369 (p) REVERT: A 360 ARG cc_start: 0.9210 (mmp80) cc_final: 0.8926 (mmm160) REVERT: A 364 GLU cc_start: 0.7799 (pt0) cc_final: 0.7270 (pm20) REVERT: A 366 ASP cc_start: 0.8179 (t0) cc_final: 0.7762 (t0) REVERT: A 368 GLN cc_start: 0.8889 (mt0) cc_final: 0.8419 (mt0) REVERT: A 371 PHE cc_start: 0.8368 (m-80) cc_final: 0.7350 (m-80) REVERT: A 381 GLU cc_start: 0.9157 (mp0) cc_final: 0.8931 (mp0) REVERT: A 389 MET cc_start: 0.8662 (ttt) cc_final: 0.8408 (tmm) REVERT: A 412 THR cc_start: 0.9265 (t) cc_final: 0.9012 (t) REVERT: B 26 TYR cc_start: 0.8288 (m-80) cc_final: 0.7952 (m-80) REVERT: B 68 ARG cc_start: 0.8868 (mmp-170) cc_final: 0.8108 (mmp-170) REVERT: B 74 LEU cc_start: 0.9201 (tp) cc_final: 0.8789 (tp) REVERT: B 145 MET cc_start: 0.9103 (mpp) cc_final: 0.8732 (mpp) REVERT: B 210 GLN cc_start: 0.9300 (mp10) cc_final: 0.8945 (mp10) REVERT: B 211 THR cc_start: 0.8953 (p) cc_final: 0.8741 (p) REVERT: B 220 ILE cc_start: 0.9760 (pt) cc_final: 0.9517 (pt) REVERT: B 236 ASP cc_start: 0.8499 (t0) cc_final: 0.8153 (t70) REVERT: B 251 MET cc_start: 0.8638 (tpt) cc_final: 0.8267 (tpt) REVERT: B 301 GLN cc_start: 0.8914 (mp-120) cc_final: 0.8344 (mp10) REVERT: B 302 LEU cc_start: 0.9100 (pp) cc_final: 0.8411 (pp) REVERT: B 303 PHE cc_start: 0.8671 (m-80) cc_final: 0.8444 (m-80) REVERT: B 305 LYS cc_start: 0.9434 (mtmt) cc_final: 0.9069 (mtpt) REVERT: B 328 THR cc_start: 0.9149 (m) cc_final: 0.8369 (p) REVERT: B 461 ARG cc_start: 0.9113 (ttp-110) cc_final: 0.8686 (ptp-110) REVERT: C 53 ARG cc_start: 0.7309 (mmt-90) cc_final: 0.6939 (tpt-90) REVERT: C 66 GLN cc_start: 0.8501 (mt0) cc_final: 0.7816 (mt0) REVERT: C 68 ARG cc_start: 0.8808 (mmt-90) cc_final: 0.8579 (mmt-90) REVERT: C 108 GLN cc_start: 0.8261 (tp-100) cc_final: 0.7939 (tp40) REVERT: C 201 PHE cc_start: 0.8251 (m-10) cc_final: 0.7948 (m-10) REVERT: C 204 MET cc_start: 0.7833 (pmm) cc_final: 0.7272 (pmm) REVERT: C 310 GLN cc_start: 0.8726 (tm-30) cc_final: 0.8428 (tm-30) REVERT: C 359 MET cc_start: 0.8379 (mmt) cc_final: 0.7921 (mmt) REVERT: C 383 MET cc_start: 0.8826 (mmt) cc_final: 0.8296 (mmt) REVERT: C 386 ILE cc_start: 0.9536 (pt) cc_final: 0.9258 (pt) REVERT: C 395 GLU cc_start: 0.9038 (tt0) cc_final: 0.8074 (tm-30) REVERT: D 40 ARG cc_start: 0.8331 (ptt180) cc_final: 0.7974 (ptp-170) REVERT: D 117 HIS cc_start: 0.8495 (t-90) cc_final: 0.7905 (t-90) REVERT: D 120 LEU cc_start: 0.8541 (mt) cc_final: 0.7898 (mt) REVERT: D 204 MET cc_start: 0.7999 (mpp) cc_final: 0.7699 (mpp) REVERT: D 206 PHE cc_start: 0.8044 (m-80) cc_final: 0.7657 (m-80) REVERT: D 355 TYR cc_start: 0.7634 (m-80) cc_final: 0.7212 (m-80) REVERT: D 361 HIS cc_start: 0.6299 (t70) cc_final: 0.5720 (t70) REVERT: D 364 GLU cc_start: 0.8647 (tm-30) cc_final: 0.8161 (tm-30) REVERT: D 445 ASN cc_start: 0.8633 (t0) cc_final: 0.8339 (t0) REVERT: D 449 LYS cc_start: 0.7943 (mmtp) cc_final: 0.7536 (mmmt) REVERT: E 41 LEU cc_start: 0.7140 (tt) cc_final: 0.6706 (tt) REVERT: E 66 GLN cc_start: 0.6229 (mt0) cc_final: 0.5739 (mt0) REVERT: E 120 LEU cc_start: 0.8733 (mt) cc_final: 0.8087 (mt) REVERT: E 185 GLU cc_start: 0.8602 (mt-10) cc_final: 0.8171 (mp0) REVERT: E 196 MET cc_start: 0.8717 (mpp) cc_final: 0.8351 (mpp) REVERT: E 232 GLN cc_start: 0.9073 (tt0) cc_final: 0.8720 (tt0) REVERT: E 233 MET cc_start: 0.9509 (ptp) cc_final: 0.8986 (ptp) REVERT: E 338 MET cc_start: 0.8963 (mpp) cc_final: 0.8605 (mpp) REVERT: E 364 GLU cc_start: 0.7416 (mm-30) cc_final: 0.6376 (mm-30) REVERT: E 365 TYR cc_start: 0.8483 (m-80) cc_final: 0.8192 (m-10) REVERT: E 397 TRP cc_start: 0.7613 (m100) cc_final: 0.7357 (m100) REVERT: F 103 GLU cc_start: 0.7420 (tp30) cc_final: 0.6905 (tp30) REVERT: F 124 ASP cc_start: 0.7675 (t70) cc_final: 0.7310 (t0) REVERT: F 125 ASP cc_start: 0.8831 (p0) cc_final: 0.8272 (p0) REVERT: F 149 GLN cc_start: 0.8772 (pt0) cc_final: 0.8408 (pt0) REVERT: F 150 THR cc_start: 0.9531 (m) cc_final: 0.8224 (m) REVERT: F 151 GLN cc_start: 0.8172 (tt0) cc_final: 0.6921 (tt0) REVERT: F 165 TRP cc_start: 0.8925 (m100) cc_final: 0.8439 (m100) REVERT: F 185 GLU cc_start: 0.8090 (tp30) cc_final: 0.7659 (mt-10) REVERT: F 192 GLN cc_start: 0.8833 (mt0) cc_final: 0.8576 (mt0) REVERT: F 196 MET cc_start: 0.7789 (mmm) cc_final: 0.7331 (mmm) REVERT: F 204 MET cc_start: 0.8501 (mpp) cc_final: 0.8253 (mpp) REVERT: F 208 ASP cc_start: 0.9389 (t0) cc_final: 0.8926 (m-30) REVERT: F 230 TYR cc_start: 0.8630 (m-80) cc_final: 0.8426 (m-80) REVERT: F 249 GLU cc_start: 0.8645 (mp0) cc_final: 0.8367 (mp0) REVERT: F 254 ARG cc_start: 0.9245 (tpt-90) cc_final: 0.8697 (tpp-160) REVERT: F 273 ILE cc_start: 0.8391 (mm) cc_final: 0.8066 (mm) REVERT: F 285 SER cc_start: 0.9352 (t) cc_final: 0.9089 (t) REVERT: F 302 LEU cc_start: 0.8958 (mt) cc_final: 0.7888 (mt) REVERT: F 334 ARG cc_start: 0.9133 (mtt90) cc_final: 0.8579 (mmt90) REVERT: F 357 GLU cc_start: 0.8440 (tm-30) cc_final: 0.7943 (tm-30) REVERT: F 397 TRP cc_start: 0.7708 (m-10) cc_final: 0.7293 (m-10) outliers start: 0 outliers final: 0 residues processed: 626 average time/residue: 0.3193 time to fit residues: 306.9391 Evaluate side-chains 524 residues out of total 2333 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 524 time to evaluate : 2.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 223 optimal weight: 8.9990 chunk 64 optimal weight: 9.9990 chunk 193 optimal weight: 40.0000 chunk 30 optimal weight: 9.9990 chunk 58 optimal weight: 8.9990 chunk 209 optimal weight: 20.0000 chunk 87 optimal weight: 6.9990 chunk 215 optimal weight: 0.6980 chunk 26 optimal weight: 5.9990 chunk 38 optimal weight: 7.9990 chunk 184 optimal weight: 6.9990 overall best weight: 5.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 323 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 212 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 258 ASN B 372 GLN ** C 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 323 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 372 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 387 HIS C 398 ASN ** C 456 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 466 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 212 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 232 GLN ** E 417 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 466 GLN ** F 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 210 GLN F 301 GLN F 317 ASN F 337 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4036 r_free = 0.4036 target = 0.134329 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.109284 restraints weight = 62967.888| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.112917 restraints weight = 37008.710| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.115435 restraints weight = 25129.936| |-----------------------------------------------------------------------------| r_work (final): 0.3784 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7232 moved from start: 0.4940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 21457 Z= 0.235 Angle : 0.729 11.553 29190 Z= 0.365 Chirality : 0.049 0.294 3146 Planarity : 0.006 0.103 3837 Dihedral : 5.928 35.201 2886 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 24.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.40 % Favored : 88.60 % Rotamer: Outliers : 0.04 % Allowed : 0.47 % Favored : 99.49 % 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: -3.07 (0.15), residues: 2658 helix: -1.97 (0.29), residues: 237 sheet: -1.35 (0.20), residues: 572 loop : -2.44 (0.13), residues: 1849 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP F 308 HIS 0.010 0.002 HIS C 35 PHE 0.043 0.002 PHE C 33 TYR 0.047 0.002 TYR E 307 ARG 0.007 0.001 ARG D 106 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5818.98 seconds wall clock time: 105 minutes 52.29 seconds (6352.29 seconds total)