Starting phenix.real_space_refine (version: 1.21rc1) on Tue Oct 10 12:34:50 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6l31_0816/10_2023/6l31_0816.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6l31_0816/10_2023/6l31_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_0816/10_2023/6l31_0816.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6l31_0816/10_2023/6l31_0816.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6l31_0816/10_2023/6l31_0816.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6l31_0816/10_2023/6l31_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: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/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: 10.71, 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: 8.33 Conformation dependent library (CDL) restraints added in 3.0 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: 1.81 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: 5.94 Time building geometry restraints manager: 8.93 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: 4.340 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: 16.780 Check model and map are aligned: 0.330 Set scattering table: 0.200 Process input model: 52.510 Find NCS groups from input model: 1.630 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 78.900 ------------------------------------------------------------------------------- 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 *********************** 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 : 2.411 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 outliers start: 53 outliers final: 19 residues processed: 729 average time/residue: 0.3284 time to fit residues: 364.5175 Evaluate side-chains 532 residues out of total 2333 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 513 time to evaluate : 2.571 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 0 residues processed: 19 average time/residue: 0.2625 time to fit residues: 11.6741 ------------------------------------------------------------------------------- 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: 0.2980 chunk 111 optimal weight: 20.0000 chunk 68 optimal weight: 0.9990 chunk 134 optimal weight: 5.9990 chunk 106 optimal weight: 6.9990 chunk 206 optimal weight: 20.0000 chunk 80 optimal weight: 6.9990 chunk 125 optimal weight: 1.9990 chunk 154 optimal weight: 10.0000 chunk 239 optimal weight: 8.9990 overall best weight: 3.2588 ------------------------------------------------------------------------------- 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 255 HIS A 258 ASN 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 ** both conformations clash, **PLEASE CHECK MANUALLY** D 139 ASN ** D 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 352 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 466 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 164 HIS E 212 ASN E 337 ASN ** E 417 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 139 ASN ** F 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 210 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: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7189 moved from start: 0.2492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 21457 Z= 0.229 Angle : 0.774 12.672 29190 Z= 0.398 Chirality : 0.049 0.279 3146 Planarity : 0.007 0.109 3837 Dihedral : 7.289 45.069 2886 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 20.42 Ramachandran Plot: Outliers : 0.19 % Allowed : 9.86 % Favored : 89.95 % Rotamer: Outliers : 0.21 % Allowed : 6.39 % Favored : 93.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.08 % Twisted Proline : 2.22 % Twisted General : 0.20 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.90 (0.14), residues: 2658 helix: -3.19 (0.24), residues: 242 sheet: -1.89 (0.19), residues: 598 loop : -2.95 (0.13), residues: 1818 *********************** 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 682 residues out of total 2333 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 677 time to evaluate : 2.340 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 outliers start: 5 outliers final: 1 residues processed: 682 average time/residue: 0.3322 time to fit residues: 343.4566 Evaluate side-chains 508 residues out of total 2333 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 507 time to evaluate : 2.442 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1812 time to fit residues: 3.6843 ------------------------------------------------------------------------------- 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: 10.0000 chunk 74 optimal weight: 20.0000 chunk 199 optimal weight: 30.0000 chunk 163 optimal weight: 8.9990 chunk 66 optimal weight: 7.9990 chunk 240 optimal weight: 5.9990 chunk 259 optimal weight: 1.9990 chunk 213 optimal weight: 0.0050 chunk 238 optimal weight: 8.9990 chunk 81 optimal weight: 7.9990 chunk 192 optimal weight: 30.0000 overall best weight: 4.8002 ------------------------------------------------------------------------------- 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 323 ASN ** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 ** D 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 352 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 361 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 466 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 139 ASN ** 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 149 GLN ** F 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 164 HIS ** F 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 212 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 301 GLN F 337 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7188 moved from start: 0.3139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 21457 Z= 0.241 Angle : 0.745 11.496 29190 Z= 0.382 Chirality : 0.048 0.313 3146 Planarity : 0.007 0.164 3837 Dihedral : 6.857 44.107 2886 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 22.22 Ramachandran Plot: Outliers : 0.11 % Allowed : 10.84 % Favored : 89.05 % Rotamer: Outliers : 0.09 % Allowed : 5.66 % 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: -3.65 (0.14), residues: 2658 helix: -2.76 (0.27), residues: 242 sheet: -1.77 (0.19), residues: 620 loop : -2.80 (0.13), residues: 1796 *********************** 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 645 residues out of total 2333 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 643 time to evaluate : 2.423 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 643 average time/residue: 0.3396 time to fit residues: 335.8266 Evaluate side-chains 505 residues out of total 2333 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 504 time to evaluate : 2.315 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.2190 time to fit residues: 3.6434 ------------------------------------------------------------------------------- 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: 1.9990 chunk 180 optimal weight: 5.9990 chunk 124 optimal weight: 30.0000 chunk 26 optimal weight: 30.0000 chunk 114 optimal weight: 20.0000 chunk 161 optimal weight: 10.0000 chunk 241 optimal weight: 30.0000 chunk 255 optimal weight: 50.0000 chunk 125 optimal weight: 10.0000 chunk 228 optimal weight: 20.0000 chunk 68 optimal weight: 20.0000 overall best weight: 9.5996 ------------------------------------------------------------------------------- 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 212 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 361 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 406 ASN A 466 GLN ** B 212 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 372 GLN ** C 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 323 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 258 ASN ** D 466 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 212 ASN E 313 GLN ** 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 31 ASN F 149 GLN F 164 HIS ** F 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 212 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 337 ASN ** F 361 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 0.7263 moved from start: 0.3609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.089 21457 Z= 0.349 Angle : 0.834 14.825 29190 Z= 0.428 Chirality : 0.051 0.347 3146 Planarity : 0.007 0.108 3837 Dihedral : 7.068 40.003 2886 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 30.54 Ramachandran Plot: Outliers : 0.08 % Allowed : 12.45 % Favored : 87.47 % Rotamer: Outliers : 0.09 % Allowed : 6.17 % Favored : 93.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.08 % Twisted Proline : 1.11 % Twisted General : 0.20 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.66 (0.14), residues: 2658 helix: -2.72 (0.26), residues: 229 sheet: -1.80 (0.19), residues: 615 loop : -2.80 (0.13), residues: 1814 *********************** 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 640 residues out of total 2333 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 638 time to evaluate : 2.432 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 outliers start: 2 outliers final: 1 residues processed: 640 average time/residue: 0.3210 time to fit residues: 313.4523 Evaluate side-chains 489 residues out of total 2333 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 488 time to evaluate : 2.354 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.2296 time to fit residues: 3.5627 ------------------------------------------------------------------------------- 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: 9.9990 chunk 144 optimal weight: 9.9990 chunk 3 optimal weight: 7.9990 chunk 190 optimal weight: 40.0000 chunk 105 optimal weight: 6.9990 chunk 217 optimal weight: 20.0000 chunk 176 optimal weight: 5.9990 chunk 0 optimal weight: 20.0000 chunk 130 optimal weight: 2.9990 chunk 229 optimal weight: 7.9990 chunk 64 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 66 GLN A 192 GLN ** A 212 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 250 GLN ** A 323 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 466 GLN ** 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 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 323 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 387 HIS C 466 GLN ** D 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 361 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 466 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 35 HIS ** 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 149 GLN F 164 HIS ** F 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 317 ASN F 337 ASN F 361 HIS ** F 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 466 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7215 moved from start: 0.3931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 21457 Z= 0.261 Angle : 0.764 14.969 29190 Z= 0.385 Chirality : 0.049 0.342 3146 Planarity : 0.006 0.106 3837 Dihedral : 6.731 38.273 2886 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 26.50 Ramachandran Plot: Outliers : 0.04 % Allowed : 11.51 % Favored : 88.45 % Rotamer: Outliers : 0.17 % Allowed : 3.99 % Favored : 95.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.08 % Twisted Proline : 1.11 % 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: -3.57 (0.15), residues: 2658 helix: -2.61 (0.26), residues: 236 sheet: -1.74 (0.20), residues: 589 loop : -2.74 (0.13), residues: 1833 *********************** 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: 4 poor density : 629 time to evaluate : 2.269 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 outliers start: 4 outliers final: 3 residues processed: 632 average time/residue: 0.3162 time to fit residues: 306.2839 Evaluate side-chains 500 residues out of total 2333 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 497 time to evaluate : 2.192 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.2089 time to fit residues: 4.1156 ------------------------------------------------------------------------------- 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: 0.2980 chunk 229 optimal weight: 30.0000 chunk 50 optimal weight: 30.0000 chunk 149 optimal weight: 30.0000 chunk 62 optimal weight: 6.9990 chunk 255 optimal weight: 20.0000 chunk 212 optimal weight: 6.9990 chunk 118 optimal weight: 8.9990 chunk 21 optimal weight: 0.9990 chunk 84 optimal weight: 9.9990 chunk 134 optimal weight: 6.9990 overall best weight: 4.4588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 142 ASN ** A 212 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 323 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 466 GLN B 121 ASN B 212 ASN ** B 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 372 GLN C 108 GLN C 255 HIS C 323 ASN ** C 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 466 GLN ** D 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 164 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 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 149 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 149 GLN F 164 HIS ** F 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 317 ASN F 337 ASN ** F 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7186 moved from start: 0.4237 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= 0.227 Angle : 0.734 11.022 29190 Z= 0.368 Chirality : 0.048 0.272 3146 Planarity : 0.006 0.105 3837 Dihedral : 6.454 36.409 2886 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 24.24 Ramachandran Plot: Outliers : 0.04 % Allowed : 10.91 % Favored : 89.05 % Rotamer: Outliers : 0.09 % Allowed : 3.13 % Favored : 96.79 % 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: -3.38 (0.15), residues: 2658 helix: -2.33 (0.29), residues: 231 sheet: -1.52 (0.21), residues: 564 loop : -2.65 (0.13), residues: 1863 *********************** 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 637 residues out of total 2333 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 635 time to evaluate : 2.594 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 outliers start: 2 outliers final: 2 residues processed: 636 average time/residue: 0.3285 time to fit residues: 318.6798 Evaluate side-chains 506 residues out of total 2333 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 504 time to evaluate : 2.575 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.2358 time to fit residues: 4.2954 ------------------------------------------------------------------------------- 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: 9.9990 chunk 28 optimal weight: 0.9990 chunk 145 optimal weight: 10.0000 chunk 186 optimal weight: 30.0000 chunk 144 optimal weight: 8.9990 chunk 215 optimal weight: 0.0570 chunk 142 optimal weight: 6.9990 chunk 254 optimal weight: 5.9990 chunk 159 optimal weight: 20.0000 chunk 155 optimal weight: 7.9990 chunk 117 optimal weight: 7.9990 overall best weight: 4.4106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 192 GLN ** A 212 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 323 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 466 GLN ** 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 C 387 HIS D 78 ASN ** D 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 466 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 212 ASN ** E 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 372 GLN ** E 417 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 149 GLN F 164 HIS ** F 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 317 ASN F 337 ASN ** F 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7174 moved from start: 0.4455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 21457 Z= 0.218 Angle : 0.736 11.935 29190 Z= 0.368 Chirality : 0.048 0.248 3146 Planarity : 0.006 0.165 3837 Dihedral : 6.280 35.340 2886 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 22.90 Ramachandran Plot: Outliers : 0.04 % Allowed : 11.06 % Favored : 88.90 % Rotamer: Outliers : 0.09 % Allowed : 1.67 % Favored : 98.24 % 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: -3.30 (0.15), residues: 2658 helix: -2.21 (0.30), residues: 225 sheet: -1.54 (0.20), residues: 597 loop : -2.59 (0.13), residues: 1836 *********************** 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: 2 poor density : 648 time to evaluate : 2.388 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 outliers start: 2 outliers final: 1 residues processed: 649 average time/residue: 0.3341 time to fit residues: 334.0087 Evaluate side-chains 521 residues out of total 2333 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 520 time to evaluate : 2.477 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.2135 time to fit residues: 3.7669 ------------------------------------------------------------------------------- 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: 40.0000 chunk 101 optimal weight: 0.1980 chunk 151 optimal weight: 0.0870 chunk 76 optimal weight: 50.0000 chunk 49 optimal weight: 1.9990 chunk 161 optimal weight: 30.0000 chunk 173 optimal weight: 40.0000 chunk 125 optimal weight: 0.0060 chunk 23 optimal weight: 5.9990 chunk 200 optimal weight: 9.9990 chunk 231 optimal weight: 40.0000 overall best weight: 1.6578 ------------------------------------------------------------------------------- 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 164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 212 ASN ** A 323 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 121 ASN ** B 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 212 ASN ** B 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 372 GLN C 108 GLN C 255 HIS D 78 ASN D 108 GLN ** D 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 164 HIS ** D 466 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 212 ASN ** E 289 ASN ** 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 149 GLN F 164 HIS ** F 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 317 ASN F 337 ASN ** F 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7119 moved from start: 0.4747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 21457 Z= 0.189 Angle : 0.731 11.776 29190 Z= 0.360 Chirality : 0.048 0.243 3146 Planarity : 0.006 0.162 3837 Dihedral : 5.972 35.038 2886 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 20.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.44 % Favored : 90.56 % 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 : 0.04 % 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: -3.15 (0.15), residues: 2658 helix: -2.20 (0.29), residues: 239 sheet: -1.39 (0.20), residues: 598 loop : -2.48 (0.13), residues: 1821 *********************** 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 649 residues out of total 2333 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 649 time to evaluate : 2.292 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 outliers start: 0 outliers final: 0 residues processed: 649 average time/residue: 0.3264 time to fit residues: 325.3025 Evaluate side-chains 528 residues out of total 2333 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 528 time to evaluate : 2.534 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.3091 ------------------------------------------------------------------------------- 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: 6.9990 chunk 222 optimal weight: 9.9990 chunk 237 optimal weight: 30.0000 chunk 142 optimal weight: 10.0000 chunk 103 optimal weight: 0.0040 chunk 186 optimal weight: 50.0000 chunk 72 optimal weight: 0.4980 chunk 214 optimal weight: 0.8980 chunk 224 optimal weight: 7.9990 chunk 236 optimal weight: 6.9990 chunk 155 optimal weight: 9.9990 overall best weight: 3.0796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 HIS A 93 GLN A 192 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 31 ASN C 108 GLN C 387 HIS D 164 HIS D 258 ASN D 315 HIS ** D 466 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 212 ASN E 258 ASN ** 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 164 HIS ** F 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 255 HIS F 317 ASN F 337 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7133 moved from start: 0.4952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 21457 Z= 0.200 Angle : 0.718 11.905 29190 Z= 0.357 Chirality : 0.048 0.228 3146 Planarity : 0.006 0.105 3837 Dihedral : 5.879 34.891 2886 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 21.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.53 % Favored : 89.47 % Rotamer: Outliers : 0.13 % Allowed : 0.90 % Favored : 98.97 % 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: -3.12 (0.15), residues: 2658 helix: -2.13 (0.29), residues: 239 sheet: -1.42 (0.20), residues: 597 loop : -2.44 (0.14), residues: 1822 *********************** 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 625 residues out of total 2333 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 622 time to evaluate : 2.251 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 outliers start: 3 outliers final: 1 residues processed: 622 average time/residue: 0.3230 time to fit residues: 309.1540 Evaluate side-chains 494 residues out of total 2333 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 493 time to evaluate : 2.452 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.2134 time to fit residues: 3.8514 ------------------------------------------------------------------------------- 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: 5.9990 chunk 153 optimal weight: 20.0000 chunk 118 optimal weight: 5.9990 chunk 174 optimal weight: 8.9990 chunk 263 optimal weight: 0.0070 chunk 242 optimal weight: 7.9990 chunk 209 optimal weight: 7.9990 chunk 21 optimal weight: 0.5980 chunk 161 optimal weight: 8.9990 chunk 128 optimal weight: 8.9990 chunk 166 optimal weight: 5.9990 overall best weight: 3.7204 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 93 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 C 466 GLN D 164 HIS ** D 466 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 212 ASN ** 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 317 ASN F 337 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7137 moved from start: 0.5079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 21457 Z= 0.206 Angle : 0.722 11.934 29190 Z= 0.357 Chirality : 0.048 0.265 3146 Planarity : 0.006 0.102 3837 Dihedral : 5.848 35.169 2886 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 22.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.12 % Favored : 89.88 % Rotamer: Outliers : 0.04 % Allowed : 0.43 % Favored : 99.53 % 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: -3.10 (0.15), residues: 2658 helix: -2.03 (0.29), residues: 239 sheet: -1.39 (0.21), residues: 567 loop : -2.44 (0.13), residues: 1852 ********************** 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 616 residues out of total 2333 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 615 time to evaluate : 2.601 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 outliers start: 1 outliers final: 1 residues processed: 616 average time/residue: 0.3332 time to fit residues: 318.5201 Evaluate side-chains 502 residues out of total 2333 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 501 time to evaluate : 2.416 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.2598 time to fit residues: 3.7330 ------------------------------------------------------------------------------- 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: 30.0000 chunk 193 optimal weight: 8.9990 chunk 30 optimal weight: 20.0000 chunk 58 optimal weight: 7.9990 chunk 209 optimal weight: 9.9990 chunk 87 optimal weight: 8.9990 chunk 215 optimal weight: 6.9990 chunk 26 optimal weight: 5.9990 chunk 38 optimal weight: 7.9990 chunk 184 optimal weight: 20.0000 overall best weight: 7.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 192 GLN ** A 323 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 372 GLN ** C 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 387 HIS ** D 361 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 466 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 212 ASN ** E 255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 258 ASN ** E 417 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 466 GLN ** F 108 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 317 ASN F 337 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.132035 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.104865 restraints weight = 64841.035| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.108431 restraints weight = 39185.052| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.110969 restraints weight = 27275.563| |-----------------------------------------------------------------------------| r_work (final): 0.3715 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7285 moved from start: 0.5125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.080 21457 Z= 0.287 Angle : 0.775 11.464 29190 Z= 0.391 Chirality : 0.049 0.295 3146 Planarity : 0.006 0.104 3837 Dihedral : 6.224 35.583 2886 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 28.23 Ramachandran Plot: Outliers : 0.08 % Allowed : 12.45 % Favored : 87.47 % 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 : 0.08 % 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: -3.26 (0.15), residues: 2658 helix: -2.07 (0.28), residues: 243 sheet: -1.49 (0.20), residues: 590 loop : -2.58 (0.13), residues: 1825 Origin is already at (0, 0, 0), no shifts will be applied Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_fail.pdb'. Return code: -15 Dumping stderr: