Starting phenix.real_space_refine (version: dev) on Tue May 17 10:07:44 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6voh_21264/05_2022/6voh_21264_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6voh_21264/05_2022/6voh_21264.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.16 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6voh_21264/05_2022/6voh_21264.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6voh_21264/05_2022/6voh_21264.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6voh_21264/05_2022/6voh_21264_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6voh_21264/05_2022/6voh_21264_updated.pdb" } resolution = 4.16 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 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 Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "E PHE 278": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 430": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g TYR 214": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4597/modules/chem_data/mon_lib" Total number of atoms: 39159 Number of models: 1 Model: "" Number of chains: 31 Chain: "A" Number of atoms: 3850 Number of conformers: 1 Conformer: "" Number of residues, atoms: 501, 3850 Classifications: {'peptide': 501} Link IDs: {'PTRANS': 16, 'TRANS': 483, 'PCIS': 1} Chain: "C" Number of atoms: 3843 Number of conformers: 1 Conformer: "" Number of residues, atoms: 500, 3843 Classifications: {'peptide': 500} Link IDs: {'PTRANS': 16, 'TRANS': 482, 'PCIS': 1} Chain: "B" Number of atoms: 3854 Number of conformers: 1 Conformer: "" Number of residues, atoms: 502, 3854 Classifications: {'peptide': 502} Link IDs: {'PTRANS': 17, 'TRANS': 484} Chain: "D" Number of atoms: 3619 Number of conformers: 1 Conformer: "" Number of residues, atoms: 478, 3619 Classifications: {'peptide': 478} Link IDs: {'PTRANS': 24, 'TRANS': 452, 'PCIS': 1} Chain: "E" Number of atoms: 3645 Number of conformers: 1 Conformer: "" Number of residues, atoms: 481, 3645 Classifications: {'peptide': 481} Link IDs: {'PTRANS': 24, 'TRANS': 455, 'PCIS': 1} Chain: "F" Number of atoms: 3636 Number of conformers: 1 Conformer: "" Number of residues, atoms: 480, 3636 Classifications: {'peptide': 480} Link IDs: {'PTRANS': 24, 'TRANS': 454, 'PCIS': 1} Chain: "d" Number of atoms: 1384 Number of conformers: 1 Conformer: "" Number of residues, atoms: 179, 1384 Classifications: {'peptide': 179} Link IDs: {'PTRANS': 4, 'TRANS': 174} Chain: "g" Number of atoms: 2508 Number of conformers: 1 Conformer: "" Number of residues, atoms: 323, 2508 Classifications: {'peptide': 323} Link IDs: {'PTRANS': 12, 'TRANS': 310} Chain: "e" Number of atoms: 1007 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1007 Classifications: {'peptide': 131} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 126} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "J" Number of atoms: 1068 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1068 Classifications: {'peptide': 136} Link IDs: {'PTRANS': 3, 'TRANS': 132} Chain: "I" Number of atoms: 1237 Number of conformers: 1 Conformer: "" Number of residues, atoms: 153, 1237 Classifications: {'peptide': 153} Link IDs: {'TRANS': 152} Chain: "a" Number of atoms: 1741 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1741 Classifications: {'peptide': 223} Link IDs: {'PTRANS': 14, 'TRANS': 208} Chain: "T" Number of atoms: 544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 544 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 3, 'TRANS': 75} Chain: "Y" Number of atoms: 544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 544 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 3, 'TRANS': 75} Chain: "X" Number of atoms: 544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 544 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 3, 'TRANS': 75} Chain: "W" Number of atoms: 544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 544 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 3, 'TRANS': 75} Chain: "V" Number of atoms: 544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 544 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 3, 'TRANS': 75} Chain: "U" Number of atoms: 544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 544 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 3, 'TRANS': 75} Chain: "Z" Number of atoms: 544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 544 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 3, 'TRANS': 75} Chain: "S" Number of atoms: 544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 544 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 3, 'TRANS': 75} Chain: "R" Number of atoms: 544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 544 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 3, 'TRANS': 75} Chain: "Q" Number of atoms: 544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 544 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 3, 'TRANS': 75} Chain: "M" Number of atoms: 544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 544 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 3, 'TRANS': 75} Chain: "N" Number of atoms: 544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 544 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 3, 'TRANS': 75} Chain: "O" Number of atoms: 544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 544 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 3, 'TRANS': 75} Chain: "P" Number of atoms: 544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 544 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 3, 'TRANS': 75} Chain: "A" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 21.30, per 1000 atoms: 0.54 Number of scatterers: 39159 At special positions: 0 Unit cell: (163.28, 204.88, 168.48, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 131 16.00 P 14 15.00 O 7486 8.00 N 6674 7.00 C 24854 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS g 240 " - pdb=" SG CYS g 246 " distance=2.05 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: 18.86 Conformation dependent library (CDL) restraints added in 6.5 seconds 10282 Ramachandran restraints generated. 5141 Oldfield, 0 Emsley, 5141 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9436 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 170 helices and 21 sheets defined 53.5% alpha, 4.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.52 Creating SS restraints... Processing helix chain 'A' and resid 9 through 24 removed outlier: 4.154A pdb=" N ILE A 12 " --> pdb=" O ILE A 9 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLU A 18 " --> pdb=" O GLU A 15 " (cutoff:3.500A) Processing helix chain 'A' and resid 152 through 155 No H-bonds generated for 'chain 'A' and resid 152 through 155' Processing helix chain 'A' and resid 176 through 186 Processing helix chain 'A' and resid 203 through 215 Processing helix chain 'A' and resid 233 through 252 Proline residue: A 240 - end of helix removed outlier: 3.902A pdb=" N PHE A 250 " --> pdb=" O LEU A 246 " (cutoff:3.500A) Processing helix chain 'A' and resid 264 through 277 Processing helix chain 'A' and resid 284 through 286 No H-bonds generated for 'chain 'A' and resid 284 through 286' Processing helix chain 'A' and resid 289 through 299 removed outlier: 4.523A pdb=" N PHE A 292 " --> pdb=" O GLY A 289 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N TYR A 293 " --> pdb=" O ASP A 290 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N LEU A 294 " --> pdb=" O VAL A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 307 through 309 No H-bonds generated for 'chain 'A' and resid 307 through 309' Processing helix chain 'A' and resid 330 through 336 Processing helix chain 'A' and resid 347 through 350 No H-bonds generated for 'chain 'A' and resid 347 through 350' Processing helix chain 'A' and resid 368 through 371 Processing helix chain 'A' and resid 374 through 379 Processing helix chain 'A' and resid 383 through 396 removed outlier: 4.137A pdb=" N GLU A 392 " --> pdb=" O ALA A 388 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 418 removed outlier: 3.699A pdb=" N ALA A 412 " --> pdb=" O GLN A 408 " (cutoff:3.500A) Processing helix chain 'A' and resid 431 through 442 removed outlier: 4.536A pdb=" N THR A 437 " --> pdb=" O GLU A 433 " (cutoff:3.500A) Processing helix chain 'A' and resid 444 through 446 No H-bonds generated for 'chain 'A' and resid 444 through 446' Processing helix chain 'A' and resid 454 through 467 Processing helix chain 'A' and resid 470 through 477 Processing helix chain 'A' and resid 484 through 503 removed outlier: 4.093A pdb=" N ALA A 488 " --> pdb=" O GLU A 484 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N LEU A 489 " --> pdb=" O GLU A 485 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LEU A 490 " --> pdb=" O ALA A 486 " (cutoff:3.500A) Processing helix chain 'C' and resid 8 through 19 removed outlier: 3.698A pdb=" N ILE C 13 " --> pdb=" O ILE C 9 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N GLU C 15 " --> pdb=" O LYS C 11 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N ARG C 16 " --> pdb=" O ILE C 12 " (cutoff:3.500A) Processing helix chain 'C' and resid 102 through 104 No H-bonds generated for 'chain 'C' and resid 102 through 104' Processing helix chain 'C' and resid 153 through 156 No H-bonds generated for 'chain 'C' and resid 153 through 156' Processing helix chain 'C' and resid 176 through 186 Processing helix chain 'C' and resid 203 through 216 Processing helix chain 'C' and resid 218 through 221 Processing helix chain 'C' and resid 233 through 252 Proline residue: C 240 - end of helix removed outlier: 3.535A pdb=" N TYR C 249 " --> pdb=" O ALA C 245 " (cutoff:3.500A) Processing helix chain 'C' and resid 264 through 277 Processing helix chain 'C' and resid 284 through 286 No H-bonds generated for 'chain 'C' and resid 284 through 286' Processing helix chain 'C' and resid 291 through 299 Processing helix chain 'C' and resid 330 through 338 Processing helix chain 'C' and resid 347 through 351 Processing helix chain 'C' and resid 374 through 399 removed outlier: 4.481A pdb=" N GLY C 381 " --> pdb=" O LYS C 377 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N LYS C 382 " --> pdb=" O LYS C 378 " (cutoff:3.500A) removed outlier: 5.155A pdb=" N ALA C 395 " --> pdb=" O ALA C 391 " (cutoff:3.500A) removed outlier: 5.618A pdb=" N PHE C 396 " --> pdb=" O GLU C 392 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ALA C 397 " --> pdb=" O LEU C 393 " (cutoff:3.500A) removed outlier: 4.709A pdb=" N GLN C 398 " --> pdb=" O GLU C 394 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N PHE C 399 " --> pdb=" O ALA C 395 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 421 removed outlier: 3.908A pdb=" N GLU C 419 " --> pdb=" O GLN C 415 " (cutoff:3.500A) Processing helix chain 'C' and resid 431 through 442 Processing helix chain 'C' and resid 452 through 468 removed outlier: 3.618A pdb=" N ARG C 455 " --> pdb=" O ASP C 452 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N TYR C 457 " --> pdb=" O VAL C 454 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLU C 460 " --> pdb=" O TYR C 457 " (cutoff:3.500A) Processing helix chain 'C' and resid 470 through 478 Processing helix chain 'C' and resid 484 through 502 Processing helix chain 'B' and resid 10 through 18 removed outlier: 3.535A pdb=" N GLU B 15 " --> pdb=" O LYS B 11 " (cutoff:3.500A) Processing helix chain 'B' and resid 152 through 157 Processing helix chain 'B' and resid 177 through 188 removed outlier: 3.585A pdb=" N GLN B 187 " --> pdb=" O THR B 183 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N GLN B 188 " --> pdb=" O ILE B 184 " (cutoff:3.500A) Processing helix chain 'B' and resid 203 through 216 Processing helix chain 'B' and resid 218 through 220 No H-bonds generated for 'chain 'B' and resid 218 through 220' Processing helix chain 'B' and resid 233 through 252 Proline residue: B 240 - end of helix removed outlier: 4.299A pdb=" N PHE B 250 " --> pdb=" O LEU B 246 " (cutoff:3.500A) Processing helix chain 'B' and resid 264 through 276 Processing helix chain 'B' and resid 284 through 286 No H-bonds generated for 'chain 'B' and resid 284 through 286' Processing helix chain 'B' and resid 291 through 299 Processing helix chain 'B' and resid 331 through 338 Processing helix chain 'B' and resid 347 through 352 Processing helix chain 'B' and resid 368 through 370 No H-bonds generated for 'chain 'B' and resid 368 through 370' Processing helix chain 'B' and resid 376 through 395 Processing helix chain 'B' and resid 411 through 420 Processing helix chain 'B' and resid 431 through 442 removed outlier: 3.903A pdb=" N GLY B 441 " --> pdb=" O THR B 437 " (cutoff:3.500A) Processing helix chain 'B' and resid 454 through 468 removed outlier: 4.463A pdb=" N GLU B 460 " --> pdb=" O LYS B 456 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N LYS B 466 " --> pdb=" O ARG B 462 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N THR B 467 " --> pdb=" O THR B 463 " (cutoff:3.500A) Processing helix chain 'B' and resid 470 through 478 Processing helix chain 'B' and resid 484 through 502 Processing helix chain 'D' and resid 104 through 106 No H-bonds generated for 'chain 'D' and resid 104 through 106' Processing helix chain 'D' and resid 154 through 158 Processing helix chain 'D' and resid 178 through 188 removed outlier: 3.837A pdb=" N ILE D 182 " --> pdb=" O LYS D 178 " (cutoff:3.500A) Processing helix chain 'D' and resid 206 through 219 Processing helix chain 'D' and resid 228 through 230 No H-bonds generated for 'chain 'D' and resid 228 through 230' Processing helix chain 'D' and resid 249 through 262 removed outlier: 3.641A pdb=" N PHE D 260 " --> pdb=" O MET D 256 " (cutoff:3.500A) Processing helix chain 'D' and resid 275 through 288 removed outlier: 3.560A pdb=" N VAL D 279 " --> pdb=" O ILE D 275 " (cutoff:3.500A) Processing helix chain 'D' and resid 305 through 311 Processing helix chain 'D' and resid 330 through 332 No H-bonds generated for 'chain 'D' and resid 330 through 332' Processing helix chain 'D' and resid 337 through 345 removed outlier: 3.887A pdb=" N THR D 342 " --> pdb=" O ALA D 338 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ALA D 344 " --> pdb=" O ALA D 340 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N HIS D 345 " --> pdb=" O THR D 341 " (cutoff:3.500A) Processing helix chain 'D' and resid 354 through 359 Processing helix chain 'D' and resid 377 through 380 No H-bonds generated for 'chain 'D' and resid 377 through 380' Processing helix chain 'D' and resid 382 through 405 removed outlier: 4.703A pdb=" N ASP D 403 " --> pdb=" O LYS D 399 " (cutoff:3.500A) removed outlier: 5.156A pdb=" N ILE D 404 " --> pdb=" O GLU D 400 " (cutoff:3.500A) Processing helix chain 'D' and resid 410 through 412 No H-bonds generated for 'chain 'D' and resid 410 through 412' Processing helix chain 'D' and resid 415 through 430 Processing helix chain 'D' and resid 451 through 462 removed outlier: 4.054A pdb=" N ARG D 456 " --> pdb=" O ALA D 452 " (cutoff:3.500A) Processing helix chain 'D' and resid 471 through 473 No H-bonds generated for 'chain 'D' and resid 471 through 473' Processing helix chain 'D' and resid 480 through 493 Processing helix chain 'E' and resid 154 through 159 Processing helix chain 'E' and resid 178 through 191 Processing helix chain 'E' and resid 206 through 219 Processing helix chain 'E' and resid 245 through 264 removed outlier: 5.486A pdb=" N GLY E 250 " --> pdb=" O ARG E 246 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N LEU E 251 " --> pdb=" O MET E 247 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N PHE E 260 " --> pdb=" O MET E 256 " (cutoff:3.500A) Processing helix chain 'E' and resid 275 through 289 Processing helix chain 'E' and resid 300 through 310 removed outlier: 4.641A pdb=" N SER E 303 " --> pdb=" O PRO E 300 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N THR E 304 " --> pdb=" O THR E 301 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N MET E 306 " --> pdb=" O SER E 303 " (cutoff:3.500A) Processing helix chain 'E' and resid 337 through 343 Processing helix chain 'E' and resid 354 through 359 Processing helix chain 'E' and resid 377 through 380 No H-bonds generated for 'chain 'E' and resid 377 through 380' Processing helix chain 'E' and resid 382 through 401 Processing helix chain 'E' and resid 415 through 431 removed outlier: 3.661A pdb=" N LEU E 419 " --> pdb=" O GLU E 415 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N THR E 420 " --> pdb=" O GLU E 416 " (cutoff:3.500A) Processing helix chain 'E' and resid 438 through 442 Processing helix chain 'E' and resid 451 through 463 Processing helix chain 'E' and resid 471 through 473 No H-bonds generated for 'chain 'E' and resid 471 through 473' Processing helix chain 'E' and resid 480 through 495 removed outlier: 4.082A pdb=" N LYS E 495 " --> pdb=" O GLU E 491 " (cutoff:3.500A) Processing helix chain 'F' and resid 154 through 158 Processing helix chain 'F' and resid 180 through 192 removed outlier: 5.166A pdb=" N LYS F 191 " --> pdb=" O ASN F 187 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N ALA F 192 " --> pdb=" O ASN F 188 " (cutoff:3.500A) Processing helix chain 'F' and resid 206 through 218 Processing helix chain 'F' and resid 227 through 229 No H-bonds generated for 'chain 'F' and resid 227 through 229' Processing helix chain 'F' and resid 245 through 247 No H-bonds generated for 'chain 'F' and resid 245 through 247' Processing helix chain 'F' and resid 249 through 262 Processing helix chain 'F' and resid 275 through 288 removed outlier: 4.778A pdb=" N ALA F 281 " --> pdb=" O PHE F 278 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N ALA F 287 " --> pdb=" O GLU F 284 " (cutoff:3.500A) Processing helix chain 'F' and resid 302 through 310 Processing helix chain 'F' and resid 330 through 332 No H-bonds generated for 'chain 'F' and resid 330 through 332' Processing helix chain 'F' and resid 337 through 340 No H-bonds generated for 'chain 'F' and resid 337 through 340' Processing helix chain 'F' and resid 342 through 345 No H-bonds generated for 'chain 'F' and resid 342 through 345' Processing helix chain 'F' and resid 354 through 358 Processing helix chain 'F' and resid 377 through 380 No H-bonds generated for 'chain 'F' and resid 377 through 380' Processing helix chain 'F' and resid 382 through 407 removed outlier: 4.659A pdb=" N ASP F 403 " --> pdb=" O LYS F 399 " (cutoff:3.500A) removed outlier: 4.951A pdb=" N ILE F 404 " --> pdb=" O GLU F 400 " (cutoff:3.500A) Processing helix chain 'F' and resid 410 through 412 No H-bonds generated for 'chain 'F' and resid 410 through 412' Processing helix chain 'F' and resid 415 through 430 Processing helix chain 'F' and resid 439 through 442 No H-bonds generated for 'chain 'F' and resid 439 through 442' Processing helix chain 'F' and resid 451 through 462 Processing helix chain 'F' and resid 471 through 473 No H-bonds generated for 'chain 'F' and resid 471 through 473' Processing helix chain 'F' and resid 480 through 495 removed outlier: 3.650A pdb=" N LYS F 495 " --> pdb=" O GLU F 491 " (cutoff:3.500A) Processing helix chain 'd' and resid 74 through 88 Processing helix chain 'd' and resid 92 through 106 Processing helix chain 'd' and resid 109 through 115 Processing helix chain 'd' and resid 122 through 136 Processing helix chain 'd' and resid 140 through 151 Processing helix chain 'd' and resid 154 through 173 removed outlier: 5.107A pdb=" N LYS d 159 " --> pdb=" O ASN d 156 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N PHE d 165 " --> pdb=" O LEU d 162 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N GLU d 166 " --> pdb=" O ASN d 163 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N THR d 173 " --> pdb=" O ASN d 170 " (cutoff:3.500A) Processing helix chain 'd' and resid 188 through 202 Processing helix chain 'd' and resid 237 through 248 Processing helix chain 'g' and resid 44 through 99 Proline residue: g 84 - end of helix removed outlier: 3.741A pdb=" N TYR g 94 " --> pdb=" O VAL g 90 " (cutoff:3.500A) Processing helix chain 'g' and resid 108 through 110 No H-bonds generated for 'chain 'g' and resid 108 through 110' Processing helix chain 'g' and resid 133 through 151 removed outlier: 3.798A pdb=" N LEU g 151 " --> pdb=" O GLU g 147 " (cutoff:3.500A) Processing helix chain 'g' and resid 162 through 170 removed outlier: 3.880A pdb=" N ARG g 170 " --> pdb=" O THR g 166 " (cutoff:3.500A) Processing helix chain 'g' and resid 188 through 203 Processing helix chain 'g' and resid 288 through 361 removed outlier: 3.963A pdb=" N LEU g 292 " --> pdb=" O PRO g 288 " (cutoff:3.500A) Proline residue: g 297 - end of helix removed outlier: 3.702A pdb=" N SER g 311 " --> pdb=" O ALA g 307 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N ASN g 361 " --> pdb=" O VAL g 357 " (cutoff:3.500A) Processing helix chain 'e' and resid 89 through 103 Processing helix chain 'e' and resid 112 through 130 removed outlier: 4.468A pdb=" N GLU e 127 " --> pdb=" O ARG e 123 " (cutoff:3.500A) removed outlier: 4.776A pdb=" N ALA e 128 " --> pdb=" O THR e 124 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N SER e 129 " --> pdb=" O ARG e 125 " (cutoff:3.500A) Processing helix chain 'J' and resid 89 through 218 removed outlier: 4.030A pdb=" N GLU J 96 " --> pdb=" O ILE J 92 " (cutoff:3.500A) Proline residue: J 111 - end of helix removed outlier: 4.042A pdb=" N ASN J 145 " --> pdb=" O GLU J 141 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N MET J 148 " --> pdb=" O ALA J 144 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ALA J 158 " --> pdb=" O GLU J 154 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N GLU J 197 " --> pdb=" O GLU J 193 " (cutoff:3.500A) removed outlier: 5.393A pdb=" N SER J 205 " --> pdb=" O LYS J 201 " (cutoff:3.500A) removed outlier: 5.026A pdb=" N GLN J 206 " --> pdb=" O SER J 202 " (cutoff:3.500A) Processing helix chain 'I' and resid 31 through 69 removed outlier: 3.538A pdb=" N ASN I 55 " --> pdb=" O ASP I 51 " (cutoff:3.500A) removed outlier: 4.768A pdb=" N GLN I 58 " --> pdb=" O ASP I 54 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N ARG I 59 " --> pdb=" O ASN I 55 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N GLU I 68 " --> pdb=" O ILE I 64 " (cutoff:3.500A) Processing helix chain 'I' and resid 72 through 103 removed outlier: 3.806A pdb=" N VAL I 97 " --> pdb=" O ASP I 93 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N GLY I 99 " --> pdb=" O PHE I 95 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N SER I 101 " --> pdb=" O VAL I 97 " (cutoff:3.500A) removed outlier: 6.045A pdb=" N GLU I 102 " --> pdb=" O ASN I 98 " (cutoff:3.500A) Processing helix chain 'I' and resid 106 through 158 removed outlier: 4.040A pdb=" N THR I 114 " --> pdb=" O LEU I 110 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LYS I 116 " --> pdb=" O ASN I 112 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N THR I 117 " --> pdb=" O SER I 113 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ILE I 129 " --> pdb=" O LYS I 125 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N GLY I 154 " --> pdb=" O GLN I 150 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N SER I 158 " --> pdb=" O GLY I 154 " (cutoff:3.500A) Processing helix chain 'I' and resid 165 through 181 Processing helix chain 'a' and resid 37 through 55 removed outlier: 3.847A pdb=" N THR a 42 " --> pdb=" O GLN a 38 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N ALA a 54 " --> pdb=" O LEU a 50 " (cutoff:3.500A) removed outlier: 5.302A pdb=" N ALA a 55 " --> pdb=" O LEU a 51 " (cutoff:3.500A) Processing helix chain 'a' and resid 67 through 84 removed outlier: 4.050A pdb=" N PHE a 71 " --> pdb=" O GLY a 67 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N TYR a 74 " --> pdb=" O ASN a 70 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N VAL a 75 " --> pdb=" O PHE a 71 " (cutoff:3.500A) Processing helix chain 'a' and resid 92 through 113 Proline residue: a 96 - end of helix removed outlier: 4.183A pdb=" N THR a 100 " --> pdb=" O PHE a 97 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N MET a 101 " --> pdb=" O ILE a 98 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N LEU a 103 " --> pdb=" O THR a 100 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N PHE a 104 " --> pdb=" O MET a 101 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N VAL a 107 " --> pdb=" O PHE a 104 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ALA a 113 " --> pdb=" O TRP a 110 " (cutoff:3.500A) Processing helix chain 'a' and resid 134 through 155 removed outlier: 3.607A pdb=" N THR a 154 " --> pdb=" O TYR a 150 " (cutoff:3.500A) Processing helix chain 'a' and resid 177 through 207 removed outlier: 3.826A pdb=" N THR a 181 " --> pdb=" O LEU a 177 " (cutoff:3.500A) Proline residue: a 183 - end of helix removed outlier: 3.547A pdb=" N ASN a 193 " --> pdb=" O ARG a 189 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N LEU a 204 " --> pdb=" O VAL a 200 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N VAL a 205 " --> pdb=" O VAL a 201 " (cutoff:3.500A) Processing helix chain 'a' and resid 213 through 243 removed outlier: 4.399A pdb=" N PHE a 218 " --> pdb=" O PRO a 215 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N THR a 223 " --> pdb=" O GLY a 220 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N GLN a 227 " --> pdb=" O SER a 224 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N ALA a 228 " --> pdb=" O GLY a 225 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ILE a 230 " --> pdb=" O GLN a 227 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ALA a 235 " --> pdb=" O ALA a 232 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ALA a 236 " --> pdb=" O THR a 233 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N LEU a 243 " --> pdb=" O GLY a 240 " (cutoff:3.500A) Processing helix chain 'T' and resid 4 through 41 removed outlier: 4.377A pdb=" N VAL T 10 " --> pdb=" O ALA T 6 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ILE T 11 " --> pdb=" O ALA T 7 " (cutoff:3.500A) removed outlier: 4.652A pdb=" N GLY T 23 " --> pdb=" O LEU T 19 " (cutoff:3.500A) Proline residue: T 24 - end of helix Processing helix chain 'T' and resid 47 through 68 removed outlier: 4.008A pdb=" N PHE T 59 " --> pdb=" O LEU T 55 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N THR T 64 " --> pdb=" O MET T 60 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N LEU T 68 " --> pdb=" O THR T 64 " (cutoff:3.500A) Processing helix chain 'T' and resid 72 through 75 No H-bonds generated for 'chain 'T' and resid 72 through 75' Processing helix chain 'Y' and resid 5 through 41 removed outlier: 4.732A pdb=" N ALA Y 13 " --> pdb=" O SER Y 9 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N GLY Y 14 " --> pdb=" O VAL Y 10 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N LEU Y 15 " --> pdb=" O ILE Y 11 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N ALA Y 20 " --> pdb=" O ALA Y 16 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N GLY Y 23 " --> pdb=" O LEU Y 19 " (cutoff:3.500A) Proline residue: Y 24 - end of helix removed outlier: 4.925A pdb=" N GLY Y 29 " --> pdb=" O GLY Y 25 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N GLN Y 34 " --> pdb=" O THR Y 30 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N GLU Y 37 " --> pdb=" O GLY Y 33 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ILE Y 39 " --> pdb=" O ALA Y 35 " (cutoff:3.500A) Processing helix chain 'Y' and resid 45 through 75 removed outlier: 4.714A pdb=" N ARG Y 50 " --> pdb=" O GLY Y 47 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LEU Y 53 " --> pdb=" O ARG Y 50 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LEU Y 54 " --> pdb=" O GLY Y 51 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N ILE Y 65 " --> pdb=" O ALA Y 62 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ALA Y 73 " --> pdb=" O VAL Y 70 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LEU Y 74 " --> pdb=" O ALA Y 71 " (cutoff:3.500A) Processing helix chain 'X' and resid 4 through 22 removed outlier: 4.198A pdb=" N ILE X 11 " --> pdb=" O ALA X 7 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N ALA X 12 " --> pdb=" O ALA X 8 " (cutoff:3.500A) Processing helix chain 'X' and resid 24 through 41 removed outlier: 3.723A pdb=" N ALA X 35 " --> pdb=" O ALA X 31 " (cutoff:3.500A) Processing helix chain 'X' and resid 45 through 75 removed outlier: 5.307A pdb=" N ARG X 50 " --> pdb=" O GLY X 47 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N GLY X 51 " --> pdb=" O LYS X 48 " (cutoff:3.500A) removed outlier: 4.878A pdb=" N LEU X 54 " --> pdb=" O GLY X 51 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N LEU X 55 " --> pdb=" O THR X 52 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLU X 61 " --> pdb=" O ALA X 58 " (cutoff:3.500A) Processing helix chain 'W' and resid 7 through 41 removed outlier: 3.690A pdb=" N GLY W 18 " --> pdb=" O GLY W 14 " (cutoff:3.500A) removed outlier: 4.759A pdb=" N GLY W 23 " --> pdb=" O LEU W 19 " (cutoff:3.500A) Proline residue: W 24 - end of helix Processing helix chain 'W' and resid 46 through 76 removed outlier: 4.056A pdb=" N GLY W 67 " --> pdb=" O LEU W 63 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N VAL W 70 " --> pdb=" O TYR W 66 " (cutoff:3.500A) Processing helix chain 'V' and resid 7 through 20 Processing helix chain 'V' and resid 23 through 41 removed outlier: 3.514A pdb=" N ILE V 39 " --> pdb=" O ALA V 35 " (cutoff:3.500A) Processing helix chain 'V' and resid 46 through 53 removed outlier: 3.518A pdb=" N ARG V 50 " --> pdb=" O GLU V 46 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N GLY V 51 " --> pdb=" O GLY V 47 " (cutoff:3.500A) Processing helix chain 'V' and resid 57 through 77 removed outlier: 3.856A pdb=" N TYR V 66 " --> pdb=" O ALA V 62 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N GLY V 67 " --> pdb=" O LEU V 63 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N LEU V 74 " --> pdb=" O VAL V 70 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N LEU V 75 " --> pdb=" O ALA V 71 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ALA V 77 " --> pdb=" O ALA V 73 " (cutoff:3.500A) Processing helix chain 'U' and resid 4 through 41 removed outlier: 4.250A pdb=" N SER U 21 " --> pdb=" O VAL U 17 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N ILE U 22 " --> pdb=" O GLY U 18 " (cutoff:3.500A) removed outlier: 4.667A pdb=" N GLY U 23 " --> pdb=" O LEU U 19 " (cutoff:3.500A) Proline residue: U 24 - end of helix removed outlier: 3.611A pdb=" N GLY U 27 " --> pdb=" O GLY U 23 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N GLY U 29 " --> pdb=" O GLY U 25 " (cutoff:3.500A) Processing helix chain 'U' and resid 46 through 75 removed outlier: 4.253A pdb=" N GLY U 67 " --> pdb=" O LEU U 63 " (cutoff:3.500A) Processing helix chain 'Z' and resid 4 through 41 removed outlier: 4.287A pdb=" N SER Z 21 " --> pdb=" O VAL Z 17 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N ILE Z 22 " --> pdb=" O GLY Z 18 " (cutoff:3.500A) removed outlier: 5.411A pdb=" N GLY Z 23 " --> pdb=" O LEU Z 19 " (cutoff:3.500A) Proline residue: Z 24 - end of helix removed outlier: 3.600A pdb=" N ARG Z 41 " --> pdb=" O GLU Z 37 " (cutoff:3.500A) Processing helix chain 'Z' and resid 43 through 75 removed outlier: 3.536A pdb=" N GLU Z 46 " --> pdb=" O PRO Z 43 " (cutoff:3.500A) removed outlier: 5.890A pdb=" N GLY Z 47 " --> pdb=" O GLU Z 44 " (cutoff:3.500A) removed outlier: 4.768A pdb=" N LEU Z 54 " --> pdb=" O GLY Z 51 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N ALA Z 58 " --> pdb=" O LEU Z 55 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N GLU Z 61 " --> pdb=" O ALA Z 58 " (cutoff:3.500A) Processing helix chain 'S' and resid 4 through 20 removed outlier: 3.996A pdb=" N ILE S 11 " --> pdb=" O ALA S 7 " (cutoff:3.500A) Processing helix chain 'S' and resid 22 through 41 removed outlier: 3.803A pdb=" N ARG S 41 " --> pdb=" O GLU S 37 " (cutoff:3.500A) Processing helix chain 'S' and resid 46 through 75 removed outlier: 4.417A pdb=" N THR S 52 " --> pdb=" O LYS S 48 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N LEU S 53 " --> pdb=" O ILE S 49 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N LEU S 55 " --> pdb=" O GLY S 51 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N GLY S 67 " --> pdb=" O LEU S 63 " (cutoff:3.500A) Processing helix chain 'R' and resid 4 through 41 removed outlier: 3.766A pdb=" N ALA R 8 " --> pdb=" O LEU R 4 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N GLY R 18 " --> pdb=" O GLY R 14 " (cutoff:3.500A) removed outlier: 4.841A pdb=" N GLY R 23 " --> pdb=" O LEU R 19 " (cutoff:3.500A) Proline residue: R 24 - end of helix removed outlier: 3.754A pdb=" N THR R 30 " --> pdb=" O VAL R 26 " (cutoff:3.500A) Processing helix chain 'R' and resid 49 through 75 removed outlier: 3.637A pdb=" N GLY R 67 " --> pdb=" O LEU R 63 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N VAL R 70 " --> pdb=" O TYR R 66 " (cutoff:3.500A) Processing helix chain 'Q' and resid 4 through 41 removed outlier: 3.842A pdb=" N ILE Q 11 " --> pdb=" O ALA Q 7 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N SER Q 21 " --> pdb=" O VAL Q 17 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N ILE Q 22 " --> pdb=" O GLY Q 18 " (cutoff:3.500A) removed outlier: 4.683A pdb=" N GLY Q 23 " --> pdb=" O LEU Q 19 " (cutoff:3.500A) Proline residue: Q 24 - end of helix Processing helix chain 'Q' and resid 46 through 75 removed outlier: 4.093A pdb=" N GLY Q 67 " --> pdb=" O LEU Q 63 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N LEU Q 75 " --> pdb=" O ALA Q 71 " (cutoff:3.500A) Processing helix chain 'M' and resid 5 through 41 removed outlier: 3.919A pdb=" N ILE M 11 " --> pdb=" O ALA M 7 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N SER M 21 " --> pdb=" O VAL M 17 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N ILE M 22 " --> pdb=" O GLY M 18 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N GLY M 23 " --> pdb=" O LEU M 19 " (cutoff:3.500A) Proline residue: M 24 - end of helix Processing helix chain 'M' and resid 46 through 75 removed outlier: 4.083A pdb=" N THR M 52 " --> pdb=" O LYS M 48 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N PHE M 59 " --> pdb=" O LEU M 55 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ILE M 65 " --> pdb=" O GLU M 61 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N TYR M 66 " --> pdb=" O ALA M 62 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N GLY M 67 " --> pdb=" O LEU M 63 " (cutoff:3.500A) Processing helix chain 'N' and resid 4 through 36 removed outlier: 4.207A pdb=" N GLY N 23 " --> pdb=" O LEU N 19 " (cutoff:3.500A) Proline residue: N 24 - end of helix Processing helix chain 'N' and resid 42 through 44 No H-bonds generated for 'chain 'N' and resid 42 through 44' Processing helix chain 'N' and resid 48 through 75 removed outlier: 3.538A pdb=" N LEU N 55 " --> pdb=" O GLY N 51 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N GLY N 67 " --> pdb=" O LEU N 63 " (cutoff:3.500A) Processing helix chain 'O' and resid 4 through 41 removed outlier: 3.612A pdb=" N ILE O 11 " --> pdb=" O ALA O 7 " (cutoff:3.500A) removed outlier: 4.926A pdb=" N GLY O 23 " --> pdb=" O LEU O 19 " (cutoff:3.500A) Proline residue: O 24 - end of helix removed outlier: 3.594A pdb=" N GLN O 34 " --> pdb=" O THR O 30 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N VAL O 36 " --> pdb=" O ALA O 32 " (cutoff:3.500A) removed outlier: 5.407A pdb=" N GLU O 37 " --> pdb=" O GLY O 33 " (cutoff:3.500A) Processing helix chain 'O' and resid 45 through 71 removed outlier: 4.730A pdb=" N ARG O 50 " --> pdb=" O GLY O 47 " (cutoff:3.500A) removed outlier: 5.141A pdb=" N LEU O 53 " --> pdb=" O ARG O 50 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N LEU O 54 " --> pdb=" O GLY O 51 " (cutoff:3.500A) removed outlier: 5.113A pdb=" N SER O 56 " --> pdb=" O LEU O 53 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N LEU O 57 " --> pdb=" O LEU O 54 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N MET O 60 " --> pdb=" O LEU O 57 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N THR O 64 " --> pdb=" O GLU O 61 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N TYR O 66 " --> pdb=" O LEU O 63 " (cutoff:3.500A) Processing helix chain 'P' and resid 4 through 41 removed outlier: 3.905A pdb=" N GLY P 18 " --> pdb=" O GLY P 14 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N GLY P 23 " --> pdb=" O LEU P 19 " (cutoff:3.500A) Proline residue: P 24 - end of helix removed outlier: 3.981A pdb=" N GLY P 27 " --> pdb=" O GLY P 23 " (cutoff:3.500A) Processing helix chain 'P' and resid 47 through 75 removed outlier: 3.511A pdb=" N LEU P 55 " --> pdb=" O GLY P 51 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N GLY P 67 " --> pdb=" O LEU P 63 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N VAL P 70 " --> pdb=" O TYR P 66 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 88 through 90 removed outlier: 6.444A pdb=" N ARG A 41 " --> pdb=" O LEU A 33 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N VAL A 75 " --> pdb=" O ALA A 64 " (cutoff:3.500A) removed outlier: 5.699A pdb=" N ALA A 64 " --> pdb=" O VAL A 75 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N GLU A 52 " --> pdb=" O ALA A 64 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 258 through 262 Processing sheet with id= C, first strand: chain 'C' and resid 72 through 75 removed outlier: 3.541A pdb=" N GLN C 34 " --> pdb=" O ARG C 41 " (cutoff:3.500A) removed outlier: 6.048A pdb=" N HIS C 43 " --> pdb=" O VAL C 32 " (cutoff:3.500A) removed outlier: 5.168A pdb=" N VAL C 32 " --> pdb=" O HIS C 43 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'C' and resid 97 through 99 Processing sheet with id= E, first strand: chain 'C' and resid 318 through 321 removed outlier: 3.541A pdb=" N GLY C 170 " --> pdb=" O VAL C 320 " (cutoff:3.500A) removed outlier: 6.038A pdb=" N ILE C 343 " --> pdb=" O ILE C 169 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 53 through 55 Processing sheet with id= G, first strand: chain 'B' and resid 193 through 198 removed outlier: 3.884A pdb=" N LEU B 258 " --> pdb=" O ILE B 193 " (cutoff:3.500A) removed outlier: 5.760A pdb=" N SER B 313 " --> pdb=" O THR B 257 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N ILE B 259 " --> pdb=" O SER B 313 " (cutoff:3.500A) removed outlier: 5.855A pdb=" N THR B 315 " --> pdb=" O ILE B 259 " (cutoff:3.500A) removed outlier: 7.158A pdb=" N TYR B 261 " --> pdb=" O THR B 315 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'D' and resid 22 through 27 removed outlier: 6.696A pdb=" N ASP D 32 " --> pdb=" O ALA D 24 " (cutoff:3.500A) removed outlier: 4.706A pdb=" N ILE D 26 " --> pdb=" O VAL D 30 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N VAL D 30 " --> pdb=" O ILE D 26 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N VAL D 77 " --> pdb=" O VAL D 65 " (cutoff:3.500A) removed outlier: 5.715A pdb=" N VAL D 65 " --> pdb=" O VAL D 77 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'D' and resid 99 through 101 removed outlier: 3.538A pdb=" N SER D 130 " --> pdb=" O VAL D 100 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'D' and resid 167 through 169 removed outlier: 6.436A pdb=" N SER D 323 " --> pdb=" O ILE D 168 " (cutoff:3.500A) No H-bonds generated for sheet with id= J Processing sheet with id= K, first strand: chain 'D' and resid 170 through 172 removed outlier: 6.012A pdb=" N THR D 350 " --> pdb=" O PHE D 171 " (cutoff:3.500A) No H-bonds generated for sheet with id= K Processing sheet with id= L, first strand: chain 'E' and resid 23 through 27 removed outlier: 6.386A pdb=" N ASP E 32 " --> pdb=" O ALA E 24 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N ILE E 26 " --> pdb=" O VAL E 30 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N VAL E 30 " --> pdb=" O ILE E 26 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N VAL E 33 " --> pdb=" O VAL E 74 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N VAL E 77 " --> pdb=" O VAL E 65 " (cutoff:3.500A) removed outlier: 5.556A pdb=" N VAL E 65 " --> pdb=" O VAL E 77 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'E' and resid 196 through 199 Processing sheet with id= N, first strand: chain 'F' and resid 23 through 27 removed outlier: 6.947A pdb=" N ASP F 32 " --> pdb=" O ALA F 24 " (cutoff:3.500A) removed outlier: 5.169A pdb=" N ILE F 26 " --> pdb=" O VAL F 30 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N VAL F 30 " --> pdb=" O ILE F 26 " (cutoff:3.500A) removed outlier: 6.078A pdb=" N VAL F 77 " --> pdb=" O VAL F 65 " (cutoff:3.500A) removed outlier: 5.481A pdb=" N VAL F 65 " --> pdb=" O VAL F 77 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N VAL F 61 " --> pdb=" O VAL F 49 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'F' and resid 99 through 101 Processing sheet with id= P, first strand: chain 'F' and resid 167 through 169 removed outlier: 6.445A pdb=" N SER F 323 " --> pdb=" O ILE F 168 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N VAL F 202 " --> pdb=" O ASP F 273 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N PHE F 199 " --> pdb=" O ALA F 233 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'd' and resid 180 through 182 Processing sheet with id= R, first strand: chain 'g' and resid 254 through 259 removed outlier: 3.679A pdb=" N THR g 265 " --> pdb=" O THR g 258 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'e' and resid 73 through 77 removed outlier: 6.359A pdb=" N ASN e 4 " --> pdb=" O ILE e 74 " (cutoff:3.500A) removed outlier: 7.229A pdb=" N ILE e 76 " --> pdb=" O ASN e 4 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N CYS e 6 " --> pdb=" O ILE e 76 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LEU e 3 " --> pdb=" O VAL e 19 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N VAL e 19 " --> pdb=" O LEU e 3 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N VAL e 7 " --> pdb=" O TRP e 15 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N TRP e 15 " --> pdb=" O VAL e 7 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N THR e 9 " --> pdb=" O SER e 13 " (cutoff:3.500A) removed outlier: 5.210A pdb=" N SER e 13 " --> pdb=" O THR e 9 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'e' and resid 40 through 42 Processing sheet with id= U, first strand: chain 'e' and resid 47 through 50 removed outlier: 3.538A pdb=" N GLY e 47 " --> pdb=" O LEU e 62 " (cutoff:3.500A) 1968 hydrogen bonds defined for protein. 5325 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: 25.28 Time building geometry restraints manager: 19.89 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 13121 1.34 - 1.47: 8096 1.47 - 1.59: 18220 1.59 - 1.71: 23 1.71 - 1.84: 249 Bond restraints: 39709 Sorted by residual: bond pdb=" C4 ATP D 601 " pdb=" C5 ATP D 601 " ideal model delta sigma weight residual 1.388 1.473 -0.085 1.00e-02 1.00e+04 7.20e+01 bond pdb=" C4 ATP A 601 " pdb=" C5 ATP A 601 " ideal model delta sigma weight residual 1.388 1.468 -0.080 1.00e-02 1.00e+04 6.47e+01 bond pdb=" C4 ATP B 601 " pdb=" C5 ATP B 601 " ideal model delta sigma weight residual 1.388 1.468 -0.080 1.00e-02 1.00e+04 6.34e+01 bond pdb=" C4 ATP C 601 " pdb=" C5 ATP C 601 " ideal model delta sigma weight residual 1.388 1.466 -0.078 1.00e-02 1.00e+04 6.06e+01 bond pdb=" C5 ATP D 601 " pdb=" C6 ATP D 601 " ideal model delta sigma weight residual 1.409 1.482 -0.073 1.00e-02 1.00e+04 5.37e+01 ... (remaining 39704 not shown) Histogram of bond angle deviations from ideal: 95.57 - 103.67: 590 103.67 - 111.77: 18802 111.77 - 119.87: 16118 119.87 - 127.97: 18189 127.97 - 136.07: 149 Bond angle restraints: 53848 Sorted by residual: angle pdb=" PB ATP C 601 " pdb=" O3B ATP C 601 " pdb=" PG ATP C 601 " ideal model delta sigma weight residual 139.87 117.60 22.27 1.00e+00 1.00e+00 4.96e+02 angle pdb=" PB ATP B 601 " pdb=" O3B ATP B 601 " pdb=" PG ATP B 601 " ideal model delta sigma weight residual 139.87 117.70 22.17 1.00e+00 1.00e+00 4.92e+02 angle pdb=" PB ATP D 601 " pdb=" O3B ATP D 601 " pdb=" PG ATP D 601 " ideal model delta sigma weight residual 139.87 119.31 20.56 1.00e+00 1.00e+00 4.23e+02 angle pdb=" PB ATP A 601 " pdb=" O3B ATP A 601 " pdb=" PG ATP A 601 " ideal model delta sigma weight residual 139.87 119.73 20.14 1.00e+00 1.00e+00 4.06e+02 angle pdb=" PA ATP D 601 " pdb=" O3A ATP D 601 " pdb=" PB ATP D 601 " ideal model delta sigma weight residual 136.83 116.72 20.11 1.00e+00 1.00e+00 4.04e+02 ... (remaining 53843 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.82: 22434 23.82 - 47.65: 1451 47.65 - 71.47: 142 71.47 - 95.30: 49 95.30 - 119.12: 3 Dihedral angle restraints: 24079 sinusoidal: 9348 harmonic: 14731 Sorted by residual: dihedral pdb=" CA PRO R 79 " pdb=" C PRO R 79 " pdb=" N PHE R 80 " pdb=" CA PHE R 80 " ideal model delta harmonic sigma weight residual -180.00 -123.70 -56.30 0 5.00e+00 4.00e-02 1.27e+02 dihedral pdb=" CA ALA D 295 " pdb=" C ALA D 295 " pdb=" N VAL D 296 " pdb=" CA VAL D 296 " ideal model delta harmonic sigma weight residual -180.00 -129.56 -50.44 0 5.00e+00 4.00e-02 1.02e+02 dihedral pdb=" CA ALA E 295 " pdb=" C ALA E 295 " pdb=" N VAL E 296 " pdb=" CA VAL E 296 " ideal model delta harmonic sigma weight residual -180.00 -131.69 -48.31 0 5.00e+00 4.00e-02 9.33e+01 ... (remaining 24076 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.070: 5541 0.070 - 0.141: 822 0.141 - 0.211: 66 0.211 - 0.281: 8 0.281 - 0.351: 3 Chirality restraints: 6440 Sorted by residual: chirality pdb=" CB ILE N 65 " pdb=" CA ILE N 65 " pdb=" CG1 ILE N 65 " pdb=" CG2 ILE N 65 " both_signs ideal model delta sigma weight residual False 2.64 2.29 0.35 2.00e-01 2.50e+01 3.09e+00 chirality pdb=" CB ILE e 69 " pdb=" CA ILE e 69 " pdb=" CG1 ILE e 69 " pdb=" CG2 ILE e 69 " both_signs ideal model delta sigma weight residual False 2.64 2.34 0.31 2.00e-01 2.50e+01 2.39e+00 chirality pdb=" CG LEU J 100 " pdb=" CB LEU J 100 " pdb=" CD1 LEU J 100 " pdb=" CD2 LEU J 100 " both_signs ideal model delta sigma weight residual False -2.59 -2.31 -0.28 2.00e-01 2.50e+01 1.99e+00 ... (remaining 6437 not shown) Planarity restraints: 6950 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU O 54 " -0.020 2.00e-02 2.50e+03 4.06e-02 1.65e+01 pdb=" C LEU O 54 " 0.070 2.00e-02 2.50e+03 pdb=" O LEU O 54 " -0.026 2.00e-02 2.50e+03 pdb=" N LEU O 55 " -0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER V 56 " -0.019 2.00e-02 2.50e+03 3.72e-02 1.38e+01 pdb=" C SER V 56 " 0.064 2.00e-02 2.50e+03 pdb=" O SER V 56 " -0.024 2.00e-02 2.50e+03 pdb=" N LEU V 57 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU T 46 " -0.018 2.00e-02 2.50e+03 3.70e-02 1.37e+01 pdb=" C GLU T 46 " 0.064 2.00e-02 2.50e+03 pdb=" O GLU T 46 " -0.024 2.00e-02 2.50e+03 pdb=" N GLY T 47 " -0.022 2.00e-02 2.50e+03 ... (remaining 6947 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.72: 2121 2.72 - 3.26: 43007 3.26 - 3.81: 66919 3.81 - 4.35: 82115 4.35 - 4.90: 135715 Nonbonded interactions: 329877 Sorted by model distance: nonbonded pdb=" O ALA F 295 " pdb=" N GLY F 297 " model vdw 2.172 2.520 nonbonded pdb=" OG1 THR d 181 " pdb=" OG1 THR d 222 " model vdw 2.176 2.440 nonbonded pdb=" OH TYR N 66 " pdb=" OE2 GLU O 61 " model vdw 2.179 2.440 nonbonded pdb=" O ALA X 20 " pdb=" OG1 THR X 64 " model vdw 2.179 2.440 nonbonded pdb=" OH TYR C 20 " pdb=" OE2 GLU d 249 " model vdw 2.213 2.440 ... (remaining 329872 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 6 through 503 or resid 601)) selection = (chain 'B' and (resid 6 through 503 or resid 601)) selection = (chain 'C' and (resid 6 through 503 or resid 601)) } ncs_group { reference = (chain 'D' and resid 17 through 494) selection = (chain 'E' and resid 17 through 494) selection = (chain 'F' and resid 17 through 494) } ncs_group { reference = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 14 5.49 5 S 131 5.16 5 C 24854 2.51 5 N 6674 2.21 5 O 7486 1.98 5 sf(0) = scattering factor at diffraction angle 0. 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: 4.300 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: 13.830 Check model and map are aligned: 0.560 Convert atoms to be neutral: 0.310 Process input model: 112.360 Find NCS groups from input model: 2.770 Set up NCS constraints: 0.460 Set refine NCS operators: 0.000 Set scattering table: 0.020 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:4.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 139.000 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7447 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 : 0.005 0.085 39709 Z= 0.348 Angle : 0.988 22.267 53848 Z= 0.609 Chirality : 0.050 0.351 6440 Planarity : 0.006 0.079 6950 Dihedral : 15.528 119.121 14640 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 14.17 Ramachandran Plot: Outliers : 0.29 % Allowed : 7.68 % Favored : 92.02 % Rotamer Outliers : 0.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.49 % 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: -3.96 (0.10), residues: 5141 helix: -2.04 (0.08), residues: 2735 sheet: -3.77 (0.19), residues: 431 loop : -3.04 (0.12), residues: 1975 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10282 Ramachandran restraints generated. 5141 Oldfield, 0 Emsley, 5141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10282 Ramachandran restraints generated. 5141 Oldfield, 0 Emsley, 5141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1034 residues out of total 4097 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 1014 time to evaluate : 4.793 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 outliers start: 20 outliers final: 4 residues processed: 1027 average time/residue: 0.5204 time to fit residues: 861.1809 Evaluate side-chains 665 residues out of total 4097 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 661 time to evaluate : 4.688 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.3589 time to fit residues: 9.0826 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 503 random chunks: chunk 424 optimal weight: 2.9990 chunk 381 optimal weight: 0.6980 chunk 211 optimal weight: 0.0980 chunk 130 optimal weight: 0.8980 chunk 257 optimal weight: 0.0870 chunk 203 optimal weight: 4.9990 chunk 394 optimal weight: 5.9990 chunk 152 optimal weight: 8.9990 chunk 239 optimal weight: 0.0770 chunk 293 optimal weight: 2.9990 chunk 456 optimal weight: 2.9990 overall best weight: 0.3716 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 423 GLN ** A 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 186 ASN C 188 GLN C 256 HIS ** C 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 409 ASN C 410 GLN ** B 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 188 ASN D 210 ASN ** D 472 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 479 ASN ** E 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 193 HIS ** F 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 299 GLN d 139 GLN d 190 HIS d 199 GLN ** d 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 301 ASN e 27 ASN I 180 ASN ** a 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 124 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 175 ASN ** Y 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 34 GLN ** W 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 28 GLN ** P 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7361 moved from start: 0.1899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.077 39709 Z= 0.212 Angle : 0.737 14.955 53848 Z= 0.372 Chirality : 0.045 0.290 6440 Planarity : 0.006 0.081 6950 Dihedral : 6.920 119.592 5573 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 18.16 Ramachandran Plot: Outliers : 0.27 % Allowed : 7.06 % Favored : 92.67 % Rotamer Outliers : 0.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.49 % 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: -2.67 (0.11), residues: 5141 helix: -0.90 (0.09), residues: 2751 sheet: -3.12 (0.22), residues: 410 loop : -2.62 (0.13), residues: 1980 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10282 Ramachandran restraints generated. 5141 Oldfield, 0 Emsley, 5141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10282 Ramachandran restraints generated. 5141 Oldfield, 0 Emsley, 5141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 948 residues out of total 4097 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 933 time to evaluate : 4.525 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 outliers start: 15 outliers final: 3 residues processed: 940 average time/residue: 0.4915 time to fit residues: 767.2490 Evaluate side-chains 654 residues out of total 4097 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 651 time to evaluate : 4.484 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.3436 time to fit residues: 8.1147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 503 random chunks: chunk 253 optimal weight: 3.9990 chunk 141 optimal weight: 4.9990 chunk 380 optimal weight: 9.9990 chunk 311 optimal weight: 0.9980 chunk 126 optimal weight: 0.6980 chunk 457 optimal weight: 8.9990 chunk 494 optimal weight: 0.9990 chunk 407 optimal weight: 5.9990 chunk 453 optimal weight: 6.9990 chunk 156 optimal weight: 9.9990 chunk 367 optimal weight: 5.9990 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 201 GLN A 389 GLN A 423 GLN C 409 ASN C 410 GLN ** B 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 188 GLN B 408 GLN ** B 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 133 HIS D 188 ASN ** D 472 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 266 GLN E 376 GLN ** F 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 299 GLN d 199 GLN ** d 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 301 ASN e 79 ASN ** a 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 175 ASN ** Y 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7454 moved from start: 0.2259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.066 39709 Z= 0.340 Angle : 0.760 10.528 53848 Z= 0.384 Chirality : 0.047 0.276 6440 Planarity : 0.006 0.072 6950 Dihedral : 6.809 115.633 5573 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 20.23 Ramachandran Plot: Outliers : 0.23 % Allowed : 8.75 % Favored : 91.01 % Rotamer Outliers : 0.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.49 % 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: -2.36 (0.11), residues: 5141 helix: -0.61 (0.09), residues: 2735 sheet: -3.20 (0.21), residues: 444 loop : -2.45 (0.13), residues: 1962 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10282 Ramachandran restraints generated. 5141 Oldfield, 0 Emsley, 5141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10282 Ramachandran restraints generated. 5141 Oldfield, 0 Emsley, 5141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 844 residues out of total 4097 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 835 time to evaluate : 4.534 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 outliers start: 9 outliers final: 5 residues processed: 843 average time/residue: 0.4968 time to fit residues: 699.2025 Evaluate side-chains 617 residues out of total 4097 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 612 time to evaluate : 4.463 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.3370 time to fit residues: 9.2375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 503 random chunks: chunk 452 optimal weight: 0.8980 chunk 344 optimal weight: 0.5980 chunk 237 optimal weight: 0.0770 chunk 50 optimal weight: 9.9990 chunk 218 optimal weight: 0.8980 chunk 307 optimal weight: 10.0000 chunk 459 optimal weight: 6.9990 chunk 486 optimal weight: 0.7980 chunk 239 optimal weight: 0.9980 chunk 435 optimal weight: 5.9990 chunk 131 optimal weight: 1.9990 overall best weight: 0.6538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 84 GLN ** A 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 273 GLN C 409 ASN C 410 GLN ** B 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 188 GLN ** B 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 472 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 479 ASN ** F 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 299 GLN ** F 389 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 134 ASN g 228 HIS g 301 ASN e 79 ASN a 86 GLN ** a 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 175 ASN Y 78 ASN X 34 GLN ** X 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 78 ASN ** R 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7370 moved from start: 0.2688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.063 39709 Z= 0.218 Angle : 0.715 14.462 53848 Z= 0.355 Chirality : 0.045 0.290 6440 Planarity : 0.005 0.073 6950 Dihedral : 6.574 116.498 5573 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 18.64 Ramachandran Plot: Outliers : 0.21 % Allowed : 7.49 % Favored : 92.30 % Rotamer Outliers : 0.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.98 % 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: -2.08 (0.11), residues: 5141 helix: -0.39 (0.09), residues: 2750 sheet: -2.99 (0.20), residues: 462 loop : -2.32 (0.13), residues: 1929 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10282 Ramachandran restraints generated. 5141 Oldfield, 0 Emsley, 5141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10282 Ramachandran restraints generated. 5141 Oldfield, 0 Emsley, 5141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 871 residues out of total 4097 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 865 time to evaluate : 4.798 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 outliers start: 6 outliers final: 0 residues processed: 868 average time/residue: 0.5150 time to fit residues: 740.8796 Evaluate side-chains 625 residues out of total 4097 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 625 time to evaluate : 4.486 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 5.9929 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 503 random chunks: chunk 404 optimal weight: 3.9990 chunk 275 optimal weight: 0.6980 chunk 7 optimal weight: 3.9990 chunk 362 optimal weight: 4.9990 chunk 200 optimal weight: 0.4980 chunk 414 optimal weight: 1.9990 chunk 336 optimal weight: 1.9990 chunk 0 optimal weight: 20.0000 chunk 248 optimal weight: 5.9990 chunk 436 optimal weight: 0.9990 chunk 122 optimal weight: 0.8980 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 423 GLN C 28 ASN ** C 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 409 ASN C 410 GLN ** B 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 188 GLN ** B 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 410 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 472 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 266 GLN ** E 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 299 GLN ** F 389 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 459 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 193 GLN ** d 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 86 GLN ** a 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 175 ASN ** Y 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 34 GLN X 78 ASN ** W 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7380 moved from start: 0.2903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.148 39709 Z= 0.247 Angle : 0.714 16.520 53848 Z= 0.359 Chirality : 0.045 0.289 6440 Planarity : 0.005 0.130 6950 Dihedral : 6.434 116.203 5573 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 18.93 Ramachandran Plot: Outliers : 0.21 % Allowed : 8.17 % Favored : 91.62 % Rotamer Outliers : 0.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.98 % Twisted General : 0.14 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.86 (0.11), residues: 5141 helix: -0.20 (0.10), residues: 2739 sheet: -2.83 (0.21), residues: 468 loop : -2.23 (0.14), residues: 1934 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10282 Ramachandran restraints generated. 5141 Oldfield, 0 Emsley, 5141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10282 Ramachandran restraints generated. 5141 Oldfield, 0 Emsley, 5141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 835 residues out of total 4097 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 832 time to evaluate : 4.470 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 outliers start: 3 outliers final: 1 residues processed: 833 average time/residue: 0.4905 time to fit residues: 685.8323 Evaluate side-chains 616 residues out of total 4097 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 615 time to evaluate : 5.257 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.3729 time to fit residues: 6.6353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 503 random chunks: chunk 163 optimal weight: 2.9990 chunk 437 optimal weight: 2.9990 chunk 96 optimal weight: 5.9990 chunk 285 optimal weight: 3.9990 chunk 120 optimal weight: 0.6980 chunk 486 optimal weight: 0.9980 chunk 403 optimal weight: 5.9990 chunk 225 optimal weight: 3.9990 chunk 40 optimal weight: 8.9990 chunk 160 optimal weight: 4.9990 chunk 255 optimal weight: 0.6980 overall best weight: 1.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 423 GLN ** C 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 409 ASN C 410 GLN ** B 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 188 GLN ** B 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 410 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 472 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 402 GLN F 66 GLN ** F 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 299 GLN ** F 389 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 459 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 58 GLN ** g 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 86 GLN ** a 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7394 moved from start: 0.3033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.586 39709 Z= 0.367 Angle : 0.836 73.899 53848 Z= 0.402 Chirality : 0.046 0.263 6440 Planarity : 0.005 0.081 6950 Dihedral : 6.427 115.637 5573 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 19.56 Ramachandran Plot: Outliers : 0.18 % Allowed : 8.38 % Favored : 91.44 % Rotamer Outliers : 0.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.82 (0.11), residues: 5141 helix: -0.17 (0.10), residues: 2739 sheet: -2.94 (0.21), residues: 466 loop : -2.17 (0.14), residues: 1936 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10282 Ramachandran restraints generated. 5141 Oldfield, 0 Emsley, 5141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10282 Ramachandran restraints generated. 5141 Oldfield, 0 Emsley, 5141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 805 residues out of total 4097 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 803 time to evaluate : 5.142 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 outliers start: 2 outliers final: 0 residues processed: 805 average time/residue: 0.4974 time to fit residues: 676.0725 Evaluate side-chains 607 residues out of total 4097 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 607 time to evaluate : 4.905 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 6.0887 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 503 random chunks: chunk 469 optimal weight: 20.0000 chunk 54 optimal weight: 0.5980 chunk 277 optimal weight: 0.9990 chunk 355 optimal weight: 9.9990 chunk 275 optimal weight: 3.9990 chunk 409 optimal weight: 4.9990 chunk 271 optimal weight: 0.6980 chunk 484 optimal weight: 0.9980 chunk 303 optimal weight: 10.0000 chunk 295 optimal weight: 0.9980 chunk 223 optimal weight: 0.9980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 410 GLN ** B 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 188 GLN ** B 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 410 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 472 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 299 GLN ** F 389 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 459 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 193 GLN ** g 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 27 ASN ** e 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 86 GLN ** a 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 34 GLN ** W 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7377 moved from start: 0.3106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.596 39709 Z= 0.347 Angle : 0.842 73.900 53848 Z= 0.400 Chirality : 0.045 0.371 6440 Planarity : 0.005 0.114 6950 Dihedral : 6.421 115.628 5573 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 20.56 Ramachandran Plot: Outliers : 0.18 % Allowed : 8.38 % Favored : 91.44 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.98 % Twisted General : 0.14 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.76 (0.11), residues: 5141 helix: -0.13 (0.10), residues: 2721 sheet: -2.89 (0.21), residues: 459 loop : -2.14 (0.14), residues: 1961 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10282 Ramachandran restraints generated. 5141 Oldfield, 0 Emsley, 5141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10282 Ramachandran restraints generated. 5141 Oldfield, 0 Emsley, 5141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 796 residues out of total 4097 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 796 time to evaluate : 4.460 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 outliers start: 0 outliers final: 0 residues processed: 796 average time/residue: 0.5006 time to fit residues: 671.4719 Evaluate side-chains 610 residues out of total 4097 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 610 time to evaluate : 4.301 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 5.6013 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 503 random chunks: chunk 299 optimal weight: 0.7980 chunk 193 optimal weight: 0.0670 chunk 289 optimal weight: 2.9990 chunk 146 optimal weight: 1.9990 chunk 95 optimal weight: 0.9980 chunk 93 optimal weight: 0.7980 chunk 308 optimal weight: 2.9990 chunk 330 optimal weight: 0.3980 chunk 239 optimal weight: 0.8980 chunk 45 optimal weight: 0.7980 chunk 381 optimal weight: 9.9990 overall best weight: 0.5718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 410 GLN ** B 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 410 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 472 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 299 GLN ** F 389 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 459 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 27 ASN a 86 GLN ** a 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7372 moved from start: 0.3148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.010 1.095 39709 Z= 0.622 Angle : 1.025 95.198 53848 Z= 0.473 Chirality : 0.046 0.567 6440 Planarity : 0.005 0.105 6950 Dihedral : 6.431 115.694 5573 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 22.30 Ramachandran Plot: Outliers : 0.19 % Allowed : 8.52 % Favored : 91.29 % Rotamer Outliers : 0.02 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.49 % Twisted General : 0.14 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.75 (0.11), residues: 5141 helix: -0.13 (0.10), residues: 2721 sheet: -2.89 (0.21), residues: 459 loop : -2.13 (0.14), residues: 1961 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10282 Ramachandran restraints generated. 5141 Oldfield, 0 Emsley, 5141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10282 Ramachandran restraints generated. 5141 Oldfield, 0 Emsley, 5141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 783 residues out of total 4097 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 782 time to evaluate : 5.946 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 outliers start: 1 outliers final: 0 residues processed: 783 average time/residue: 0.5188 time to fit residues: 690.7351 Evaluate side-chains 600 residues out of total 4097 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 600 time to evaluate : 4.578 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 6.2183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 503 random chunks: chunk 441 optimal weight: 10.0000 chunk 464 optimal weight: 5.9990 chunk 423 optimal weight: 7.9990 chunk 451 optimal weight: 0.9980 chunk 271 optimal weight: 0.7980 chunk 196 optimal weight: 0.9990 chunk 354 optimal weight: 9.9990 chunk 138 optimal weight: 0.9990 chunk 408 optimal weight: 5.9990 chunk 427 optimal weight: 7.9990 chunk 450 optimal weight: 6.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 443 ASN C 28 ASN ** C 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 409 ASN C 410 GLN ** B 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 188 GLN B 273 GLN ** B 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 410 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 472 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 266 GLN F 299 GLN ** F 389 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 459 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 193 GLN d 227 ASN g 99 GLN g 331 ASN e 27 ASN a 109 ASN ** a 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7417 moved from start: 0.3209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.810 39709 Z= 0.489 Angle : 0.877 72.888 53848 Z= 0.423 Chirality : 0.046 0.331 6440 Planarity : 0.005 0.090 6950 Dihedral : 6.438 114.644 5573 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 20.12 Ramachandran Plot: Outliers : 0.19 % Allowed : 8.81 % Favored : 90.99 % Rotamer Outliers : 0.05 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.77 (0.11), residues: 5141 helix: -0.13 (0.10), residues: 2709 sheet: -2.91 (0.21), residues: 478 loop : -2.13 (0.14), residues: 1954 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10282 Ramachandran restraints generated. 5141 Oldfield, 0 Emsley, 5141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10282 Ramachandran restraints generated. 5141 Oldfield, 0 Emsley, 5141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 780 residues out of total 4097 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 778 time to evaluate : 4.980 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 outliers start: 2 outliers final: 0 residues processed: 780 average time/residue: 0.4944 time to fit residues: 651.4189 Evaluate side-chains 601 residues out of total 4097 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 601 time to evaluate : 4.921 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 6.2123 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 503 random chunks: chunk 296 optimal weight: 4.9990 chunk 477 optimal weight: 0.8980 chunk 291 optimal weight: 3.9990 chunk 226 optimal weight: 0.9980 chunk 332 optimal weight: 5.9990 chunk 501 optimal weight: 4.9990 chunk 461 optimal weight: 30.0000 chunk 399 optimal weight: 0.9980 chunk 41 optimal weight: 0.5980 chunk 308 optimal weight: 0.9980 chunk 244 optimal weight: 0.9980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 409 ASN C 410 GLN ** B 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 410 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 25 GLN ** D 472 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 133 HIS F 299 GLN ** F 389 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 459 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 58 GLN a 109 ASN ** a 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 78 ASN X 42 GLN ** W 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7379 moved from start: 0.3354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.685 39709 Z= 0.382 Angle : 0.871 72.116 53848 Z= 0.420 Chirality : 0.046 0.511 6440 Planarity : 0.005 0.096 6950 Dihedral : 6.425 116.760 5573 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 19.20 Ramachandran Plot: Outliers : 0.21 % Allowed : 8.17 % Favored : 91.62 % Rotamer Outliers : 0.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.98 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.61 (0.11), residues: 5141 helix: -0.03 (0.10), residues: 2719 sheet: -2.86 (0.21), residues: 464 loop : -2.01 (0.14), residues: 1958 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10282 Ramachandran restraints generated. 5141 Oldfield, 0 Emsley, 5141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10282 Ramachandran restraints generated. 5141 Oldfield, 0 Emsley, 5141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 783 residues out of total 4097 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 782 time to evaluate : 4.560 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 outliers start: 1 outliers final: 0 residues processed: 783 average time/residue: 0.4863 time to fit residues: 646.4425 Evaluate side-chains 592 residues out of total 4097 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 592 time to evaluate : 4.536 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 6.0969 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 503 random chunks: chunk 316 optimal weight: 0.6980 chunk 425 optimal weight: 1.9990 chunk 122 optimal weight: 1.9990 chunk 367 optimal weight: 10.0000 chunk 58 optimal weight: 2.9990 chunk 110 optimal weight: 0.4980 chunk 399 optimal weight: 3.9990 chunk 167 optimal weight: 1.9990 chunk 410 optimal weight: 6.9990 chunk 50 optimal weight: 0.9990 chunk 73 optimal weight: 0.5980 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 201 GLN ** C 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 410 GLN ** B 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 148 GLN B 188 GLN ** B 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 334 ASN ** B 410 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 434 GLN D 25 GLN ** D 472 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 396 GLN ** F 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 299 GLN ** F 389 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 459 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 193 GLN d 227 ASN ** g 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 109 ASN ** a 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 78 ASN ** U 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.140998 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.136921 restraints weight = 73483.458| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.134171 restraints weight = 120027.546| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.133334 restraints weight = 219991.556| |-----------------------------------------------------------------------------| r_work (final): 0.3716 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7205 moved from start: 0.3574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.658 39709 Z= 0.330 Angle : 0.829 69.679 53848 Z= 0.402 Chirality : 0.046 0.408 6440 Planarity : 0.005 0.081 6950 Dihedral : 6.346 118.456 5573 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 19.11 Ramachandran Plot: Outliers : 0.19 % Allowed : 8.11 % Favored : 91.69 % Rotamer Outliers : 0.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.98 % 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: -1.55 (0.12), residues: 5141 helix: 0.01 (0.10), residues: 2715 sheet: -2.85 (0.21), residues: 451 loop : -1.98 (0.14), residues: 1975 =============================================================================== Job complete usr+sys time: 10701.07 seconds wall clock time: 192 minutes 43.32 seconds (11563.32 seconds total)