Starting phenix.real_space_refine (version: dev) on Fri Feb 24 22:56:56 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y5a_33614/02_2023/7y5a_33614_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y5a_33614/02_2023/7y5a_33614.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y5a_33614/02_2023/7y5a_33614.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y5a_33614/02_2023/7y5a_33614.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y5a_33614/02_2023/7y5a_33614_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y5a_33614/02_2023/7y5a_33614_updated.pdb" } resolution = 3.5 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= 0.002 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 Process input model Symmetric amino acids flipped Residue "A TYR 231": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 281": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 86": "OE1" <-> "OE2" Residue "B ASP 119": "OD1" <-> "OD2" Residue "B PHE 302": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 303": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 507": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 511": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 295": "OE1" <-> "OE2" Residue "C PHE 354": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 116": "OE1" <-> "OE2" Residue "D TYR 309": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 314": "OD1" <-> "OD2" Residue "D TYR 315": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 347": "OD1" <-> "OD2" Residue "D TYR 366": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 42": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 150": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 217": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 257": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 315": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 366": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 447": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 257": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 279": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 456": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 239": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.19s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 23975 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 3766 Number of conformers: 1 Conformer: "" Number of residues, atoms: 500, 3766 Classifications: {'peptide': 500} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 22, 'TRANS': 477} Chain breaks: 1 Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 21 Planarities with less than four sites: {'GLU:plan': 5, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 29 Chain: "B" Number of atoms: 3713 Number of conformers: 1 Conformer: "" Number of residues, atoms: 493, 3713 Classifications: {'peptide': 493} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 20, 'TRANS': 472} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 16 Chain: "C" Number of atoms: 3643 Number of conformers: 1 Conformer: "" Number of residues, atoms: 489, 3643 Classifications: {'peptide': 489} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 20, 'TRANS': 468} Chain breaks: 1 Unresolved non-hydrogen bonds: 54 Unresolved non-hydrogen angles: 65 Unresolved non-hydrogen dihedrals: 43 Planarities with less than four sites: {'GLU:plan': 8, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 41 Chain: "D" Number of atoms: 3495 Number of conformers: 1 Conformer: "" Number of residues, atoms: 464, 3495 Classifications: {'peptide': 464} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 23, 'TRANS': 440} Unresolved non-hydrogen bonds: 59 Unresolved non-hydrogen angles: 73 Unresolved non-hydrogen dihedrals: 45 Planarities with less than four sites: {'GLU:plan': 8, 'ASP:plan': 6} Unresolved non-hydrogen planarities: 50 Chain: "E" Number of atoms: 3486 Number of conformers: 1 Conformer: "" Number of residues, atoms: 464, 3486 Classifications: {'peptide': 464} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PTRANS': 23, 'TRANS': 440} Unresolved non-hydrogen bonds: 68 Unresolved non-hydrogen angles: 87 Unresolved non-hydrogen dihedrals: 49 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 5, 'ASN:plan1': 1, 'ASP:plan': 11} Unresolved non-hydrogen planarities: 64 Chain: "F" Number of atoms: 3525 Number of conformers: 1 Conformer: "" Number of residues, atoms: 464, 3525 Classifications: {'peptide': 464} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 23, 'TRANS': 440} Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 21 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 4, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 29 Chain: "G" Number of atoms: 2195 Number of conformers: 1 Conformer: "" Number of residues, atoms: 290, 2195 Classifications: {'peptide': 290} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 9, 'TRANS': 280} Chain breaks: 2 Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 46 Unresolved non-hydrogen dihedrals: 28 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 5, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 30 Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 13.67, per 1000 atoms: 0.57 Number of scatterers: 23975 At special positions: 0 Unit cell: (129.8, 156.2, 135.3, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 74 16.00 P 13 15.00 Mg 5 11.99 O 4600 8.00 N 4198 7.00 C 15085 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 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: 9.95 Conformation dependent library (CDL) restraints added in 3.6 seconds 6284 Ramachandran restraints generated. 3142 Oldfield, 0 Emsley, 3142 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5754 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 113 helices and 17 sheets defined 40.1% alpha, 11.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.66 Creating SS restraints... Processing helix chain 'A' and resid 82 through 84 No H-bonds generated for 'chain 'A' and resid 82 through 84' Processing helix chain 'A' and resid 104 through 106 No H-bonds generated for 'chain 'A' and resid 104 through 106' Processing helix chain 'A' and resid 139 through 141 No H-bonds generated for 'chain 'A' and resid 139 through 141' Processing helix chain 'A' and resid 154 through 159 Processing helix chain 'A' and resid 180 through 195 removed outlier: 4.459A pdb=" N ARG A 190 " --> pdb=" O ILE A 186 " (cutoff:3.500A) removed outlier: 5.412A pdb=" N GLU A 191 " --> pdb=" O LEU A 187 " (cutoff:3.500A) removed outlier: 4.935A pdb=" N ALA A 192 " --> pdb=" O ASN A 188 " (cutoff:3.500A) Processing helix chain 'A' and resid 213 through 225 Processing helix chain 'A' and resid 243 through 262 Proline residue: A 250 - end of helix removed outlier: 4.104A pdb=" N GLY A 253 " --> pdb=" O ALA A 249 " (cutoff:3.500A) Processing helix chain 'A' and resid 275 through 287 Processing helix chain 'A' and resid 294 through 296 No H-bonds generated for 'chain 'A' and resid 294 through 296' Processing helix chain 'A' and resid 301 through 311 removed outlier: 3.881A pdb=" N HIS A 305 " --> pdb=" O VAL A 301 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N ARG A 311 " --> pdb=" O ARG A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 340 through 347 removed outlier: 3.576A pdb=" N SER A 347 " --> pdb=" O THR A 343 " (cutoff:3.500A) Processing helix chain 'A' and resid 357 through 362 Processing helix chain 'A' and resid 378 through 380 No H-bonds generated for 'chain 'A' and resid 378 through 380' Processing helix chain 'A' and resid 384 through 390 Processing helix chain 'A' and resid 393 through 407 removed outlier: 4.224A pdb=" N ALA A 405 " --> pdb=" O ARG A 401 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N PHE A 406 " --> pdb=" O GLU A 402 " (cutoff:3.500A) Processing helix chain 'A' and resid 415 through 431 removed outlier: 3.558A pdb=" N LEU A 431 " --> pdb=" O LEU A 427 " (cutoff:3.500A) Processing helix chain 'A' and resid 441 through 452 Processing helix chain 'A' and resid 454 through 456 No H-bonds generated for 'chain 'A' and resid 454 through 456' Processing helix chain 'A' and resid 465 through 477 removed outlier: 3.652A pdb=" N VAL A 475 " --> pdb=" O LEU A 471 " (cutoff:3.500A) Processing helix chain 'A' and resid 480 through 489 removed outlier: 4.163A pdb=" N THR A 489 " --> pdb=" O ILE A 486 " (cutoff:3.500A) Processing helix chain 'A' and resid 494 through 510 removed outlier: 3.795A pdb=" N LYS A 509 " --> pdb=" O ASN A 505 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N GLY A 510 " --> pdb=" O GLU A 506 " (cutoff:3.500A) Processing helix chain 'B' and resid 154 through 157 No H-bonds generated for 'chain 'B' and resid 154 through 157' Processing helix chain 'B' and resid 178 through 194 removed outlier: 4.435A pdb=" N GLN B 189 " --> pdb=" O THR B 185 " (cutoff:3.500A) removed outlier: 5.674A pdb=" N ARG B 190 " --> pdb=" O ILE B 186 " (cutoff:3.500A) removed outlier: 6.115A pdb=" N GLU B 191 " --> pdb=" O LEU B 187 " (cutoff:3.500A) removed outlier: 5.312A pdb=" N ALA B 192 " --> pdb=" O ASN B 188 " (cutoff:3.500A) Processing helix chain 'B' and resid 213 through 226 Processing helix chain 'B' and resid 228 through 231 Processing helix chain 'B' and resid 245 through 247 No H-bonds generated for 'chain 'B' and resid 245 through 247' Processing helix chain 'B' and resid 249 through 263 removed outlier: 3.770A pdb=" N HIS B 259 " --> pdb=" O ALA B 255 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N TRP B 260 " --> pdb=" O ILE B 256 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N ASN B 263 " --> pdb=" O HIS B 259 " (cutoff:3.500A) Processing helix chain 'B' and resid 275 through 287 Processing helix chain 'B' and resid 294 through 296 No H-bonds generated for 'chain 'B' and resid 294 through 296' Processing helix chain 'B' and resid 302 through 309 Processing helix chain 'B' and resid 340 through 348 Processing helix chain 'B' and resid 357 through 362 Processing helix chain 'B' and resid 384 through 407 removed outlier: 3.887A pdb=" N GLY B 391 " --> pdb=" O LYS B 387 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N SER B 392 " --> pdb=" O GLU B 388 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N LEU B 395 " --> pdb=" O GLY B 391 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ASP B 396 " --> pdb=" O SER B 392 " (cutoff:3.500A) removed outlier: 5.834A pdb=" N ALA B 405 " --> pdb=" O ARG B 401 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N PHE B 406 " --> pdb=" O GLU B 402 " (cutoff:3.500A) removed outlier: 5.099A pdb=" N ALA B 407 " --> pdb=" O LEU B 403 " (cutoff:3.500A) Processing helix chain 'B' and resid 415 through 430 Processing helix chain 'B' and resid 441 through 453 Processing helix chain 'B' and resid 461 through 478 removed outlier: 3.849A pdb=" N GLN B 465 " --> pdb=" O VAL B 461 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ARG B 466 " --> pdb=" O GLU B 462 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N GLU B 468 " --> pdb=" O VAL B 464 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N SER B 469 " --> pdb=" O GLN B 465 " (cutoff:3.500A) Processing helix chain 'B' and resid 480 through 489 removed outlier: 3.684A pdb=" N THR B 489 " --> pdb=" O ILE B 486 " (cutoff:3.500A) Processing helix chain 'B' and resid 494 through 510 removed outlier: 3.987A pdb=" N LYS B 509 " --> pdb=" O ASN B 505 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N GLY B 510 " --> pdb=" O GLU B 506 " (cutoff:3.500A) Processing helix chain 'C' and resid 154 through 157 No H-bonds generated for 'chain 'C' and resid 154 through 157' Processing helix chain 'C' and resid 179 through 195 removed outlier: 4.453A pdb=" N GLN C 189 " --> pdb=" O THR C 185 " (cutoff:3.500A) removed outlier: 5.374A pdb=" N ARG C 190 " --> pdb=" O ILE C 186 " (cutoff:3.500A) removed outlier: 5.874A pdb=" N GLU C 191 " --> pdb=" O LEU C 187 " (cutoff:3.500A) removed outlier: 5.263A pdb=" N ALA C 192 " --> pdb=" O ASN C 188 " (cutoff:3.500A) Processing helix chain 'C' and resid 213 through 225 Processing helix chain 'C' and resid 243 through 263 Proline residue: C 250 - end of helix removed outlier: 4.128A pdb=" N ILE C 256 " --> pdb=" O THR C 252 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N GLY C 257 " --> pdb=" O GLY C 253 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N TYR C 262 " --> pdb=" O GLN C 258 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N ASN C 263 " --> pdb=" O HIS C 259 " (cutoff:3.500A) Processing helix chain 'C' and resid 275 through 287 Processing helix chain 'C' and resid 294 through 296 No H-bonds generated for 'chain 'C' and resid 294 through 296' Processing helix chain 'C' and resid 301 through 311 Processing helix chain 'C' and resid 340 through 348 Processing helix chain 'C' and resid 357 through 362 removed outlier: 3.649A pdb=" N GLN C 362 " --> pdb=" O ASP C 358 " (cutoff:3.500A) Processing helix chain 'C' and resid 384 through 389 Processing helix chain 'C' and resid 393 through 407 Processing helix chain 'C' and resid 415 through 431 removed outlier: 3.551A pdb=" N LEU C 431 " --> pdb=" O LEU C 427 " (cutoff:3.500A) Processing helix chain 'C' and resid 441 through 453 Processing helix chain 'C' and resid 461 through 477 removed outlier: 4.930A pdb=" N GLN C 465 " --> pdb=" O GLU C 462 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N ARG C 466 " --> pdb=" O ASP C 463 " (cutoff:3.500A) removed outlier: 4.888A pdb=" N LEU C 471 " --> pdb=" O GLU C 468 " (cutoff:3.500A) Processing helix chain 'C' and resid 480 through 489 removed outlier: 4.267A pdb=" N THR C 489 " --> pdb=" O ILE C 486 " (cutoff:3.500A) Processing helix chain 'C' and resid 494 through 505 Processing helix chain 'C' and resid 508 through 510 No H-bonds generated for 'chain 'C' and resid 508 through 510' Processing helix chain 'D' and resid 142 through 146 Processing helix chain 'D' and resid 166 through 177 Processing helix chain 'D' and resid 194 through 206 Processing helix chain 'D' and resid 210 through 212 No H-bonds generated for 'chain 'D' and resid 210 through 212' Processing helix chain 'D' and resid 224 through 228 removed outlier: 3.995A pdb=" N MET D 228 " --> pdb=" O PRO D 224 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 224 through 228' Processing helix chain 'D' and resid 230 through 244 Processing helix chain 'D' and resid 256 through 269 removed outlier: 4.359A pdb=" N GLU D 265 " --> pdb=" O ALA D 262 " (cutoff:3.500A) Processing helix chain 'D' and resid 283 through 293 Processing helix chain 'D' and resid 311 through 313 No H-bonds generated for 'chain 'D' and resid 311 through 313' Processing helix chain 'D' and resid 318 through 325 removed outlier: 4.131A pdb=" N THR D 322 " --> pdb=" O PRO D 318 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N THR D 323 " --> pdb=" O ALA D 319 " (cutoff:3.500A) Processing helix chain 'D' and resid 336 through 339 No H-bonds generated for 'chain 'D' and resid 336 through 339' Processing helix chain 'D' and resid 348 through 350 No H-bonds generated for 'chain 'D' and resid 348 through 350' Processing helix chain 'D' and resid 363 through 389 removed outlier: 4.245A pdb=" N ILE D 385 " --> pdb=" O ASP D 381 " (cutoff:3.500A) removed outlier: 5.199A pdb=" N ILE D 388 " --> pdb=" O ASP D 384 " (cutoff:3.500A) Processing helix chain 'D' and resid 391 through 393 No H-bonds generated for 'chain 'D' and resid 391 through 393' Processing helix chain 'D' and resid 396 through 411 Processing helix chain 'D' and resid 420 through 423 No H-bonds generated for 'chain 'D' and resid 420 through 423' Processing helix chain 'D' and resid 432 through 444 Processing helix chain 'D' and resid 447 through 449 No H-bonds generated for 'chain 'D' and resid 447 through 449' Processing helix chain 'D' and resid 452 through 455 Processing helix chain 'D' and resid 462 through 469 Processing helix chain 'E' and resid 142 through 145 No H-bonds generated for 'chain 'E' and resid 142 through 145' Processing helix chain 'E' and resid 166 through 179 Processing helix chain 'E' and resid 194 through 207 Processing helix chain 'E' and resid 226 through 243 removed outlier: 4.871A pdb=" N ALA E 231 " --> pdb=" O ARG E 227 " (cutoff:3.500A) Processing helix chain 'E' and resid 256 through 270 removed outlier: 4.093A pdb=" N THR E 260 " --> pdb=" O ILE E 256 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N GLN E 261 " --> pdb=" O PHE E 257 " (cutoff:3.500A) Processing helix chain 'E' and resid 283 through 293 Processing helix chain 'E' and resid 318 through 325 removed outlier: 3.728A pdb=" N ALA E 325 " --> pdb=" O ALA E 321 " (cutoff:3.500A) Processing helix chain 'E' and resid 358 through 386 removed outlier: 7.664A pdb=" N ASP E 363 " --> pdb=" O ALA E 359 " (cutoff:3.500A) removed outlier: 8.891A pdb=" N GLU E 364 " --> pdb=" O ILE E 360 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N HIS E 365 " --> pdb=" O VAL E 361 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N TYR E 366 " --> pdb=" O GLY E 362 " (cutoff:3.500A) Processing helix chain 'E' and resid 391 through 393 No H-bonds generated for 'chain 'E' and resid 391 through 393' Processing helix chain 'E' and resid 396 through 411 Processing helix chain 'E' and resid 417 through 420 No H-bonds generated for 'chain 'E' and resid 417 through 420' Processing helix chain 'E' and resid 432 through 443 Processing helix chain 'E' and resid 447 through 449 No H-bonds generated for 'chain 'E' and resid 447 through 449' Processing helix chain 'E' and resid 452 through 456 Processing helix chain 'E' and resid 461 through 470 Processing helix chain 'F' and resid 142 through 146 Processing helix chain 'F' and resid 166 through 177 Processing helix chain 'F' and resid 194 through 205 Processing helix chain 'F' and resid 224 through 228 removed outlier: 3.723A pdb=" N MET F 228 " --> pdb=" O GLY F 225 " (cutoff:3.500A) Processing helix chain 'F' and resid 230 through 243 Processing helix chain 'F' and resid 256 through 270 Processing helix chain 'F' and resid 283 through 291 Processing helix chain 'F' and resid 311 through 313 No H-bonds generated for 'chain 'F' and resid 311 through 313' Processing helix chain 'F' and resid 318 through 326 removed outlier: 3.936A pdb=" N THR F 323 " --> pdb=" O ALA F 319 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N ALA F 325 " --> pdb=" O ALA F 321 " (cutoff:3.500A) removed outlier: 5.167A pdb=" N HIS F 326 " --> pdb=" O THR F 322 " (cutoff:3.500A) Processing helix chain 'F' and resid 335 through 340 Processing helix chain 'F' and resid 348 through 350 No H-bonds generated for 'chain 'F' and resid 348 through 350' Processing helix chain 'F' and resid 363 through 388 removed outlier: 4.144A pdb=" N ARG F 367 " --> pdb=" O ASP F 363 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N VAL F 368 " --> pdb=" O GLU F 364 " (cutoff:3.500A) removed outlier: 4.744A pdb=" N ASP F 384 " --> pdb=" O LYS F 380 " (cutoff:3.500A) removed outlier: 5.274A pdb=" N ILE F 385 " --> pdb=" O ASP F 381 " (cutoff:3.500A) Processing helix chain 'F' and resid 396 through 411 Processing helix chain 'F' and resid 419 through 421 No H-bonds generated for 'chain 'F' and resid 419 through 421' Processing helix chain 'F' and resid 432 through 444 Processing helix chain 'F' and resid 452 through 454 No H-bonds generated for 'chain 'F' and resid 452 through 454' Processing helix chain 'F' and resid 461 through 469 removed outlier: 3.872A pdb=" N GLU F 469 " --> pdb=" O ALA F 465 " (cutoff:3.500A) Processing helix chain 'G' and resid 5 through 60 removed outlier: 3.838A pdb=" N ALA G 38 " --> pdb=" O ALA G 34 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ARG G 39 " --> pdb=" O LYS G 35 " (cutoff:3.500A) Proline residue: G 45 - end of helix removed outlier: 4.392A pdb=" N ALA G 60 " --> pdb=" O GLU G 56 " (cutoff:3.500A) Processing helix chain 'G' and resid 66 through 68 No H-bonds generated for 'chain 'G' and resid 66 through 68' Processing helix chain 'G' and resid 92 through 110 removed outlier: 3.836A pdb=" N VAL G 96 " --> pdb=" O TYR G 92 " (cutoff:3.500A) Processing helix chain 'G' and resid 121 through 129 removed outlier: 3.507A pdb=" N PHE G 129 " --> pdb=" O GLY G 125 " (cutoff:3.500A) Processing helix chain 'G' and resid 147 through 164 removed outlier: 4.058A pdb=" N GLY G 164 " --> pdb=" O ALA G 160 " (cutoff:3.500A) Processing helix chain 'G' and resid 228 through 301 Proline residue: G 237 - end of helix removed outlier: 4.581A pdb=" N ASP G 272 " --> pdb=" O ASP G 268 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N LEU G 273 " --> pdb=" O ASN G 269 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 33 through 37 removed outlier: 3.598A pdb=" N THR A 33 " --> pdb=" O GLU A 45 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N GLU A 45 " --> pdb=" O THR A 33 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N HIS A 43 " --> pdb=" O ILE A 35 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N ALA A 37 " --> pdb=" O ILE A 41 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N ILE A 41 " --> pdb=" O ALA A 37 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N ASN A 68 " --> pdb=" O GLY A 75 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N VAL A 77 " --> pdb=" O ALA A 66 " (cutoff:3.500A) removed outlier: 5.336A pdb=" N ALA A 66 " --> pdb=" O VAL A 77 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 99 through 102 Processing sheet with id= C, first strand: chain 'A' and resid 352 through 355 removed outlier: 6.795A pdb=" N LEU A 169 " --> pdb=" O CYS A 353 " (cutoff:3.500A) removed outlier: 8.034A pdb=" N LEU A 355 " --> pdb=" O LEU A 169 " (cutoff:3.500A) removed outlier: 7.124A pdb=" N ILE A 171 " --> pdb=" O LEU A 355 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N THR A 325 " --> pdb=" O VAL A 267 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N PHE A 271 " --> pdb=" O LEU A 327 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ILE A 329 " --> pdb=" O PHE A 271 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N ARG A 203 " --> pdb=" O LEU A 268 " (cutoff:3.500A) removed outlier: 7.940A pdb=" N VAL A 270 " --> pdb=" O ARG A 203 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N VAL A 205 " --> pdb=" O VAL A 270 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 41 through 44 removed outlier: 4.262A pdb=" N ASN B 68 " --> pdb=" O GLY B 75 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N VAL B 77 " --> pdb=" O ALA B 66 " (cutoff:3.500A) removed outlier: 5.946A pdb=" N ALA B 66 " --> pdb=" O VAL B 77 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N LEU B 79 " --> pdb=" O GLY B 64 " (cutoff:3.500A) removed outlier: 5.313A pdb=" N GLY B 64 " --> pdb=" O LEU B 79 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 351 through 354 removed outlier: 3.974A pdb=" N GLN B 168 " --> pdb=" O GLY B 326 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N ILE B 170 " --> pdb=" O PRO B 328 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ILE B 330 " --> pdb=" O ILE B 170 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N GLY B 172 " --> pdb=" O ILE B 330 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ILE B 329 " --> pdb=" O PHE B 271 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'C' and resid 31 through 33 removed outlier: 3.717A pdb=" N LEU C 67 " --> pdb=" O GLY C 75 " (cutoff:3.500A) removed outlier: 7.134A pdb=" N GLY C 75 " --> pdb=" O LEU C 67 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ASP C 36 " --> pdb=" O HIS C 43 " (cutoff:3.500A) removed outlier: 6.165A pdb=" N GLU C 45 " --> pdb=" O VAL C 34 " (cutoff:3.500A) removed outlier: 5.966A pdb=" N VAL C 34 " --> pdb=" O GLU C 45 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'C' and resid 99 through 102 Processing sheet with id= H, first strand: chain 'C' and resid 109 through 112 removed outlier: 3.863A pdb=" N ARG C 109 " --> pdb=" O THR C 232 " (cutoff:3.500A) removed outlier: 9.182A pdb=" N THR C 233 " --> pdb=" O VAL C 202 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N CYS C 204 " --> pdb=" O THR C 233 " (cutoff:3.500A) removed outlier: 8.257A pdb=" N VAL C 235 " --> pdb=" O CYS C 204 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N TYR C 206 " --> pdb=" O VAL C 235 " (cutoff:3.500A) removed outlier: 7.894A pdb=" N ALA C 237 " --> pdb=" O TYR C 206 " (cutoff:3.500A) removed outlier: 6.012A pdb=" N ALA C 208 " --> pdb=" O ALA C 237 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N HIS C 266 " --> pdb=" O ARG C 203 " (cutoff:3.500A) removed outlier: 8.163A pdb=" N VAL C 205 " --> pdb=" O HIS C 266 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N LEU C 268 " --> pdb=" O VAL C 205 " (cutoff:3.500A) removed outlier: 8.233A pdb=" N VAL C 207 " --> pdb=" O LEU C 268 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N VAL C 270 " --> pdb=" O VAL C 207 " (cutoff:3.500A) removed outlier: 8.140A pdb=" N ILE C 209 " --> pdb=" O VAL C 270 " (cutoff:3.500A) removed outlier: 5.364A pdb=" N SER C 323 " --> pdb=" O VAL C 267 " (cutoff:3.500A) removed outlier: 7.141A pdb=" N ILE C 269 " --> pdb=" O SER C 323 " (cutoff:3.500A) removed outlier: 6.266A pdb=" N THR C 325 " --> pdb=" O ILE C 269 " (cutoff:3.500A) removed outlier: 7.688A pdb=" N PHE C 271 " --> pdb=" O THR C 325 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N LEU C 327 " --> pdb=" O PHE C 271 " (cutoff:3.500A) removed outlier: 7.043A pdb=" N GLN C 168 " --> pdb=" O PRO C 328 " (cutoff:3.500A) removed outlier: 8.374A pdb=" N ILE C 330 " --> pdb=" O GLN C 168 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N ILE C 170 " --> pdb=" O ILE C 330 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'D' and resid 11 through 16 removed outlier: 6.832A pdb=" N ASP D 21 " --> pdb=" O VAL D 13 " (cutoff:3.500A) removed outlier: 5.164A pdb=" N ILE D 15 " --> pdb=" O VAL D 19 " (cutoff:3.500A) removed outlier: 7.548A pdb=" N VAL D 19 " --> pdb=" O ILE D 15 " (cutoff:3.500A) removed outlier: 6.178A pdb=" N ILE D 65 " --> pdb=" O VAL D 53 " (cutoff:3.500A) removed outlier: 5.510A pdb=" N VAL D 53 " --> pdb=" O ILE D 65 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'D' and resid 155 through 158 removed outlier: 7.856A pdb=" N ILE D 156 " --> pdb=" O ILE D 302 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N SER D 304 " --> pdb=" O ILE D 156 " (cutoff:3.500A) removed outlier: 8.264A pdb=" N LEU D 158 " --> pdb=" O SER D 304 " (cutoff:3.500A) removed outlier: 7.019A pdb=" N GLN D 306 " --> pdb=" O LEU D 158 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N VAL D 249 " --> pdb=" O THR D 303 " (cutoff:3.500A) removed outlier: 8.072A pdb=" N MET D 305 " --> pdb=" O VAL D 249 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N LEU D 251 " --> pdb=" O MET D 305 " (cutoff:3.500A) removed outlier: 8.328A pdb=" N ALA D 307 " --> pdb=" O LEU D 251 " (cutoff:3.500A) removed outlier: 7.257A pdb=" N ILE D 253 " --> pdb=" O ALA D 307 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N THR D 184 " --> pdb=" O LEU D 250 " (cutoff:3.500A) removed outlier: 8.347A pdb=" N PHE D 252 " --> pdb=" O THR D 184 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N VAL D 186 " --> pdb=" O PHE D 252 " (cutoff:3.500A) removed outlier: 8.570A pdb=" N ASP D 254 " --> pdb=" O VAL D 186 " (cutoff:3.500A) removed outlier: 7.708A pdb=" N ALA D 188 " --> pdb=" O ASP D 254 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ALA D 214 " --> pdb=" O SER D 185 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N PHE D 187 " --> pdb=" O ALA D 214 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N VAL D 216 " --> pdb=" O PHE D 187 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N GLY D 191 " --> pdb=" O GLY D 218 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'E' and resid 11 through 14 removed outlier: 6.697A pdb=" N ASP E 21 " --> pdb=" O VAL E 13 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N ILE E 65 " --> pdb=" O VAL E 53 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N VAL E 53 " --> pdb=" O ILE E 65 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'E' and resid 87 through 90 removed outlier: 3.898A pdb=" N GLU E 116 " --> pdb=" O VAL E 90 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'E' and resid 329 through 332 removed outlier: 3.518A pdb=" N PHE E 159 " --> pdb=" O THR E 331 " (cutoff:3.500A) removed outlier: 8.282A pdb=" N ILE E 156 " --> pdb=" O ILE E 302 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N SER E 304 " --> pdb=" O ILE E 156 " (cutoff:3.500A) removed outlier: 7.553A pdb=" N LEU E 158 " --> pdb=" O SER E 304 " (cutoff:3.500A) removed outlier: 5.690A pdb=" N GLN E 306 " --> pdb=" O LEU E 158 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N VAL E 249 " --> pdb=" O THR E 303 " (cutoff:3.500A) removed outlier: 8.837A pdb=" N MET E 305 " --> pdb=" O VAL E 249 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N LEU E 251 " --> pdb=" O MET E 305 " (cutoff:3.500A) removed outlier: 8.609A pdb=" N ALA E 307 " --> pdb=" O LEU E 251 " (cutoff:3.500A) removed outlier: 8.066A pdb=" N ILE E 253 " --> pdb=" O ALA E 307 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N THR E 184 " --> pdb=" O LEU E 250 " (cutoff:3.500A) removed outlier: 7.849A pdb=" N PHE E 252 " --> pdb=" O THR E 184 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N VAL E 186 " --> pdb=" O PHE E 252 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N ALA E 214 " --> pdb=" O PHE E 187 " (cutoff:3.500A) removed outlier: 8.187A pdb=" N GLY E 189 " --> pdb=" O ALA E 214 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N VAL E 216 " --> pdb=" O GLY E 189 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'F' and resid 11 through 15 removed outlier: 6.974A pdb=" N ASP F 21 " --> pdb=" O VAL F 13 " (cutoff:3.500A) removed outlier: 5.971A pdb=" N ILE F 65 " --> pdb=" O VAL F 53 " (cutoff:3.500A) removed outlier: 5.475A pdb=" N VAL F 53 " --> pdb=" O ILE F 65 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LYS F 47 " --> pdb=" O ILE F 40 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'F' and resid 87 through 89 Processing sheet with id= P, first strand: chain 'F' and resid 329 through 332 removed outlier: 4.186A pdb=" N ALA F 329 " --> pdb=" O LYS F 155 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ALA F 157 " --> pdb=" O ALA F 329 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N THR F 331 " --> pdb=" O ALA F 157 " (cutoff:3.500A) removed outlier: 8.524A pdb=" N ILE F 156 " --> pdb=" O ILE F 302 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N SER F 304 " --> pdb=" O ILE F 156 " (cutoff:3.500A) removed outlier: 8.243A pdb=" N LEU F 158 " --> pdb=" O SER F 304 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N GLN F 306 " --> pdb=" O LEU F 158 " (cutoff:3.500A) removed outlier: 8.071A pdb=" N GLY F 160 " --> pdb=" O GLN F 306 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N VAL F 308 " --> pdb=" O GLY F 160 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N VAL F 249 " --> pdb=" O THR F 303 " (cutoff:3.500A) removed outlier: 8.269A pdb=" N MET F 305 " --> pdb=" O VAL F 249 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N LEU F 251 " --> pdb=" O MET F 305 " (cutoff:3.500A) removed outlier: 8.320A pdb=" N ALA F 307 " --> pdb=" O LEU F 251 " (cutoff:3.500A) removed outlier: 7.202A pdb=" N ILE F 253 " --> pdb=" O ALA F 307 " (cutoff:3.500A) removed outlier: 8.993A pdb=" N TYR F 309 " --> pdb=" O ILE F 253 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N THR F 184 " --> pdb=" O LEU F 250 " (cutoff:3.500A) removed outlier: 8.576A pdb=" N PHE F 252 " --> pdb=" O THR F 184 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N VAL F 186 " --> pdb=" O PHE F 252 " (cutoff:3.500A) removed outlier: 8.689A pdb=" N ASP F 254 " --> pdb=" O VAL F 186 " (cutoff:3.500A) removed outlier: 7.598A pdb=" N ALA F 188 " --> pdb=" O ASP F 254 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N ALA F 214 " --> pdb=" O PHE F 187 " (cutoff:3.500A) removed outlier: 8.567A pdb=" N GLY F 189 " --> pdb=" O ALA F 214 " (cutoff:3.500A) removed outlier: 7.240A pdb=" N VAL F 216 " --> pdb=" O GLY F 189 " (cutoff:3.500A) removed outlier: 8.475A pdb=" N GLY F 191 " --> pdb=" O VAL F 216 " (cutoff:3.500A) removed outlier: 8.682A pdb=" N GLY F 218 " --> pdb=" O GLY F 191 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'G' and resid 196 through 202 removed outlier: 8.803A pdb=" N HIS G 184 " --> pdb=" O ARG G 76 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N GLY G 78 " --> pdb=" O HIS G 184 " (cutoff:3.500A) removed outlier: 7.946A pdb=" N VAL G 186 " --> pdb=" O GLY G 78 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N LEU G 80 " --> pdb=" O VAL G 186 " (cutoff:3.500A) removed outlier: 8.756A pdb=" N THR G 188 " --> pdb=" O LEU G 80 " (cutoff:3.500A) removed outlier: 9.361A pdb=" N VAL G 82 " --> pdb=" O THR G 188 " (cutoff:3.500A) removed outlier: 12.314A pdb=" N PHE G 190 " --> pdb=" O VAL G 82 " (cutoff:3.500A) removed outlier: 6.196A pdb=" N ASP G 113 " --> pdb=" O ALA G 77 " (cutoff:3.500A) removed outlier: 7.523A pdb=" N VAL G 79 " --> pdb=" O ASP G 113 " (cutoff:3.500A) removed outlier: 6.144A pdb=" N VAL G 115 " --> pdb=" O VAL G 79 " (cutoff:3.500A) removed outlier: 7.686A pdb=" N VAL G 81 " --> pdb=" O VAL G 115 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N TYR G 117 " --> pdb=" O VAL G 81 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N GLU G 136 " --> pdb=" O VAL G 118 " (cutoff:3.500A) 886 hydrogen bonds defined for protein. 2493 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: 7.69 Time building geometry restraints manager: 10.60 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 8159 1.34 - 1.46: 4843 1.46 - 1.58: 11226 1.58 - 1.70: 19 1.70 - 1.81: 130 Bond restraints: 24377 Sorted by residual: bond pdb=" CA HIS D 326 " pdb=" C HIS D 326 " ideal model delta sigma weight residual 1.526 1.510 0.016 1.20e-02 6.94e+03 1.83e+00 bond pdb=" N SER D 119 " pdb=" CA SER D 119 " ideal model delta sigma weight residual 1.457 1.473 -0.016 1.29e-02 6.01e+03 1.55e+00 bond pdb=" CA SER C 437 " pdb=" CB SER C 437 " ideal model delta sigma weight residual 1.522 1.530 -0.008 7.00e-03 2.04e+04 1.22e+00 bond pdb=" C PHE F 343 " pdb=" N PRO F 344 " ideal model delta sigma weight residual 1.335 1.350 -0.015 1.36e-02 5.41e+03 1.16e+00 bond pdb=" CA VAL D 277 " pdb=" C VAL D 277 " ideal model delta sigma weight residual 1.523 1.536 -0.013 1.27e-02 6.20e+03 1.12e+00 ... (remaining 24372 not shown) Histogram of bond angle deviations from ideal: 96.82 - 105.42: 500 105.42 - 114.01: 14273 114.01 - 122.61: 15605 122.61 - 131.21: 2646 131.21 - 139.81: 51 Bond angle restraints: 33075 Sorted by residual: angle pdb=" N TRP D 118 " pdb=" CA TRP D 118 " pdb=" C TRP D 118 " ideal model delta sigma weight residual 108.34 114.95 -6.61 1.31e+00 5.83e-01 2.55e+01 angle pdb=" C PHE C 340 " pdb=" N ILE C 341 " pdb=" CA ILE C 341 " ideal model delta sigma weight residual 120.33 123.34 -3.01 8.00e-01 1.56e+00 1.41e+01 angle pdb=" N ILE D 120 " pdb=" CA ILE D 120 " pdb=" C ILE D 120 " ideal model delta sigma weight residual 113.53 110.13 3.40 9.80e-01 1.04e+00 1.20e+01 angle pdb=" CB MET E 67 " pdb=" CG MET E 67 " pdb=" SD MET E 67 " ideal model delta sigma weight residual 112.70 122.41 -9.71 3.00e+00 1.11e-01 1.05e+01 angle pdb=" C PHE A 340 " pdb=" N ILE A 341 " pdb=" CA ILE A 341 " ideal model delta sigma weight residual 120.33 122.92 -2.59 8.00e-01 1.56e+00 1.05e+01 ... (remaining 33070 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.84: 13231 17.84 - 35.69: 1136 35.69 - 53.53: 214 53.53 - 71.37: 45 71.37 - 89.22: 32 Dihedral angle restraints: 14658 sinusoidal: 5697 harmonic: 8961 Sorted by residual: dihedral pdb=" CA ARG E 258 " pdb=" C ARG E 258 " pdb=" N PHE E 259 " pdb=" CA PHE E 259 " ideal model delta harmonic sigma weight residual 180.00 161.44 18.56 0 5.00e+00 4.00e-02 1.38e+01 dihedral pdb=" CA GLY D 263 " pdb=" C GLY D 263 " pdb=" N SER D 264 " pdb=" CA SER D 264 " ideal model delta harmonic sigma weight residual 180.00 -162.02 -17.98 0 5.00e+00 4.00e-02 1.29e+01 dihedral pdb=" CA ILE B 383 " pdb=" C ILE B 383 " pdb=" N LYS B 384 " pdb=" CA LYS B 384 " ideal model delta harmonic sigma weight residual -180.00 -163.15 -16.85 0 5.00e+00 4.00e-02 1.14e+01 ... (remaining 14655 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 2579 0.034 - 0.067: 840 0.067 - 0.101: 284 0.101 - 0.135: 124 0.135 - 0.168: 4 Chirality restraints: 3831 Sorted by residual: chirality pdb=" CA TRP D 118 " pdb=" N TRP D 118 " pdb=" C TRP D 118 " pdb=" CB TRP D 118 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.09e-01 chirality pdb=" CB VAL B 102 " pdb=" CA VAL B 102 " pdb=" CG1 VAL B 102 " pdb=" CG2 VAL B 102 " both_signs ideal model delta sigma weight residual False -2.63 -2.47 -0.16 2.00e-01 2.50e+01 6.47e-01 chirality pdb=" CG LEU D 146 " pdb=" CB LEU D 146 " pdb=" CD1 LEU D 146 " pdb=" CD2 LEU D 146 " both_signs ideal model delta sigma weight residual False -2.59 -2.44 -0.15 2.00e-01 2.50e+01 5.40e-01 ... (remaining 3828 not shown) Planarity restraints: 4320 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL E 310 " -0.041 5.00e-02 4.00e+02 6.23e-02 6.20e+00 pdb=" N PRO E 311 " 0.108 5.00e-02 4.00e+02 pdb=" CA PRO E 311 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO E 311 " -0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL D 430 " -0.030 5.00e-02 4.00e+02 4.57e-02 3.33e+00 pdb=" N PRO D 431 " 0.079 5.00e-02 4.00e+02 pdb=" CA PRO D 431 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO D 431 " -0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL E 430 " 0.029 5.00e-02 4.00e+02 4.48e-02 3.21e+00 pdb=" N PRO E 431 " -0.078 5.00e-02 4.00e+02 pdb=" CA PRO E 431 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO E 431 " 0.025 5.00e-02 4.00e+02 ... (remaining 4317 not shown) Histogram of nonbonded interaction distances: 1.99 - 2.57: 211 2.57 - 3.15: 20127 3.15 - 3.73: 37453 3.73 - 4.32: 47354 4.32 - 4.90: 79044 Nonbonded interactions: 184189 Sorted by model distance: nonbonded pdb=" O2B ATP A 600 " pdb="MG MG A 601 " model vdw 1.986 2.170 nonbonded pdb=" O1A ATP B 600 " pdb="MG MG B 601 " model vdw 2.014 2.170 nonbonded pdb=" O2B ATP B 600 " pdb="MG MG B 601 " model vdw 2.026 2.170 nonbonded pdb=" O1G ATP B 600 " pdb="MG MG B 601 " model vdw 2.059 2.170 nonbonded pdb=" O3B ADP F 600 " pdb="MG MG F 601 " model vdw 2.074 2.170 ... (remaining 184184 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 29 and (name N or name CA or name C or name O or name CB \ )) or resid 30 through 44 or (resid 45 and (name N or name CA or name C or name \ O or name CB )) or resid 46 through 132 or (resid 133 and (name N or name CA or \ name C or name O or name CB )) or resid 134 through 355 or (resid 356 and (name \ N or name CA or name C or name O or name CB )) or resid 357 or (resid 358 and (n \ ame N or name CA or name C or name O or name CB )) or resid 359 through 400 or ( \ resid 401 through 402 and (name N or name CA or name C or name O or name CB )) o \ r resid 403 through 410 or resid 414 through 416 or (resid 417 through 419 and ( \ name N or name CA or name C or name O or name CB )) or resid 420 through 461 or \ (resid 462 through 463 and (name N or name CA or name C or name O or name CB )) \ or resid 464 through 467 or (resid 468 and (name N or name CA or name C or name \ O or name CB )) or resid 469 or (resid 470 and (name N or name CA or name C or n \ ame O or name CB )) or resid 471 through 475 or (resid 476 through 477 and (name \ N or name CA or name C or name O or name CB )) or resid 478 through 494 or (res \ id 495 through 499 and (name N or name CA or name C or name O or name CB )) or r \ esid 500 through 505 or (resid 506 and (name N or name CA or name C or name O or \ name CB )) or resid 507 through 515 or resid 537 through 538 or resid 540 or re \ sid 600 through 601)) selection = (chain 'B' and ((resid 29 and (name N or name CA or name C or name O or name CB \ )) or resid 30 through 44 or (resid 45 and (name N or name CA or name C or name \ O or name CB )) or resid 46 through 132 or (resid 133 and (name N or name CA or \ name C or name O or name CB )) or resid 134 through 190 or (resid 191 through 19 \ 2 and (name N or name CA or name C or name O or name CB )) or resid 193 through \ 316 or (resid 317 and (name N or name CA or name C or name O or name CB )) or re \ sid 318 through 355 or (resid 356 and (name N or name CA or name C or name O or \ name CB )) or resid 357 or (resid 358 and (name N or name CA or name C or name O \ or name CB )) or resid 359 through 401 or (resid 402 and (name N or name CA or \ name C or name O or name CB )) or resid 403 through 410 or resid 414 through 416 \ or (resid 417 through 419 and (name N or name CA or name C or name O or name CB \ )) or resid 420 through 456 or (resid 457 and (name N or name CA or name C or n \ ame O or name CB )) or resid 458 through 467 or (resid 468 and (name N or name C \ A or name C or name O or name CB )) or resid 469 through 475 or (resid 476 throu \ gh 477 and (name N or name CA or name C or name O or name CB )) or resid 478 thr \ ough 493 or (resid 494 through 499 and (name N or name CA or name C or name O or \ name CB )) or resid 500 through 505 or (resid 506 and (name N or name CA or nam \ e C or name O or name CB )) or resid 507 through 514 or (resid 515 and (name N o \ r name CA or name C or name O or name CB )) or resid 518 through 520 or resid 60 \ 0 through 601)) selection = (chain 'C' and (resid 29 through 190 or (resid 191 through 192 and (name N or na \ me CA or name C or name O or name CB )) or resid 193 through 316 or (resid 317 a \ nd (name N or name CA or name C or name O or name CB )) or resid 318 through 400 \ or (resid 401 through 402 and (name N or name CA or name C or name O or name CB \ )) or resid 403 through 456 or (resid 457 and (name N or name CA or name C or n \ ame O or name CB )) or resid 458 through 469 or (resid 470 and (name N or name C \ A or name C or name O or name CB )) or resid 471 through 493 or (resid 494 throu \ gh 499 and (name N or name CA or name C or name O or name CB )) or resid 500 thr \ ough 515 or resid 518 through 520 or resid 600 through 601)) } ncs_group { reference = (chain 'D' and (resid 8 through 103 or (resid 104 through 105 and (name N or nam \ e CA or name C or name O or name CB )) or resid 106 or (resid 107 through 108 an \ d (name N or name CA or name C or name O or name CB )) or resid 109 through 113 \ or (resid 114 and (name N or name CA or name C or name O or name CB )) or resid \ 115 through 198 or (resid 199 and (name N or name CA or name C or name O or name \ CB )) or resid 200 through 202 or (resid 203 and (name N or name CA or name C o \ r name O or name CB )) or resid 204 through 205 or (resid 206 through 207 and (n \ ame N or name CA or name C or name O or name CB )) or resid 208 through 285 or ( \ resid 286 and (name N or name CA or name C or name O or name CB )) or resid 287 \ through 362 or (resid 363 through 364 and (name N or name CA or name C or name O \ or name CB )) or resid 365 through 369 or (resid 370 through 371 and (name N or \ name CA or name C or name O or name CB )) or resid 372 through 380 or (resid 38 \ 1 and (name N or name CA or name C or name O or name CB )) or resid 382 through \ 391 or (resid 392 through 393 and (name N or name CA or name C or name O or name \ CB )) or resid 394 through 402 or (resid 403 and (name N or name CA or name C o \ r name O or name CB )) or resid 404 through 424 or (resid 425 and (name N or nam \ e CA or name C or name O or name CB )) or resid 426 through 471)) selection = (chain 'E' and (resid 8 through 104 or (resid 105 and (name N or name CA or name \ C or name O or name CB )) or resid 106 through 137 or (resid 138 and (name N or \ name CA or name C or name O or name CB )) or resid 139 through 220 or (resid 22 \ 1 through 222 and (name N or name CA or name C or name O or name CB )) or resid \ 223 through 285 or (resid 286 and (name N or name CA or name C or name O or name \ CB )) or resid 287 through 288 or (resid 289 and (name N or name CA or name C o \ r name O or name CB )) or resid 290 through 291 or (resid 292 and (name N or nam \ e CA or name C or name O or name CB )) or resid 293 through 370 or (resid 371 an \ d (name N or name CA or name C or name O or name CB )) or resid 372 through 395 \ or (resid 396 through 398 and (name N or name CA or name C or name O or name CB \ )) or resid 399 through 461 or (resid 462 through 463 and (name N or name CA or \ name C or name O or name CB )) or resid 464 through 465 or (resid 466 and (name \ N or name CA or name C or name O or name CB )) or resid 467 through 471)) selection = (chain 'F' and (resid 8 through 103 or (resid 104 through 105 and (name N or nam \ e CA or name C or name O or name CB )) or resid 106 through 107 or (resid 108 an \ d (name N or name CA or name C or name O or name CB )) or resid 109 through 113 \ or (resid 114 and (name N or name CA or name C or name O or name CB )) or resid \ 115 through 134 or (resid 135 and (name N or name CA or name C or name O or name \ CB )) or resid 136 through 137 or (resid 138 and (name N or name CA or name C o \ r name O or name CB )) or resid 139 through 198 or (resid 199 and (name N or nam \ e CA or name C or name O or name CB )) or resid 200 through 202 or (resid 203 an \ d (name N or name CA or name C or name O or name CB )) or resid 204 through 205 \ or (resid 206 through 207 and (name N or name CA or name C or name O or name CB \ )) or resid 208 through 220 or (resid 221 through 222 and (name N or name CA or \ name C or name O or name CB )) or resid 223 through 291 or (resid 292 and (name \ N or name CA or name C or name O or name CB )) or resid 293 through 369 or (resi \ d 370 through 371 and (name N or name CA or name C or name O or name CB )) or re \ sid 372 through 380 or (resid 381 and (name N or name CA or name C or name O or \ name CB )) or resid 382 through 383 or (resid 384 and (name N or name CA or name \ C or name O or name CB )) or resid 385 through 391 or (resid 392 through 393 an \ d (name N or name CA or name C or name O or name CB )) or resid 394 through 395 \ or (resid 396 through 398 and (name N or name CA or name C or name O or name CB \ )) or resid 399 through 402 or (resid 403 and (name N or name CA or name C or na \ me O or name CB )) or resid 404 through 432 or (resid 433 and (name N or name CA \ or name C or name O or name CB )) or resid 434 through 461 or (resid 462 throug \ h 463 and (name N or name CA or name C or name O or name CB )) or resid 464 thro \ ugh 465 or (resid 466 and (name N or name CA or name C or name O or name CB )) o \ r resid 467 through 471)) } 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: 6 Type Number sf(0) Gaussians P 13 5.49 5 Mg 5 5.21 5 S 74 5.16 5 C 15085 2.51 5 N 4198 2.21 5 O 4600 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: 1.940 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: 7.970 Check model and map are aligned: 0.360 Process input model: 60.390 Find NCS groups from input model: 1.840 Set up NCS constraints: 0.130 Set refine NCS operators: 0.000 Set scattering table: 0.230 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 75.540 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8500 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 : 0.003 0.031 24377 Z= 0.170 Angle : 0.595 9.708 33075 Z= 0.322 Chirality : 0.041 0.168 3831 Planarity : 0.004 0.062 4320 Dihedral : 14.472 89.218 8904 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer Outliers : 0.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.45 (0.15), residues: 3142 helix: 1.55 (0.15), residues: 1218 sheet: 0.71 (0.25), residues: 401 loop : -0.86 (0.16), residues: 1523 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6284 Ramachandran restraints generated. 3142 Oldfield, 0 Emsley, 3142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6284 Ramachandran restraints generated. 3142 Oldfield, 0 Emsley, 3142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 2561 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 120 time to evaluate : 3.088 Fit side-chains revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 120 average time/residue: 0.3248 time to fit residues: 66.6033 Evaluate side-chains 99 residues out of total 2561 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 99 time to evaluate : 2.977 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.0367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 265 optimal weight: 5.9990 chunk 237 optimal weight: 7.9990 chunk 132 optimal weight: 5.9990 chunk 81 optimal weight: 0.3980 chunk 160 optimal weight: 9.9990 chunk 127 optimal weight: 10.0000 chunk 246 optimal weight: 0.3980 chunk 95 optimal weight: 0.9990 chunk 149 optimal weight: 5.9990 chunk 183 optimal weight: 2.9990 chunk 285 optimal weight: 4.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 382 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 326 HIS ** E 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8527 moved from start: 0.0537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.025 24377 Z= 0.192 Angle : 0.514 7.447 33075 Z= 0.261 Chirality : 0.041 0.148 3831 Planarity : 0.004 0.043 4320 Dihedral : 4.744 88.530 3427 Min Nonbonded Distance : 1.909 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer Outliers : 0.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.50 (0.15), residues: 3142 helix: 1.57 (0.15), residues: 1245 sheet: 0.66 (0.25), residues: 390 loop : -0.81 (0.16), residues: 1507 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6284 Ramachandran restraints generated. 3142 Oldfield, 0 Emsley, 3142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6284 Ramachandran restraints generated. 3142 Oldfield, 0 Emsley, 3142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 2561 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 105 time to evaluate : 2.900 Fit side-chains revert: symmetry clash outliers start: 6 outliers final: 4 residues processed: 109 average time/residue: 0.3328 time to fit residues: 62.0239 Evaluate side-chains 104 residues out of total 2561 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 100 time to evaluate : 2.992 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 4 outliers final: 1 residues processed: 4 average time/residue: 0.2637 time to fit residues: 5.7810 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 158 optimal weight: 9.9990 chunk 88 optimal weight: 10.0000 chunk 237 optimal weight: 10.0000 chunk 194 optimal weight: 8.9990 chunk 78 optimal weight: 0.5980 chunk 285 optimal weight: 4.9990 chunk 308 optimal weight: 6.9990 chunk 254 optimal weight: 5.9990 chunk 283 optimal weight: 0.9990 chunk 97 optimal weight: 9.9990 chunk 229 optimal weight: 8.9990 overall best weight: 3.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 335 ASN A 382 GLN ** B 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 382 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 326 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 52 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8595 moved from start: 0.1059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.032 24377 Z= 0.343 Angle : 0.590 7.676 33075 Z= 0.305 Chirality : 0.042 0.172 3831 Planarity : 0.004 0.054 4320 Dihedral : 5.061 88.580 3427 Min Nonbonded Distance : 1.883 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer Outliers : 0.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.35 (0.15), residues: 3142 helix: 1.47 (0.15), residues: 1219 sheet: 0.54 (0.25), residues: 400 loop : -0.89 (0.16), residues: 1523 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6284 Ramachandran restraints generated. 3142 Oldfield, 0 Emsley, 3142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6284 Ramachandran restraints generated. 3142 Oldfield, 0 Emsley, 3142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 2561 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 102 time to evaluate : 2.916 Fit side-chains outliers start: 15 outliers final: 7 residues processed: 112 average time/residue: 0.3337 time to fit residues: 63.9732 Evaluate side-chains 105 residues out of total 2561 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 98 time to evaluate : 3.007 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.2621 time to fit residues: 7.3331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 282 optimal weight: 5.9990 chunk 214 optimal weight: 5.9990 chunk 148 optimal weight: 2.9990 chunk 31 optimal weight: 3.9990 chunk 136 optimal weight: 0.9990 chunk 191 optimal weight: 5.9990 chunk 286 optimal weight: 0.9980 chunk 303 optimal weight: 8.9990 chunk 149 optimal weight: 7.9990 chunk 271 optimal weight: 0.6980 chunk 81 optimal weight: 1.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 335 ASN B 43 HIS ** C 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 382 GLN ** D 326 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 171 GLN ** E 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8553 moved from start: 0.0997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.034 24377 Z= 0.164 Angle : 0.504 8.012 33075 Z= 0.256 Chirality : 0.040 0.142 3831 Planarity : 0.003 0.059 4320 Dihedral : 4.813 88.928 3427 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer Outliers : 0.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.53 (0.15), residues: 3142 helix: 1.59 (0.15), residues: 1232 sheet: 0.65 (0.25), residues: 411 loop : -0.79 (0.16), residues: 1499 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6284 Ramachandran restraints generated. 3142 Oldfield, 0 Emsley, 3142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6284 Ramachandran restraints generated. 3142 Oldfield, 0 Emsley, 3142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 2561 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 109 time to evaluate : 2.985 Fit side-chains outliers start: 16 outliers final: 8 residues processed: 122 average time/residue: 0.3263 time to fit residues: 67.5545 Evaluate side-chains 113 residues out of total 2561 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 105 time to evaluate : 2.787 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.2133 time to fit residues: 6.9959 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 252 optimal weight: 5.9990 chunk 172 optimal weight: 6.9990 chunk 4 optimal weight: 8.9990 chunk 225 optimal weight: 10.0000 chunk 125 optimal weight: 0.8980 chunk 259 optimal weight: 1.9990 chunk 209 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 154 optimal weight: 10.0000 chunk 272 optimal weight: 2.9990 chunk 76 optimal weight: 3.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 335 ASN ** B 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 55 GLN ** D 326 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 171 GLN ** E 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 55 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8580 moved from start: 0.1192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.026 24377 Z= 0.251 Angle : 0.537 9.468 33075 Z= 0.274 Chirality : 0.041 0.152 3831 Planarity : 0.004 0.053 4320 Dihedral : 4.872 86.695 3427 Min Nonbonded Distance : 1.897 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer Outliers : 0.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.48 (0.15), residues: 3142 helix: 1.55 (0.15), residues: 1231 sheet: 0.61 (0.25), residues: 417 loop : -0.81 (0.16), residues: 1494 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6284 Ramachandran restraints generated. 3142 Oldfield, 0 Emsley, 3142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6284 Ramachandran restraints generated. 3142 Oldfield, 0 Emsley, 3142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 2561 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 104 time to evaluate : 2.805 Fit side-chains outliers start: 24 outliers final: 13 residues processed: 125 average time/residue: 0.3219 time to fit residues: 68.5661 Evaluate side-chains 113 residues out of total 2561 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 100 time to evaluate : 2.687 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.2118 time to fit residues: 8.8077 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 102 optimal weight: 10.0000 chunk 273 optimal weight: 0.8980 chunk 59 optimal weight: 3.9990 chunk 178 optimal weight: 10.0000 chunk 74 optimal weight: 2.9990 chunk 303 optimal weight: 9.9990 chunk 252 optimal weight: 5.9990 chunk 140 optimal weight: 2.9990 chunk 25 optimal weight: 6.9990 chunk 100 optimal weight: 3.9990 chunk 159 optimal weight: 9.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 335 ASN ** B 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 171 GLN ** D 326 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8591 moved from start: 0.1355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.029 24377 Z= 0.264 Angle : 0.551 9.170 33075 Z= 0.282 Chirality : 0.041 0.157 3831 Planarity : 0.004 0.054 4320 Dihedral : 4.955 87.182 3427 Min Nonbonded Distance : 1.891 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer Outliers : 1.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.45 (0.15), residues: 3142 helix: 1.50 (0.15), residues: 1234 sheet: 0.65 (0.24), residues: 424 loop : -0.84 (0.16), residues: 1484 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6284 Ramachandran restraints generated. 3142 Oldfield, 0 Emsley, 3142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6284 Ramachandran restraints generated. 3142 Oldfield, 0 Emsley, 3142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 2561 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 104 time to evaluate : 2.644 Fit side-chains revert: symmetry clash outliers start: 30 outliers final: 15 residues processed: 131 average time/residue: 0.3206 time to fit residues: 71.5042 Evaluate side-chains 116 residues out of total 2561 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 101 time to evaluate : 2.917 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 0 residues processed: 15 average time/residue: 0.2356 time to fit residues: 10.6206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 292 optimal weight: 9.9990 chunk 34 optimal weight: 1.9990 chunk 173 optimal weight: 8.9990 chunk 221 optimal weight: 8.9990 chunk 171 optimal weight: 10.0000 chunk 255 optimal weight: 2.9990 chunk 169 optimal weight: 2.9990 chunk 302 optimal weight: 9.9990 chunk 189 optimal weight: 6.9990 chunk 184 optimal weight: 0.7980 chunk 139 optimal weight: 7.9990 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 335 ASN B 68 ASN ** D 326 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8600 moved from start: 0.1492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.031 24377 Z= 0.279 Angle : 0.562 10.012 33075 Z= 0.287 Chirality : 0.041 0.162 3831 Planarity : 0.004 0.052 4320 Dihedral : 5.017 87.592 3427 Min Nonbonded Distance : 1.884 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer Outliers : 0.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.39 (0.15), residues: 3142 helix: 1.47 (0.15), residues: 1234 sheet: 0.56 (0.25), residues: 419 loop : -0.87 (0.16), residues: 1489 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6284 Ramachandran restraints generated. 3142 Oldfield, 0 Emsley, 3142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6284 Ramachandran restraints generated. 3142 Oldfield, 0 Emsley, 3142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 2561 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 103 time to evaluate : 2.875 Fit side-chains outliers start: 21 outliers final: 10 residues processed: 119 average time/residue: 0.3349 time to fit residues: 67.9554 Evaluate side-chains 110 residues out of total 2561 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 100 time to evaluate : 2.887 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.2334 time to fit residues: 8.0664 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 187 optimal weight: 10.0000 chunk 120 optimal weight: 7.9990 chunk 180 optimal weight: 0.9990 chunk 91 optimal weight: 7.9990 chunk 59 optimal weight: 1.9990 chunk 58 optimal weight: 0.9980 chunk 192 optimal weight: 4.9990 chunk 206 optimal weight: 9.9990 chunk 149 optimal weight: 0.4980 chunk 28 optimal weight: 7.9990 chunk 237 optimal weight: 1.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 335 ASN ** B 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 326 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8555 moved from start: 0.1425 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.029 24377 Z= 0.153 Angle : 0.514 10.565 33075 Z= 0.258 Chirality : 0.040 0.139 3831 Planarity : 0.003 0.053 4320 Dihedral : 4.860 88.658 3427 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer Outliers : 0.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.54 (0.15), residues: 3142 helix: 1.62 (0.15), residues: 1231 sheet: 0.73 (0.25), residues: 405 loop : -0.82 (0.16), residues: 1506 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6284 Ramachandran restraints generated. 3142 Oldfield, 0 Emsley, 3142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6284 Ramachandran restraints generated. 3142 Oldfield, 0 Emsley, 3142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 2561 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 109 time to evaluate : 3.899 Fit side-chains outliers start: 8 outliers final: 2 residues processed: 114 average time/residue: 0.3574 time to fit residues: 69.5920 Evaluate side-chains 105 residues out of total 2561 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 103 time to evaluate : 2.828 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.2901 time to fit residues: 5.1655 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 275 optimal weight: 4.9990 chunk 289 optimal weight: 0.7980 chunk 264 optimal weight: 1.9990 chunk 282 optimal weight: 3.9990 chunk 169 optimal weight: 10.0000 chunk 122 optimal weight: 8.9990 chunk 221 optimal weight: 4.9990 chunk 86 optimal weight: 3.9990 chunk 254 optimal weight: 10.0000 chunk 266 optimal weight: 8.9990 chunk 281 optimal weight: 2.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 335 ASN ** D 326 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 415 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8589 moved from start: 0.1550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.030 24377 Z= 0.252 Angle : 0.552 10.130 33075 Z= 0.280 Chirality : 0.041 0.156 3831 Planarity : 0.004 0.053 4320 Dihedral : 4.974 87.101 3427 Min Nonbonded Distance : 1.895 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer Outliers : 0.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.49 (0.15), residues: 3142 helix: 1.58 (0.15), residues: 1232 sheet: 0.68 (0.25), residues: 412 loop : -0.85 (0.16), residues: 1498 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6284 Ramachandran restraints generated. 3142 Oldfield, 0 Emsley, 3142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6284 Ramachandran restraints generated. 3142 Oldfield, 0 Emsley, 3142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 2561 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 103 time to evaluate : 2.844 Fit side-chains outliers start: 7 outliers final: 2 residues processed: 109 average time/residue: 0.3412 time to fit residues: 63.4798 Evaluate side-chains 100 residues out of total 2561 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 98 time to evaluate : 2.911 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.2180 time to fit residues: 4.6363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 185 optimal weight: 5.9990 chunk 298 optimal weight: 0.9990 chunk 182 optimal weight: 0.7980 chunk 141 optimal weight: 0.0570 chunk 207 optimal weight: 1.9990 chunk 312 optimal weight: 0.9980 chunk 287 optimal weight: 7.9990 chunk 249 optimal weight: 0.5980 chunk 25 optimal weight: 3.9990 chunk 192 optimal weight: 8.9990 chunk 152 optimal weight: 6.9990 overall best weight: 0.6900 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 326 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8538 moved from start: 0.1502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.038 24377 Z= 0.134 Angle : 0.511 10.372 33075 Z= 0.254 Chirality : 0.040 0.140 3831 Planarity : 0.003 0.050 4320 Dihedral : 4.743 88.319 3427 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer Outliers : 0.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.60 (0.15), residues: 3142 helix: 1.64 (0.15), residues: 1235 sheet: 0.87 (0.24), residues: 426 loop : -0.83 (0.16), residues: 1481 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6284 Ramachandran restraints generated. 3142 Oldfield, 0 Emsley, 3142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6284 Ramachandran restraints generated. 3142 Oldfield, 0 Emsley, 3142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 2561 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 105 time to evaluate : 2.891 Fit side-chains outliers start: 2 outliers final: 2 residues processed: 106 average time/residue: 0.3415 time to fit residues: 62.0884 Evaluate side-chains 106 residues out of total 2561 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 104 time to evaluate : 2.994 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.2692 time to fit residues: 4.9253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 197 optimal weight: 3.9990 chunk 265 optimal weight: 0.9990 chunk 76 optimal weight: 4.9990 chunk 229 optimal weight: 9.9990 chunk 36 optimal weight: 9.9990 chunk 69 optimal weight: 0.0270 chunk 249 optimal weight: 0.0970 chunk 104 optimal weight: 6.9990 chunk 256 optimal weight: 9.9990 chunk 31 optimal weight: 0.5980 chunk 45 optimal weight: 8.9990 overall best weight: 1.1440 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 335 ASN ** B 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 382 GLN ** D 326 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.051141 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2884 r_free = 0.2884 target = 0.042075 restraints weight = 138461.844| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2925 r_free = 0.2925 target = 0.043312 restraints weight = 72960.541| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2953 r_free = 0.2953 target = 0.044152 restraints weight = 46805.792| |-----------------------------------------------------------------------------| r_work (final): 0.2951 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8544 moved from start: 0.1537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.034 24377 Z= 0.145 Angle : 0.506 10.198 33075 Z= 0.251 Chirality : 0.040 0.136 3831 Planarity : 0.003 0.044 4320 Dihedral : 4.645 86.893 3427 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer Outliers : 0.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.64 (0.15), residues: 3142 helix: 1.63 (0.15), residues: 1248 sheet: 0.97 (0.25), residues: 406 loop : -0.79 (0.16), residues: 1488 =============================================================================== Job complete usr+sys time: 3020.92 seconds wall clock time: 57 minutes 37.58 seconds (3457.58 seconds total)