Starting phenix.real_space_refine (version: dev) on Tue May 17 05:18:35 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6oqt_20169/05_2022/6oqt_20169_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6oqt_20169/05_2022/6oqt_20169.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6oqt_20169/05_2022/6oqt_20169.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6oqt_20169/05_2022/6oqt_20169.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6oqt_20169/05_2022/6oqt_20169_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6oqt_20169/05_2022/6oqt_20169_neut_updated.pdb" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "F TYR 297": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 405": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4597/modules/chem_data/mon_lib" Total number of atoms: 36971 Number of models: 1 Model: "" Number of chains: 28 Chain: "W" Number of atoms: 1320 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1320 Classifications: {'peptide': 173} Link IDs: {'PTRANS': 3, 'TRANS': 169} Chain: "C" Number of atoms: 3869 Number of conformers: 1 Conformer: "" Number of residues, atoms: 512, 3869 Classifications: {'peptide': 512} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 17, 'TRANS': 493, 'PCIS': 1} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "B" Number of atoms: 3871 Number of conformers: 1 Conformer: "" Number of residues, atoms: 513, 3871 Classifications: {'peptide': 513} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 17, 'TRANS': 494, 'PCIS': 1} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "A" Number of atoms: 3832 Number of conformers: 1 Conformer: "" Number of residues, atoms: 508, 3832 Classifications: {'peptide': 508} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 17, 'TRANS': 489, 'PCIS': 1} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "X" Number of atoms: 1210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1210 Classifications: {'peptide': 156} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 153} Chain: "H" Number of atoms: 1034 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1034 Classifications: {'peptide': 136} Link IDs: {'PTRANS': 4, 'TRANS': 131} Chain: "G" Number of atoms: 2186 Number of conformers: 1 Conformer: "" Number of residues, atoms: 284, 2186 Classifications: {'peptide': 284} Link IDs: {'PTRANS': 7, 'TRANS': 274, 'PCIS': 2} Chain: "F" Number of atoms: 3520 Number of conformers: 1 Conformer: "" Number of residues, atoms: 458, 3520 Classifications: {'peptide': 458} Link IDs: {'PTRANS': 19, 'TRANS': 437, 'PCIS': 1} Chain: "E" Number of atoms: 3533 Number of conformers: 1 Conformer: "" Number of residues, atoms: 460, 3533 Classifications: {'peptide': 460} Link IDs: {'PTRANS': 19, 'TRANS': 439, 'PCIS': 1} Chain: "D" Number of atoms: 3533 Number of conformers: 1 Conformer: "" Number of residues, atoms: 460, 3533 Classifications: {'peptide': 460} Link IDs: {'PTRANS': 19, 'TRANS': 439, 'PCIS': 1} Chain: "J" Number of atoms: 557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 557 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 3, 'TRANS': 73} Chain: "L" Number of atoms: 557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 557 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 3, 'TRANS': 73} Chain: "M" Number of atoms: 557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 557 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 3, 'TRANS': 73} Chain: "N" Number of atoms: 557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 557 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 3, 'TRANS': 73} Chain: "O" Number of atoms: 557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 557 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 3, 'TRANS': 73} Chain: "P" Number of atoms: 557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 557 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 3, 'TRANS': 73} Chain: "Q" Number of atoms: 557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 557 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 3, 'TRANS': 73} Chain: "R" Number of atoms: 552 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 552 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 3, 'TRANS': 72} Chain: "Y" Number of atoms: 1210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1210 Classifications: {'peptide': 156} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 153} Chain: "a" Number of atoms: 2104 Number of conformers: 1 Conformer: "" Number of residues, atoms: 266, 2104 Classifications: {'peptide': 266} Link IDs: {'PTRANS': 14, 'TRANS': 250, 'PCIS': 1} Chain: "I" Number of atoms: 557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 557 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 3, 'TRANS': 73} Chain: "S" Number of atoms: 557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 557 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 3, 'TRANS': 73} 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: "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: "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: "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} Chain: "E" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {'PO4': 1, ' MG': 1, 'ADP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 20.58, per 1000 atoms: 0.56 Number of scatterers: 36971 At special positions: 0 Unit cell: (176.956, 219.037, 138.112, 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 180 16.00 P 16 15.00 Mg 5 11.99 O 6968 8.00 N 6317 7.00 C 23485 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: 17.14 Conformation dependent library (CDL) restraints added in 6.4 seconds 9614 Ramachandran restraints generated. 4807 Oldfield, 0 Emsley, 4807 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8818 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 183 helices and 26 sheets defined 55.6% alpha, 10.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.75 Creating SS restraints... Processing helix chain 'W' and resid 8 through 20 Processing helix chain 'W' and resid 24 through 39 removed outlier: 3.971A pdb=" N LYS W 39 " --> pdb=" O ALA W 35 " (cutoff:3.500A) Processing helix chain 'W' and resid 41 through 46 removed outlier: 3.563A pdb=" N GLU W 45 " --> pdb=" O GLU W 41 " (cutoff:3.500A) Processing helix chain 'W' and resid 53 through 63 removed outlier: 3.901A pdb=" N GLU W 58 " --> pdb=" O GLU W 54 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N VAL W 63 " --> pdb=" O SER W 59 " (cutoff:3.500A) Processing helix chain 'W' and resid 71 through 81 Processing helix chain 'W' and resid 85 through 102 Proline residue: W 89 - end of helix removed outlier: 4.061A pdb=" N LEU W 92 " --> pdb=" O PRO W 89 " (cutoff:3.500A) Processing helix chain 'W' and resid 120 through 131 removed outlier: 3.683A pdb=" N LYS W 130 " --> pdb=" O ALA W 126 " (cutoff:3.500A) Processing helix chain 'W' and resid 163 through 171 Processing helix chain 'C' and resid 9 through 17 Processing helix chain 'C' and resid 101 through 103 No H-bonds generated for 'chain 'C' and resid 101 through 103' Processing helix chain 'C' and resid 136 through 138 No H-bonds generated for 'chain 'C' and resid 136 through 138' Processing helix chain 'C' and resid 151 through 156 removed outlier: 3.671A pdb=" N MET C 156 " --> pdb=" O ALA C 152 " (cutoff:3.500A) Processing helix chain 'C' and resid 175 through 188 removed outlier: 4.091A pdb=" N GLN C 186 " --> pdb=" O ALA C 182 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N ARG C 187 " --> pdb=" O ILE C 183 " (cutoff:3.500A) removed outlier: 5.303A pdb=" N ASP C 188 " --> pdb=" O ILE C 184 " (cutoff:3.500A) Processing helix chain 'C' and resid 202 through 214 removed outlier: 3.821A pdb=" N ASN C 207 " --> pdb=" O SER C 203 " (cutoff:3.500A) Processing helix chain 'C' and resid 218 through 220 No H-bonds generated for 'chain 'C' and resid 218 through 220' Processing helix chain 'C' and resid 232 through 236 Processing helix chain 'C' and resid 238 through 252 removed outlier: 3.669A pdb=" N TYR C 248 " --> pdb=" O ALA C 244 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N PHE C 249 " --> pdb=" O MET C 245 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N ARG C 252 " --> pdb=" O TYR C 248 " (cutoff:3.500A) Processing helix chain 'C' and resid 266 through 276 Processing helix chain 'C' and resid 283 through 285 No H-bonds generated for 'chain 'C' and resid 283 through 285' Processing helix chain 'C' and resid 288 through 300 removed outlier: 4.287A pdb=" N PHE C 291 " --> pdb=" O GLY C 288 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LEU C 293 " --> pdb=" O VAL C 290 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N SER C 295 " --> pdb=" O TYR C 292 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N ARG C 296 " --> pdb=" O LEU C 293 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N GLU C 299 " --> pdb=" O ARG C 296 " (cutoff:3.500A) Processing helix chain 'C' and resid 306 through 312 Processing helix chain 'C' and resid 333 through 335 No H-bonds generated for 'chain 'C' and resid 333 through 335' Processing helix chain 'C' and resid 340 through 348 removed outlier: 3.608A pdb=" N ASN C 344 " --> pdb=" O PHE C 340 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N SER C 347 " --> pdb=" O THR C 343 " (cutoff:3.500A) Processing helix chain 'C' and resid 357 through 361 Processing helix chain 'C' and resid 378 through 381 Processing helix chain 'C' and resid 384 through 412 removed outlier: 3.773A pdb=" N GLY C 391 " --> pdb=" O LYS C 387 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N GLY C 392 " --> pdb=" O LYS C 388 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ILE C 393 " --> pdb=" O LEU C 389 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N THR C 395 " --> pdb=" O GLY C 391 " (cutoff:3.500A) removed outlier: 5.097A pdb=" N ALA C 405 " --> pdb=" O ARG C 401 " (cutoff:3.500A) removed outlier: 6.185A pdb=" N PHE C 406 " --> pdb=" O GLU C 402 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N SER C 407 " --> pdb=" O LEU C 403 " (cutoff:3.500A) removed outlier: 4.689A pdb=" N GLN C 408 " --> pdb=" O ALA C 404 " (cutoff:3.500A) removed outlier: 4.839A pdb=" N PHE C 409 " --> pdb=" O ALA C 405 " (cutoff:3.500A) removed outlier: 5.938A pdb=" N SER C 411 " --> pdb=" O SER C 407 " (cutoff:3.500A) removed outlier: 7.398A pdb=" N ASP C 412 " --> pdb=" O GLN C 408 " (cutoff:3.500A) Processing helix chain 'C' and resid 415 through 431 removed outlier: 4.354A pdb=" N GLN C 420 " --> pdb=" O ALA C 416 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N LYS C 426 " --> pdb=" O ASP C 422 " (cutoff:3.500A) Processing helix chain 'C' and resid 441 through 452 Processing helix chain 'C' and resid 455 through 457 No H-bonds generated for 'chain 'C' and resid 455 through 457' Processing helix chain 'C' and resid 461 through 478 removed outlier: 3.665A pdb=" N ILE C 464 " --> pdb=" O LEU C 461 " (cutoff:3.500A) removed outlier: 4.986A pdb=" N GLY C 465 " --> pdb=" O SER C 462 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ASP C 478 " --> pdb=" O VAL C 475 " (cutoff:3.500A) Processing helix chain 'C' and resid 480 through 489 removed outlier: 3.653A pdb=" N GLN C 488 " --> pdb=" O GLN C 484 " (cutoff:3.500A) Processing helix chain 'C' and resid 494 through 510 Processing helix chain 'B' and resid 5 through 17 removed outlier: 3.643A pdb=" N ILE B 12 " --> pdb=" O ILE B 8 " (cutoff:3.500A) Processing helix chain 'B' and resid 101 through 103 No H-bonds generated for 'chain 'B' and resid 101 through 103' Processing helix chain 'B' and resid 151 through 156 Processing helix chain 'B' and resid 175 through 188 removed outlier: 3.752A pdb=" N ALA B 182 " --> pdb=" O LEU B 178 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLN B 186 " --> pdb=" O ALA B 182 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N ARG B 187 " --> pdb=" O ILE B 183 " (cutoff:3.500A) removed outlier: 5.346A pdb=" N ASP B 188 " --> pdb=" O ILE B 184 " (cutoff:3.500A) Processing helix chain 'B' and resid 202 through 214 Processing helix chain 'B' and resid 217 through 220 Processing helix chain 'B' and resid 232 through 252 Proline residue: B 239 - end of helix removed outlier: 3.670A pdb=" N TYR B 248 " --> pdb=" O ALA B 244 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N PHE B 249 " --> pdb=" O MET B 245 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ARG B 252 " --> pdb=" O TYR B 248 " (cutoff:3.500A) Processing helix chain 'B' and resid 263 through 277 removed outlier: 3.501A pdb=" N LEU B 277 " --> pdb=" O ILE B 273 " (cutoff:3.500A) Processing helix chain 'B' and resid 283 through 285 No H-bonds generated for 'chain 'B' and resid 283 through 285' Processing helix chain 'B' and resid 288 through 300 removed outlier: 4.404A pdb=" N PHE B 291 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N LEU B 293 " --> pdb=" O VAL B 290 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N ARG B 296 " --> pdb=" O LEU B 293 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N GLU B 299 " --> pdb=" O ARG B 296 " (cutoff:3.500A) Processing helix chain 'B' and resid 306 through 312 Processing helix chain 'B' and resid 333 through 335 No H-bonds generated for 'chain 'B' and resid 333 through 335' Processing helix chain 'B' and resid 340 through 346 Processing helix chain 'B' and resid 357 through 361 Processing helix chain 'B' and resid 378 through 381 Processing helix chain 'B' and resid 384 through 390 Processing helix chain 'B' and resid 393 through 406 removed outlier: 3.712A pdb=" N GLU B 402 " --> pdb=" O ALA B 398 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N ALA B 405 " --> pdb=" O ARG B 401 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 431 Processing helix chain 'B' and resid 441 through 452 Processing helix chain 'B' and resid 461 through 477 removed outlier: 3.695A pdb=" N ILE B 464 " --> pdb=" O LEU B 461 " (cutoff:3.500A) removed outlier: 5.055A pdb=" N GLY B 465 " --> pdb=" O SER B 462 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N VAL B 475 " --> pdb=" O LEU B 472 " (cutoff:3.500A) Processing helix chain 'B' and resid 480 through 486 Processing helix chain 'B' and resid 494 through 510 Processing helix chain 'A' and resid 7 through 19 Processing helix chain 'A' and resid 101 through 103 No H-bonds generated for 'chain 'A' and resid 101 through 103' Processing helix chain 'A' and resid 136 through 138 No H-bonds generated for 'chain 'A' and resid 136 through 138' Processing helix chain 'A' and resid 151 through 156 removed outlier: 3.573A pdb=" N SER A 155 " --> pdb=" O LYS A 151 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N MET A 156 " --> pdb=" O ALA A 152 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 151 through 156' Processing helix chain 'A' and resid 175 through 188 removed outlier: 3.997A pdb=" N GLN A 186 " --> pdb=" O ALA A 182 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N ARG A 187 " --> pdb=" O ILE A 183 " (cutoff:3.500A) removed outlier: 5.527A pdb=" N ASP A 188 " --> pdb=" O ILE A 184 " (cutoff:3.500A) Processing helix chain 'A' and resid 202 through 214 Processing helix chain 'A' and resid 218 through 220 No H-bonds generated for 'chain 'A' and resid 218 through 220' Processing helix chain 'A' and resid 232 through 251 Proline residue: A 239 - end of helix removed outlier: 3.715A pdb=" N TYR A 248 " --> pdb=" O ALA A 244 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N PHE A 249 " --> pdb=" O MET A 245 " (cutoff:3.500A) Processing helix chain 'A' and resid 263 through 277 removed outlier: 4.045A pdb=" N LEU A 277 " --> pdb=" O ILE A 273 " (cutoff:3.500A) Processing helix chain 'A' and resid 283 through 285 No H-bonds generated for 'chain 'A' and resid 283 through 285' Processing helix chain 'A' and resid 290 through 300 removed outlier: 3.605A pdb=" N HIS A 294 " --> pdb=" O VAL A 290 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LEU A 297 " --> pdb=" O LEU A 293 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N ARG A 300 " --> pdb=" O ARG A 296 " (cutoff:3.500A) Processing helix chain 'A' and resid 306 through 312 Processing helix chain 'A' and resid 333 through 335 No H-bonds generated for 'chain 'A' and resid 333 through 335' Processing helix chain 'A' and resid 340 through 347 removed outlier: 3.662A pdb=" N SER A 347 " --> pdb=" O THR A 343 " (cutoff:3.500A) Processing helix chain 'A' and resid 357 through 361 Processing helix chain 'A' and resid 378 through 381 Processing helix chain 'A' and resid 384 through 389 Processing helix chain 'A' and resid 393 through 406 removed outlier: 3.760A pdb=" N GLU A 402 " --> pdb=" O ALA A 398 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ALA A 405 " --> pdb=" O ARG A 401 " (cutoff:3.500A) Processing helix chain 'A' and resid 415 through 430 removed outlier: 3.667A pdb=" N GLN A 420 " --> pdb=" O ALA A 416 " (cutoff:3.500A) Processing helix chain 'A' and resid 441 through 452 Processing helix chain 'A' and resid 461 through 478 removed outlier: 4.436A pdb=" N GLY A 465 " --> pdb=" O LEU A 461 " (cutoff:3.500A) removed outlier: 5.251A pdb=" N SER A 466 " --> pdb=" O SER A 462 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ARG A 477 " --> pdb=" O ALA A 473 " (cutoff:3.500A) Processing helix chain 'A' and resid 480 through 489 Processing helix chain 'A' and resid 494 through 509 removed outlier: 3.566A pdb=" N LYS A 499 " --> pdb=" O GLU A 495 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N ALA A 509 " --> pdb=" O ASP A 505 " (cutoff:3.500A) Processing helix chain 'X' and resid 5 through 24 removed outlier: 3.719A pdb=" N GLN X 10 " --> pdb=" O ILE X 7 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N VAL X 15 " --> pdb=" O ILE X 12 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N LEU X 16 " --> pdb=" O ALA X 13 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N PHE X 20 " --> pdb=" O PHE X 17 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LYS X 23 " --> pdb=" O PHE X 20 " (cutoff:3.500A) Processing helix chain 'X' and resid 26 through 135 removed outlier: 3.541A pdb=" N ALA X 32 " --> pdb=" O PRO X 28 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ILE X 33 " --> pdb=" O LEU X 29 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N ARG X 36 " --> pdb=" O ALA X 32 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N HIS X 51 " --> pdb=" O ALA X 47 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N LEU X 54 " --> pdb=" O ALA X 50 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N SER X 60 " --> pdb=" O LEU X 56 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ILE X 76 " --> pdb=" O ALA X 72 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N GLN X 96 " --> pdb=" O ALA X 92 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N LYS X 114 " --> pdb=" O GLU X 110 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N GLU X 119 " --> pdb=" O ARG X 115 " (cutoff:3.500A) removed outlier: 4.850A pdb=" N LYS X 122 " --> pdb=" O GLU X 118 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N GLN X 123 " --> pdb=" O GLU X 119 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N ALA X 125 " --> pdb=" O ARG X 121 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N ILE X 126 " --> pdb=" O LYS X 122 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N VAL X 129 " --> pdb=" O ALA X 125 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ALA X 132 " --> pdb=" O ALA X 128 " (cutoff:3.500A) Processing helix chain 'X' and resid 143 through 145 No H-bonds generated for 'chain 'X' and resid 143 through 145' Processing helix chain 'X' and resid 148 through 155 Processing helix chain 'H' and resid 88 through 102 removed outlier: 3.694A pdb=" N ALA H 92 " --> pdb=" O ASP H 88 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ALA H 101 " --> pdb=" O ALA H 97 " (cutoff:3.500A) Processing helix chain 'H' and resid 112 through 124 Processing helix chain 'H' and resid 130 through 132 No H-bonds generated for 'chain 'H' and resid 130 through 132' Processing helix chain 'G' and resid 2 through 57 removed outlier: 3.658A pdb=" N ALA G 39 " --> pdb=" O GLN G 35 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N SER G 41 " --> pdb=" O ARG G 37 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N ARG G 42 " --> pdb=" O MET G 38 " (cutoff:3.500A) Proline residue: G 43 - end of helix removed outlier: 3.755A pdb=" N HIS G 57 " --> pdb=" O GLY G 53 " (cutoff:3.500A) Processing helix chain 'G' and resid 65 through 67 No H-bonds generated for 'chain 'G' and resid 65 through 67' Processing helix chain 'G' and resid 90 through 107 removed outlier: 3.566A pdb=" N THR G 104 " --> pdb=" O ALA G 100 " (cutoff:3.500A) Processing helix chain 'G' and resid 119 through 128 Processing helix chain 'G' and resid 145 through 160 removed outlier: 5.285A pdb=" N GLY G 150 " --> pdb=" O SER G 146 " (cutoff:3.500A) Proline residue: G 151 - end of helix Processing helix chain 'G' and resid 199 through 202 removed outlier: 3.890A pdb=" N SER G 202 " --> pdb=" O LYS G 199 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 199 through 202' Processing helix chain 'G' and resid 211 through 282 removed outlier: 3.590A pdb=" N ASP G 216 " --> pdb=" O LYS G 212 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N THR G 217 " --> pdb=" O ALA G 213 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N VAL G 244 " --> pdb=" O ALA G 240 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N LYS G 258 " --> pdb=" O GLY G 254 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N GLU G 259 " --> pdb=" O SER G 255 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N LEU G 262 " --> pdb=" O LYS G 258 " (cutoff:3.500A) Processing helix chain 'F' and resid 81 through 83 No H-bonds generated for 'chain 'F' and resid 81 through 83' Processing helix chain 'F' and resid 116 through 118 No H-bonds generated for 'chain 'F' and resid 116 through 118' Processing helix chain 'F' and resid 131 through 136 Processing helix chain 'F' and resid 157 through 166 Processing helix chain 'F' and resid 183 through 195 Processing helix chain 'F' and resid 199 through 201 No H-bonds generated for 'chain 'F' and resid 199 through 201' Processing helix chain 'F' and resid 213 through 232 removed outlier: 4.919A pdb=" N ALA F 220 " --> pdb=" O ARG F 216 " (cutoff:3.500A) removed outlier: 5.252A pdb=" N LEU F 221 " --> pdb=" O LEU F 217 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N MET F 226 " --> pdb=" O THR F 222 " (cutoff:3.500A) Processing helix chain 'F' and resid 244 through 258 removed outlier: 3.991A pdb=" N ALA F 250 " --> pdb=" O TYR F 247 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N GLU F 253 " --> pdb=" O ALA F 250 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N SER F 255 " --> pdb=" O THR F 252 " (cutoff:3.500A) removed outlier: 4.891A pdb=" N ALA F 256 " --> pdb=" O GLU F 253 " (cutoff:3.500A) Processing helix chain 'F' and resid 271 through 279 removed outlier: 3.965A pdb=" N LEU F 278 " --> pdb=" O GLU F 274 " (cutoff:3.500A) Processing helix chain 'F' and resid 299 through 301 No H-bonds generated for 'chain 'F' and resid 299 through 301' Processing helix chain 'F' and resid 306 through 314 removed outlier: 4.525A pdb=" N ALA F 313 " --> pdb=" O ALA F 309 " (cutoff:3.500A) removed outlier: 4.777A pdb=" N HIS F 314 " --> pdb=" O THR F 310 " (cutoff:3.500A) Processing helix chain 'F' and resid 323 through 328 removed outlier: 4.320A pdb=" N LEU F 328 " --> pdb=" O GLN F 324 " (cutoff:3.500A) Processing helix chain 'F' and resid 346 through 377 removed outlier: 7.340A pdb=" N GLN F 351 " --> pdb=" O LEU F 347 " (cutoff:3.500A) removed outlier: 9.341A pdb=" N GLU F 352 " --> pdb=" O VAL F 348 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N HIS F 353 " --> pdb=" O VAL F 349 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LYS F 371 " --> pdb=" O TYR F 367 " (cutoff:3.500A) removed outlier: 4.839A pdb=" N ASP F 372 " --> pdb=" O GLN F 368 " (cutoff:3.500A) removed outlier: 5.228A pdb=" N ILE F 373 " --> pdb=" O GLU F 369 " (cutoff:3.500A) Processing helix chain 'F' and resid 379 through 381 No H-bonds generated for 'chain 'F' and resid 379 through 381' Processing helix chain 'F' and resid 386 through 400 Processing helix chain 'F' and resid 408 through 411 No H-bonds generated for 'chain 'F' and resid 408 through 411' Processing helix chain 'F' and resid 420 through 432 removed outlier: 3.727A pdb=" N ARG F 425 " --> pdb=" O LYS F 421 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N GLY F 426 " --> pdb=" O ASP F 422 " (cutoff:3.500A) Processing helix chain 'F' and resid 440 through 442 No H-bonds generated for 'chain 'F' and resid 440 through 442' Processing helix chain 'F' and resid 449 through 458 removed outlier: 4.015A pdb=" N LYS F 457 " --> pdb=" O VAL F 453 " (cutoff:3.500A) removed outlier: 4.541A pdb=" N LYS F 458 " --> pdb=" O GLU F 454 " (cutoff:3.500A) Processing helix chain 'E' and resid 81 through 83 No H-bonds generated for 'chain 'E' and resid 81 through 83' Processing helix chain 'E' and resid 131 through 136 Processing helix chain 'E' and resid 155 through 168 Processing helix chain 'E' and resid 183 through 196 removed outlier: 3.788A pdb=" N SER E 196 " --> pdb=" O GLU E 192 " (cutoff:3.500A) Processing helix chain 'E' and resid 199 through 201 No H-bonds generated for 'chain 'E' and resid 199 through 201' Processing helix chain 'E' and resid 213 through 233 removed outlier: 5.066A pdb=" N ALA E 220 " --> pdb=" O ARG E 216 " (cutoff:3.500A) removed outlier: 4.865A pdb=" N LEU E 221 " --> pdb=" O LEU E 217 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N GLU E 233 " --> pdb=" O LYS E 229 " (cutoff:3.500A) Processing helix chain 'E' and resid 244 through 258 removed outlier: 3.582A pdb=" N GLY E 251 " --> pdb=" O TYR E 247 " (cutoff:3.500A) Processing helix chain 'E' and resid 271 through 279 removed outlier: 3.756A pdb=" N LEU E 278 " --> pdb=" O GLU E 274 " (cutoff:3.500A) Processing helix chain 'E' and resid 299 through 301 No H-bonds generated for 'chain 'E' and resid 299 through 301' Processing helix chain 'E' and resid 306 through 312 Processing helix chain 'E' and resid 323 through 327 Processing helix chain 'E' and resid 346 through 349 No H-bonds generated for 'chain 'E' and resid 346 through 349' Processing helix chain 'E' and resid 351 through 377 removed outlier: 4.391A pdb=" N GLU E 369 " --> pdb=" O GLN E 365 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N ASP E 372 " --> pdb=" O GLN E 368 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ILE E 376 " --> pdb=" O ASP E 372 " (cutoff:3.500A) Processing helix chain 'E' and resid 379 through 381 No H-bonds generated for 'chain 'E' and resid 379 through 381' Processing helix chain 'E' and resid 384 through 399 removed outlier: 3.627A pdb=" N LEU E 388 " --> pdb=" O GLU E 384 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N VAL E 389 " --> pdb=" O GLU E 385 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ALA E 391 " --> pdb=" O LYS E 387 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N LYS E 395 " --> pdb=" O ALA E 391 " (cutoff:3.500A) Processing helix chain 'E' and resid 408 through 411 No H-bonds generated for 'chain 'E' and resid 408 through 411' Processing helix chain 'E' and resid 420 through 431 Processing helix chain 'E' and resid 440 through 442 No H-bonds generated for 'chain 'E' and resid 440 through 442' Processing helix chain 'E' and resid 449 through 457 removed outlier: 3.925A pdb=" N GLU E 454 " --> pdb=" O GLU E 450 " (cutoff:3.500A) Processing helix chain 'D' and resid 81 through 83 No H-bonds generated for 'chain 'D' and resid 81 through 83' Processing helix chain 'D' and resid 131 through 136 Processing helix chain 'D' and resid 155 through 169 Processing helix chain 'D' and resid 183 through 195 Processing helix chain 'D' and resid 199 through 201 No H-bonds generated for 'chain 'D' and resid 199 through 201' Processing helix chain 'D' and resid 213 through 233 removed outlier: 5.024A pdb=" N ALA D 220 " --> pdb=" O ARG D 216 " (cutoff:3.500A) removed outlier: 4.765A pdb=" N LEU D 221 " --> pdb=" O LEU D 217 " (cutoff:3.500A) Processing helix chain 'D' and resid 244 through 257 Processing helix chain 'D' and resid 271 through 279 Processing helix chain 'D' and resid 299 through 301 No H-bonds generated for 'chain 'D' and resid 299 through 301' Processing helix chain 'D' and resid 306 through 311 Processing helix chain 'D' and resid 323 through 327 Processing helix chain 'D' and resid 346 through 377 removed outlier: 7.368A pdb=" N GLN D 351 " --> pdb=" O LEU D 347 " (cutoff:3.500A) removed outlier: 9.075A pdb=" N GLU D 352 " --> pdb=" O VAL D 348 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N HIS D 353 " --> pdb=" O VAL D 349 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N ASP D 372 " --> pdb=" O GLN D 368 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N ILE D 373 " --> pdb=" O GLU D 369 " (cutoff:3.500A) Processing helix chain 'D' and resid 379 through 381 No H-bonds generated for 'chain 'D' and resid 379 through 381' Processing helix chain 'D' and resid 386 through 399 Processing helix chain 'D' and resid 407 through 411 removed outlier: 3.743A pdb=" N THR D 411 " --> pdb=" O GLU D 408 " (cutoff:3.500A) Processing helix chain 'D' and resid 420 through 431 Processing helix chain 'D' and resid 440 through 443 Processing helix chain 'D' and resid 449 through 456 Processing helix chain 'J' and resid 4 through 41 removed outlier: 5.074A pdb=" N LEU J 9 " --> pdb=" O MET J 6 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N TYR J 10 " --> pdb=" O ASP J 7 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ILE J 28 " --> pdb=" O ALA J 25 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N ALA J 40 " --> pdb=" O GLU J 37 " (cutoff:3.500A) Processing helix chain 'J' and resid 46 through 76 removed outlier: 4.123A pdb=" N LEU J 59 " --> pdb=" O ILE J 55 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N ALA J 62 " --> pdb=" O GLY J 58 " (cutoff:3.500A) removed outlier: 5.007A pdb=" N ILE J 63 " --> pdb=" O LEU J 59 " (cutoff:3.500A) Proline residue: J 64 - end of helix Processing helix chain 'L' and resid 7 through 41 Processing helix chain 'L' and resid 43 through 76 removed outlier: 3.518A pdb=" N ILE L 46 " --> pdb=" O PRO L 43 " (cutoff:3.500A) Proline residue: L 47 - end of helix removed outlier: 3.875A pdb=" N ASP L 61 " --> pdb=" O GLY L 58 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N ILE L 63 " --> pdb=" O VAL L 60 " (cutoff:3.500A) Proline residue: L 64 - end of helix Processing helix chain 'M' and resid 4 through 41 removed outlier: 3.976A pdb=" N LEU M 8 " --> pdb=" O LEU M 4 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LYS M 34 " --> pdb=" O ILE M 30 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ARG M 41 " --> pdb=" O GLU M 37 " (cutoff:3.500A) Processing helix chain 'M' and resid 43 through 76 Proline residue: M 47 - end of helix removed outlier: 4.014A pdb=" N MET M 57 " --> pdb=" O PHE M 54 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N ILE M 63 " --> pdb=" O VAL M 60 " (cutoff:3.500A) Proline residue: M 64 - end of helix removed outlier: 3.544A pdb=" N PHE M 76 " --> pdb=" O TYR M 73 " (cutoff:3.500A) Processing helix chain 'N' and resid 4 through 41 removed outlier: 4.318A pdb=" N LEU N 8 " --> pdb=" O ASN N 5 " (cutoff:3.500A) removed outlier: 5.240A pdb=" N LEU N 9 " --> pdb=" O MET N 6 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N ALA N 12 " --> pdb=" O LEU N 9 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N GLU N 37 " --> pdb=" O LYS N 34 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ALA N 40 " --> pdb=" O GLU N 37 " (cutoff:3.500A) Processing helix chain 'N' and resid 43 through 76 Proline residue: N 47 - end of helix removed outlier: 3.642A pdb=" N GLY N 58 " --> pdb=" O ILE N 55 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N ASP N 61 " --> pdb=" O GLY N 58 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ALA N 62 " --> pdb=" O LEU N 59 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N ILE N 63 " --> pdb=" O VAL N 60 " (cutoff:3.500A) Proline residue: N 64 - end of helix removed outlier: 3.505A pdb=" N VAL N 68 " --> pdb=" O MET N 65 " (cutoff:3.500A) Processing helix chain 'O' and resid 5 through 41 removed outlier: 4.664A pdb=" N LEU O 9 " --> pdb=" O MET O 6 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N LEU O 19 " --> pdb=" O MET O 16 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ILE O 28 " --> pdb=" O ALA O 25 " (cutoff:3.500A) Processing helix chain 'O' and resid 46 through 60 removed outlier: 3.582A pdb=" N LEU O 59 " --> pdb=" O ILE O 55 " (cutoff:3.500A) Processing helix chain 'O' and resid 62 through 76 Processing helix chain 'P' and resid 6 through 41 removed outlier: 3.514A pdb=" N TYR P 10 " --> pdb=" O MET P 6 " (cutoff:3.500A) Processing helix chain 'P' and resid 46 through 76 removed outlier: 3.751A pdb=" N LEU P 59 " --> pdb=" O ILE P 55 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N ALA P 62 " --> pdb=" O GLY P 58 " (cutoff:3.500A) removed outlier: 4.893A pdb=" N ILE P 63 " --> pdb=" O LEU P 59 " (cutoff:3.500A) Proline residue: P 64 - end of helix removed outlier: 3.673A pdb=" N LEU P 70 " --> pdb=" O ILE P 66 " (cutoff:3.500A) Processing helix chain 'Q' and resid 4 through 6 No H-bonds generated for 'chain 'Q' and resid 4 through 6' Processing helix chain 'Q' and resid 8 through 41 Processing helix chain 'Q' and resid 43 through 76 Proline residue: Q 47 - end of helix removed outlier: 3.937A pdb=" N MET Q 57 " --> pdb=" O PHE Q 54 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N GLY Q 58 " --> pdb=" O ILE Q 55 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N ILE Q 63 " --> pdb=" O VAL Q 60 " (cutoff:3.500A) Proline residue: Q 64 - end of helix Processing helix chain 'R' and resid 6 through 41 Processing helix chain 'R' and resid 46 through 76 removed outlier: 3.631A pdb=" N LEU R 59 " --> pdb=" O ILE R 55 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ALA R 62 " --> pdb=" O GLY R 58 " (cutoff:3.500A) removed outlier: 4.978A pdb=" N ILE R 63 " --> pdb=" O LEU R 59 " (cutoff:3.500A) Proline residue: R 64 - end of helix Processing helix chain 'Y' and resid 3 through 24 removed outlier: 3.764A pdb=" N ILE Y 12 " --> pdb=" O LEU Y 8 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ALA Y 13 " --> pdb=" O GLY Y 9 " (cutoff:3.500A) Processing helix chain 'Y' and resid 26 through 139 removed outlier: 3.593A pdb=" N THR Y 62 " --> pdb=" O LYS Y 58 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N ASP Y 63 " --> pdb=" O ALA Y 59 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N ASP Y 88 " --> pdb=" O SER Y 84 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LYS Y 91 " --> pdb=" O LEU Y 87 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N GLN Y 96 " --> pdb=" O ALA Y 92 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N GLN Y 106 " --> pdb=" O VAL Y 102 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N ALA Y 107 " --> pdb=" O ALA Y 103 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N GLU Y 108 " --> pdb=" O GLN Y 104 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N GLU Y 110 " --> pdb=" O GLN Y 106 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N VAL Y 129 " --> pdb=" O ALA Y 125 " (cutoff:3.500A) Processing helix chain 'Y' and resid 142 through 155 removed outlier: 3.606A pdb=" N ASP Y 147 " --> pdb=" O ALA Y 143 " (cutoff:3.500A) Processing helix chain 'a' and resid 8 through 16 removed outlier: 3.699A pdb=" N LEU a 16 " --> pdb=" O ILE a 12 " (cutoff:3.500A) Processing helix chain 'a' and resid 43 through 64 removed outlier: 3.840A pdb=" N VAL a 63 " --> pdb=" O LEU a 59 " (cutoff:3.500A) Processing helix chain 'a' and resid 74 through 93 removed outlier: 3.727A pdb=" N ALA a 78 " --> pdb=" O LYS a 74 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ILE a 79 " --> pdb=" O PHE a 75 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N MET a 93 " --> pdb=" O SER a 89 " (cutoff:3.500A) Processing helix chain 'a' and resid 100 through 120 removed outlier: 4.136A pdb=" N ASP a 119 " --> pdb=" O MET a 115 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N LEU a 120 " --> pdb=" O ASN a 116 " (cutoff:3.500A) Processing helix chain 'a' and resid 123 through 132 Proline residue: a 127 - end of helix removed outlier: 3.587A pdb=" N GLU a 131 " --> pdb=" O PRO a 127 " (cutoff:3.500A) Processing helix chain 'a' and resid 143 through 145 No H-bonds generated for 'chain 'a' and resid 143 through 145' Processing helix chain 'a' and resid 147 through 180 removed outlier: 3.516A pdb=" N ILE a 159 " --> pdb=" O LEU a 155 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N LYS a 169 " --> pdb=" O SER a 165 " (cutoff:3.500A) removed outlier: 8.181A pdb=" N ILE a 171 " --> pdb=" O LYS a 167 " (cutoff:3.500A) removed outlier: 9.202A pdb=" N GLY a 172 " --> pdb=" O MET a 168 " (cutoff:3.500A) Processing helix chain 'a' and resid 186 through 227 Proline residue: a 190 - end of helix removed outlier: 3.958A pdb=" N LEU a 193 " --> pdb=" O PRO a 190 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N GLU a 196 " --> pdb=" O LEU a 193 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N SER a 202 " --> pdb=" O SER a 199 " (cutoff:3.500A) Proline residue: a 204 - end of helix Processing helix chain 'a' and resid 234 through 268 Proline residue: a 240 - end of helix removed outlier: 4.167A pdb=" N LEU a 247 " --> pdb=" O ILE a 243 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ILE a 248 " --> pdb=" O PHE a 244 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N ALA a 253 " --> pdb=" O ILE a 249 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N PHE a 256 " --> pdb=" O GLN a 252 " (cutoff:3.500A) Processing helix chain 'I' and resid 4 through 7 No H-bonds generated for 'chain 'I' and resid 4 through 7' Processing helix chain 'I' and resid 9 through 41 removed outlier: 3.508A pdb=" N ARG I 41 " --> pdb=" O GLU I 37 " (cutoff:3.500A) Processing helix chain 'I' and resid 43 through 76 Proline residue: I 47 - end of helix removed outlier: 3.734A pdb=" N ARG I 50 " --> pdb=" O PRO I 47 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N PHE I 53 " --> pdb=" O ARG I 50 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N VAL I 56 " --> pdb=" O PHE I 53 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N GLY I 58 " --> pdb=" O ILE I 55 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ASP I 61 " --> pdb=" O GLY I 58 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N ILE I 63 " --> pdb=" O VAL I 60 " (cutoff:3.500A) Proline residue: I 64 - end of helix removed outlier: 3.518A pdb=" N GLY I 69 " --> pdb=" O ILE I 66 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N LEU I 70 " --> pdb=" O ALA I 67 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N TYR I 73 " --> pdb=" O LEU I 70 " (cutoff:3.500A) Processing helix chain 'S' and resid 6 through 41 removed outlier: 3.698A pdb=" N TYR S 10 " --> pdb=" O MET S 6 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N MET S 11 " --> pdb=" O ASP S 7 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N LYS S 34 " --> pdb=" O ILE S 30 " (cutoff:3.500A) Processing helix chain 'S' and resid 43 through 60 removed outlier: 3.628A pdb=" N ILE S 46 " --> pdb=" O PRO S 43 " (cutoff:3.500A) Proline residue: S 47 - end of helix removed outlier: 4.051A pdb=" N ARG S 50 " --> pdb=" O PRO S 47 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ILE S 55 " --> pdb=" O GLN S 52 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N GLY S 58 " --> pdb=" O ILE S 55 " (cutoff:3.500A) Processing helix chain 'S' and resid 62 through 76 Processing sheet with id= A, first strand: chain 'W' and resid 135 through 142 Processing sheet with id= B, first strand: chain 'C' and resid 87 through 89 removed outlier: 6.402A pdb=" N ARG C 40 " --> pdb=" O VAL C 32 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N VAL C 34 " --> pdb=" O VAL C 38 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N VAL C 38 " --> pdb=" O VAL C 34 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N SER C 70 " --> pdb=" O GLU C 67 " (cutoff:3.500A) removed outlier: 7.093A pdb=" N VAL C 74 " --> pdb=" O ALA C 63 " (cutoff:3.500A) removed outlier: 6.016A pdb=" N ALA C 63 " --> pdb=" O VAL C 74 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N ARG C 59 " --> pdb=" O LEU C 55 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'C' and resid 96 through 98 Processing sheet with id= D, first strand: chain 'C' and resid 107 through 109 removed outlier: 8.378A pdb=" N VAL C 108 " --> pdb=" O THR C 221 " (cutoff:3.500A) removed outlier: 6.209A pdb=" N VAL C 223 " --> pdb=" O VAL C 108 " (cutoff:3.500A) removed outlier: 8.871A pdb=" N ILE C 222 " --> pdb=" O ILE C 191 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N CYS C 193 " --> pdb=" O ILE C 222 " (cutoff:3.500A) removed outlier: 8.244A pdb=" N VAL C 224 " --> pdb=" O CYS C 193 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N TYR C 195 " --> pdb=" O VAL C 224 " (cutoff:3.500A) removed outlier: 7.857A pdb=" N ALA C 226 " --> pdb=" O TYR C 195 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N ALA C 197 " --> pdb=" O ALA C 226 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N ASP C 255 " --> pdb=" O LYS C 192 " (cutoff:3.500A) removed outlier: 8.233A pdb=" N ILE C 194 " --> pdb=" O ASP C 255 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N LEU C 257 " --> pdb=" O ILE C 194 " (cutoff:3.500A) removed outlier: 7.697A pdb=" N VAL C 196 " --> pdb=" O LEU C 257 " (cutoff:3.500A) removed outlier: 6.224A pdb=" N ILE C 259 " --> pdb=" O VAL C 196 " (cutoff:3.500A) removed outlier: 7.283A pdb=" N ILE C 198 " --> pdb=" O ILE C 259 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N ASP C 261 " --> pdb=" O ILE C 198 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N SER C 323 " --> pdb=" O ALA C 256 " (cutoff:3.500A) removed outlier: 7.833A pdb=" N ILE C 258 " --> pdb=" O SER C 323 " (cutoff:3.500A) removed outlier: 6.144A pdb=" N THR C 325 " --> pdb=" O ILE C 258 " (cutoff:3.500A) removed outlier: 7.356A pdb=" N TYR C 260 " --> pdb=" O THR C 325 " (cutoff:3.500A) No H-bonds generated for sheet with id= D Processing sheet with id= E, first strand: chain 'C' and resid 352 through 355 removed outlier: 6.576A pdb=" N LEU C 166 " --> pdb=" O ILE C 353 " (cutoff:3.500A) removed outlier: 7.513A pdb=" N LEU C 355 " --> pdb=" O LEU C 166 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N ILE C 168 " --> pdb=" O LEU C 355 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 87 through 90 removed outlier: 4.595A pdb=" N ASN B 27 " --> pdb=" O CYS B 90 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N ARG B 40 " --> pdb=" O VAL B 32 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N VAL B 34 " --> pdb=" O VAL B 38 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N VAL B 38 " --> pdb=" O VAL B 34 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N VAL B 74 " --> pdb=" O ALA B 63 " (cutoff:3.500A) removed outlier: 5.950A pdb=" N ALA B 63 " --> pdb=" O VAL B 74 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N ARG B 59 " --> pdb=" O LEU B 55 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 96 through 98 Processing sheet with id= H, first strand: chain 'B' and resid 352 through 355 removed outlier: 6.509A pdb=" N LEU B 166 " --> pdb=" O ILE B 353 " (cutoff:3.500A) removed outlier: 7.451A pdb=" N LEU B 355 " --> pdb=" O LEU B 166 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N ILE B 168 " --> pdb=" O LEU B 355 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 221 through 226 removed outlier: 6.858A pdb=" N CYS B 193 " --> pdb=" O ILE B 222 " (cutoff:3.500A) removed outlier: 8.152A pdb=" N VAL B 224 " --> pdb=" O CYS B 193 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N TYR B 195 " --> pdb=" O VAL B 224 " (cutoff:3.500A) removed outlier: 7.768A pdb=" N ALA B 226 " --> pdb=" O TYR B 195 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N ALA B 197 " --> pdb=" O ALA B 226 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N SER B 323 " --> pdb=" O ALA B 256 " (cutoff:3.500A) removed outlier: 7.918A pdb=" N ILE B 258 " --> pdb=" O SER B 323 " (cutoff:3.500A) removed outlier: 6.144A pdb=" N THR B 325 " --> pdb=" O ILE B 258 " (cutoff:3.500A) removed outlier: 7.677A pdb=" N TYR B 260 " --> pdb=" O THR B 325 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'A' and resid 87 through 89 removed outlier: 6.350A pdb=" N ARG A 40 " --> pdb=" O VAL A 32 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N VAL A 34 " --> pdb=" O VAL A 38 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N VAL A 38 " --> pdb=" O VAL A 34 " (cutoff:3.500A) removed outlier: 7.073A pdb=" N VAL A 74 " --> pdb=" O ALA A 63 " (cutoff:3.500A) removed outlier: 5.821A pdb=" N ALA A 63 " --> pdb=" O VAL A 74 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ARG A 59 " --> pdb=" O LEU A 55 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'A' and resid 96 through 98 Processing sheet with id= L, first strand: chain 'A' and resid 352 through 355 removed outlier: 6.608A pdb=" N LEU A 166 " --> pdb=" O ILE A 353 " (cutoff:3.500A) removed outlier: 7.509A pdb=" N LEU A 355 " --> pdb=" O LEU A 166 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N ILE A 168 " --> pdb=" O LEU A 355 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'A' and resid 221 through 226 removed outlier: 6.825A pdb=" N CYS A 193 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 7.975A pdb=" N VAL A 224 " --> pdb=" O CYS A 193 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N TYR A 195 " --> pdb=" O VAL A 224 " (cutoff:3.500A) removed outlier: 7.828A pdb=" N ALA A 226 " --> pdb=" O TYR A 195 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N ALA A 197 " --> pdb=" O ALA A 226 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N SER A 323 " --> pdb=" O ALA A 256 " (cutoff:3.500A) removed outlier: 7.963A pdb=" N ILE A 258 " --> pdb=" O SER A 323 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N THR A 325 " --> pdb=" O ILE A 258 " (cutoff:3.500A) removed outlier: 7.777A pdb=" N TYR A 260 " --> pdb=" O THR A 325 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N LEU A 327 " --> pdb=" O TYR A 260 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'H' and resid 41 through 45 removed outlier: 3.618A pdb=" N GLY H 67 " --> pdb=" O ILE H 45 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ILE H 68 " --> pdb=" O LEU H 79 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N HIS H 5 " --> pdb=" O VAL H 76 " (cutoff:3.500A) removed outlier: 8.154A pdb=" N VAL H 78 " --> pdb=" O HIS H 5 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N ASP H 7 " --> pdb=" O VAL H 78 " (cutoff:3.500A) removed outlier: 7.164A pdb=" N VAL H 53 " --> pdb=" O GLU H 21 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N ILE H 23 " --> pdb=" O ARG H 51 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N ARG H 51 " --> pdb=" O ILE H 23 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'H' and resid 22 through 27 Processing sheet with id= P, first strand: chain 'G' and resid 180 through 188 removed outlier: 6.558A pdb=" N LEU G 167 " --> pdb=" O LEU G 187 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N LYS G 166 " --> pdb=" O ARG G 74 " (cutoff:3.500A) removed outlier: 5.567A pdb=" N ASN G 172 " --> pdb=" O VAL G 80 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N GLN G 111 " --> pdb=" O VAL G 75 " (cutoff:3.500A) removed outlier: 8.263A pdb=" N TYR G 77 " --> pdb=" O GLN G 111 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N ASP G 113 " --> pdb=" O TYR G 77 " (cutoff:3.500A) removed outlier: 7.386A pdb=" N VAL G 79 " --> pdb=" O ASP G 113 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N ALA G 115 " --> pdb=" O VAL G 79 " (cutoff:3.500A) removed outlier: 7.558A pdb=" N MET G 116 " --> pdb=" O VAL G 133 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N GLN G 135 " --> pdb=" O MET G 116 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'F' and resid 3 through 9 removed outlier: 6.558A pdb=" N ASP F 14 " --> pdb=" O VAL F 6 " (cutoff:3.500A) removed outlier: 4.803A pdb=" N VAL F 8 " --> pdb=" O VAL F 12 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N VAL F 12 " --> pdb=" O VAL F 8 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N ILE F 54 " --> pdb=" O VAL F 42 " (cutoff:3.500A) removed outlier: 5.576A pdb=" N VAL F 42 " --> pdb=" O ILE F 54 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'F' and resid 76 through 79 removed outlier: 4.804A pdb=" N GLU F 105 " --> pdb=" O VAL F 79 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'F' and resid 317 through 320 removed outlier: 7.911A pdb=" N VAL F 145 " --> pdb=" O ILE F 290 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N SER F 292 " --> pdb=" O VAL F 145 " (cutoff:3.500A) removed outlier: 7.926A pdb=" N LEU F 147 " --> pdb=" O SER F 292 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N GLN F 294 " --> pdb=" O LEU F 147 " (cutoff:3.500A) removed outlier: 7.937A pdb=" N GLY F 149 " --> pdb=" O GLN F 294 " (cutoff:3.500A) removed outlier: 6.225A pdb=" N VAL F 296 " --> pdb=" O GLY F 149 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'E' and resid 4 through 9 removed outlier: 6.474A pdb=" N ASP E 14 " --> pdb=" O VAL E 6 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N VAL E 8 " --> pdb=" O VAL E 12 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N VAL E 12 " --> pdb=" O VAL E 8 " (cutoff:3.500A) removed outlier: 6.208A pdb=" N ILE E 54 " --> pdb=" O VAL E 42 " (cutoff:3.500A) removed outlier: 5.617A pdb=" N VAL E 42 " --> pdb=" O ILE E 54 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'E' and resid 76 through 78 Processing sheet with id= V, first strand: chain 'E' and resid 317 through 319 removed outlier: 8.546A pdb=" N VAL E 145 " --> pdb=" O ILE E 290 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N SER E 292 " --> pdb=" O VAL E 145 " (cutoff:3.500A) removed outlier: 7.729A pdb=" N LEU E 147 " --> pdb=" O SER E 292 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N GLN E 294 " --> pdb=" O LEU E 147 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'D' and resid 3 through 9 removed outlier: 6.486A pdb=" N ASP D 14 " --> pdb=" O VAL D 6 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N VAL D 8 " --> pdb=" O VAL D 12 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N VAL D 12 " --> pdb=" O VAL D 8 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N ILE D 54 " --> pdb=" O VAL D 42 " (cutoff:3.500A) removed outlier: 5.646A pdb=" N VAL D 42 " --> pdb=" O ILE D 54 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N GLU D 36 " --> pdb=" O ASN D 33 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'D' and resid 76 through 78 Processing sheet with id= Y, first strand: chain 'D' and resid 317 through 320 removed outlier: 8.765A pdb=" N VAL D 145 " --> pdb=" O ILE D 290 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N SER D 292 " --> pdb=" O VAL D 145 " (cutoff:3.500A) removed outlier: 7.986A pdb=" N LEU D 147 " --> pdb=" O SER D 292 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N GLN D 294 " --> pdb=" O LEU D 147 " (cutoff:3.500A) removed outlier: 8.130A pdb=" N GLY D 149 " --> pdb=" O GLN D 294 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N VAL D 296 " --> pdb=" O GLY D 149 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'a' and resid 20 through 22 1941 hydrogen bonds defined for protein. 4869 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: 13.94 Time building geometry restraints manager: 18.30 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 6333 1.30 - 1.42: 8611 1.42 - 1.55: 22200 1.55 - 1.68: 24 1.68 - 1.81: 360 Bond restraints: 37528 Sorted by residual: bond pdb=" C4 ATP A 600 " pdb=" C5 ATP A 600 " ideal model delta sigma weight residual 1.388 1.460 -0.072 1.00e-02 1.00e+04 5.21e+01 bond pdb=" C4 ATP B 600 " pdb=" C5 ATP B 600 " ideal model delta sigma weight residual 1.388 1.459 -0.071 1.00e-02 1.00e+04 5.09e+01 bond pdb=" C4 ATP C 600 " pdb=" C5 ATP C 600 " ideal model delta sigma weight residual 1.388 1.459 -0.071 1.00e-02 1.00e+04 5.01e+01 bond pdb=" C5 ATP B 600 " pdb=" C6 ATP B 600 " ideal model delta sigma weight residual 1.409 1.471 -0.062 1.00e-02 1.00e+04 3.85e+01 bond pdb=" C VAL F 205 " pdb=" O VAL F 205 " ideal model delta sigma weight residual 1.237 1.170 0.066 1.07e-02 8.73e+03 3.84e+01 ... (remaining 37523 not shown) Histogram of bond angle deviations from ideal: 97.88 - 105.57: 843 105.57 - 113.26: 21099 113.26 - 120.95: 19048 120.95 - 128.65: 9611 128.65 - 136.34: 196 Bond angle restraints: 50797 Sorted by residual: angle pdb=" PB ATP B 600 " pdb=" O3B ATP B 600 " pdb=" PG ATP B 600 " ideal model delta sigma weight residual 139.87 118.69 21.18 1.00e+00 1.00e+00 4.49e+02 angle pdb=" PB ATP A 600 " pdb=" O3B ATP A 600 " pdb=" PG ATP A 600 " ideal model delta sigma weight residual 139.87 118.75 21.12 1.00e+00 1.00e+00 4.46e+02 angle pdb=" PB ATP C 600 " pdb=" O3B ATP C 600 " pdb=" PG ATP C 600 " ideal model delta sigma weight residual 139.87 119.39 20.48 1.00e+00 1.00e+00 4.19e+02 angle pdb=" PA ATP A 600 " pdb=" O3A ATP A 600 " pdb=" PB ATP A 600 " ideal model delta sigma weight residual 136.83 117.42 19.41 1.00e+00 1.00e+00 3.77e+02 angle pdb=" PA ATP B 600 " pdb=" O3A ATP B 600 " pdb=" PB ATP B 600 " ideal model delta sigma weight residual 136.83 120.69 16.14 1.00e+00 1.00e+00 2.61e+02 ... (remaining 50792 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.39: 21943 29.39 - 58.77: 669 58.77 - 88.16: 80 88.16 - 117.54: 4 117.54 - 146.93: 5 Dihedral angle restraints: 22701 sinusoidal: 8917 harmonic: 13784 Sorted by residual: dihedral pdb=" O1B ADP D 500 " pdb=" O3A ADP D 500 " pdb=" PB ADP D 500 " pdb=" PA ADP D 500 " ideal model delta sinusoidal sigma weight residual 300.00 153.07 146.93 1 2.00e+01 2.50e-03 4.41e+01 dihedral pdb=" O2A ADP F 500 " pdb=" O3A ADP F 500 " pdb=" PA ADP F 500 " pdb=" PB ADP F 500 " ideal model delta sinusoidal sigma weight residual -60.00 85.51 -145.51 1 2.00e+01 2.50e-03 4.38e+01 dihedral pdb=" C5' ADP D 500 " pdb=" O5' ADP D 500 " pdb=" PA ADP D 500 " pdb=" O2A ADP D 500 " ideal model delta sinusoidal sigma weight residual 300.00 166.99 133.02 1 2.00e+01 2.50e-03 4.04e+01 ... (remaining 22698 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.094: 5534 0.094 - 0.188: 362 0.188 - 0.282: 18 0.282 - 0.376: 4 0.376 - 0.469: 2 Chirality restraints: 5920 Sorted by residual: chirality pdb=" CA GLN B 511 " pdb=" N GLN B 511 " pdb=" C GLN B 511 " pdb=" CB GLN B 511 " both_signs ideal model delta sigma weight residual False 2.51 2.04 0.47 2.00e-01 2.50e+01 5.51e+00 chirality pdb=" CA LEU a 178 " pdb=" N LEU a 178 " pdb=" C LEU a 178 " pdb=" CB LEU a 178 " both_signs ideal model delta sigma weight residual False 2.51 2.08 0.43 2.00e-01 2.50e+01 4.64e+00 chirality pdb=" CA ASP C 261 " pdb=" N ASP C 261 " pdb=" C ASP C 261 " pdb=" CB ASP C 261 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.59e+00 ... (remaining 5917 not shown) Planarity restraints: 6550 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA D 264 " 0.024 2.00e-02 2.50e+03 4.86e-02 2.36e+01 pdb=" C ALA D 264 " -0.084 2.00e-02 2.50e+03 pdb=" O ALA D 264 " 0.030 2.00e-02 2.50e+03 pdb=" N VAL D 265 " 0.030 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP A 261 " -0.022 2.00e-02 2.50e+03 4.36e-02 1.90e+01 pdb=" C ASP A 261 " 0.075 2.00e-02 2.50e+03 pdb=" O ASP A 261 " -0.027 2.00e-02 2.50e+03 pdb=" N ASP A 262 " -0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA E 264 " 0.021 2.00e-02 2.50e+03 4.25e-02 1.81e+01 pdb=" C ALA E 264 " -0.074 2.00e-02 2.50e+03 pdb=" O ALA E 264 " 0.027 2.00e-02 2.50e+03 pdb=" N VAL E 265 " 0.026 2.00e-02 2.50e+03 ... (remaining 6547 not shown) Histogram of nonbonded interaction distances: 1.78 - 2.41: 46 2.41 - 3.03: 24595 3.03 - 3.65: 53379 3.65 - 4.28: 84573 4.28 - 4.90: 142032 Nonbonded interactions: 304625 Sorted by model distance: nonbonded pdb=" O2G ATP C 600 " pdb="MG MG C 601 " model vdw 1.781 2.170 nonbonded pdb=" O2B ATP A 600 " pdb="MG MG A 601 " model vdw 1.852 2.170 nonbonded pdb=" OG1 THR C 176 " pdb="MG MG C 601 " model vdw 1.860 2.170 nonbonded pdb=" O3 PO4 D 501 " pdb="MG MG D 502 " model vdw 1.870 2.170 nonbonded pdb=" O2G ATP B 600 " pdb="MG MG B 601 " model vdw 1.888 2.170 ... (remaining 304620 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 4 through 408 or (resid 409 through 410 and (name N or nam \ e CA or name C or name O or name CB )) or resid 411 through 511 or resid 600 thr \ ough 601)) selection = (chain 'B' and (resid 4 through 511 or resid 600 through 601)) selection = (chain 'C' and (resid 4 through 408 or (resid 409 through 410 and (name N or nam \ e CA or name C or name O or name CB )) or resid 411 through 511 or resid 600 thr \ ough 601)) } ncs_group { reference = (chain 'D' and (resid 2 through 459 or resid 500)) selection = (chain 'E' and (resid 2 through 459 or resid 500)) selection = (chain 'F' and (resid 2 through 459 or resid 500)) } ncs_group { reference = (chain 'I' and resid 3 through 78) selection = (chain 'J' and resid 3 through 78) selection = (chain 'L' and resid 3 through 78) selection = (chain 'M' and resid 3 through 78) selection = (chain 'N' and resid 3 through 78) selection = (chain 'O' and resid 3 through 78) selection = (chain 'P' and resid 3 through 78) selection = (chain 'Q' and resid 3 through 78) selection = chain 'R' selection = (chain 'S' and resid 3 through 78) } ncs_group { reference = chain 'X' selection = chain 'Y' } 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 16 5.49 5 Mg 5 5.21 5 S 180 5.16 5 C 23485 2.51 5 N 6317 2.21 5 O 6968 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 individual isotropic 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: 1.830 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: 0.040 Extract box with map and model: 12.680 Check model and map are aligned: 0.610 Convert atoms to be neutral: 0.310 Process input model: 98.480 Find NCS groups from input model: 2.710 Set up NCS constraints: 0.270 Set refine NCS operators: 0.000 Set scattering table: 0.020 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 119.760 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8762 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 : 0.008 0.114 37528 Z= 0.510 Angle : 0.855 21.180 50797 Z= 0.552 Chirality : 0.050 0.469 5920 Planarity : 0.004 0.049 6550 Dihedral : 14.363 146.931 13883 Min Nonbonded Distance : 1.781 Molprobity Statistics. All-atom Clashscore : 3.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer Outliers : 1.96 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 5.03 % 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: -2.11 (0.11), residues: 4807 helix: -1.46 (0.09), residues: 2654 sheet: -0.52 (0.20), residues: 538 loop : -1.26 (0.14), residues: 1615 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9614 Ramachandran restraints generated. 4807 Oldfield, 0 Emsley, 4807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9614 Ramachandran restraints generated. 4807 Oldfield, 0 Emsley, 4807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 825 residues out of total 3849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 750 time to evaluate : 4.774 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 75 outliers final: 32 residues processed: 813 average time/residue: 0.5055 time to fit residues: 654.4684 Evaluate side-chains 633 residues out of total 3849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 601 time to evaluate : 4.479 Switching outliers to nearest non-outliers outliers start: 32 outliers final: 0 residues processed: 32 average time/residue: 0.3164 time to fit residues: 25.2161 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 473 random chunks: chunk 399 optimal weight: 0.7980 chunk 358 optimal weight: 0.9980 chunk 198 optimal weight: 0.8980 chunk 122 optimal weight: 0.9990 chunk 241 optimal weight: 2.9990 chunk 191 optimal weight: 2.9990 chunk 370 optimal weight: 0.8980 chunk 143 optimal weight: 1.9990 chunk 225 optimal weight: 0.8980 chunk 275 optimal weight: 0.9990 chunk 429 optimal weight: 0.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: W 67 GLN W 71 ASN C 123 HIS C 333 GLN C 369 ASN B 4 ASN ** B 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 26 HIS B 58 ASN B 147 GLN B 186 GLN B 333 GLN B 488 GLN A 4 ASN A 65 ASN A 147 GLN A 344 ASN A 408 GLN X 123 GLN H 104 HIS ** H 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 35 GLN G 57 HIS G 64 HIS F 279 GLN E 7 GLN D 279 GLN J 3 ASN ** J 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 3 ASN ** Y 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 132 HIS a 181 GLN Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8716 moved from start: 0.1769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.077 37528 Z= 0.195 Angle : 0.605 7.927 50797 Z= 0.319 Chirality : 0.043 0.222 5920 Planarity : 0.005 0.069 6550 Dihedral : 6.738 131.013 5248 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer Outliers : 2.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.03 % 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: -0.47 (0.12), residues: 4807 helix: -0.04 (0.10), residues: 2688 sheet: -0.32 (0.21), residues: 534 loop : -0.50 (0.15), residues: 1585 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9614 Ramachandran restraints generated. 4807 Oldfield, 0 Emsley, 4807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9614 Ramachandran restraints generated. 4807 Oldfield, 0 Emsley, 4807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 757 residues out of total 3849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 672 time to evaluate : 4.317 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 85 outliers final: 32 residues processed: 715 average time/residue: 0.4880 time to fit residues: 567.3779 Evaluate side-chains 633 residues out of total 3849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 601 time to evaluate : 4.649 Switching outliers to nearest non-outliers outliers start: 32 outliers final: 0 residues processed: 32 average time/residue: 0.3932 time to fit residues: 28.2067 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 473 random chunks: chunk 238 optimal weight: 10.0000 chunk 133 optimal weight: 5.9990 chunk 357 optimal weight: 5.9990 chunk 292 optimal weight: 1.9990 chunk 118 optimal weight: 0.9990 chunk 430 optimal weight: 5.9990 chunk 464 optimal weight: 6.9990 chunk 383 optimal weight: 4.9990 chunk 426 optimal weight: 3.9990 chunk 146 optimal weight: 1.9990 chunk 345 optimal weight: 0.8980 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 511 GLN ** B 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 488 GLN A 358 ASN H 5 HIS H 104 HIS H 127 GLN G 57 HIS F 368 GLN D 243 ASN ** Y 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 78 GLN ** Y 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8727 moved from start: 0.2132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.080 37528 Z= 0.270 Angle : 0.582 9.067 50797 Z= 0.304 Chirality : 0.043 0.192 5920 Planarity : 0.005 0.071 6550 Dihedral : 6.217 122.378 5248 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer Outliers : 1.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.03 % 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: 0.02 (0.12), residues: 4807 helix: 0.41 (0.10), residues: 2692 sheet: -0.22 (0.21), residues: 532 loop : -0.34 (0.16), residues: 1583 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9614 Ramachandran restraints generated. 4807 Oldfield, 0 Emsley, 4807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9614 Ramachandran restraints generated. 4807 Oldfield, 0 Emsley, 4807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 683 residues out of total 3849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 624 time to evaluate : 4.788 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 59 outliers final: 24 residues processed: 660 average time/residue: 0.4860 time to fit residues: 522.0908 Evaluate side-chains 609 residues out of total 3849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 585 time to evaluate : 4.902 Switching outliers to nearest non-outliers outliers start: 24 outliers final: 0 residues processed: 24 average time/residue: 0.3265 time to fit residues: 20.9023 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 473 random chunks: chunk 425 optimal weight: 10.0000 chunk 323 optimal weight: 0.8980 chunk 223 optimal weight: 0.8980 chunk 47 optimal weight: 0.9990 chunk 205 optimal weight: 10.0000 chunk 288 optimal weight: 4.9990 chunk 431 optimal weight: 10.0000 chunk 457 optimal weight: 1.9990 chunk 225 optimal weight: 0.9990 chunk 409 optimal weight: 0.9990 chunk 123 optimal weight: 5.9990 overall best weight: 0.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 104 HIS G 57 HIS F 324 GLN ** Y 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 78 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8702 moved from start: 0.2496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.075 37528 Z= 0.180 Angle : 0.548 13.188 50797 Z= 0.284 Chirality : 0.041 0.254 5920 Planarity : 0.004 0.060 6550 Dihedral : 5.809 116.063 5248 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer Outliers : 1.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.03 % 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: 0.38 (0.12), residues: 4807 helix: 0.74 (0.10), residues: 2671 sheet: -0.15 (0.21), residues: 532 loop : -0.23 (0.16), residues: 1604 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9614 Ramachandran restraints generated. 4807 Oldfield, 0 Emsley, 4807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9614 Ramachandran restraints generated. 4807 Oldfield, 0 Emsley, 4807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 692 residues out of total 3849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 634 time to evaluate : 4.690 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 58 outliers final: 19 residues processed: 669 average time/residue: 0.4986 time to fit residues: 548.2484 Evaluate side-chains 612 residues out of total 3849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 593 time to evaluate : 4.723 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 0 residues processed: 19 average time/residue: 0.3368 time to fit residues: 18.5099 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 473 random chunks: chunk 380 optimal weight: 0.5980 chunk 259 optimal weight: 0.9980 chunk 6 optimal weight: 0.9980 chunk 340 optimal weight: 4.9990 chunk 188 optimal weight: 5.9990 chunk 390 optimal weight: 0.7980 chunk 316 optimal weight: 0.9980 chunk 0 optimal weight: 7.9990 chunk 233 optimal weight: 6.9990 chunk 410 optimal weight: 0.7980 chunk 115 optimal weight: 5.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: W 73 GLN C 479 HIS ** B 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 10 GLN X 106 GLN H 104 HIS G 54 HIS G 57 HIS F 7 GLN ** Y 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 87 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8692 moved from start: 0.2750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.065 37528 Z= 0.171 Angle : 0.538 13.075 50797 Z= 0.278 Chirality : 0.041 0.190 5920 Planarity : 0.004 0.047 6550 Dihedral : 5.526 112.515 5248 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer Outliers : 1.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.03 % 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: 0.59 (0.12), residues: 4807 helix: 0.96 (0.10), residues: 2657 sheet: -0.09 (0.21), residues: 540 loop : -0.21 (0.16), residues: 1610 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9614 Ramachandran restraints generated. 4807 Oldfield, 0 Emsley, 4807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9614 Ramachandran restraints generated. 4807 Oldfield, 0 Emsley, 4807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 676 residues out of total 3849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 626 time to evaluate : 4.791 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 50 outliers final: 22 residues processed: 652 average time/residue: 0.5163 time to fit residues: 552.9369 Evaluate side-chains 613 residues out of total 3849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 591 time to evaluate : 4.519 Switching outliers to nearest non-outliers outliers start: 22 outliers final: 0 residues processed: 22 average time/residue: 0.4009 time to fit residues: 22.1107 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 473 random chunks: chunk 153 optimal weight: 0.0030 chunk 411 optimal weight: 3.9990 chunk 90 optimal weight: 6.9990 chunk 268 optimal weight: 0.0980 chunk 112 optimal weight: 6.9990 chunk 457 optimal weight: 0.9980 chunk 379 optimal weight: 9.9990 chunk 211 optimal weight: 1.9990 chunk 38 optimal weight: 0.7980 chunk 151 optimal weight: 0.8980 chunk 240 optimal weight: 3.9990 overall best weight: 0.5590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 479 HIS X 10 GLN H 104 HIS G 57 HIS F 7 GLN F 437 HIS ** Y 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8675 moved from start: 0.2986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.082 37528 Z= 0.159 Angle : 0.541 13.640 50797 Z= 0.276 Chirality : 0.041 0.216 5920 Planarity : 0.004 0.080 6550 Dihedral : 5.327 109.326 5248 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer Outliers : 0.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.03 % 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: 0.71 (0.12), residues: 4807 helix: 1.05 (0.10), residues: 2660 sheet: -0.05 (0.21), residues: 542 loop : -0.14 (0.16), residues: 1605 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9614 Ramachandran restraints generated. 4807 Oldfield, 0 Emsley, 4807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9614 Ramachandran restraints generated. 4807 Oldfield, 0 Emsley, 4807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 669 residues out of total 3849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 631 time to evaluate : 5.097 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 38 outliers final: 15 residues processed: 646 average time/residue: 0.5051 time to fit residues: 535.7772 Evaluate side-chains 602 residues out of total 3849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 587 time to evaluate : 4.589 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 0 residues processed: 15 average time/residue: 0.3343 time to fit residues: 15.6030 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 473 random chunks: chunk 441 optimal weight: 0.3980 chunk 51 optimal weight: 2.9990 chunk 260 optimal weight: 3.9990 chunk 334 optimal weight: 4.9990 chunk 258 optimal weight: 1.9990 chunk 385 optimal weight: 0.9980 chunk 255 optimal weight: 0.9980 chunk 455 optimal weight: 3.9990 chunk 285 optimal weight: 0.9980 chunk 277 optimal weight: 0.8980 chunk 210 optimal weight: 1.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 42 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 104 GLN H 5 HIS H 104 HIS G 57 HIS F 7 GLN ** Y 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8679 moved from start: 0.3104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.068 37528 Z= 0.172 Angle : 0.544 12.109 50797 Z= 0.277 Chirality : 0.041 0.168 5920 Planarity : 0.004 0.045 6550 Dihedral : 5.215 109.007 5248 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer Outliers : 1.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.03 % 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: 0.77 (0.12), residues: 4807 helix: 1.10 (0.10), residues: 2658 sheet: -0.01 (0.21), residues: 540 loop : -0.12 (0.16), residues: 1609 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9614 Ramachandran restraints generated. 4807 Oldfield, 0 Emsley, 4807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9614 Ramachandran restraints generated. 4807 Oldfield, 0 Emsley, 4807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 644 residues out of total 3849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 605 time to evaluate : 4.958 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 39 outliers final: 19 residues processed: 619 average time/residue: 0.4926 time to fit residues: 498.1709 Evaluate side-chains 614 residues out of total 3849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 595 time to evaluate : 4.610 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 0 residues processed: 19 average time/residue: 0.3553 time to fit residues: 18.4607 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 473 random chunks: chunk 282 optimal weight: 3.9990 chunk 182 optimal weight: 0.1980 chunk 272 optimal weight: 0.8980 chunk 137 optimal weight: 4.9990 chunk 89 optimal weight: 4.9990 chunk 88 optimal weight: 0.6980 chunk 289 optimal weight: 0.9980 chunk 310 optimal weight: 1.9990 chunk 225 optimal weight: 2.9990 chunk 42 optimal weight: 0.9980 chunk 358 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 42 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 106 GLN H 104 HIS G 57 HIS ** Y 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 85 GLN a 15 HIS ** a 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8673 moved from start: 0.3232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.056 37528 Z= 0.166 Angle : 0.545 12.469 50797 Z= 0.278 Chirality : 0.041 0.199 5920 Planarity : 0.004 0.107 6550 Dihedral : 5.061 108.043 5248 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer Outliers : 0.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.03 % 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: 0.84 (0.12), residues: 4807 helix: 1.16 (0.10), residues: 2658 sheet: 0.04 (0.21), residues: 542 loop : -0.09 (0.16), residues: 1607 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9614 Ramachandran restraints generated. 4807 Oldfield, 0 Emsley, 4807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9614 Ramachandran restraints generated. 4807 Oldfield, 0 Emsley, 4807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 640 residues out of total 3849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 618 time to evaluate : 4.842 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 22 outliers final: 8 residues processed: 629 average time/residue: 0.5144 time to fit residues: 533.2489 Evaluate side-chains 600 residues out of total 3849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 592 time to evaluate : 4.495 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.3569 time to fit residues: 11.2982 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 473 random chunks: chunk 414 optimal weight: 2.9990 chunk 436 optimal weight: 3.9990 chunk 398 optimal weight: 4.9990 chunk 424 optimal weight: 6.9990 chunk 255 optimal weight: 1.9990 chunk 185 optimal weight: 9.9990 chunk 333 optimal weight: 10.0000 chunk 130 optimal weight: 0.5980 chunk 383 optimal weight: 0.0370 chunk 401 optimal weight: 0.9980 chunk 423 optimal weight: 9.9990 overall best weight: 1.3262 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 42 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 104 GLN H 104 HIS F 7 GLN M 3 ASN ** Y 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 3 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8688 moved from start: 0.3242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.059 37528 Z= 0.208 Angle : 0.574 12.446 50797 Z= 0.292 Chirality : 0.042 0.214 5920 Planarity : 0.004 0.099 6550 Dihedral : 5.048 109.775 5248 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer Outliers : 0.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.03 % 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: 0.86 (0.12), residues: 4807 helix: 1.16 (0.10), residues: 2656 sheet: 0.04 (0.21), residues: 541 loop : -0.06 (0.16), residues: 1610 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9614 Ramachandran restraints generated. 4807 Oldfield, 0 Emsley, 4807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9614 Ramachandran restraints generated. 4807 Oldfield, 0 Emsley, 4807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 618 residues out of total 3849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 601 time to evaluate : 4.552 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 17 outliers final: 7 residues processed: 608 average time/residue: 0.5047 time to fit residues: 503.0344 Evaluate side-chains 599 residues out of total 3849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 592 time to evaluate : 4.521 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.3230 time to fit residues: 10.3403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 473 random chunks: chunk 278 optimal weight: 5.9990 chunk 449 optimal weight: 7.9990 chunk 274 optimal weight: 3.9990 chunk 213 optimal weight: 4.9990 chunk 312 optimal weight: 0.9980 chunk 471 optimal weight: 1.9990 chunk 433 optimal weight: 10.0000 chunk 375 optimal weight: 1.9990 chunk 38 optimal weight: 3.9990 chunk 289 optimal weight: 0.7980 chunk 230 optimal weight: 9.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 42 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 104 GLN H 24 GLN H 104 HIS Y 10 GLN ** Y 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8708 moved from start: 0.3172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.062 37528 Z= 0.262 Angle : 0.595 11.877 50797 Z= 0.302 Chirality : 0.043 0.230 5920 Planarity : 0.004 0.094 6550 Dihedral : 5.172 110.541 5248 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer Outliers : 0.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.03 % 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: 0.81 (0.12), residues: 4807 helix: 1.11 (0.10), residues: 2672 sheet: 0.04 (0.21), residues: 544 loop : -0.08 (0.16), residues: 1591 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9614 Ramachandran restraints generated. 4807 Oldfield, 0 Emsley, 4807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9614 Ramachandran restraints generated. 4807 Oldfield, 0 Emsley, 4807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 605 residues out of total 3849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 595 time to evaluate : 4.656 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 10 outliers final: 5 residues processed: 598 average time/residue: 0.5047 time to fit residues: 498.4705 Evaluate side-chains 596 residues out of total 3849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 591 time to evaluate : 4.709 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.3332 time to fit residues: 9.2816 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 473 random chunks: chunk 298 optimal weight: 2.9990 chunk 399 optimal weight: 0.8980 chunk 114 optimal weight: 0.9990 chunk 345 optimal weight: 2.9990 chunk 55 optimal weight: 1.9990 chunk 104 optimal weight: 7.9990 chunk 375 optimal weight: 0.9990 chunk 157 optimal weight: 3.9990 chunk 385 optimal weight: 0.9990 chunk 47 optimal weight: 5.9990 chunk 69 optimal weight: 0.4980 overall best weight: 0.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 42 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 104 HIS F 7 GLN L 42 GLN ** Y 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.090152 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2833 r_free = 0.2833 target = 0.063598 restraints weight = 77749.855| |-----------------------------------------------------------------------------| r_work (start): 0.2823 rms_B_bonded: 2.17 r_work: 0.2811 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.2799 rms_B_bonded: 1.94 restraints_weight: 0.2500 r_work: 0.2788 rms_B_bonded: 1.96 restraints_weight: 0.1250 r_work: 0.2776 rms_B_bonded: 2.02 restraints_weight: 0.0625 r_work: 0.2764 rms_B_bonded: 2.11 restraints_weight: 0.0312 r_work: 0.2751 rms_B_bonded: 2.23 restraints_weight: 0.0156 r_work: 0.2737 rms_B_bonded: 2.38 restraints_weight: 0.0078 r_work: 0.2722 rms_B_bonded: 2.55 restraints_weight: 0.0039 r_work: 0.2707 rms_B_bonded: 2.75 restraints_weight: 0.0020 r_work: 0.2690 rms_B_bonded: 2.99 restraints_weight: 0.0010 r_work: 0.2672 rms_B_bonded: 3.25 restraints_weight: 0.0005 r_work: 0.2653 rms_B_bonded: 3.56 restraints_weight: 0.0002 r_work: 0.2633 rms_B_bonded: 3.90 restraints_weight: 0.0001 r_work: 0.2611 rms_B_bonded: 4.29 restraints_weight: 0.0001 r_work: 0.2587 rms_B_bonded: 4.72 restraints_weight: 0.0000 r_work (final): 0.2587 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8913 moved from start: 0.3344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.057 37528 Z= 0.177 Angle : 0.572 11.560 50797 Z= 0.290 Chirality : 0.042 0.225 5920 Planarity : 0.004 0.091 6550 Dihedral : 5.040 106.676 5248 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer Outliers : 0.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.03 % 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: 0.89 (0.12), residues: 4807 helix: 1.20 (0.10), residues: 2661 sheet: 0.04 (0.22), residues: 540 loop : -0.08 (0.16), residues: 1606 =============================================================================== Job complete usr+sys time: 9404.07 seconds wall clock time: 169 minutes 25.76 seconds (10165.76 seconds total)