Starting phenix.real_space_refine (version: dev) on Tue May 17 05:11:31 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6oqs_20168/05_2022/6oqs_20168_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6oqs_20168/05_2022/6oqs_20168.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6oqs_20168/05_2022/6oqs_20168.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6oqs_20168/05_2022/6oqs_20168.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6oqs_20168/05_2022/6oqs_20168_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6oqs_20168/05_2022/6oqs_20168_neut_updated.pdb" } resolution = 3.3 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 "C TYR 308": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 417": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 240": "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} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 153} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 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: "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: "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: "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: "Y" Number of atoms: 1210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1210 Classifications: {'peptide': 156} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 153} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 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: "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: 20.78, per 1000 atoms: 0.56 Number of scatterers: 36971 At special positions: 0 Unit cell: (176.956, 220.116, 139.191, 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: 16.35 Conformation dependent library (CDL) restraints added in 6.0 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 56.1% alpha, 9.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.74 Creating SS restraints... Processing helix chain 'W' and resid 8 through 20 Processing helix chain 'W' and resid 24 through 37 Processing helix chain 'W' and resid 41 through 48 removed outlier: 3.581A pdb=" N GLU W 45 " --> pdb=" O GLU W 41 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N SER W 48 " --> pdb=" O ALA W 44 " (cutoff:3.500A) Processing helix chain 'W' and resid 53 through 62 removed outlier: 3.632A pdb=" N GLU W 58 " --> pdb=" O GLU W 54 " (cutoff:3.500A) Processing helix chain 'W' and resid 71 through 82 Processing helix chain 'W' and resid 85 through 102 Proline residue: W 89 - end of helix removed outlier: 3.963A pdb=" N LEU W 92 " --> pdb=" O PRO W 89 " (cutoff:3.500A) Processing helix chain 'W' and resid 120 through 131 removed outlier: 3.614A 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: 3.586A pdb=" N MET C 156 " --> pdb=" O ALA C 152 " (cutoff:3.500A) Processing helix chain 'C' and resid 175 through 186 removed outlier: 4.082A pdb=" N GLN C 186 " --> pdb=" O ALA C 182 " (cutoff:3.500A) Processing helix chain 'C' and resid 202 through 214 removed outlier: 3.843A 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 252 Proline residue: C 239 - end of helix removed outlier: 3.815A pdb=" N TYR C 248 " --> pdb=" O ALA C 244 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N PHE C 249 " --> pdb=" O MET C 245 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ARG C 252 " --> pdb=" O TYR C 248 " (cutoff:3.500A) Processing helix chain 'C' and resid 263 through 276 removed outlier: 3.806A pdb=" N VAL C 268 " --> pdb=" O SER C 264 " (cutoff:3.500A) 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: 4.231A pdb=" N PHE C 291 " --> pdb=" O GLY C 288 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N TYR C 292 " --> pdb=" O ASP C 289 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N SER C 295 " --> pdb=" O TYR C 292 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N ARG C 296 " --> pdb=" O LEU C 293 " (cutoff:3.500A) removed outlier: 4.583A 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: 4.007A 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: 3.930A pdb=" N GLY C 391 " --> pdb=" O LYS C 387 " (cutoff:3.500A) removed outlier: 4.695A pdb=" N GLY C 392 " --> pdb=" O LYS C 388 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N ILE C 393 " --> pdb=" O LEU C 389 " (cutoff:3.500A) removed outlier: 4.995A pdb=" N ALA C 405 " --> pdb=" O ARG C 401 " (cutoff:3.500A) removed outlier: 6.061A pdb=" N PHE C 406 " --> pdb=" O GLU C 402 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N SER C 407 " --> pdb=" O LEU C 403 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N GLN C 408 " --> pdb=" O ALA C 404 " (cutoff:3.500A) removed outlier: 5.019A pdb=" N PHE C 409 " --> pdb=" O ALA C 405 " (cutoff:3.500A) removed outlier: 6.071A pdb=" N SER C 411 " --> pdb=" O SER C 407 " (cutoff:3.500A) removed outlier: 7.256A pdb=" N ASP C 412 " --> pdb=" O GLN C 408 " (cutoff:3.500A) Processing helix chain 'C' and resid 415 through 431 removed outlier: 4.344A pdb=" N GLN C 420 " --> pdb=" O ALA C 416 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LEU C 431 " --> pdb=" O VAL C 427 " (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: 3.506A pdb=" N ILE C 464 " --> pdb=" O LEU C 461 " (cutoff:3.500A) removed outlier: 4.987A pdb=" N GLY C 465 " --> pdb=" O SER C 462 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ASP C 478 " --> pdb=" O VAL C 475 " (cutoff:3.500A) Processing helix chain 'C' and resid 480 through 489 removed outlier: 3.631A 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 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: 3.632A pdb=" N GLN B 186 " --> pdb=" O ALA B 182 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N ARG B 187 " --> pdb=" O ILE B 183 " (cutoff:3.500A) removed outlier: 5.329A 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 removed outlier: 3.516A pdb=" N LEU B 237 " --> pdb=" O ALA B 233 " (cutoff:3.500A) Proline residue: B 239 - end of helix removed outlier: 3.665A pdb=" N TYR B 248 " --> pdb=" O ALA B 244 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N PHE B 249 " --> pdb=" O MET B 245 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ARG B 252 " --> pdb=" O TYR B 248 " (cutoff:3.500A) Processing helix chain 'B' and resid 263 through 277 removed outlier: 3.678A pdb=" N ALA B 267 " --> pdb=" O LEU B 263 " (cutoff:3.500A) removed outlier: 3.620A 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: 4.349A pdb=" N PHE B 291 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 3.734A 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: 4.458A 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 348 Processing helix chain 'B' and resid 357 through 361 Processing helix chain 'B' and resid 378 through 381 removed outlier: 3.625A pdb=" N ALA B 381 " --> pdb=" O GLY B 378 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 378 through 381' Processing helix chain 'B' and resid 384 through 390 Processing helix chain 'B' and resid 393 through 407 removed outlier: 3.678A pdb=" N ALA B 405 " --> pdb=" O ARG B 401 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N PHE B 406 " --> pdb=" O GLU B 402 " (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 464 through 477 Processing helix chain 'B' and resid 480 through 486 Processing helix chain 'B' and resid 494 through 510 Processing helix chain 'A' and resid 5 through 19 removed outlier: 3.678A pdb=" N SER A 9 " --> pdb=" O SER A 5 " (cutoff:3.500A) 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 Processing helix chain 'A' and resid 175 through 188 removed outlier: 4.035A pdb=" N GLN A 186 " --> pdb=" O ALA A 182 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N ARG A 187 " --> pdb=" O ILE A 183 " (cutoff:3.500A) removed outlier: 5.455A 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: 3.549A pdb=" N TYR A 248 " --> pdb=" O ALA A 244 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N PHE A 249 " --> pdb=" O MET A 245 " (cutoff:3.500A) Processing helix chain 'A' and resid 263 through 277 removed outlier: 3.658A pdb=" N VAL A 268 " --> pdb=" O SER A 264 " (cutoff:3.500A) removed outlier: 3.880A 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: 3.510A pdb=" N HIS A 294 " --> pdb=" O VAL A 290 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LEU A 297 " --> pdb=" O LEU A 293 " (cutoff:3.500A) removed outlier: 4.620A 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 340 through 348 removed outlier: 3.522A 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 407 removed outlier: 3.810A pdb=" N GLU A 402 " --> pdb=" O ALA A 398 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ALA A 405 " --> pdb=" O ARG A 401 " (cutoff:3.500A) Processing helix chain 'A' and resid 415 through 431 removed outlier: 3.634A 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: 4.401A pdb=" N GLY A 465 " --> pdb=" O LEU A 461 " (cutoff:3.500A) removed outlier: 5.213A pdb=" N SER A 466 " --> pdb=" O SER A 462 " (cutoff:3.500A) removed outlier: 3.730A 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: 3.635A pdb=" N LYS A 499 " --> pdb=" O GLU A 495 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N ALA A 509 " --> pdb=" O ASP A 505 " (cutoff:3.500A) Processing helix chain 'X' and resid 5 through 135 removed outlier: 4.104A pdb=" N GLN X 10 " --> pdb=" O ILE X 7 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N PHE X 14 " --> pdb=" O ALA X 11 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N LEU X 16 " --> pdb=" O ALA X 13 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N PHE X 20 " --> pdb=" O PHE X 17 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N CYS X 21 " --> pdb=" O VAL X 18 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LYS X 23 " --> pdb=" O PHE X 20 " (cutoff:3.500A) removed outlier: 4.984A pdb=" N VAL X 25 " --> pdb=" O MET X 22 " (cutoff:3.500A) removed outlier: 5.098A pdb=" N TRP X 26 " --> pdb=" O LYS X 23 " (cutoff:3.500A) Proline residue: X 27 - end of helix removed outlier: 3.515A pdb=" N MET X 30 " --> pdb=" O PRO X 27 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N LYS X 38 " --> pdb=" O LYS X 35 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ASP X 42 " --> pdb=" O GLU X 39 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ALA X 50 " --> pdb=" O ALA X 47 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N HIS X 51 " --> pdb=" O GLU X 48 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LEU X 54 " --> pdb=" O HIS X 51 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N ASP X 88 " --> pdb=" O GLN X 85 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N GLN X 106 " --> pdb=" O ALA X 103 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N GLU X 110 " --> pdb=" O ALA X 107 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N GLU X 118 " --> pdb=" O ARG X 115 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ARG X 121 " --> pdb=" O GLU X 118 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N VAL X 124 " --> pdb=" O ARG X 121 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N ALA X 125 " --> pdb=" O LYS X 122 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N ALA X 128 " --> pdb=" O ALA X 125 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ILE X 135 " --> pdb=" O ALA X 132 " (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 removed outlier: 3.703A pdb=" N LEU X 152 " --> pdb=" O ILE X 148 " (cutoff:3.500A) Processing helix chain 'H' and resid 90 through 103 Processing helix chain 'H' and resid 112 through 124 removed outlier: 3.645A pdb=" N GLN H 116 " --> pdb=" O VAL H 112 " (cutoff:3.500A) Processing helix chain 'H' and resid 130 through 133 No H-bonds generated for 'chain 'H' and resid 130 through 133' Processing helix chain 'G' and resid 2 through 57 removed outlier: 3.751A pdb=" N MET G 25 " --> pdb=" O LYS G 21 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N SER G 41 " --> pdb=" O ARG G 37 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N ARG G 42 " --> pdb=" O MET G 38 " (cutoff:3.500A) Proline residue: G 43 - end of helix removed outlier: 3.629A pdb=" N LYS G 50 " --> pdb=" O GLU G 46 " (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 88 through 107 removed outlier: 4.551A pdb=" N ASN G 91 " --> pdb=" O GLY G 88 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ASN G 93 " --> pdb=" O LEU G 90 " (cutoff:3.500A) Processing helix chain 'G' and resid 119 through 128 Processing helix chain 'G' and resid 145 through 160 removed outlier: 3.566A pdb=" N ILE G 149 " --> pdb=" O LEU G 145 " (cutoff:3.500A) removed outlier: 5.369A 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: 4.280A 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: 3.598A pdb=" N ASP G 216 " --> pdb=" O LYS G 212 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N THR G 217 " --> pdb=" O ALA G 213 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N VAL G 244 " --> pdb=" O ALA G 240 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N LYS G 258 " --> pdb=" O GLY G 254 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N GLU G 259 " --> pdb=" O SER G 255 " (cutoff:3.500A) removed outlier: 4.132A 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 167 Processing helix chain 'F' and resid 183 through 196 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: 4.835A pdb=" N ALA F 220 " --> pdb=" O ARG F 216 " (cutoff:3.500A) removed outlier: 5.257A pdb=" N LEU F 221 " --> pdb=" O LEU F 217 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N MET F 226 " --> pdb=" O THR F 222 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N PHE F 230 " --> pdb=" O MET F 226 " (cutoff:3.500A) Processing helix chain 'F' and resid 244 through 258 removed outlier: 3.909A pdb=" N ALA F 250 " --> pdb=" O TYR F 247 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N GLU F 253 " --> pdb=" O ALA F 250 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N SER F 255 " --> pdb=" O THR F 252 " (cutoff:3.500A) removed outlier: 4.859A pdb=" N ALA F 256 " --> pdb=" O GLU F 253 " (cutoff:3.500A) Processing helix chain 'F' and resid 271 through 279 removed outlier: 3.750A 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: 4.522A pdb=" N ALA F 313 " --> pdb=" O ALA F 309 " (cutoff:3.500A) removed outlier: 4.950A pdb=" N HIS F 314 " --> pdb=" O THR F 310 " (cutoff:3.500A) Processing helix chain 'F' and resid 323 through 328 removed outlier: 4.148A pdb=" N LEU F 328 " --> pdb=" O GLN F 324 " (cutoff:3.500A) Processing helix chain 'F' and resid 346 through 349 No H-bonds generated for 'chain 'F' and resid 346 through 349' Processing helix chain 'F' and resid 351 through 369 Processing helix chain 'F' and resid 371 through 377 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 384 through 399 removed outlier: 3.648A pdb=" N VAL F 390 " --> pdb=" O ASP F 386 " (cutoff:3.500A) Processing helix chain 'F' and resid 405 through 411 removed outlier: 3.791A pdb=" N GLU F 408 " --> pdb=" O PHE F 405 " (cutoff:3.500A) removed outlier: 4.650A pdb=" N VAL F 409 " --> pdb=" O VAL F 406 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N THR F 411 " --> pdb=" O GLU F 408 " (cutoff:3.500A) Processing helix chain 'F' and resid 420 through 432 removed outlier: 3.732A pdb=" N ARG F 425 " --> pdb=" O LYS F 421 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N GLY F 426 " --> pdb=" O ASP F 422 " (cutoff:3.500A) Processing helix chain 'F' and resid 440 through 443 Processing helix chain 'F' and resid 449 through 458 removed outlier: 3.976A pdb=" N LYS F 457 " --> pdb=" O VAL F 453 " (cutoff:3.500A) removed outlier: 4.166A 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: 3.945A 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: 4.999A pdb=" N ALA E 220 " --> pdb=" O ARG E 216 " (cutoff:3.500A) removed outlier: 4.754A pdb=" N LEU E 221 " --> pdb=" O LEU E 217 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N LYS E 229 " --> pdb=" O THR E 225 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLU E 233 " --> pdb=" O LYS E 229 " (cutoff:3.500A) Processing helix chain 'E' and resid 244 through 258 removed outlier: 3.576A pdb=" N GLY E 251 " --> pdb=" O TYR E 247 " (cutoff:3.500A) Processing helix chain 'E' and resid 271 through 279 removed outlier: 3.696A 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 311 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: 4.301A pdb=" N GLU E 369 " --> pdb=" O GLN E 365 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N ASP E 372 " --> pdb=" O GLN E 368 " (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: 3.793A pdb=" N LYS E 395 " --> pdb=" O ALA E 391 " (cutoff:3.500A) Processing helix chain 'E' and resid 407 through 411 removed outlier: 3.546A pdb=" N THR E 411 " --> pdb=" O GLU E 408 " (cutoff:3.500A) Processing helix chain 'E' and resid 420 through 432 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: 4.060A 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 170 Processing helix chain 'D' and resid 183 through 196 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: 5.239A pdb=" N ALA D 220 " --> pdb=" O ARG D 216 " (cutoff:3.500A) removed outlier: 4.973A pdb=" N LEU D 221 " --> pdb=" O LEU D 217 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N GLU D 233 " --> pdb=" O LYS D 229 " (cutoff:3.500A) Processing helix chain 'D' and resid 244 through 257 Processing helix chain 'D' and resid 271 through 281 removed outlier: 4.324A pdb=" N ARG D 281 " --> pdb=" O VAL D 277 " (cutoff:3.500A) 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 328 Processing helix chain 'D' and resid 346 through 349 No H-bonds generated for 'chain 'D' and resid 346 through 349' Processing helix chain 'D' and resid 351 through 376 removed outlier: 4.402A pdb=" N ASP D 372 " --> pdb=" O GLN D 368 " (cutoff:3.500A) removed outlier: 4.238A 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 408 through 411 No H-bonds generated for 'chain 'D' and resid 408 through 411' 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 458 removed outlier: 3.627A pdb=" N LYS D 458 " --> pdb=" O GLU D 454 " (cutoff:3.500A) Processing helix chain 'I' and resid 4 through 41 removed outlier: 3.774A pdb=" N MET I 11 " --> pdb=" O ASP I 7 " (cutoff:3.500A) Processing helix chain 'I' and resid 43 through 76 removed outlier: 3.731A pdb=" N ILE I 46 " --> pdb=" O PRO I 43 " (cutoff:3.500A) Proline residue: I 47 - end of helix removed outlier: 4.093A pdb=" N ARG I 50 " --> pdb=" O PRO I 47 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N MET I 57 " --> pdb=" O PHE I 54 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLY I 58 " --> pdb=" O ILE I 55 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N ASP I 61 " --> pdb=" O GLY I 58 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N ILE I 63 " --> pdb=" O VAL I 60 " (cutoff:3.500A) Proline residue: I 64 - end of helix Processing helix chain 'J' and resid 4 through 41 removed outlier: 3.713A pdb=" N LEU J 8 " --> pdb=" O LEU J 4 " (cutoff:3.500A) Processing helix chain 'J' and resid 46 through 60 removed outlier: 3.809A pdb=" N LEU J 59 " --> pdb=" O ILE J 55 " (cutoff:3.500A) Processing helix chain 'J' and resid 62 through 76 Processing helix chain 'L' and resid 4 through 41 removed outlier: 3.722A pdb=" N VAL L 15 " --> pdb=" O ALA L 12 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ALA L 24 " --> pdb=" O ALA L 21 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N GLY L 27 " --> pdb=" O ALA L 24 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ILE L 28 " --> pdb=" O ALA L 25 " (cutoff:3.500A) Processing helix chain 'L' and resid 43 through 76 removed outlier: 3.799A pdb=" N ILE L 46 " --> pdb=" O PRO L 43 " (cutoff:3.500A) Proline residue: L 47 - end of helix removed outlier: 4.045A pdb=" N ARG L 50 " --> pdb=" O PRO L 47 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N MET L 57 " --> pdb=" O PHE L 54 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N GLY L 58 " --> pdb=" O ILE L 55 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N ASP L 61 " --> pdb=" O GLY L 58 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N ILE L 63 " --> pdb=" O VAL L 60 " (cutoff:3.500A) Proline residue: L 64 - end of helix removed outlier: 3.646A pdb=" N MET L 75 " --> pdb=" O LEU L 72 " (cutoff:3.500A) Processing helix chain 'M' and resid 4 through 41 removed outlier: 3.512A pdb=" N MET M 11 " --> pdb=" O ASP M 7 " (cutoff:3.500A) Processing helix chain 'M' and resid 43 through 60 Proline residue: M 47 - end of helix removed outlier: 4.160A pdb=" N ARG M 50 " --> pdb=" O PRO M 47 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N PHE M 53 " --> pdb=" O ARG M 50 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N GLY M 58 " --> pdb=" O ILE M 55 " (cutoff:3.500A) Processing helix chain 'M' and resid 63 through 76 Processing helix chain 'N' and resid 4 through 41 removed outlier: 4.520A pdb=" N LEU N 9 " --> pdb=" O ASN N 5 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N TYR N 10 " --> pdb=" O MET N 6 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N MET N 11 " --> pdb=" O ASP N 7 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N MET N 16 " --> pdb=" O ALA N 12 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ALA N 21 " --> pdb=" O MET N 17 " (cutoff:3.500A) Processing helix chain 'N' and resid 43 through 76 Proline residue: N 47 - end of helix removed outlier: 4.257A pdb=" N ARG N 50 " --> pdb=" O PRO N 47 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N GLY N 58 " --> pdb=" O ILE N 55 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N ASP N 61 " --> pdb=" O GLY N 58 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N ILE N 63 " --> pdb=" O VAL N 60 " (cutoff:3.500A) Proline residue: N 64 - end of helix Processing helix chain 'O' and resid 4 through 41 removed outlier: 3.515A pdb=" N MET O 17 " --> pdb=" O ALA O 14 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LEU O 19 " --> pdb=" O MET O 16 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLY O 23 " --> pdb=" O ALA O 20 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ALA O 24 " --> pdb=" O ALA O 21 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N GLY O 27 " --> pdb=" O ALA O 24 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ILE O 28 " --> pdb=" O ALA O 25 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ALA O 40 " --> pdb=" O GLU O 37 " (cutoff:3.500A) Processing helix chain 'O' and resid 46 through 76 removed outlier: 3.799A pdb=" N THR O 51 " --> pdb=" O PRO O 47 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N PHE O 54 " --> pdb=" O ARG O 50 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N LEU O 59 " --> pdb=" O ILE O 55 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ASP O 61 " --> pdb=" O MET O 57 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N ALA O 62 " --> pdb=" O GLY O 58 " (cutoff:3.500A) removed outlier: 4.818A pdb=" N ILE O 63 " --> pdb=" O LEU O 59 " (cutoff:3.500A) Proline residue: O 64 - end of helix Processing helix chain 'P' and resid 4 through 41 removed outlier: 3.866A pdb=" N LEU P 8 " --> pdb=" O LEU P 4 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N LEU P 9 " --> pdb=" O ASN P 5 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ALA P 21 " --> pdb=" O MET P 17 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N ILE P 28 " --> pdb=" O ALA P 24 " (cutoff:3.500A) Processing helix chain 'P' and resid 45 through 76 removed outlier: 3.517A pdb=" N LEU P 49 " --> pdb=" O ILE P 46 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N GLY P 58 " --> pdb=" O ILE P 55 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N ILE P 63 " --> pdb=" O VAL P 60 " (cutoff:3.500A) Proline residue: P 64 - end of helix Processing helix chain 'Q' and resid 4 through 41 removed outlier: 3.547A pdb=" N LEU Q 8 " --> pdb=" O LEU Q 4 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N LEU Q 9 " --> pdb=" O ASN Q 5 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N TYR Q 10 " --> pdb=" O MET Q 6 " (cutoff:3.500A) Processing helix chain 'Q' and resid 43 through 76 Proline residue: Q 47 - end of helix removed outlier: 4.209A pdb=" N ARG Q 50 " --> pdb=" O PRO Q 47 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N PHE Q 54 " --> pdb=" O THR Q 51 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N ASP Q 61 " --> pdb=" O GLY Q 58 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N ILE Q 63 " --> pdb=" O VAL Q 60 " (cutoff:3.500A) Proline residue: Q 64 - end of helix removed outlier: 3.616A pdb=" N PHE Q 76 " --> pdb=" O TYR Q 73 " (cutoff:3.500A) Processing helix chain 'R' and resid 4 through 41 removed outlier: 3.755A pdb=" N LEU R 8 " --> pdb=" O LEU R 4 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N LEU R 9 " --> pdb=" O ASN R 5 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ALA R 21 " --> pdb=" O MET R 17 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ILE R 28 " --> pdb=" O ALA R 24 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N LYS R 34 " --> pdb=" O ILE R 30 " (cutoff:3.500A) Processing helix chain 'R' and resid 45 through 76 removed outlier: 3.860A pdb=" N ARG R 50 " --> pdb=" O PRO R 47 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N ILE R 63 " --> pdb=" O VAL R 60 " (cutoff:3.500A) Proline residue: R 64 - end of helix removed outlier: 3.504A pdb=" N VAL R 74 " --> pdb=" O GLY R 71 " (cutoff:3.500A) Processing helix chain 'S' and resid 6 through 41 removed outlier: 4.555A pdb=" N TYR S 10 " --> pdb=" O ASP S 7 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N VAL S 15 " --> pdb=" O ALA S 12 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ALA S 24 " --> pdb=" O ALA S 21 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ILE S 28 " --> pdb=" O ALA S 25 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ARG S 41 " --> pdb=" O GLY S 38 " (cutoff:3.500A) Processing helix chain 'S' and resid 43 through 60 Proline residue: S 47 - end of helix removed outlier: 3.504A pdb=" N MET S 57 " --> pdb=" O PHE S 54 " (cutoff:3.500A) Processing helix chain 'S' and resid 62 through 76 Processing helix chain 'Y' and resid 3 through 24 removed outlier: 3.829A pdb=" N LYS Y 23 " --> pdb=" O LEU Y 19 " (cutoff:3.500A) Processing helix chain 'Y' and resid 26 through 139 removed outlier: 3.730A pdb=" N ALA Y 70 " --> pdb=" O LYS Y 66 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N GLN Y 73 " --> pdb=" O LYS Y 69 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N ARG Y 98 " --> pdb=" O ALA Y 94 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N THR Y 99 " --> pdb=" O GLU Y 95 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N LYS Y 100 " --> pdb=" O GLN Y 96 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N GLN Y 123 " --> pdb=" O GLU Y 119 " (cutoff:3.500A) Processing helix chain 'Y' and resid 142 through 153 Processing helix chain 'a' and resid 8 through 16 removed outlier: 3.604A pdb=" N GLY a 13 " --> pdb=" O GLN a 9 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N LEU a 16 " --> pdb=" O ILE a 12 " (cutoff:3.500A) Processing helix chain 'a' and resid 43 through 64 removed outlier: 3.731A pdb=" N VAL a 63 " --> pdb=" O LEU a 59 " (cutoff:3.500A) Processing helix chain 'a' and resid 74 through 93 removed outlier: 3.797A pdb=" N ALA a 78 " --> pdb=" O LYS a 74 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N VAL a 82 " --> pdb=" O ALA a 78 " (cutoff:3.500A) Processing helix chain 'a' and resid 100 through 120 removed outlier: 4.460A pdb=" N ASP a 119 " --> pdb=" O MET a 115 " (cutoff:3.500A) removed outlier: 4.478A 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 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: 3.666A pdb=" N LYS a 169 " --> pdb=" O SER a 165 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N ILE a 171 " --> pdb=" O LYS a 167 " (cutoff:3.500A) removed outlier: 9.460A pdb=" N GLY a 172 " --> pdb=" O MET a 168 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N GLY a 173 " --> pdb=" O LYS a 169 " (cutoff:3.500A) Processing helix chain 'a' and resid 189 through 228 removed outlier: 3.995A pdb=" N ILE a 194 " --> pdb=" O PRO a 190 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N LYS a 203 " --> pdb=" O SER a 199 " (cutoff:3.500A) Proline residue: a 204 - end of helix removed outlier: 3.698A pdb=" N LEU a 211 " --> pdb=" O LEU a 207 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ASN a 214 " --> pdb=" O ARG a 210 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N ILE a 221 " --> pdb=" O ALA a 217 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N PHE a 222 " --> pdb=" O GLY a 218 " (cutoff:3.500A) Processing helix chain 'a' and resid 231 through 233 No H-bonds generated for 'chain 'a' and resid 231 through 233' Processing helix chain 'a' and resid 235 through 268 Proline residue: a 240 - end of helix removed outlier: 4.035A pdb=" N PHE a 244 " --> pdb=" O PRO a 240 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N LEU a 247 " --> pdb=" O ILE a 243 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N THR a 250 " --> pdb=" O ILE a 246 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N PHE a 256 " --> pdb=" O GLN a 252 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N SER a 268 " --> pdb=" O LEU a 264 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'W' and resid 135 through 142 removed outlier: 3.723A pdb=" N ASN W 139 " --> pdb=" O VAL W 108 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N VAL W 110 " --> pdb=" O ASN W 139 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'C' and resid 28 through 30 removed outlier: 4.185A pdb=" N MET C 52 " --> pdb=" O THR C 91 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N ARG C 59 " --> pdb=" O LEU C 55 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N GLY C 72 " --> pdb=" O LEU C 64 " (cutoff:3.500A) removed outlier: 4.885A pdb=" N LEU C 66 " --> pdb=" O SER C 70 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N SER C 70 " --> pdb=" O LEU C 66 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ARG C 40 " --> pdb=" O SER C 33 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N SER C 33 " --> pdb=" O ARG C 40 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N HIS C 42 " --> pdb=" O ILE C 31 " (cutoff:3.500A) removed outlier: 5.702A pdb=" N ILE C 31 " --> pdb=" O HIS C 42 " (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: 8.330A pdb=" N VAL C 108 " --> pdb=" O THR C 221 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N VAL C 223 " --> pdb=" O VAL C 108 " (cutoff:3.500A) removed outlier: 8.950A pdb=" N ILE C 222 " --> pdb=" O ILE C 191 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N CYS C 193 " --> pdb=" O ILE C 222 " (cutoff:3.500A) removed outlier: 8.206A pdb=" N VAL C 224 " --> pdb=" O CYS C 193 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N TYR C 195 " --> pdb=" O VAL C 224 " (cutoff:3.500A) removed outlier: 7.831A pdb=" N ALA C 226 " --> pdb=" O TYR C 195 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N ALA C 197 " --> pdb=" O ALA C 226 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N ASP C 255 " --> pdb=" O LYS C 192 " (cutoff:3.500A) removed outlier: 8.221A pdb=" N ILE C 194 " --> pdb=" O ASP C 255 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N LEU C 257 " --> pdb=" O ILE C 194 " (cutoff:3.500A) removed outlier: 7.631A pdb=" N VAL C 196 " --> pdb=" O LEU C 257 " (cutoff:3.500A) removed outlier: 6.192A pdb=" N ILE C 259 " --> pdb=" O VAL C 196 " (cutoff:3.500A) removed outlier: 7.178A pdb=" N ILE C 198 " --> pdb=" O ILE C 259 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N ASP C 261 " --> pdb=" O ILE C 198 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N SER C 323 " --> pdb=" O ALA C 256 " (cutoff:3.500A) removed outlier: 7.767A pdb=" N ILE C 258 " --> pdb=" O SER C 323 " (cutoff:3.500A) removed outlier: 6.005A pdb=" N THR C 325 " --> pdb=" O ILE C 258 " (cutoff:3.500A) removed outlier: 7.302A 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 351 through 355 removed outlier: 3.567A pdb=" N LEU C 166 " --> pdb=" O GLY C 351 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 87 through 90 removed outlier: 4.648A pdb=" N ASN B 27 " --> pdb=" O CYS B 90 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N ARG B 40 " --> pdb=" O VAL B 32 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N VAL B 34 " --> pdb=" O VAL B 38 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N VAL B 38 " --> pdb=" O VAL B 34 " (cutoff:3.500A) removed outlier: 6.992A pdb=" N VAL B 74 " --> pdb=" O ALA B 63 " (cutoff:3.500A) removed outlier: 5.930A pdb=" N ALA B 63 " --> pdb=" O VAL B 74 " (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 107 through 109 removed outlier: 8.053A pdb=" N VAL B 108 " --> pdb=" O THR B 221 " (cutoff:3.500A) removed outlier: 6.142A pdb=" N VAL B 223 " --> pdb=" O VAL B 108 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N CYS B 193 " --> pdb=" O ILE B 222 " (cutoff:3.500A) removed outlier: 8.197A pdb=" N VAL B 224 " --> pdb=" O CYS B 193 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N TYR B 195 " --> pdb=" O VAL B 224 " (cutoff:3.500A) removed outlier: 7.908A pdb=" N ALA B 226 " --> pdb=" O TYR B 195 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N ALA B 197 " --> pdb=" O ALA B 226 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N SER B 323 " --> pdb=" O ALA B 256 " (cutoff:3.500A) removed outlier: 7.826A pdb=" N ILE B 258 " --> pdb=" O SER B 323 " (cutoff:3.500A) removed outlier: 6.208A pdb=" N THR B 325 " --> pdb=" O ILE B 258 " (cutoff:3.500A) removed outlier: 7.743A pdb=" N TYR B 260 " --> pdb=" O THR B 325 " (cutoff:3.500A) Processing sheet with id= I, 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: 7.293A pdb=" N LEU B 355 " --> pdb=" O LEU B 166 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N ILE B 168 " --> pdb=" O LEU B 355 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'A' and resid 87 through 89 removed outlier: 6.354A pdb=" N ARG A 40 " --> pdb=" O VAL A 32 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N VAL A 34 " --> pdb=" O VAL A 38 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N VAL A 38 " --> pdb=" O VAL A 34 " (cutoff:3.500A) removed outlier: 7.040A pdb=" N VAL A 74 " --> pdb=" O ALA A 63 " (cutoff:3.500A) removed outlier: 5.743A pdb=" N ALA A 63 " --> pdb=" O VAL A 74 " (cutoff:3.500A) removed outlier: 3.750A 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: 6.845A pdb=" N LEU A 166 " --> pdb=" O ILE A 353 " (cutoff:3.500A) removed outlier: 7.610A pdb=" N LEU A 355 " --> pdb=" O LEU A 166 " (cutoff:3.500A) removed outlier: 6.813A 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: 6.859A pdb=" N CYS A 193 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 8.072A pdb=" N VAL A 224 " --> pdb=" O CYS A 193 " (cutoff:3.500A) removed outlier: 6.158A pdb=" N TYR A 195 " --> pdb=" O VAL A 224 " (cutoff:3.500A) removed outlier: 7.748A pdb=" N ALA A 226 " --> pdb=" O TYR A 195 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N ALA A 197 " --> pdb=" O ALA A 226 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N SER A 323 " --> pdb=" O ALA A 256 " (cutoff:3.500A) removed outlier: 8.136A pdb=" N ILE A 258 " --> pdb=" O SER A 323 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N THR A 325 " --> pdb=" O ILE A 258 " (cutoff:3.500A) removed outlier: 7.879A pdb=" N TYR A 260 " --> pdb=" O THR A 325 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N LEU A 327 " --> pdb=" O TYR A 260 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'H' and resid 5 through 9 removed outlier: 3.611A pdb=" N ILE H 68 " --> pdb=" O LEU H 79 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N GLY H 67 " --> pdb=" O ILE H 45 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'H' and resid 30 through 35 removed outlier: 7.330A pdb=" N VAL H 53 " --> pdb=" O GLU H 21 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N ILE H 23 " --> pdb=" O ARG H 51 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N ARG H 51 " --> pdb=" O ILE H 23 " (cutoff:3.500A) removed outlier: 5.855A pdb=" N VAL H 25 " --> pdb=" O MET H 49 " (cutoff:3.500A) removed outlier: 8.873A pdb=" N MET H 49 " --> pdb=" O VAL H 25 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'G' and resid 180 through 188 removed outlier: 6.578A pdb=" N LEU G 167 " --> pdb=" O LEU G 187 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N LYS G 166 " --> pdb=" O ARG G 74 " (cutoff:3.500A) removed outlier: 5.654A pdb=" N ASN G 172 " --> pdb=" O VAL G 80 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N GLN G 111 " --> pdb=" O VAL G 75 " (cutoff:3.500A) removed outlier: 8.266A pdb=" N TYR G 77 " --> pdb=" O GLN G 111 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N ASP G 113 " --> pdb=" O TYR G 77 " (cutoff:3.500A) removed outlier: 7.472A pdb=" N VAL G 79 " --> pdb=" O ASP G 113 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N ALA G 115 " --> pdb=" O VAL G 79 " (cutoff:3.500A) removed outlier: 7.588A pdb=" N MET G 116 " --> pdb=" O VAL G 133 " (cutoff:3.500A) removed outlier: 4.369A 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: 6.552A pdb=" N ASP F 14 " --> pdb=" O VAL F 6 " (cutoff:3.500A) removed outlier: 4.739A pdb=" N VAL F 8 " --> pdb=" O VAL F 12 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N VAL F 12 " --> pdb=" O VAL F 8 " (cutoff:3.500A) removed outlier: 6.125A pdb=" N ILE F 54 " --> pdb=" O VAL F 42 " (cutoff:3.500A) removed outlier: 5.558A 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 78 Processing sheet with id= S, first strand: chain 'F' and resid 317 through 320 removed outlier: 8.042A pdb=" N VAL F 145 " --> pdb=" O ILE F 290 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N SER F 292 " --> pdb=" O VAL F 145 " (cutoff:3.500A) removed outlier: 8.000A pdb=" N LEU F 147 " --> pdb=" O SER F 292 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N GLN F 294 " --> pdb=" O LEU F 147 " (cutoff:3.500A) removed outlier: 8.023A pdb=" N GLY F 149 " --> pdb=" O GLN F 294 " (cutoff:3.500A) removed outlier: 6.201A 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: 6.424A pdb=" N ASP E 14 " --> pdb=" O VAL E 6 " (cutoff:3.500A) removed outlier: 4.419A 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: 6.222A pdb=" N ILE E 54 " --> pdb=" O VAL E 42 " (cutoff:3.500A) removed outlier: 5.593A 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 79 removed outlier: 4.840A pdb=" N GLU E 105 " --> pdb=" O VAL E 79 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'E' and resid 317 through 319 removed outlier: 8.452A pdb=" N VAL E 145 " --> pdb=" O ILE E 290 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N SER E 292 " --> pdb=" O VAL E 145 " (cutoff:3.500A) removed outlier: 7.683A pdb=" N LEU E 147 " --> pdb=" O SER E 292 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N GLN E 294 " --> pdb=" O LEU E 147 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'D' and resid 4 through 9 removed outlier: 6.606A pdb=" N ASP D 14 " --> pdb=" O VAL D 6 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N VAL D 8 " --> pdb=" O VAL D 12 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N VAL D 12 " --> pdb=" O VAL D 8 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N ILE D 54 " --> pdb=" O VAL D 42 " (cutoff:3.500A) removed outlier: 5.638A pdb=" N VAL D 42 " --> pdb=" O ILE D 54 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'D' and resid 76 through 79 removed outlier: 4.653A pdb=" N GLU D 105 " --> pdb=" O VAL D 79 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'D' and resid 317 through 320 removed outlier: 8.802A pdb=" N VAL D 145 " --> pdb=" O ILE D 290 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N SER D 292 " --> pdb=" O VAL D 145 " (cutoff:3.500A) removed outlier: 8.128A pdb=" N LEU D 147 " --> pdb=" O SER D 292 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N GLN D 294 " --> pdb=" O LEU D 147 " (cutoff:3.500A) removed outlier: 8.242A pdb=" N GLY D 149 " --> pdb=" O GLN D 294 " (cutoff:3.500A) removed outlier: 6.335A 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 1959 hydrogen bonds defined for protein. 4638 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: 13.54 Time building geometry restraints manager: 16.96 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.29: 6331 1.29 - 1.42: 8590 1.42 - 1.55: 22222 1.55 - 1.68: 25 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 1.462 -0.074 1.00e-02 1.00e+04 5.54e+01 bond pdb=" C4 ATP B 600 " pdb=" C5 ATP B 600 " ideal model delta sigma weight residual 1.388 1.461 -0.073 1.00e-02 1.00e+04 5.32e+01 bond pdb=" C4 ATP C 600 " pdb=" C5 ATP C 600 " ideal model delta sigma weight residual 1.388 1.460 -0.072 1.00e-02 1.00e+04 5.14e+01 bond pdb=" C5 ATP A 600 " pdb=" C6 ATP A 600 " ideal model delta sigma weight residual 1.409 1.475 -0.066 1.00e-02 1.00e+04 4.32e+01 bond pdb=" C ASP B 261 " pdb=" O ASP B 261 " ideal model delta sigma weight residual 1.237 1.162 0.075 1.17e-02 7.31e+03 4.12e+01 ... (remaining 37523 not shown) Histogram of bond angle deviations from ideal: 98.23 - 105.85: 858 105.85 - 113.46: 21332 113.46 - 121.08: 19409 121.08 - 128.70: 9002 128.70 - 136.31: 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 139.87 116.20 23.67 1.00e+00 1.00e+00 5.60e+02 angle pdb=" PB ATP A 600 " pdb=" O3B ATP A 600 " pdb=" PG ATP A 600 " ideal model delta sigma weight residual 139.87 118.09 21.78 1.00e+00 1.00e+00 4.74e+02 angle pdb=" PB ATP C 600 " pdb=" O3B ATP C 600 " pdb=" PG ATP C 600 " ideal model delta sigma weight residual 139.87 118.42 21.45 1.00e+00 1.00e+00 4.60e+02 angle pdb=" PA ATP C 600 " pdb=" O3A ATP C 600 " pdb=" PB ATP C 600 " ideal model delta sigma weight residual 136.83 116.65 20.18 1.00e+00 1.00e+00 4.07e+02 angle pdb=" PA ATP A 600 " pdb=" O3A ATP A 600 " pdb=" PB ATP A 600 " ideal model delta sigma weight residual 136.83 116.74 20.09 1.00e+00 1.00e+00 4.04e+02 ... (remaining 50792 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.54: 22006 30.54 - 61.08: 620 61.08 - 91.62: 70 91.62 - 122.16: 2 122.16 - 152.70: 3 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 300.00 147.29 152.70 1 2.00e+01 2.50e-03 4.53e+01 dihedral pdb=" C5' ADP E 500 " pdb=" O5' ADP E 500 " pdb=" PA ADP E 500 " pdb=" O2A ADP E 500 " ideal model delta sinusoidal sigma weight residual 300.00 155.99 144.01 1 2.00e+01 2.50e-03 4.34e+01 dihedral pdb=" O2A ADP D 500 " pdb=" O3A ADP D 500 " pdb=" PA ADP D 500 " pdb=" PB ADP D 500 " ideal model delta sinusoidal sigma weight residual -60.00 65.65 -125.65 1 2.00e+01 2.50e-03 3.80e+01 ... (remaining 22698 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.071: 5208 0.071 - 0.141: 672 0.141 - 0.212: 32 0.212 - 0.283: 6 0.283 - 0.353: 2 Chirality restraints: 5920 Sorted by residual: 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 2.16 0.35 2.00e-01 2.50e+01 3.12e+00 chirality pdb=" CA VAL a 29 " pdb=" N VAL a 29 " pdb=" C VAL a 29 " pdb=" CB VAL a 29 " both_signs ideal model delta sigma weight residual False 2.44 2.75 -0.31 2.00e-01 2.50e+01 2.44e+00 chirality pdb=" CA ASP B 261 " pdb=" N ASP B 261 " pdb=" C ASP B 261 " pdb=" CB ASP B 261 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.28 2.00e-01 2.50e+01 1.91e+00 ... (remaining 5917 not shown) Planarity restraints: 6550 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS H 100 " 0.023 2.00e-02 2.50e+03 4.66e-02 2.17e+01 pdb=" C LYS H 100 " -0.081 2.00e-02 2.50e+03 pdb=" O LYS H 100 " 0.030 2.00e-02 2.50e+03 pdb=" N ALA H 101 " 0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN C 18 " -0.018 2.00e-02 2.50e+03 3.51e-02 1.23e+01 pdb=" C GLN C 18 " 0.061 2.00e-02 2.50e+03 pdb=" O GLN C 18 " -0.022 2.00e-02 2.50e+03 pdb=" N PHE C 19 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PRO G 191 " -0.015 2.00e-02 2.50e+03 3.12e-02 9.75e+00 pdb=" C PRO G 191 " 0.054 2.00e-02 2.50e+03 pdb=" O PRO G 191 " -0.021 2.00e-02 2.50e+03 pdb=" N ALA G 192 " -0.018 2.00e-02 2.50e+03 ... (remaining 6547 not shown) Histogram of nonbonded interaction distances: 1.85 - 2.46: 138 2.46 - 3.07: 27408 3.07 - 3.68: 53704 3.68 - 4.29: 83303 4.29 - 4.90: 140189 Nonbonded interactions: 304742 Sorted by model distance: nonbonded pdb=" O2G ATP B 600 " pdb="MG MG B 601 " model vdw 1.849 2.170 nonbonded pdb=" OG1 THR C 176 " pdb="MG MG C 601 " model vdw 1.854 2.170 nonbonded pdb=" O2B ATP A 600 " pdb="MG MG A 601 " model vdw 1.872 2.170 nonbonded pdb=" O2G ATP A 600 " pdb="MG MG A 601 " model vdw 1.890 2.170 nonbonded pdb=" OG1 THR A 176 " pdb="MG MG A 601 " model vdw 1.915 2.170 ... (remaining 304737 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: 2.800 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.030 Extract box with map and model: 12.600 Check model and map are aligned: 0.550 Convert atoms to be neutral: 0.300 Process input model: 96.080 Find NCS groups from input model: 2.910 Set up NCS constraints: 0.260 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: 0.000 Load rotamer database and sin/cos tables:3.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 118.730 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8576 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 0.112 37528 Z= 0.499 Angle : 0.846 23.673 50797 Z= 0.551 Chirality : 0.048 0.353 5920 Planarity : 0.004 0.049 6550 Dihedral : 14.373 152.702 13883 Min Nonbonded Distance : 1.849 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.52 % Favored : 97.46 % Rotamer Outliers : 1.80 % 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: -2.20 (0.11), residues: 4807 helix: -1.35 (0.09), residues: 2630 sheet: -0.80 (0.20), residues: 539 loop : -1.55 (0.14), residues: 1638 *********************** 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 935 residues out of total 3851 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 866 time to evaluate : 4.681 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 69 outliers final: 28 residues processed: 923 average time/residue: 0.5126 time to fit residues: 750.2376 Evaluate side-chains 624 residues out of total 3851 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 596 time to evaluate : 4.646 Switching outliers to nearest non-outliers outliers start: 28 outliers final: 0 residues processed: 28 average time/residue: 0.3328 time to fit residues: 23.2261 ------------------------------------------------------------------------------- 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: 6.9990 chunk 358 optimal weight: 5.9990 chunk 198 optimal weight: 1.9990 chunk 122 optimal weight: 4.9990 chunk 241 optimal weight: 0.7980 chunk 191 optimal weight: 1.9990 chunk 370 optimal weight: 5.9990 chunk 143 optimal weight: 0.7980 chunk 225 optimal weight: 2.9990 chunk 275 optimal weight: 2.9990 chunk 429 optimal weight: 0.0980 overall best weight: 1.1384 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** C 408 GLN B 14 GLN B 26 HIS B 147 GLN B 186 GLN A 65 ASN A 147 GLN A 344 ASN A 484 GLN X 80 ASN H 5 HIS H 56 HIS G 54 HIS G 274 GLN F 32 GLN F 324 GLN F 368 GLN D 121 ASN ** D 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 52 GLN O 3 ASN R 5 ASN S 5 ASN ** S 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 37 GLN Y 73 GLN a 5 ASN a 116 ASN a 132 HIS a 185 HIS ** a 245 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8558 moved from start: 0.2182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.103 37528 Z= 0.216 Angle : 0.640 10.110 50797 Z= 0.333 Chirality : 0.043 0.268 5920 Planarity : 0.005 0.053 6550 Dihedral : 6.338 140.839 5248 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer Outliers : 2.29 % 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: -0.61 (0.12), residues: 4807 helix: -0.03 (0.10), residues: 2655 sheet: -0.34 (0.21), residues: 538 loop : -0.82 (0.15), residues: 1614 *********************** 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 734 residues out of total 3851 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 646 time to evaluate : 4.473 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 outliers start: 88 outliers final: 45 residues processed: 695 average time/residue: 0.4845 time to fit residues: 548.1632 Evaluate side-chains 615 residues out of total 3851 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 570 time to evaluate : 4.908 Switching outliers to nearest non-outliers outliers start: 45 outliers final: 0 residues processed: 45 average time/residue: 0.3366 time to fit residues: 34.3111 ------------------------------------------------------------------------------- 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: 0.9990 chunk 133 optimal weight: 3.9990 chunk 357 optimal weight: 7.9990 chunk 292 optimal weight: 2.9990 chunk 118 optimal weight: 2.9990 chunk 430 optimal weight: 0.9990 chunk 464 optimal weight: 5.9990 chunk 383 optimal weight: 8.9990 chunk 426 optimal weight: 9.9990 chunk 146 optimal weight: 5.9990 chunk 345 optimal weight: 6.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** W 73 GLN C 333 GLN ** X 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 72 GLN G 64 HIS D 121 ASN J 3 ASN L 42 GLN ** O 3 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 52 GLN ** S 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 10 GLN Y 64 GLN ** a 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 18 ASN a 185 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8589 moved from start: 0.2574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.051 37528 Z= 0.287 Angle : 0.614 9.146 50797 Z= 0.316 Chirality : 0.043 0.264 5920 Planarity : 0.005 0.046 6550 Dihedral : 5.911 114.832 5248 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer Outliers : 2.19 % 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: -0.19 (0.12), residues: 4807 helix: 0.37 (0.10), residues: 2641 sheet: -0.24 (0.21), residues: 539 loop : -0.70 (0.15), residues: 1627 *********************** 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 678 residues out of total 3851 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 594 time to evaluate : 4.617 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 outliers start: 84 outliers final: 39 residues processed: 653 average time/residue: 0.4811 time to fit residues: 513.8478 Evaluate side-chains 597 residues out of total 3851 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 558 time to evaluate : 4.140 Switching outliers to nearest non-outliers outliers start: 39 outliers final: 0 residues processed: 39 average time/residue: 0.3154 time to fit residues: 28.8390 ------------------------------------------------------------------------------- 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: 0.0470 chunk 323 optimal weight: 1.9990 chunk 223 optimal weight: 1.9990 chunk 47 optimal weight: 4.9990 chunk 205 optimal weight: 9.9990 chunk 288 optimal weight: 5.9990 chunk 431 optimal weight: 0.6980 chunk 457 optimal weight: 0.9980 chunk 225 optimal weight: 2.9990 chunk 409 optimal weight: 6.9990 chunk 123 optimal weight: 6.9990 overall best weight: 1.1482 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 511 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 444 GLN X 2 ASN X 64 GLN ** D 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 3 ASN ** O 3 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 52 GLN ** Y 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 123 GLN a 185 HIS ** a 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 245 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8567 moved from start: 0.2960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.053 37528 Z= 0.183 Angle : 0.567 10.296 50797 Z= 0.289 Chirality : 0.042 0.349 5920 Planarity : 0.004 0.047 6550 Dihedral : 5.620 106.200 5248 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer Outliers : 1.67 % 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: 0.13 (0.12), residues: 4807 helix: 0.66 (0.10), residues: 2622 sheet: -0.12 (0.22), residues: 521 loop : -0.60 (0.15), residues: 1664 *********************** 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 668 residues out of total 3851 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 604 time to evaluate : 4.947 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 64 outliers final: 29 residues processed: 650 average time/residue: 0.4879 time to fit residues: 517.6097 Evaluate side-chains 589 residues out of total 3851 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 560 time to evaluate : 4.474 Switching outliers to nearest non-outliers outliers start: 29 outliers final: 0 residues processed: 29 average time/residue: 0.3308 time to fit residues: 23.8978 ------------------------------------------------------------------------------- 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: 5.9990 chunk 259 optimal weight: 5.9990 chunk 6 optimal weight: 6.9990 chunk 340 optimal weight: 3.9990 chunk 188 optimal weight: 8.9990 chunk 390 optimal weight: 5.9990 chunk 316 optimal weight: 0.9990 chunk 0 optimal weight: 7.9990 chunk 233 optimal weight: 3.9990 chunk 410 optimal weight: 7.9990 chunk 115 optimal weight: 4.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 511 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 444 GLN A 493 ASN ** X 2 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 80 ASN F 324 GLN L 42 GLN ** O 3 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 3 ASN a 185 HIS ** a 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8624 moved from start: 0.3106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.069 37528 Z= 0.422 Angle : 0.650 10.467 50797 Z= 0.333 Chirality : 0.045 0.291 5920 Planarity : 0.005 0.100 6550 Dihedral : 5.817 109.918 5248 Min Nonbonded Distance : 1.895 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer Outliers : 2.19 % 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: 0.05 (0.12), residues: 4807 helix: 0.62 (0.10), residues: 2630 sheet: -0.18 (0.22), residues: 523 loop : -0.70 (0.15), residues: 1654 *********************** 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 651 residues out of total 3851 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 567 time to evaluate : 5.055 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 84 outliers final: 51 residues processed: 611 average time/residue: 0.5009 time to fit residues: 501.2749 Evaluate side-chains 591 residues out of total 3851 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 540 time to evaluate : 4.744 Switching outliers to nearest non-outliers outliers start: 51 outliers final: 0 residues processed: 51 average time/residue: 0.3504 time to fit residues: 39.5620 ------------------------------------------------------------------------------- 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: 0.9980 chunk 411 optimal weight: 20.0000 chunk 90 optimal weight: 2.9990 chunk 268 optimal weight: 4.9990 chunk 112 optimal weight: 6.9990 chunk 457 optimal weight: 0.9980 chunk 379 optimal weight: 3.9990 chunk 211 optimal weight: 0.9980 chunk 38 optimal weight: 4.9990 chunk 151 optimal weight: 0.9990 chunk 240 optimal weight: 0.9980 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: W 67 GLN B 484 GLN ** B 511 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 444 GLN X 2 ASN X 85 GLN H 75 ASN ** D 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 42 GLN ** O 3 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 3 ASN ** a 15 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 185 HIS ** a 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8576 moved from start: 0.3369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.052 37528 Z= 0.172 Angle : 0.571 9.563 50797 Z= 0.289 Chirality : 0.042 0.344 5920 Planarity : 0.004 0.056 6550 Dihedral : 5.521 107.416 5248 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer Outliers : 1.17 % 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: 0.31 (0.12), residues: 4807 helix: 0.86 (0.10), residues: 2622 sheet: -0.08 (0.22), residues: 510 loop : -0.59 (0.15), residues: 1675 *********************** 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 624 residues out of total 3851 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 579 time to evaluate : 4.993 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 45 outliers final: 15 residues processed: 611 average time/residue: 0.4867 time to fit residues: 485.8176 Evaluate side-chains 561 residues out of total 3851 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 546 time to evaluate : 4.633 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 0 residues processed: 15 average time/residue: 0.3574 time to fit residues: 16.1568 ------------------------------------------------------------------------------- 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: 0.7980 chunk 51 optimal weight: 0.7980 chunk 260 optimal weight: 3.9990 chunk 334 optimal weight: 9.9990 chunk 258 optimal weight: 0.0060 chunk 385 optimal weight: 0.9990 chunk 255 optimal weight: 2.9990 chunk 455 optimal weight: 0.9990 chunk 285 optimal weight: 10.0000 chunk 277 optimal weight: 0.3980 chunk 210 optimal weight: 0.9990 overall best weight: 0.5998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 14 GLN ** B 511 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 444 GLN H 72 GLN H 75 ASN ** D 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 42 GLN ** O 3 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 42 GLN ** S 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 20 GLN a 116 ASN a 185 HIS ** a 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8559 moved from start: 0.3581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.040 37528 Z= 0.157 Angle : 0.575 12.480 50797 Z= 0.288 Chirality : 0.041 0.276 5920 Planarity : 0.004 0.057 6550 Dihedral : 5.321 105.123 5248 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer Outliers : 0.94 % 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: 0.49 (0.12), residues: 4807 helix: 1.01 (0.10), residues: 2614 sheet: 0.00 (0.22), residues: 520 loop : -0.54 (0.15), residues: 1673 *********************** 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 620 residues out of total 3851 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 584 time to evaluate : 4.702 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 36 outliers final: 12 residues processed: 607 average time/residue: 0.5073 time to fit residues: 502.1016 Evaluate side-chains 558 residues out of total 3851 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 546 time to evaluate : 4.929 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.3751 time to fit residues: 14.5865 ------------------------------------------------------------------------------- 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: 10.0000 chunk 182 optimal weight: 1.9990 chunk 272 optimal weight: 5.9990 chunk 137 optimal weight: 4.9990 chunk 89 optimal weight: 0.9980 chunk 88 optimal weight: 0.1980 chunk 289 optimal weight: 0.6980 chunk 310 optimal weight: 20.0000 chunk 225 optimal weight: 0.9980 chunk 42 optimal weight: 0.9990 chunk 358 optimal weight: 2.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 511 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 444 GLN H 75 ASN L 5 ASN L 42 GLN M 3 ASN ** O 3 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 116 ASN a 185 HIS ** a 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8556 moved from start: 0.3751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.038 37528 Z= 0.164 Angle : 0.580 12.590 50797 Z= 0.290 Chirality : 0.041 0.242 5920 Planarity : 0.004 0.060 6550 Dihedral : 5.219 105.042 5248 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer Outliers : 0.70 % 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: 1.08 (0.11), residues: 2610 sheet: 0.07 (0.22), residues: 502 loop : -0.48 (0.15), residues: 1695 *********************** 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 593 residues out of total 3851 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 566 time to evaluate : 4.238 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 27 outliers final: 12 residues processed: 580 average time/residue: 0.5197 time to fit residues: 493.0542 Evaluate side-chains 563 residues out of total 3851 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 551 time to evaluate : 4.992 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.3517 time to fit residues: 14.0355 ------------------------------------------------------------------------------- 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: 9.9990 chunk 436 optimal weight: 6.9990 chunk 398 optimal weight: 10.0000 chunk 424 optimal weight: 7.9990 chunk 255 optimal weight: 0.8980 chunk 185 optimal weight: 0.8980 chunk 333 optimal weight: 9.9990 chunk 130 optimal weight: 0.7980 chunk 383 optimal weight: 20.0000 chunk 401 optimal weight: 0.9980 chunk 423 optimal weight: 2.9990 overall best weight: 1.3182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 511 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 444 GLN H 72 GLN H 75 ASN ** D 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 361 GLN ** I 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 42 GLN L 52 GLN M 5 ASN ** O 3 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 52 GLN ** Y 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 116 ASN a 185 HIS ** a 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8568 moved from start: 0.3817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.039 37528 Z= 0.196 Angle : 0.593 13.935 50797 Z= 0.295 Chirality : 0.042 0.235 5920 Planarity : 0.004 0.053 6550 Dihedral : 5.209 106.873 5248 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer Outliers : 0.60 % 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: 0.63 (0.12), residues: 4807 helix: 1.14 (0.11), residues: 2604 sheet: 0.06 (0.22), residues: 504 loop : -0.50 (0.15), residues: 1699 *********************** 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 581 residues out of total 3851 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 558 time to evaluate : 4.950 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 23 outliers final: 13 residues processed: 567 average time/residue: 0.5489 time to fit residues: 511.7488 Evaluate side-chains 557 residues out of total 3851 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 544 time to evaluate : 4.565 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.3779 time to fit residues: 15.0101 ------------------------------------------------------------------------------- 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: 8.9990 chunk 449 optimal weight: 20.0000 chunk 274 optimal weight: 6.9990 chunk 213 optimal weight: 2.9990 chunk 312 optimal weight: 1.9990 chunk 471 optimal weight: 3.9990 chunk 433 optimal weight: 8.9990 chunk 375 optimal weight: 6.9990 chunk 38 optimal weight: 3.9990 chunk 289 optimal weight: 0.9980 chunk 230 optimal weight: 1.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 511 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 42 GLN ** O 3 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 52 GLN a 116 ASN a 185 HIS ** a 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8594 moved from start: 0.3792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.042 37528 Z= 0.280 Angle : 0.620 12.320 50797 Z= 0.309 Chirality : 0.043 0.308 5920 Planarity : 0.005 0.095 6550 Dihedral : 5.326 110.166 5248 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer Outliers : 0.31 % 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: 0.55 (0.12), residues: 4807 helix: 1.07 (0.10), residues: 2628 sheet: -0.01 (0.23), residues: 496 loop : -0.53 (0.15), residues: 1683 ********************** 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 561 residues out of total 3851 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 549 time to evaluate : 5.001 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: 12 outliers final: 6 residues processed: 554 average time/residue: 0.5233 time to fit residues: 473.3024 Evaluate side-chains 539 residues out of total 3851 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 533 time to evaluate : 4.459 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.3522 time to fit residues: 9.9865 ------------------------------------------------------------------------------- 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: 3.9990 chunk 399 optimal weight: 0.6980 chunk 114 optimal weight: 6.9990 chunk 345 optimal weight: 3.9990 chunk 55 optimal weight: 8.9990 chunk 104 optimal weight: 0.9990 chunk 375 optimal weight: 6.9990 chunk 157 optimal weight: 0.1980 chunk 385 optimal weight: 5.9990 chunk 47 optimal weight: 5.9990 chunk 69 optimal weight: 0.6980 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 511 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 444 GLN H 55 GLN H 72 GLN H 75 ASN H 104 HIS D 361 GLN ** I 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 42 GLN ** O 3 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 52 GLN a 116 ASN a 185 HIS ** a 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.096175 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2937 r_free = 0.2937 target = 0.067750 restraints weight = 83151.889| |-----------------------------------------------------------------------------| r_work (start): 0.2930 rms_B_bonded: 2.14 r_work: 0.2916 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.2903 rms_B_bonded: 1.91 restraints_weight: 0.2500 r_work: 0.2891 rms_B_bonded: 1.94 restraints_weight: 0.1250 r_work: 0.2878 rms_B_bonded: 2.03 restraints_weight: 0.0625 r_work: 0.2864 rms_B_bonded: 2.15 restraints_weight: 0.0312 r_work: 0.2848 rms_B_bonded: 2.31 restraints_weight: 0.0156 r_work: 0.2832 rms_B_bonded: 2.51 restraints_weight: 0.0078 r_work: 0.2815 rms_B_bonded: 2.75 restraints_weight: 0.0039 r_work: 0.2795 rms_B_bonded: 3.04 restraints_weight: 0.0020 r_work: 0.2774 rms_B_bonded: 3.37 restraints_weight: 0.0010 r_work: 0.2751 rms_B_bonded: 3.76 restraints_weight: 0.0005 r_work: 0.2726 rms_B_bonded: 4.22 restraints_weight: 0.0002 r_work: 0.2699 rms_B_bonded: 4.75 restraints_weight: 0.0001 r_work (final): 0.2699 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8884 moved from start: 0.3916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.062 37528 Z= 0.197 Angle : 0.603 12.411 50797 Z= 0.298 Chirality : 0.042 0.304 5920 Planarity : 0.004 0.054 6550 Dihedral : 5.191 110.383 5248 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 8.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % 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: 0.61 (0.12), residues: 4807 helix: 1.11 (0.10), residues: 2629 sheet: 0.02 (0.22), residues: 504 loop : -0.50 (0.15), residues: 1674 =============================================================================== Job complete usr+sys time: 9177.40 seconds wall clock time: 165 minutes 36.63 seconds (9936.63 seconds total)