Starting phenix.real_space_refine on Tue Apr 16 03:24:00 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p2y_13174/04_2024/7p2y_13174_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p2y_13174/04_2024/7p2y_13174.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p2y_13174/04_2024/7p2y_13174.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p2y_13174/04_2024/7p2y_13174.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p2y_13174/04_2024/7p2y_13174_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p2y_13174/04_2024/7p2y_13174_updated.pdb" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.011 sd= 1.066 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 12 5.49 5 Mg 4 5.21 5 S 147 5.16 5 C 23664 2.51 5 N 6317 2.21 5 O 7028 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 454": "OE1" <-> "OE2" Residue "A GLU 489": "OE1" <-> "OE2" Residue "A GLU 498": "OE1" <-> "OE2" Residue "B ARG 477": "NH1" <-> "NH2" Residue "B GLU 489": "OE1" <-> "OE2" Residue "C GLU 416": "OE1" <-> "OE2" Residue "C ARG 477": "NH1" <-> "NH2" Residue "D ARG 20": "NH1" <-> "NH2" Residue "D ARG 217": "NH1" <-> "NH2" Residue "D ARG 240": "NH1" <-> "NH2" Residue "D ARG 371": "NH1" <-> "NH2" Residue "E ARG 251": "NH1" <-> "NH2" Residue "E GLU 258": "OE1" <-> "OE2" Residue "E ARG 363": "NH1" <-> "NH2" Residue "F ARG 5": "NH1" <-> "NH2" Residue "F ARG 20": "NH1" <-> "NH2" Residue "F ARG 181": "NH1" <-> "NH2" Residue "F GLU 357": "OE1" <-> "OE2" Residue "G GLU 36": "OE1" <-> "OE2" Residue "H GLU 2": "OE1" <-> "OE2" Residue "O GLU 2": "OE1" <-> "OE2" Residue "R GLU 36": "OE1" <-> "OE2" Residue "S GLU 36": "OE1" <-> "OE2" Residue "a ARG 182": "NH1" <-> "NH2" Residue "a GLU 192": "OE1" <-> "OE2" Residue "a GLU 217": "OE1" <-> "OE2" Residue "a ARG 224": "NH1" <-> "NH2" Residue "b ARG 91": "NH1" <-> "NH2" Residue "d GLU 98": "OE1" <-> "OE2" Residue "e ARG 51": "NH1" <-> "NH2" Residue "e GLU 55": "OE1" <-> "OE2" Residue "e ARG 85": "NH1" <-> "NH2" Residue "g ARG 66": "NH1" <-> "NH2" Residue "g ARG 224": "NH1" <-> "NH2" Residue "p ARG 121": "NH1" <-> "NH2" Time to flip residues: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 37172 Number of models: 1 Model: "" Number of chains: 30 Chain: "A" Number of atoms: 3846 Number of conformers: 1 Conformer: "" Number of residues, atoms: 509, 3846 Classifications: {'peptide': 509} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 490} Chain: "B" Number of atoms: 3892 Number of conformers: 1 Conformer: "" Number of residues, atoms: 514, 3892 Classifications: {'peptide': 514} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 495} Chain: "C" Number of atoms: 3850 Number of conformers: 1 Conformer: "" Number of residues, atoms: 509, 3850 Classifications: {'peptide': 509} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 491} Chain: "D" Number of atoms: 3525 Number of conformers: 1 Conformer: "" Number of residues, atoms: 463, 3525 Classifications: {'peptide': 463} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 440} Chain: "E" Number of atoms: 3525 Number of conformers: 1 Conformer: "" Number of residues, atoms: 463, 3525 Classifications: {'peptide': 463} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 22, 'TRANS': 440} Chain: "F" Number of atoms: 3533 Number of conformers: 1 Conformer: "" Number of residues, atoms: 464, 3533 Classifications: {'peptide': 464} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 441} Chain: "G" Number of atoms: 577 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 577 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 4, 'TRANS': 74} Chain: "H" Number of atoms: 577 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 577 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 4, 'TRANS': 74} Chain: "J" Number of atoms: 585 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 585 Classifications: {'peptide': 80} Link IDs: {'PTRANS': 4, 'TRANS': 75} Chain: "K" Number of atoms: 585 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 585 Classifications: {'peptide': 80} Link IDs: {'PTRANS': 4, 'TRANS': 75} Chain: "L" Number of atoms: 585 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 585 Classifications: {'peptide': 80} Link IDs: {'PTRANS': 4, 'TRANS': 75} Chain: "O" Number of atoms: 585 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 585 Classifications: {'peptide': 80} Link IDs: {'PTRANS': 4, 'TRANS': 75} Chain: "P" Number of atoms: 577 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 577 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 4, 'TRANS': 74} Chain: "Q" Number of atoms: 577 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 577 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 4, 'TRANS': 74} Chain: "R" Number of atoms: 585 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 585 Classifications: {'peptide': 80} Link IDs: {'PTRANS': 4, 'TRANS': 75} Chain: "S" Number of atoms: 585 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 585 Classifications: {'peptide': 80} Link IDs: {'PTRANS': 4, 'TRANS': 75} Chain: "a" Number of atoms: 2104 Number of conformers: 1 Conformer: "" Number of residues, atoms: 277, 2104 Classifications: {'peptide': 277} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 15, 'TRANS': 261} Unresolved non-hydrogen bonds: 87 Unresolved non-hydrogen angles: 114 Unresolved non-hydrogen dihedrals: 80 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'TYR:plan': 1, 'TRP:plan': 1, 'ASP:plan': 1, 'PHE:plan': 2, 'GLU:plan': 3, 'HIS:plan': 3} Unresolved non-hydrogen planarities: 58 Chain: "b" Number of atoms: 1162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 154, 1162 Classifications: {'peptide': 154} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 2, 'TRANS': 151} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "d" Number of atoms: 1347 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 1347 Classifications: {'peptide': 174} Link IDs: {'PTRANS': 6, 'TRANS': 167} Chain: "e" Number of atoms: 1010 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 1010 Classifications: {'peptide': 138} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 132} Chain: "g" Number of atoms: 2243 Number of conformers: 1 Conformer: "" Number of residues, atoms: 288, 2243 Classifications: {'peptide': 288} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 279} Chain: "p" Number of atoms: 1185 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 1185 Classifications: {'peptide': 155} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 152} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 5 Unusual residues: {'PO4': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 19.79, per 1000 atoms: 0.53 Number of scatterers: 37172 At special positions: 0 Unit cell: (136.85, 137.7, 239.7, 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 147 16.00 P 12 15.00 Mg 4 11.99 O 7028 8.00 N 6317 7.00 C 23664 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: 15.06 Conformation dependent library (CDL) restraints added in 7.3 seconds 9720 Ramachandran restraints generated. 4860 Oldfield, 0 Emsley, 4860 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8930 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 182 helices and 25 sheets defined 54.7% alpha, 8.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 7.65 Creating SS restraints... Processing helix chain 'A' and resid 4 through 14 Processing helix chain 'A' and resid 18 through 25 removed outlier: 3.597A pdb=" N THR A 22 " --> pdb=" O GLY A 18 " (cutoff:3.500A) Processing helix chain 'A' and resid 80 through 82 No H-bonds generated for 'chain 'A' and resid 80 through 82' Processing helix chain 'A' and resid 102 through 104 No H-bonds generated for 'chain 'A' and resid 102 through 104' Processing helix chain 'A' and resid 153 through 157 Processing helix chain 'A' and resid 176 through 188 removed outlier: 3.861A pdb=" N GLN A 187 " --> pdb=" O ALA A 183 " (cutoff:3.500A) removed outlier: 4.732A pdb=" N LYS A 188 " --> pdb=" O ILE A 184 " (cutoff:3.500A) Processing helix chain 'A' and resid 203 through 215 Processing helix chain 'A' and resid 218 through 221 removed outlier: 3.587A pdb=" N TYR A 221 " --> pdb=" O ALA A 218 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 218 through 221' Processing helix chain 'A' and resid 233 through 253 Proline residue: A 240 - end of helix removed outlier: 3.727A pdb=" N TYR A 249 " --> pdb=" O THR A 245 " (cutoff:3.500A) removed outlier: 4.986A pdb=" N PHE A 250 " --> pdb=" O MET A 246 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N ARG A 251 " --> pdb=" O GLY A 247 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ARG A 253 " --> pdb=" O TYR A 249 " (cutoff:3.500A) Processing helix chain 'A' and resid 264 through 278 removed outlier: 3.515A pdb=" N LEU A 278 " --> pdb=" O ILE A 274 " (cutoff:3.500A) Processing helix chain 'A' and resid 284 through 286 No H-bonds generated for 'chain 'A' and resid 284 through 286' Processing helix chain 'A' and resid 291 through 299 removed outlier: 3.737A pdb=" N HIS A 295 " --> pdb=" O VAL A 291 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N LEU A 298 " --> pdb=" O LEU A 294 " (cutoff:3.500A) Processing helix chain 'A' and resid 307 through 313 Processing helix chain 'A' and resid 341 through 347 Processing helix chain 'A' and resid 358 through 362 Processing helix chain 'A' and resid 379 through 382 Processing helix chain 'A' and resid 385 through 390 Processing helix chain 'A' and resid 394 through 407 removed outlier: 3.578A pdb=" N GLU A 403 " --> pdb=" O ALA A 399 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 431 removed outlier: 3.509A pdb=" N GLN A 426 " --> pdb=" O LEU A 422 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N ARG A 427 " --> pdb=" O GLU A 423 " (cutoff:3.500A) Processing helix chain 'A' and resid 442 through 453 removed outlier: 3.604A pdb=" N SER A 448 " --> pdb=" O ASP A 444 " (cutoff:3.500A) Processing helix chain 'A' and resid 465 through 479 Processing helix chain 'A' and resid 481 through 489 Processing helix chain 'A' and resid 495 through 510 Processing helix chain 'B' and resid 10 through 18 Processing helix chain 'B' and resid 22 through 27 removed outlier: 3.541A pdb=" N LYS B 27 " --> pdb=" O SER B 23 " (cutoff:3.500A) Processing helix chain 'B' and resid 137 through 139 No H-bonds generated for 'chain 'B' and resid 137 through 139' Processing helix chain 'B' and resid 152 through 157 removed outlier: 3.562A pdb=" N THR B 156 " --> pdb=" O LYS B 152 " (cutoff:3.500A) Processing helix chain 'B' and resid 176 through 187 removed outlier: 4.049A pdb=" N GLN B 187 " --> pdb=" O ALA B 183 " (cutoff:3.500A) Processing helix chain 'B' and resid 203 through 215 Processing helix chain 'B' and resid 233 through 253 Proline residue: B 240 - end of helix removed outlier: 4.342A pdb=" N PHE B 250 " --> pdb=" O MET B 246 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ARG B 251 " --> pdb=" O GLY B 247 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N ARG B 253 " --> pdb=" O TYR B 249 " (cutoff:3.500A) Processing helix chain 'B' and resid 264 through 278 Processing helix chain 'B' and resid 284 through 286 No H-bonds generated for 'chain 'B' and resid 284 through 286' Processing helix chain 'B' and resid 291 through 301 removed outlier: 3.704A pdb=" N ARG B 297 " --> pdb=" O TYR B 293 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N LEU B 298 " --> pdb=" O LEU B 294 " (cutoff:3.500A) removed outlier: 4.639A pdb=" N ARG B 301 " --> pdb=" O ARG B 297 " (cutoff:3.500A) Processing helix chain 'B' and resid 307 through 313 Processing helix chain 'B' and resid 334 through 336 No H-bonds generated for 'chain 'B' and resid 334 through 336' Processing helix chain 'B' and resid 341 through 349 removed outlier: 3.597A pdb=" N ILE B 349 " --> pdb=" O ASN B 345 " (cutoff:3.500A) Processing helix chain 'B' and resid 358 through 362 Processing helix chain 'B' and resid 379 through 382 Processing helix chain 'B' and resid 385 through 403 removed outlier: 4.776A pdb=" N GLY B 392 " --> pdb=" O LYS B 388 " (cutoff:3.500A) removed outlier: 5.557A pdb=" N GLY B 393 " --> pdb=" O LYS B 389 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N ILE B 394 " --> pdb=" O LEU B 390 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 409 removed outlier: 3.501A pdb=" N GLN B 409 " --> pdb=" O ALA B 406 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 431 Processing helix chain 'B' and resid 442 through 453 Processing helix chain 'B' and resid 462 through 479 removed outlier: 5.023A pdb=" N VAL B 466 " --> pdb=" O LYS B 463 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N GLU B 479 " --> pdb=" O PHE B 476 " (cutoff:3.500A) Processing helix chain 'B' and resid 481 through 489 Processing helix chain 'B' and resid 495 through 510 Processing helix chain 'C' and resid 8 through 19 Processing helix chain 'C' and resid 80 through 82 No H-bonds generated for 'chain 'C' and resid 80 through 82' Processing helix chain 'C' and resid 154 through 157 No H-bonds generated for 'chain 'C' and resid 154 through 157' Processing helix chain 'C' and resid 176 through 188 removed outlier: 3.829A pdb=" N GLN C 187 " --> pdb=" O ALA C 183 " (cutoff:3.500A) removed outlier: 4.862A pdb=" N LYS C 188 " --> pdb=" O ILE C 184 " (cutoff:3.500A) Processing helix chain 'C' and resid 203 through 215 Processing helix chain 'C' and resid 233 through 253 Proline residue: C 240 - end of helix removed outlier: 3.589A pdb=" N MET C 246 " --> pdb=" O SER C 242 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N PHE C 250 " --> pdb=" O MET C 246 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ARG C 251 " --> pdb=" O GLY C 247 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N ARG C 253 " --> pdb=" O TYR C 249 " (cutoff:3.500A) Processing helix chain 'C' and resid 264 through 277 Processing helix chain 'C' and resid 284 through 286 No H-bonds generated for 'chain 'C' and resid 284 through 286' Processing helix chain 'C' and resid 291 through 301 removed outlier: 3.900A pdb=" N LEU C 298 " --> pdb=" O LEU C 294 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N ARG C 301 " --> pdb=" O ARG C 297 " (cutoff:3.500A) Processing helix chain 'C' and resid 307 through 313 Processing helix chain 'C' and resid 341 through 349 removed outlier: 3.665A pdb=" N ILE C 349 " --> pdb=" O ASN C 345 " (cutoff:3.500A) Processing helix chain 'C' and resid 358 through 362 Processing helix chain 'C' and resid 379 through 382 Processing helix chain 'C' and resid 385 through 403 removed outlier: 4.718A pdb=" N GLY C 392 " --> pdb=" O LYS C 388 " (cutoff:3.500A) removed outlier: 5.780A pdb=" N GLY C 393 " --> pdb=" O LYS C 389 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N ILE C 394 " --> pdb=" O LEU C 390 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 410 removed outlier: 5.090A pdb=" N GLN C 409 " --> pdb=" O ALA C 406 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 432 Processing helix chain 'C' and resid 442 through 453 Processing helix chain 'C' and resid 462 through 479 removed outlier: 5.242A pdb=" N VAL C 466 " --> pdb=" O LYS C 463 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ASP C 467 " --> pdb=" O LYS C 464 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N GLU C 479 " --> pdb=" O PHE C 476 " (cutoff:3.500A) Processing helix chain 'C' and resid 481 through 490 Processing helix chain 'C' and resid 495 through 511 Processing helix chain 'D' and resid 80 through 82 No H-bonds generated for 'chain 'D' and resid 80 through 82' Processing helix chain 'D' and resid 130 through 135 Processing helix chain 'D' and resid 154 through 165 Processing helix chain 'D' and resid 182 through 194 Processing helix chain 'D' and resid 198 through 200 No H-bonds generated for 'chain 'D' and resid 198 through 200' Processing helix chain 'D' and resid 212 through 216 Processing helix chain 'D' and resid 219 through 230 removed outlier: 3.516A pdb=" N ALA D 226 " --> pdb=" O GLY D 222 " (cutoff:3.500A) Processing helix chain 'D' and resid 249 through 258 removed outlier: 3.692A pdb=" N ALA D 255 " --> pdb=" O TYR D 252 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N GLU D 258 " --> pdb=" O ALA D 255 " (cutoff:3.500A) Processing helix chain 'D' and resid 261 through 263 No H-bonds generated for 'chain 'D' and resid 261 through 263' Processing helix chain 'D' and resid 276 through 286 removed outlier: 4.028A pdb=" N LEU D 283 " --> pdb=" O GLU D 279 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N ARG D 286 " --> pdb=" O VAL D 282 " (cutoff:3.500A) Processing helix chain 'D' and resid 304 through 306 No H-bonds generated for 'chain 'D' and resid 304 through 306' Processing helix chain 'D' and resid 311 through 319 removed outlier: 5.118A pdb=" N ALA D 318 " --> pdb=" O ALA D 314 " (cutoff:3.500A) removed outlier: 4.801A pdb=" N HIS D 319 " --> pdb=" O THR D 315 " (cutoff:3.500A) Processing helix chain 'D' and resid 328 through 332 Processing helix chain 'D' and resid 351 through 354 No H-bonds generated for 'chain 'D' and resid 351 through 354' Processing helix chain 'D' and resid 356 through 381 removed outlier: 4.716A pdb=" N ASP D 377 " --> pdb=" O LYS D 373 " (cutoff:3.500A) removed outlier: 4.843A pdb=" N ILE D 378 " --> pdb=" O GLU D 374 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N ALA D 380 " --> pdb=" O LYS D 376 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ILE D 381 " --> pdb=" O ASP D 377 " (cutoff:3.500A) Processing helix chain 'D' and resid 384 through 386 No H-bonds generated for 'chain 'D' and resid 384 through 386' Processing helix chain 'D' and resid 389 through 404 Processing helix chain 'D' and resid 412 through 414 No H-bonds generated for 'chain 'D' and resid 412 through 414' Processing helix chain 'D' and resid 425 through 437 Processing helix chain 'D' and resid 445 through 448 Processing helix chain 'D' and resid 454 through 463 Processing helix chain 'E' and resid 80 through 82 No H-bonds generated for 'chain 'E' and resid 80 through 82' Processing helix chain 'E' and resid 130 through 135 Processing helix chain 'E' and resid 154 through 168 Processing helix chain 'E' and resid 182 through 194 Processing helix chain 'E' and resid 198 through 200 No H-bonds generated for 'chain 'E' and resid 198 through 200' Processing helix chain 'E' and resid 212 through 231 removed outlier: 5.440A pdb=" N ALA E 219 " --> pdb=" O ARG E 215 " (cutoff:3.500A) removed outlier: 4.816A pdb=" N LEU E 220 " --> pdb=" O LEU E 216 " (cutoff:3.500A) Processing helix chain 'E' and resid 250 through 262 removed outlier: 3.530A pdb=" N GLY E 256 " --> pdb=" O TYR E 252 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N VAL E 259 " --> pdb=" O ALA E 255 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N ALA E 261 " --> pdb=" O THR E 257 " (cutoff:3.500A) removed outlier: 4.724A pdb=" N LEU E 262 " --> pdb=" O GLU E 258 " (cutoff:3.500A) Processing helix chain 'E' and resid 276 through 284 Processing helix chain 'E' and resid 304 through 306 No H-bonds generated for 'chain 'E' and resid 304 through 306' Processing helix chain 'E' and resid 311 through 317 removed outlier: 3.898A pdb=" N THR E 316 " --> pdb=" O SER E 312 " (cutoff:3.500A) Processing helix chain 'E' and resid 328 through 332 Processing helix chain 'E' and resid 351 through 354 No H-bonds generated for 'chain 'E' and resid 351 through 354' Processing helix chain 'E' and resid 356 through 372 Processing helix chain 'E' and resid 374 through 382 removed outlier: 4.134A pdb=" N ASP E 377 " --> pdb=" O GLU E 374 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ILE E 378 " --> pdb=" O LEU E 375 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N LEU E 382 " --> pdb=" O ILE E 379 " (cutoff:3.500A) Processing helix chain 'E' and resid 392 through 404 Processing helix chain 'E' and resid 425 through 437 Processing helix chain 'E' and resid 445 through 448 Processing helix chain 'E' and resid 454 through 463 Processing helix chain 'F' and resid 80 through 82 No H-bonds generated for 'chain 'F' and resid 80 through 82' Processing helix chain 'F' and resid 115 through 117 No H-bonds generated for 'chain 'F' and resid 115 through 117' Processing helix chain 'F' and resid 154 through 168 Processing helix chain 'F' and resid 182 through 194 Processing helix chain 'F' and resid 196 through 200 removed outlier: 3.824A pdb=" N ASP F 199 " --> pdb=" O ASN F 196 " (cutoff:3.500A) Processing helix chain 'F' and resid 212 through 231 removed outlier: 5.129A pdb=" N ALA F 219 " --> pdb=" O ARG F 215 " (cutoff:3.500A) removed outlier: 4.708A pdb=" N LEU F 220 " --> pdb=" O LEU F 216 " (cutoff:3.500A) Processing helix chain 'F' and resid 249 through 263 Processing helix chain 'F' and resid 276 through 284 removed outlier: 3.774A pdb=" N LEU F 283 " --> pdb=" O GLU F 279 " (cutoff:3.500A) Processing helix chain 'F' and resid 304 through 306 No H-bonds generated for 'chain 'F' and resid 304 through 306' Processing helix chain 'F' and resid 311 through 318 removed outlier: 4.095A pdb=" N ALA F 318 " --> pdb=" O ALA F 314 " (cutoff:3.500A) Processing helix chain 'F' and resid 328 through 332 Processing helix chain 'F' and resid 357 through 382 removed outlier: 4.275A pdb=" N ASP F 377 " --> pdb=" O LYS F 373 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N ILE F 378 " --> pdb=" O GLU F 374 " (cutoff:3.500A) Processing helix chain 'F' and resid 384 through 386 No H-bonds generated for 'chain 'F' and resid 384 through 386' Processing helix chain 'F' and resid 389 through 404 Processing helix chain 'F' and resid 411 through 415 removed outlier: 3.635A pdb=" N VAL F 414 " --> pdb=" O VAL F 411 " (cutoff:3.500A) Processing helix chain 'F' and resid 428 through 436 Processing helix chain 'F' and resid 445 through 448 Processing helix chain 'F' and resid 454 through 463 Processing helix chain 'G' and resid 3 through 40 removed outlier: 3.852A pdb=" N GLY G 19 " --> pdb=" O LEU G 15 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N GLY G 28 " --> pdb=" O ALA G 24 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ARG G 33 " --> pdb=" O LEU G 29 " (cutoff:3.500A) Processing helix chain 'G' and resid 42 through 59 removed outlier: 3.513A pdb=" N ALA G 45 " --> pdb=" O PRO G 42 " (cutoff:3.500A) Proline residue: G 46 - end of helix Processing helix chain 'G' and resid 61 through 75 Processing helix chain 'H' and resid 3 through 40 removed outlier: 3.680A pdb=" N GLY H 19 " --> pdb=" O LEU H 15 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ARG H 33 " --> pdb=" O LEU H 29 " (cutoff:3.500A) Processing helix chain 'H' and resid 42 through 75 removed outlier: 3.752A pdb=" N ALA H 45 " --> pdb=" O PRO H 42 " (cutoff:3.500A) Proline residue: H 46 - end of helix removed outlier: 3.924A pdb=" N ASP H 60 " --> pdb=" O GLY H 57 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N ALA H 61 " --> pdb=" O LEU H 58 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N VAL H 62 " --> pdb=" O LEU H 59 " (cutoff:3.500A) Proline residue: H 63 - end of helix Processing helix chain 'J' and resid 2 through 40 removed outlier: 3.597A pdb=" N GLY J 19 " --> pdb=" O LEU J 15 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLY J 28 " --> pdb=" O ALA J 24 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N ARG J 33 " --> pdb=" O LEU J 29 " (cutoff:3.500A) Processing helix chain 'J' and resid 42 through 59 Proline residue: J 46 - end of helix Processing helix chain 'J' and resid 61 through 75 Processing helix chain 'K' and resid 2 through 40 removed outlier: 3.770A pdb=" N ARG K 33 " --> pdb=" O LEU K 29 " (cutoff:3.500A) Processing helix chain 'K' and resid 42 through 59 removed outlier: 3.816A pdb=" N ALA K 45 " --> pdb=" O PRO K 42 " (cutoff:3.500A) Proline residue: K 46 - end of helix Processing helix chain 'K' and resid 61 through 75 Processing helix chain 'L' and resid 2 through 40 removed outlier: 3.548A pdb=" N GLY L 19 " --> pdb=" O LEU L 15 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N ARG L 33 " --> pdb=" O LEU L 29 " (cutoff:3.500A) Processing helix chain 'L' and resid 42 through 59 Proline residue: L 46 - end of helix removed outlier: 3.658A pdb=" N MET L 52 " --> pdb=" O GLN L 49 " (cutoff:3.500A) Processing helix chain 'L' and resid 61 through 75 Processing helix chain 'O' and resid 2 through 40 removed outlier: 3.691A pdb=" N ILE O 16 " --> pdb=" O SER O 12 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ILE O 25 " --> pdb=" O LEU O 21 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ARG O 33 " --> pdb=" O LEU O 29 " (cutoff:3.500A) Processing helix chain 'O' and resid 42 through 59 removed outlier: 4.012A pdb=" N ALA O 45 " --> pdb=" O PRO O 42 " (cutoff:3.500A) Proline residue: O 46 - end of helix removed outlier: 3.508A pdb=" N MET O 52 " --> pdb=" O GLN O 49 " (cutoff:3.500A) Processing helix chain 'O' and resid 61 through 75 Processing helix chain 'P' and resid 3 through 40 removed outlier: 3.746A pdb=" N ARG P 33 " --> pdb=" O LEU P 29 " (cutoff:3.500A) Processing helix chain 'P' and resid 42 through 59 Proline residue: P 46 - end of helix Processing helix chain 'P' and resid 61 through 75 Processing helix chain 'Q' and resid 3 through 40 removed outlier: 3.590A pdb=" N GLY Q 19 " --> pdb=" O LEU Q 15 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ARG Q 33 " --> pdb=" O LEU Q 29 " (cutoff:3.500A) Processing helix chain 'Q' and resid 42 through 59 Proline residue: Q 46 - end of helix Processing helix chain 'Q' and resid 61 through 74 Processing helix chain 'R' and resid 2 through 40 removed outlier: 3.614A pdb=" N GLY R 19 " --> pdb=" O LEU R 15 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ARG R 33 " --> pdb=" O LEU R 29 " (cutoff:3.500A) Processing helix chain 'R' and resid 42 through 59 removed outlier: 3.773A pdb=" N ALA R 45 " --> pdb=" O PRO R 42 " (cutoff:3.500A) Proline residue: R 46 - end of helix Processing helix chain 'R' and resid 61 through 75 Processing helix chain 'S' and resid 2 through 40 removed outlier: 3.702A pdb=" N GLY S 19 " --> pdb=" O LEU S 15 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ILE S 25 " --> pdb=" O LEU S 21 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N GLY S 28 " --> pdb=" O ALA S 24 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ARG S 33 " --> pdb=" O LEU S 29 " (cutoff:3.500A) Processing helix chain 'S' and resid 42 through 59 removed outlier: 3.738A pdb=" N ALA S 45 " --> pdb=" O PRO S 42 " (cutoff:3.500A) Proline residue: S 46 - end of helix Processing helix chain 'S' and resid 61 through 75 removed outlier: 3.543A pdb=" N GLY S 68 " --> pdb=" O MET S 64 " (cutoff:3.500A) Processing helix chain 'a' and resid 16 through 25 Processing helix chain 'a' and resid 29 through 32 Processing helix chain 'a' and resid 53 through 72 removed outlier: 4.325A pdb=" N ILE a 62 " --> pdb=" O GLY a 58 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N PHE a 63 " --> pdb=" O LEU a 59 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N VAL a 70 " --> pdb=" O LEU a 66 " (cutoff:3.500A) Processing helix chain 'a' and resid 81 through 100 Processing helix chain 'a' and resid 108 through 127 removed outlier: 3.530A pdb=" N MET a 125 " --> pdb=" O LEU a 121 " (cutoff:3.500A) removed outlier: 4.643A pdb=" N ASP a 126 " --> pdb=" O MET a 122 " (cutoff:3.500A) removed outlier: 4.977A pdb=" N LEU a 127 " --> pdb=" O ASN a 123 " (cutoff:3.500A) Processing helix chain 'a' and resid 132 through 143 removed outlier: 4.378A pdb=" N PHE a 139 " --> pdb=" O GLN a 135 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N VAL a 140 " --> pdb=" O VAL a 136 " (cutoff:3.500A) Processing helix chain 'a' and resid 148 through 153 removed outlier: 3.688A pdb=" N TYR a 153 " --> pdb=" O PRO a 149 " (cutoff:3.500A) Processing helix chain 'a' and resid 162 through 180 removed outlier: 3.628A pdb=" N VAL a 172 " --> pdb=" O MET a 168 " (cutoff:3.500A) Processing helix chain 'a' and resid 186 through 190 Processing helix chain 'a' and resid 202 through 208 Processing helix chain 'a' and resid 211 through 247 removed outlier: 4.593A pdb=" N PHE a 221 " --> pdb=" O GLU a 217 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N ALA a 223 " --> pdb=" O VAL a 219 " (cutoff:3.500A) removed outlier: 5.969A pdb=" N ARG a 224 " --> pdb=" O THR a 220 " (cutoff:3.500A) Proline residue: a 225 - end of helix removed outlier: 3.833A pdb=" N ALA a 247 " --> pdb=" O PHE a 243 " (cutoff:3.500A) Processing helix chain 'a' and resid 256 through 287 Proline residue: a 260 - end of helix removed outlier: 3.963A pdb=" N THR a 270 " --> pdb=" O ILE a 266 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N LEU a 271 " --> pdb=" O LEU a 267 " (cutoff:3.500A) Processing helix chain 'b' and resid 7 through 22 Processing helix chain 'b' and resid 25 through 138 removed outlier: 3.568A pdb=" N ALA b 32 " --> pdb=" O PRO b 28 " (cutoff:3.500A) removed outlier: 4.853A pdb=" N ILE b 33 " --> pdb=" O LEU b 29 " (cutoff:3.500A) removed outlier: 4.683A pdb=" N SER b 34 " --> pdb=" O ILE b 30 " (cutoff:3.500A) removed outlier: 4.680A pdb=" N GLU b 35 " --> pdb=" O ASN b 31 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N ARG b 36 " --> pdb=" O ALA b 32 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N ALA b 46 " --> pdb=" O ASP b 42 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N LYS b 49 " --> pdb=" O ASN b 45 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N ALA b 50 " --> pdb=" O ALA b 46 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N GLU b 64 " --> pdb=" O GLN b 60 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N LEU b 65 " --> pdb=" O VAL b 61 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N ALA b 83 " --> pdb=" O ALA b 79 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ALA b 84 " --> pdb=" O ASN b 80 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N GLN b 85 " --> pdb=" O ARG b 81 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N SER b 115 " --> pdb=" O GLN b 111 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N GLU b 119 " --> pdb=" O SER b 115 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N GLU b 133 " --> pdb=" O VAL b 129 " (cutoff:3.500A) removed outlier: 4.797A pdb=" N LYS b 134 " --> pdb=" O THR b 130 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N ILE b 135 " --> pdb=" O GLY b 131 " (cutoff:3.500A) removed outlier: 4.782A pdb=" N LEU b 136 " --> pdb=" O ALA b 132 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N ASN b 137 " --> pdb=" O GLU b 133 " (cutoff:3.500A) Processing helix chain 'd' and resid 4 through 22 removed outlier: 3.712A pdb=" N ARG d 9 " --> pdb=" O LEU d 5 " (cutoff:3.500A) Proline residue: d 10 - end of helix Processing helix chain 'd' and resid 25 through 40 Processing helix chain 'd' and resid 42 through 48 Processing helix chain 'd' and resid 55 through 66 Processing helix chain 'd' and resid 72 through 83 Processing helix chain 'd' and resid 87 through 104 Proline residue: d 91 - end of helix Processing helix chain 'd' and resid 120 through 133 removed outlier: 3.975A pdb=" N LYS d 132 " --> pdb=" O SER d 128 " (cutoff:3.500A) removed outlier: 4.606A pdb=" N ARG d 133 " --> pdb=" O ALA d 129 " (cutoff:3.500A) Processing helix chain 'd' and resid 165 through 175 removed outlier: 3.630A pdb=" N ARG d 173 " --> pdb=" O GLU d 170 " (cutoff:3.500A) Processing helix chain 'e' and resid 91 through 126 removed outlier: 4.661A pdb=" N GLU e 96 " --> pdb=" O ALA e 93 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N LYS e 109 " --> pdb=" O ALA e 106 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ASP e 113 " --> pdb=" O SER e 110 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N SER e 114 " --> pdb=" O ASP e 111 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ALA e 115 " --> pdb=" O LEU e 112 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N ALA e 116 " --> pdb=" O ASP e 113 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N ALA e 117 " --> pdb=" O SER e 114 " (cutoff:3.500A) removed outlier: 5.231A pdb=" N LEU e 118 " --> pdb=" O ALA e 115 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N ALA e 119 " --> pdb=" O ALA e 116 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ALA e 120 " --> pdb=" O ALA e 117 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N LEU e 121 " --> pdb=" O LEU e 118 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N THR e 124 " --> pdb=" O LEU e 121 " (cutoff:3.500A) Processing helix chain 'e' and resid 129 through 134 removed outlier: 4.412A pdb=" N ILE e 134 " --> pdb=" O THR e 130 " (cutoff:3.500A) Processing helix chain 'g' and resid 4 through 59 removed outlier: 3.843A pdb=" N ALA g 40 " --> pdb=" O GLN g 36 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N GLN g 41 " --> pdb=" O GLU g 37 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N GLY g 42 " --> pdb=" O ARG g 38 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N ARG g 43 " --> pdb=" O MET g 39 " (cutoff:3.500A) Proline residue: g 44 - end of helix Processing helix chain 'g' and resid 91 through 108 removed outlier: 3.692A pdb=" N GLU g 108 " --> pdb=" O LYS g 104 " (cutoff:3.500A) Processing helix chain 'g' and resid 120 through 128 Processing helix chain 'g' and resid 146 through 161 removed outlier: 4.582A pdb=" N GLY g 151 " --> pdb=" O GLU g 147 " (cutoff:3.500A) removed outlier: 5.529A pdb=" N SER g 152 " --> pdb=" O GLN g 148 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N VAL g 153 " --> pdb=" O LEU g 149 " (cutoff:3.500A) Processing helix chain 'g' and resid 214 through 287 removed outlier: 3.763A pdb=" N GLU g 236 " --> pdb=" O GLN g 232 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ASN g 237 " --> pdb=" O GLY g 233 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N LEU g 265 " --> pdb=" O LYS g 261 " (cutoff:3.500A) Processing helix chain 'p' and resid 3 through 138 removed outlier: 3.718A pdb=" N GLY p 9 " --> pdb=" O LEU p 5 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LYS p 23 " --> pdb=" O ALA p 19 " (cutoff:3.500A) Proline residue: p 27 - end of helix removed outlier: 3.849A pdb=" N GLN p 58 " --> pdb=" O LEU p 54 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N ALA p 59 " --> pdb=" O ALA p 55 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N ALA p 67 " --> pdb=" O GLN p 63 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N ASN p 80 " --> pdb=" O ILE p 76 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ARG p 81 " --> pdb=" O GLU p 77 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N GLU p 99 " --> pdb=" O ALA p 95 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N ARG p 121 " --> pdb=" O ARG p 117 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N GLN p 122 " --> pdb=" O GLU p 118 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N GLN p 123 " --> pdb=" O GLU p 119 " (cutoff:3.500A) Processing helix chain 'p' and resid 143 through 155 removed outlier: 4.050A pdb=" N ALA p 154 " --> pdb=" O SER p 150 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 89 through 91 removed outlier: 4.395A pdb=" N PHE A 61 " --> pdb=" O LEU A 77 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N MET A 34 " --> pdb=" O ARG A 41 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 97 through 100 removed outlier: 3.615A pdb=" N VAL A 100 " --> pdb=" O LEU A 126 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N LEU A 126 " --> pdb=" O VAL A 100 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 330 through 332 removed outlier: 6.458A pdb=" N ILE A 168 " --> pdb=" O ILE A 331 " (cutoff:3.500A) removed outlier: 7.975A pdb=" N ILE A 169 " --> pdb=" O GLY A 352 " (cutoff:3.500A) removed outlier: 5.966A pdb=" N ILE A 354 " --> pdb=" O ILE A 169 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 257 through 262 removed outlier: 6.478A pdb=" N LYS A 193 " --> pdb=" O LEU A 258 " (cutoff:3.500A) removed outlier: 8.296A pdb=" N ILE A 260 " --> pdb=" O LYS A 193 " (cutoff:3.500A) removed outlier: 7.043A pdb=" N VAL A 195 " --> pdb=" O ILE A 260 " (cutoff:3.500A) removed outlier: 7.907A pdb=" N ASP A 262 " --> pdb=" O VAL A 195 " (cutoff:3.500A) removed outlier: 7.192A pdb=" N VAL A 197 " --> pdb=" O ASP A 262 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 89 through 91 removed outlier: 5.959A pdb=" N HIS B 43 " --> pdb=" O ILE B 32 " (cutoff:3.500A) removed outlier: 5.749A pdb=" N ILE B 32 " --> pdb=" O HIS B 43 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 97 through 100 removed outlier: 4.043A pdb=" N LEU B 126 " --> pdb=" O VAL B 100 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 353 through 356 removed outlier: 6.944A pdb=" N LEU B 167 " --> pdb=" O ILE B 354 " (cutoff:3.500A) removed outlier: 7.748A pdb=" N LEU B 356 " --> pdb=" O LEU B 167 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N ILE B 169 " --> pdb=" O LEU B 356 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 257 through 261 removed outlier: 6.334A pdb=" N LYS B 193 " --> pdb=" O LEU B 258 " (cutoff:3.500A) removed outlier: 8.112A pdb=" N ILE B 260 " --> pdb=" O LYS B 193 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N VAL B 195 " --> pdb=" O ILE B 260 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'C' and resid 29 through 31 removed outlier: 6.570A pdb=" N GLY C 73 " --> pdb=" O LEU C 65 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N MET C 34 " --> pdb=" O ARG C 41 " (cutoff:3.500A) removed outlier: 6.042A pdb=" N HIS C 43 " --> pdb=" O ILE C 32 " (cutoff:3.500A) removed outlier: 5.863A pdb=" N ILE C 32 " --> pdb=" O HIS C 43 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'C' and resid 97 through 100 removed outlier: 3.999A pdb=" N LEU C 126 " --> pdb=" O VAL C 100 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'C' and resid 353 through 356 removed outlier: 7.100A pdb=" N LEU C 167 " --> pdb=" O ILE C 354 " (cutoff:3.500A) removed outlier: 7.877A pdb=" N LEU C 356 " --> pdb=" O LEU C 167 " (cutoff:3.500A) removed outlier: 7.014A pdb=" N ILE C 169 " --> pdb=" O LEU C 356 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'C' and resid 257 through 262 removed outlier: 6.481A pdb=" N LYS C 193 " --> pdb=" O LEU C 258 " (cutoff:3.500A) removed outlier: 8.137A pdb=" N ILE C 260 " --> pdb=" O LYS C 193 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N VAL C 195 " --> pdb=" O ILE C 260 " (cutoff:3.500A) removed outlier: 7.649A pdb=" N ASP C 262 " --> pdb=" O VAL C 195 " (cutoff:3.500A) removed outlier: 7.032A pdb=" N VAL C 197 " --> pdb=" O ASP C 262 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'D' and resid 3 through 5 removed outlier: 6.807A pdb=" N ARG D 51 " --> pdb=" O GLN D 42 " (cutoff:3.500A) removed outlier: 5.122A pdb=" N GLN D 44 " --> pdb=" O VAL D 49 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N VAL D 49 " --> pdb=" O GLN D 44 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ILE D 10 " --> pdb=" O VAL D 13 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ASP D 15 " --> pdb=" O GLN D 8 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N GLN D 8 " --> pdb=" O ASP D 15 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N GLU D 17 " --> pdb=" O ILE D 6 " (cutoff:3.500A) removed outlier: 6.032A pdb=" N ILE D 6 " --> pdb=" O GLU D 17 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'D' and resid 75 through 77 Processing sheet with id= O, first strand: chain 'D' and resid 322 through 325 removed outlier: 7.659A pdb=" N VAL D 144 " --> pdb=" O ILE D 295 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N SER D 297 " --> pdb=" O VAL D 144 " (cutoff:3.500A) removed outlier: 8.001A pdb=" N LEU D 146 " --> pdb=" O SER D 297 " (cutoff:3.500A) removed outlier: 7.220A pdb=" N GLN D 299 " --> pdb=" O LEU D 146 " (cutoff:3.500A) removed outlier: 8.068A pdb=" N GLY D 148 " --> pdb=" O GLN D 299 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N VAL D 301 " --> pdb=" O GLY D 148 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N VAL D 242 " --> pdb=" O THR D 296 " (cutoff:3.500A) removed outlier: 8.160A pdb=" N ILE D 298 " --> pdb=" O VAL D 242 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N LEU D 244 " --> pdb=" O ILE D 298 " (cutoff:3.500A) removed outlier: 8.057A pdb=" N ALA D 300 " --> pdb=" O LEU D 244 " (cutoff:3.500A) removed outlier: 6.994A pdb=" N VAL D 246 " --> pdb=" O ALA D 300 " (cutoff:3.500A) removed outlier: 8.636A pdb=" N TYR D 302 " --> pdb=" O VAL D 246 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N LEU D 172 " --> pdb=" O LEU D 243 " (cutoff:3.500A) removed outlier: 8.554A pdb=" N PHE D 245 " --> pdb=" O LEU D 172 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N VAL D 174 " --> pdb=" O PHE D 245 " (cutoff:3.500A) removed outlier: 8.131A pdb=" N ASP D 247 " --> pdb=" O VAL D 174 " (cutoff:3.500A) removed outlier: 7.595A pdb=" N ALA D 176 " --> pdb=" O ASP D 247 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'E' and resid 5 through 10 removed outlier: 6.760A pdb=" N ASP E 15 " --> pdb=" O ILE E 7 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N ILE E 9 " --> pdb=" O VAL E 13 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N VAL E 13 " --> pdb=" O ILE E 9 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ARG E 51 " --> pdb=" O GLN E 43 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N ILE E 53 " --> pdb=" O VAL E 41 " (cutoff:3.500A) removed outlier: 5.990A pdb=" N VAL E 41 " --> pdb=" O ILE E 53 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'E' and resid 75 through 77 Processing sheet with id= R, first strand: chain 'E' and resid 322 through 325 removed outlier: 3.500A pdb=" N ALA E 322 " --> pdb=" O LYS E 143 " (cutoff:3.500A) removed outlier: 8.665A pdb=" N VAL E 144 " --> pdb=" O ILE E 295 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N SER E 297 " --> pdb=" O VAL E 144 " (cutoff:3.500A) removed outlier: 8.207A pdb=" N LEU E 146 " --> pdb=" O SER E 297 " (cutoff:3.500A) removed outlier: 7.361A pdb=" N GLN E 299 " --> pdb=" O LEU E 146 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'F' and resid 5 through 10 removed outlier: 6.612A pdb=" N ASP F 15 " --> pdb=" O ILE F 7 " (cutoff:3.500A) removed outlier: 4.586A pdb=" N ILE F 9 " --> pdb=" O VAL F 13 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N VAL F 13 " --> pdb=" O ILE F 9 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N ILE F 53 " --> pdb=" O VAL F 41 " (cutoff:3.500A) removed outlier: 5.656A pdb=" N VAL F 41 " --> pdb=" O ILE F 53 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N MET F 55 " --> pdb=" O LEU F 39 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N LEU F 39 " --> pdb=" O MET F 55 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'F' and resid 75 through 78 removed outlier: 4.473A pdb=" N GLU F 104 " --> pdb=" O VAL F 78 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'F' and resid 322 through 325 removed outlier: 3.778A pdb=" N ALA F 322 " --> pdb=" O LYS F 143 " (cutoff:3.500A) removed outlier: 8.305A pdb=" N VAL F 144 " --> pdb=" O ILE F 295 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N SER F 297 " --> pdb=" O VAL F 144 " (cutoff:3.500A) removed outlier: 7.455A pdb=" N LEU F 146 " --> pdb=" O SER F 297 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N GLN F 299 " --> pdb=" O LEU F 146 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ASP F 247 " --> pdb=" O ALA F 176 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N VAL F 178 " --> pdb=" O ASP F 247 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'd' and resid 137 through 144 removed outlier: 3.633A pdb=" N VAL d 108 " --> pdb=" O THR d 137 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N THR d 139 " --> pdb=" O VAL d 108 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N VAL d 110 " --> pdb=" O THR d 139 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'e' and resid 41 through 45 removed outlier: 3.532A pdb=" N LEU e 69 " --> pdb=" O THR e 43 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N GLY e 67 " --> pdb=" O LEU e 45 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N GLN e 5 " --> pdb=" O VAL e 76 " (cutoff:3.500A) removed outlier: 7.750A pdb=" N VAL e 78 " --> pdb=" O GLN e 5 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N ASP e 7 " --> pdb=" O VAL e 78 " (cutoff:3.500A) removed outlier: 7.452A pdb=" N ALA e 80 " --> pdb=" O ASP e 7 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N VAL e 9 " --> pdb=" O ALA e 80 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N SER e 10 " --> pdb=" O SER e 14 " (cutoff:3.500A) removed outlier: 5.403A pdb=" N SER e 14 " --> pdb=" O SER e 10 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'e' and resid 31 through 34 removed outlier: 3.630A pdb=" N MET e 22 " --> pdb=" O LEU e 53 " (cutoff:3.500A) removed outlier: 5.389A pdb=" N LYS e 26 " --> pdb=" O PRO e 49 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'g' and resid 181 through 187 removed outlier: 3.723A pdb=" N ARG g 167 " --> pdb=" O ARG g 75 " (cutoff:3.500A) removed outlier: 6.066A pdb=" N ASN g 173 " --> pdb=" O VAL g 81 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N GLU g 112 " --> pdb=" O VAL g 76 " (cutoff:3.500A) removed outlier: 8.313A pdb=" N TYR g 78 " --> pdb=" O GLU g 112 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N GLN g 114 " --> pdb=" O TYR g 78 " (cutoff:3.500A) removed outlier: 7.788A pdb=" N ILE g 80 " --> pdb=" O GLN g 114 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N ALA g 116 " --> pdb=" O ILE g 80 " (cutoff:3.500A) removed outlier: 7.518A pdb=" N LEU g 117 " --> pdb=" O LEU g 134 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N ALA g 136 " --> pdb=" O LEU g 117 " (cutoff:3.500A) 1970 hydrogen bonds defined for protein. 5247 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: 14.58 Time building geometry restraints manager: 16.05 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 12421 1.34 - 1.46: 7221 1.46 - 1.58: 17817 1.58 - 1.70: 18 1.70 - 1.82: 277 Bond restraints: 37754 Sorted by residual: bond pdb=" C1' ADP D 502 " pdb=" N9 ADP D 502 " ideal model delta sigma weight residual 1.485 1.339 0.146 2.00e-02 2.50e+03 5.36e+01 bond pdb=" O3A ATP C 602 " pdb=" PB ATP C 602 " ideal model delta sigma weight residual 1.592 1.663 -0.071 1.10e-02 8.26e+03 4.19e+01 bond pdb=" O3A ATP A 601 " pdb=" PB ATP A 601 " ideal model delta sigma weight residual 1.592 1.663 -0.071 1.10e-02 8.26e+03 4.14e+01 bond pdb=" O3A ATP B 601 " pdb=" PB ATP B 601 " ideal model delta sigma weight residual 1.592 1.662 -0.070 1.10e-02 8.26e+03 4.08e+01 bond pdb=" C5 ATP B 601 " pdb=" N7 ATP B 601 " ideal model delta sigma weight residual 1.387 1.335 0.052 1.00e-02 1.00e+04 2.70e+01 ... (remaining 37749 not shown) Histogram of bond angle deviations from ideal: 97.02 - 105.30: 794 105.30 - 113.59: 21473 113.59 - 121.88: 21521 121.88 - 130.17: 7304 130.17 - 138.45: 93 Bond angle restraints: 51185 Sorted by residual: angle pdb=" C5 ATP A 601 " pdb=" C4 ATP A 601 " pdb=" N3 ATP A 601 " ideal model delta sigma weight residual 126.80 119.27 7.53 1.00e+00 1.00e+00 5.67e+01 angle pdb=" C5 ATP B 601 " pdb=" C4 ATP B 601 " pdb=" N3 ATP B 601 " ideal model delta sigma weight residual 126.80 119.29 7.51 1.00e+00 1.00e+00 5.64e+01 angle pdb=" C5 ATP C 602 " pdb=" C4 ATP C 602 " pdb=" N3 ATP C 602 " ideal model delta sigma weight residual 126.80 119.33 7.47 1.00e+00 1.00e+00 5.58e+01 angle pdb=" PB ATP B 601 " pdb=" O3B ATP B 601 " pdb=" PG ATP B 601 " ideal model delta sigma weight residual 139.87 132.72 7.15 1.00e+00 1.00e+00 5.12e+01 angle pdb=" PB ATP C 602 " pdb=" O3B ATP C 602 " pdb=" PG ATP C 602 " ideal model delta sigma weight residual 139.87 132.79 7.08 1.00e+00 1.00e+00 5.01e+01 ... (remaining 51180 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.81: 22447 31.81 - 63.62: 360 63.62 - 95.43: 38 95.43 - 127.23: 0 127.23 - 159.04: 1 Dihedral angle restraints: 22846 sinusoidal: 8902 harmonic: 13944 Sorted by residual: dihedral pdb=" O1B ADP D 502 " pdb=" O3A ADP D 502 " pdb=" PB ADP D 502 " pdb=" PA ADP D 502 " ideal model delta sinusoidal sigma weight residual 300.00 140.95 159.04 1 2.00e+01 2.50e-03 4.64e+01 dihedral pdb=" CA GLY E 206 " pdb=" C GLY E 206 " pdb=" N GLN E 207 " pdb=" CA GLN E 207 " ideal model delta harmonic sigma weight residual -180.00 -157.33 -22.67 0 5.00e+00 4.00e-02 2.06e+01 dihedral pdb=" CA ASP F 194 " pdb=" C ASP F 194 " pdb=" N SER F 195 " pdb=" CA SER F 195 " ideal model delta harmonic sigma weight residual 180.00 157.54 22.46 0 5.00e+00 4.00e-02 2.02e+01 ... (remaining 22843 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 4842 0.053 - 0.106: 986 0.106 - 0.159: 164 0.159 - 0.212: 3 0.212 - 0.266: 2 Chirality restraints: 5997 Sorted by residual: chirality pdb=" C1' ADP D 502 " pdb=" C2' ADP D 502 " pdb=" N9 ADP D 502 " pdb=" O4' ADP D 502 " both_signs ideal model delta sigma weight residual False 2.48 2.22 0.27 2.00e-01 2.50e+01 1.76e+00 chirality pdb=" C2' ADP D 502 " pdb=" C1' ADP D 502 " pdb=" C3' ADP D 502 " pdb=" O2' ADP D 502 " both_signs ideal model delta sigma weight residual False -2.51 -2.75 0.24 2.00e-01 2.50e+01 1.47e+00 chirality pdb=" CA MET E 159 " pdb=" N MET E 159 " pdb=" C MET E 159 " pdb=" CB MET E 159 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 9.13e-01 ... (remaining 5994 not shown) Planarity restraints: 6637 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA MET p 22 " 0.014 2.00e-02 2.50e+03 2.73e-02 7.43e+00 pdb=" C MET p 22 " -0.047 2.00e-02 2.50e+03 pdb=" O MET p 22 " 0.018 2.00e-02 2.50e+03 pdb=" N LYS p 23 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA b 19 " 0.009 2.00e-02 2.50e+03 1.89e-02 3.58e+00 pdb=" C ALA b 19 " -0.033 2.00e-02 2.50e+03 pdb=" O ALA b 19 " 0.012 2.00e-02 2.50e+03 pdb=" N PHE b 20 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR a 23 " 0.013 2.00e-02 2.50e+03 1.32e-02 3.51e+00 pdb=" CG TYR a 23 " -0.033 2.00e-02 2.50e+03 pdb=" CD1 TYR a 23 " 0.010 2.00e-02 2.50e+03 pdb=" CD2 TYR a 23 " 0.007 2.00e-02 2.50e+03 pdb=" CE1 TYR a 23 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TYR a 23 " 0.001 2.00e-02 2.50e+03 pdb=" CZ TYR a 23 " 0.006 2.00e-02 2.50e+03 pdb=" OH TYR a 23 " -0.002 2.00e-02 2.50e+03 ... (remaining 6634 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 467 2.65 - 3.21: 36792 3.21 - 3.78: 55262 3.78 - 4.34: 76415 4.34 - 4.90: 126233 Nonbonded interactions: 295169 Sorted by model distance: nonbonded pdb=" OG1 THR A 177 " pdb="MG MG A 602 " model vdw 2.088 2.170 nonbonded pdb=" OG1 THR B 177 " pdb="MG MG B 602 " model vdw 2.095 2.170 nonbonded pdb=" OG1 THR C 177 " pdb="MG MG C 601 " model vdw 2.096 2.170 nonbonded pdb=" O2B ATP A 601 " pdb="MG MG A 602 " model vdw 2.096 2.170 nonbonded pdb="MG MG D 501 " pdb=" O1B ADP D 502 " model vdw 2.126 2.170 ... (remaining 295164 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and resid 6 through 511) selection = (chain 'B' and resid 6 through 511) selection = (chain 'C' and resid 6 through 511) } ncs_group { reference = (chain 'D' and resid 2 through 464) selection = (chain 'E' and resid 2 through 464) selection = (chain 'F' and resid 2 through 464) } ncs_group { reference = chain 'G' selection = chain 'H' selection = (chain 'J' and resid 2 through 80) selection = (chain 'K' and resid 2 through 80) selection = (chain 'L' and resid 2 through 80) selection = (chain 'O' and resid 2 through 80) selection = chain 'P' selection = chain 'Q' selection = (chain 'R' and resid 2 through 80) selection = (chain 'S' and resid 2 through 80) } ncs_group { reference = chain 'b' selection = (chain 'p' and ((resid 3 through 7 and (name N or name CA or name C or name O or \ name CB )) or resid 8 through 155 or (resid 156 and (name N or name CA or name \ C or name O or name CB or name CG or name CD1 or name CD2)))) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.75 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: 5.860 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 21.790 Check model and map are aligned: 0.600 Set scattering table: 0.340 Process input model: 99.980 Find NCS groups from input model: 2.700 Set up NCS constraints: 0.240 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:3.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 134.690 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8477 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 : 0.004 0.146 37754 Z= 0.295 Angle : 0.698 17.078 51185 Z= 0.415 Chirality : 0.043 0.266 5997 Planarity : 0.004 0.044 6637 Dihedral : 12.081 159.042 13916 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 10.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 0.08 % Allowed : 0.23 % Favored : 99.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.54 % 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: 0.12 (0.12), residues: 4860 helix: 1.32 (0.10), residues: 2621 sheet: -0.98 (0.20), residues: 578 loop : -1.52 (0.15), residues: 1661 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP a 261 HIS 0.005 0.001 HIS a 17 PHE 0.031 0.002 PHE a 101 TYR 0.033 0.001 TYR a 23 ARG 0.013 0.001 ARG b 36 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9720 Ramachandran restraints generated. 4860 Oldfield, 0 Emsley, 4860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9720 Ramachandran restraints generated. 4860 Oldfield, 0 Emsley, 4860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 473 residues out of total 3858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 470 time to evaluate : 4.202 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: C 110 ASP cc_start: 0.8388 (t70) cc_final: 0.8005 (t0) REVERT: C 337 ASP cc_start: 0.8860 (t70) cc_final: 0.8655 (t0) REVERT: F 210 GLU cc_start: 0.8584 (OUTLIER) cc_final: 0.8285 (mt-10) REVERT: G 64 MET cc_start: 0.9439 (mmp) cc_final: 0.9201 (mmp) REVERT: H 36 GLU cc_start: 0.8899 (tt0) cc_final: 0.8604 (tm-30) REVERT: H 52 MET cc_start: 0.9179 (tmm) cc_final: 0.8918 (tmm) REVERT: H 60 ASP cc_start: 0.8807 (m-30) cc_final: 0.8518 (m-30) REVERT: H 64 MET cc_start: 0.9099 (mmp) cc_final: 0.8658 (mmm) REVERT: J 36 GLU cc_start: 0.8337 (mm-30) cc_final: 0.7633 (mm-30) REVERT: J 52 MET cc_start: 0.9418 (tmm) cc_final: 0.9203 (tmm) REVERT: K 52 MET cc_start: 0.9080 (tmm) cc_final: 0.8576 (tmm) REVERT: O 36 GLU cc_start: 0.8905 (tm-30) cc_final: 0.8373 (tm-30) REVERT: O 52 MET cc_start: 0.9049 (tmm) cc_final: 0.8753 (tmm) REVERT: Q 52 MET cc_start: 0.9280 (tmm) cc_final: 0.8940 (tmm) REVERT: R 49 GLN cc_start: 0.9290 (tt0) cc_final: 0.8948 (tt0) REVERT: R 52 MET cc_start: 0.9153 (tmm) cc_final: 0.8856 (tmm) REVERT: S 49 GLN cc_start: 0.9101 (tt0) cc_final: 0.8810 (mt0) REVERT: a 100 THR cc_start: 0.9070 (p) cc_final: 0.8647 (p) REVERT: a 123 ASN cc_start: 0.8797 (t0) cc_final: 0.8171 (t0) REVERT: a 126 ASP cc_start: 0.8398 (m-30) cc_final: 0.7726 (m-30) REVERT: a 221 PHE cc_start: 0.8208 (p90) cc_final: 0.7941 (p90) REVERT: a 236 MET cc_start: 0.8535 (mmp) cc_final: 0.8084 (mmp) REVERT: a 240 GLU cc_start: 0.8886 (pt0) cc_final: 0.8580 (pt0) REVERT: b 16 PHE cc_start: 0.8218 (m-10) cc_final: 0.7548 (m-10) REVERT: b 17 PHE cc_start: 0.8988 (t80) cc_final: 0.8618 (t80) REVERT: b 45 ASN cc_start: 0.7998 (OUTLIER) cc_final: 0.6890 (p0) REVERT: b 54 LEU cc_start: 0.9173 (mm) cc_final: 0.8873 (tp) REVERT: d 69 ASP cc_start: 0.8978 (m-30) cc_final: 0.7780 (t0) REVERT: d 83 ASP cc_start: 0.8983 (m-30) cc_final: 0.8757 (m-30) REVERT: e 5 GLN cc_start: 0.8130 (tp-100) cc_final: 0.7814 (tp-100) REVERT: e 7 ASP cc_start: 0.8193 (m-30) cc_final: 0.7876 (m-30) REVERT: e 22 MET cc_start: 0.7765 (tmm) cc_final: 0.7474 (tmm) REVERT: e 99 LYS cc_start: 0.8864 (mmmm) cc_final: 0.8531 (mmtt) REVERT: e 103 GLN cc_start: 0.9217 (tm-30) cc_final: 0.8917 (tm-30) REVERT: e 113 ASP cc_start: 0.8571 (t0) cc_final: 0.8348 (t0) REVERT: g 156 MET cc_start: 0.8332 (mmm) cc_final: 0.8098 (mmt) REVERT: p 14 PHE cc_start: 0.9017 (m-80) cc_final: 0.8564 (m-80) REVERT: p 53 ASP cc_start: 0.9179 (m-30) cc_final: 0.8200 (m-30) REVERT: p 129 VAL cc_start: 0.8956 (t) cc_final: 0.8716 (m) outliers start: 3 outliers final: 0 residues processed: 473 average time/residue: 0.5628 time to fit residues: 426.3475 Evaluate side-chains 365 residues out of total 3858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 363 time to evaluate : 4.021 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 210 GLU Chi-restraints excluded: chain b residue 45 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 405 optimal weight: 2.9990 chunk 363 optimal weight: 0.0670 chunk 201 optimal weight: 0.0370 chunk 124 optimal weight: 3.9990 chunk 245 optimal weight: 0.7980 chunk 194 optimal weight: 5.9990 chunk 376 optimal weight: 0.6980 chunk 145 optimal weight: 5.9990 chunk 228 optimal weight: 7.9990 chunk 280 optimal weight: 5.9990 chunk 435 optimal weight: 8.9990 overall best weight: 0.9198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 426 GLN C 201 GLN ** E 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 41 GLN S 41 GLN ** a 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 37 GLN ** b 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8454 moved from start: 0.1112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 37754 Z= 0.179 Angle : 0.572 7.889 51185 Z= 0.297 Chirality : 0.042 0.241 5997 Planarity : 0.004 0.054 6637 Dihedral : 6.905 178.761 5377 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 0.68 % Allowed : 5.29 % Favored : 94.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.54 % 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: 4860 helix: 1.38 (0.10), residues: 2632 sheet: -0.50 (0.20), residues: 599 loop : -1.45 (0.15), residues: 1629 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP a 255 HIS 0.004 0.001 HIS D 358 PHE 0.021 0.001 PHE b 16 TYR 0.015 0.001 TYR a 283 ARG 0.007 0.000 ARG p 91 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9720 Ramachandran restraints generated. 4860 Oldfield, 0 Emsley, 4860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9720 Ramachandran restraints generated. 4860 Oldfield, 0 Emsley, 4860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 454 residues out of total 3858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 428 time to evaluate : 4.094 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: C 110 ASP cc_start: 0.8300 (t70) cc_final: 0.7974 (t0) REVERT: G 60 ASP cc_start: 0.8733 (t0) cc_final: 0.7789 (t0) REVERT: G 64 MET cc_start: 0.9377 (mmp) cc_final: 0.8829 (mmp) REVERT: H 36 GLU cc_start: 0.8971 (tt0) cc_final: 0.8650 (tm-30) REVERT: H 40 ARG cc_start: 0.9013 (mmm-85) cc_final: 0.8541 (mmm-85) REVERT: H 60 ASP cc_start: 0.8764 (m-30) cc_final: 0.8271 (m-30) REVERT: H 64 MET cc_start: 0.9040 (mmp) cc_final: 0.8655 (mmm) REVERT: J 36 GLU cc_start: 0.8408 (mm-30) cc_final: 0.7806 (mm-30) REVERT: K 52 MET cc_start: 0.9102 (tmm) cc_final: 0.8702 (tmm) REVERT: L 52 MET cc_start: 0.9585 (tmm) cc_final: 0.9325 (tmm) REVERT: O 36 GLU cc_start: 0.8728 (tm-30) cc_final: 0.7857 (tm-30) REVERT: R 49 GLN cc_start: 0.9193 (tt0) cc_final: 0.8984 (tt0) REVERT: R 52 MET cc_start: 0.9218 (tmm) cc_final: 0.8988 (tmm) REVERT: S 14 ILE cc_start: 0.9352 (tp) cc_final: 0.9148 (tp) REVERT: S 18 PHE cc_start: 0.9093 (m-10) cc_final: 0.8830 (m-10) REVERT: S 52 MET cc_start: 0.9245 (tmm) cc_final: 0.9012 (tmm) REVERT: a 21 MET cc_start: 0.9351 (mmp) cc_final: 0.8822 (ptm) REVERT: a 123 ASN cc_start: 0.8900 (t0) cc_final: 0.8184 (t0) REVERT: a 131 ASP cc_start: 0.8215 (p0) cc_final: 0.8011 (p0) REVERT: a 168 MET cc_start: 0.9300 (mmm) cc_final: 0.8881 (mmm) REVERT: a 184 LYS cc_start: 0.7929 (mppt) cc_final: 0.7108 (tptp) REVERT: a 235 ASN cc_start: 0.7869 (m-40) cc_final: 0.7450 (m-40) REVERT: a 236 MET cc_start: 0.8570 (mmp) cc_final: 0.7027 (mtm) REVERT: a 237 TYR cc_start: 0.9375 (t80) cc_final: 0.9173 (t80) REVERT: a 240 GLU cc_start: 0.8834 (pt0) cc_final: 0.8564 (pt0) REVERT: a 277 MET cc_start: 0.9435 (tmm) cc_final: 0.9101 (tmm) REVERT: b 17 PHE cc_start: 0.9028 (t80) cc_final: 0.8340 (t80) REVERT: b 99 GLU cc_start: 0.8754 (tm-30) cc_final: 0.8291 (mm-30) REVERT: d 69 ASP cc_start: 0.8968 (m-30) cc_final: 0.7811 (t0) REVERT: e 22 MET cc_start: 0.8202 (tmm) cc_final: 0.7358 (tmm) REVERT: e 103 GLN cc_start: 0.9030 (tm-30) cc_final: 0.8803 (tm-30) REVERT: e 113 ASP cc_start: 0.8598 (t0) cc_final: 0.8311 (t0) REVERT: p 53 ASP cc_start: 0.8701 (m-30) cc_final: 0.8430 (m-30) REVERT: p 129 VAL cc_start: 0.8894 (t) cc_final: 0.8637 (m) REVERT: p 134 LYS cc_start: 0.8865 (mmmm) cc_final: 0.8561 (mmmm) outliers start: 26 outliers final: 13 residues processed: 440 average time/residue: 0.5335 time to fit residues: 380.9315 Evaluate side-chains 389 residues out of total 3858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 376 time to evaluate : 4.033 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 329 ASP Chi-restraints excluded: chain H residue 79 PHE Chi-restraints excluded: chain J residue 67 VAL Chi-restraints excluded: chain P residue 79 PHE Chi-restraints excluded: chain a residue 17 HIS Chi-restraints excluded: chain a residue 157 VAL Chi-restraints excluded: chain a residue 284 LEU Chi-restraints excluded: chain d residue 166 LEU Chi-restraints excluded: chain e residue 58 THR Chi-restraints excluded: chain e residue 61 ILE Chi-restraints excluded: chain e residue 81 ASP Chi-restraints excluded: chain g residue 39 MET Chi-restraints excluded: chain p residue 4 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 242 optimal weight: 7.9990 chunk 135 optimal weight: 0.6980 chunk 362 optimal weight: 2.9990 chunk 296 optimal weight: 4.9990 chunk 120 optimal weight: 3.9990 chunk 436 optimal weight: 6.9990 chunk 471 optimal weight: 3.9990 chunk 388 optimal weight: 6.9990 chunk 433 optimal weight: 3.9990 chunk 148 optimal weight: 0.9980 chunk 350 optimal weight: 0.9980 overall best weight: 1.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 169 HIS J 41 GLN P 41 GLN ** a 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 173 ASN ** p 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** p 138 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8473 moved from start: 0.1372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 37754 Z= 0.247 Angle : 0.563 8.324 51185 Z= 0.290 Chirality : 0.042 0.206 5997 Planarity : 0.004 0.045 6637 Dihedral : 6.432 172.002 5372 Min Nonbonded Distance : 1.860 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 0.91 % Allowed : 7.96 % Favored : 91.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.54 % 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: 0.34 (0.12), residues: 4860 helix: 1.35 (0.10), residues: 2643 sheet: -0.37 (0.20), residues: 605 loop : -1.41 (0.15), residues: 1612 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP g 206 HIS 0.003 0.001 HIS A 295 PHE 0.021 0.001 PHE G 53 TYR 0.018 0.001 TYR g 204 ARG 0.010 0.000 ARG p 81 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9720 Ramachandran restraints generated. 4860 Oldfield, 0 Emsley, 4860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9720 Ramachandran restraints generated. 4860 Oldfield, 0 Emsley, 4860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 438 residues out of total 3858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 403 time to evaluate : 4.254 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: G 52 MET cc_start: 0.9594 (tmm) cc_final: 0.9393 (tmm) REVERT: G 60 ASP cc_start: 0.8739 (t0) cc_final: 0.8077 (t0) REVERT: G 64 MET cc_start: 0.9396 (mmp) cc_final: 0.8657 (mmp) REVERT: H 36 GLU cc_start: 0.8991 (tt0) cc_final: 0.8716 (tm-30) REVERT: H 40 ARG cc_start: 0.9038 (mmm-85) cc_final: 0.8473 (mmm-85) REVERT: H 41 GLN cc_start: 0.8391 (mm-40) cc_final: 0.8189 (mm-40) REVERT: H 60 ASP cc_start: 0.8771 (m-30) cc_final: 0.8534 (m-30) REVERT: H 64 MET cc_start: 0.9047 (mmp) cc_final: 0.8644 (mmm) REVERT: J 36 GLU cc_start: 0.8442 (mm-30) cc_final: 0.7802 (mm-30) REVERT: K 52 MET cc_start: 0.9150 (tmm) cc_final: 0.8684 (tmm) REVERT: L 1 MET cc_start: 0.8106 (ppp) cc_final: 0.7883 (ppp) REVERT: L 52 MET cc_start: 0.9597 (tmm) cc_final: 0.9395 (tmm) REVERT: O 36 GLU cc_start: 0.8761 (tm-30) cc_final: 0.7908 (tm-30) REVERT: R 52 MET cc_start: 0.9271 (tmm) cc_final: 0.9025 (tmm) REVERT: S 18 PHE cc_start: 0.9048 (m-10) cc_final: 0.8779 (m-10) REVERT: S 52 MET cc_start: 0.9268 (tmm) cc_final: 0.9038 (tmm) REVERT: a 122 MET cc_start: 0.8940 (mtp) cc_final: 0.8738 (mtp) REVERT: a 123 ASN cc_start: 0.8886 (t0) cc_final: 0.8522 (t0) REVERT: a 125 MET cc_start: 0.8691 (tpp) cc_final: 0.8455 (tpp) REVERT: a 168 MET cc_start: 0.9219 (mmm) cc_final: 0.8708 (mmm) REVERT: a 179 TYR cc_start: 0.8486 (OUTLIER) cc_final: 0.7778 (t80) REVERT: a 184 LYS cc_start: 0.7934 (mppt) cc_final: 0.7170 (tptp) REVERT: a 237 TYR cc_start: 0.9416 (t80) cc_final: 0.9070 (t80) REVERT: a 240 GLU cc_start: 0.8842 (pt0) cc_final: 0.8539 (pt0) REVERT: a 277 MET cc_start: 0.9406 (tmm) cc_final: 0.9181 (tmm) REVERT: b 17 PHE cc_start: 0.8951 (t80) cc_final: 0.8601 (t80) REVERT: d 69 ASP cc_start: 0.8995 (m-30) cc_final: 0.7816 (t0) REVERT: d 83 ASP cc_start: 0.8776 (m-30) cc_final: 0.8533 (m-30) REVERT: e 22 MET cc_start: 0.8276 (tmm) cc_final: 0.7463 (tmm) REVERT: e 103 GLN cc_start: 0.9018 (tm-30) cc_final: 0.8771 (tm-30) REVERT: e 113 ASP cc_start: 0.8567 (t0) cc_final: 0.8288 (t0) REVERT: p 53 ASP cc_start: 0.8699 (m-30) cc_final: 0.8368 (m-30) REVERT: p 81 ARG cc_start: 0.8548 (tmm-80) cc_final: 0.8064 (tmm-80) REVERT: p 129 VAL cc_start: 0.8871 (t) cc_final: 0.8564 (m) REVERT: p 134 LYS cc_start: 0.8873 (mmmm) cc_final: 0.8640 (mmmm) outliers start: 35 outliers final: 24 residues processed: 426 average time/residue: 0.5283 time to fit residues: 365.3579 Evaluate side-chains 392 residues out of total 3858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 367 time to evaluate : 4.482 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 263 ASP Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain C residue 318 VAL Chi-restraints excluded: chain D residue 345 THR Chi-restraints excluded: chain F residue 325 VAL Chi-restraints excluded: chain F residue 329 ASP Chi-restraints excluded: chain F residue 379 ILE Chi-restraints excluded: chain F residue 423 VAL Chi-restraints excluded: chain H residue 79 PHE Chi-restraints excluded: chain P residue 79 PHE Chi-restraints excluded: chain S residue 67 VAL Chi-restraints excluded: chain a residue 152 VAL Chi-restraints excluded: chain a residue 163 ASN Chi-restraints excluded: chain a residue 179 TYR Chi-restraints excluded: chain a residue 284 LEU Chi-restraints excluded: chain b residue 66 ASP Chi-restraints excluded: chain d residue 166 LEU Chi-restraints excluded: chain e residue 58 THR Chi-restraints excluded: chain e residue 61 ILE Chi-restraints excluded: chain e residue 81 ASP Chi-restraints excluded: chain g residue 39 MET Chi-restraints excluded: chain g residue 150 THR Chi-restraints excluded: chain g residue 189 VAL Chi-restraints excluded: chain p residue 4 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 431 optimal weight: 10.0000 chunk 328 optimal weight: 0.9990 chunk 226 optimal weight: 7.9990 chunk 48 optimal weight: 0.9990 chunk 208 optimal weight: 0.0770 chunk 293 optimal weight: 10.0000 chunk 438 optimal weight: 0.7980 chunk 463 optimal weight: 0.8980 chunk 228 optimal weight: 0.0770 chunk 415 optimal weight: 5.9990 chunk 125 optimal weight: 4.9990 overall best weight: 0.5698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 272 GLN ** b 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8437 moved from start: 0.1644 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 37754 Z= 0.152 Angle : 0.531 10.106 51185 Z= 0.273 Chirality : 0.041 0.190 5997 Planarity : 0.004 0.044 6637 Dihedral : 6.128 159.913 5372 Min Nonbonded Distance : 1.893 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 0.91 % Allowed : 9.34 % Favored : 89.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.47 (0.12), residues: 4860 helix: 1.38 (0.10), residues: 2646 sheet: -0.09 (0.21), residues: 598 loop : -1.31 (0.15), residues: 1616 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP g 206 HIS 0.003 0.000 HIS D 358 PHE 0.019 0.001 PHE G 53 TYR 0.012 0.001 TYR g 204 ARG 0.006 0.000 ARG d 175 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9720 Ramachandran restraints generated. 4860 Oldfield, 0 Emsley, 4860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9720 Ramachandran restraints generated. 4860 Oldfield, 0 Emsley, 4860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 447 residues out of total 3858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 412 time to evaluate : 4.122 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 49 MET cc_start: 0.8223 (mtm) cc_final: 0.7883 (mtp) REVERT: C 110 ASP cc_start: 0.8240 (t70) cc_final: 0.7900 (t0) REVERT: G 60 ASP cc_start: 0.8724 (t0) cc_final: 0.8396 (t0) REVERT: G 64 MET cc_start: 0.9361 (mmp) cc_final: 0.8813 (mmp) REVERT: H 36 GLU cc_start: 0.8985 (tt0) cc_final: 0.8700 (tm-30) REVERT: H 40 ARG cc_start: 0.8979 (mmm-85) cc_final: 0.8520 (mmm-85) REVERT: H 52 MET cc_start: 0.9375 (tmm) cc_final: 0.9129 (tmm) REVERT: H 60 ASP cc_start: 0.8648 (m-30) cc_final: 0.8241 (m-30) REVERT: H 64 MET cc_start: 0.9031 (mmp) cc_final: 0.8667 (mmm) REVERT: J 36 GLU cc_start: 0.8382 (mm-30) cc_final: 0.7729 (mm-30) REVERT: K 52 MET cc_start: 0.9140 (tmm) cc_final: 0.8675 (tmm) REVERT: O 36 GLU cc_start: 0.8736 (tm-30) cc_final: 0.7886 (tm-30) REVERT: R 52 MET cc_start: 0.9272 (tmm) cc_final: 0.9018 (tmm) REVERT: R 64 MET cc_start: 0.9161 (mmm) cc_final: 0.8700 (mmm) REVERT: S 18 PHE cc_start: 0.9072 (m-10) cc_final: 0.8868 (m-10) REVERT: a 21 MET cc_start: 0.9297 (mmp) cc_final: 0.8736 (ptm) REVERT: a 122 MET cc_start: 0.8875 (mtp) cc_final: 0.8668 (mtp) REVERT: a 123 ASN cc_start: 0.8820 (t0) cc_final: 0.8287 (t0) REVERT: a 125 MET cc_start: 0.8754 (tpp) cc_final: 0.8504 (tpp) REVERT: a 168 MET cc_start: 0.9222 (mmm) cc_final: 0.8820 (mmm) REVERT: a 179 TYR cc_start: 0.8414 (OUTLIER) cc_final: 0.7714 (t80) REVERT: a 184 LYS cc_start: 0.7948 (mppt) cc_final: 0.7292 (tptp) REVERT: a 236 MET cc_start: 0.8494 (mmp) cc_final: 0.6904 (mtm) REVERT: a 240 GLU cc_start: 0.8774 (pt0) cc_final: 0.8401 (pt0) REVERT: a 277 MET cc_start: 0.9372 (tmm) cc_final: 0.9112 (tmm) REVERT: b 12 ILE cc_start: 0.9196 (mt) cc_final: 0.8502 (tt) REVERT: b 17 PHE cc_start: 0.8969 (t80) cc_final: 0.8481 (t80) REVERT: b 49 LYS cc_start: 0.8859 (ptpt) cc_final: 0.8417 (tptt) REVERT: d 69 ASP cc_start: 0.8978 (m-30) cc_final: 0.7896 (t0) REVERT: e 22 MET cc_start: 0.8257 (tmm) cc_final: 0.7538 (tmm) REVERT: e 103 GLN cc_start: 0.8994 (tm-30) cc_final: 0.8756 (tm-30) REVERT: e 113 ASP cc_start: 0.8552 (t0) cc_final: 0.8272 (t0) REVERT: p 53 ASP cc_start: 0.8698 (m-30) cc_final: 0.8405 (m-30) REVERT: p 81 ARG cc_start: 0.8517 (tmm-80) cc_final: 0.8072 (tmm-80) REVERT: p 129 VAL cc_start: 0.8774 (t) cc_final: 0.8526 (m) REVERT: p 134 LYS cc_start: 0.8864 (mmmm) cc_final: 0.8609 (mmmm) outliers start: 35 outliers final: 18 residues processed: 432 average time/residue: 0.5394 time to fit residues: 375.2891 Evaluate side-chains 392 residues out of total 3858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 373 time to evaluate : 4.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 49 MET Chi-restraints excluded: chain F residue 266 MET Chi-restraints excluded: chain F residue 329 ASP Chi-restraints excluded: chain F residue 379 ILE Chi-restraints excluded: chain F residue 423 VAL Chi-restraints excluded: chain H residue 79 PHE Chi-restraints excluded: chain P residue 79 PHE Chi-restraints excluded: chain S residue 27 PHE Chi-restraints excluded: chain a residue 152 VAL Chi-restraints excluded: chain a residue 157 VAL Chi-restraints excluded: chain a residue 179 TYR Chi-restraints excluded: chain a residue 284 LEU Chi-restraints excluded: chain b residue 117 ARG Chi-restraints excluded: chain d residue 166 LEU Chi-restraints excluded: chain e residue 61 ILE Chi-restraints excluded: chain e residue 81 ASP Chi-restraints excluded: chain e residue 110 SER Chi-restraints excluded: chain g residue 39 MET Chi-restraints excluded: chain g residue 138 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 386 optimal weight: 10.0000 chunk 263 optimal weight: 5.9990 chunk 6 optimal weight: 0.0670 chunk 345 optimal weight: 7.9990 chunk 191 optimal weight: 4.9990 chunk 395 optimal weight: 6.9990 chunk 320 optimal weight: 3.9990 chunk 0 optimal weight: 20.0000 chunk 236 optimal weight: 10.0000 chunk 416 optimal weight: 4.9990 chunk 117 optimal weight: 3.9990 overall best weight: 3.6126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_failure.pdb'. Return code: -15 Dumping stderr: