Starting phenix.real_space_refine (version: 1.21rc1) on Mon May 15 16:02:23 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p3w_13186/05_2023/7p3w_13186_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p3w_13186/05_2023/7p3w_13186.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p3w_13186/05_2023/7p3w_13186.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p3w_13186/05_2023/7p3w_13186.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p3w_13186/05_2023/7p3w_13186_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p3w_13186/05_2023/7p3w_13186_updated.pdb" } resolution = 4.3 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= 0.008 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 11 5.49 5 Mg 4 5.21 5 S 147 5.16 5 C 23656 2.51 5 N 6313 2.21 5 O 7018 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 97": "OE1" <-> "OE2" Residue "A GLU 215": "OE1" <-> "OE2" Residue "A GLU 311": "OE1" <-> "OE2" Residue "A PHE 355": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 403": "OE1" <-> "OE2" Residue "A ARG 477": "NH1" <-> "NH2" Residue "A GLU 489": "OE1" <-> "OE2" Residue "A GLU 498": "OE1" <-> "OE2" Residue "B GLU 8": "OE1" <-> "OE2" Residue "B GLU 68": "OE1" <-> "OE2" Residue "B GLU 285": "OE1" <-> "OE2" Residue "B GLU 311": "OE1" <-> "OE2" Residue "B PHE 468": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 489": "OE1" <-> "OE2" Residue "C GLU 55": "OE1" <-> "OE2" Residue "C GLU 166": "OE1" <-> "OE2" Residue "C GLU 214": "OE1" <-> "OE2" Residue "C GLU 285": "OE1" <-> "OE2" Residue "C GLU 300": "OE1" <-> "OE2" Residue "C GLU 308": "OE1" <-> "OE2" Residue "C GLU 423": "OE1" <-> "OE2" Residue "C ARG 477": "NH1" <-> "NH2" Residue "D GLU 103": "OE1" <-> "OE2" Residue "D GLU 160": "OE1" <-> "OE2" Residue "D ARG 251": "NH1" <-> "NH2" Residue "D ARG 363": "NH1" <-> "NH2" Residue "D GLU 456": "OE1" <-> "OE2" Residue "D GLU 462": "OE1" <-> "OE2" Residue "E ARG 5": "NH1" <-> "NH2" Residue "E ARG 20": "NH1" <-> "NH2" Residue "E GLU 40": "OE1" <-> "OE2" Residue "E ARG 181": "NH1" <-> "NH2" Residue "E GLU 235": "OE1" <-> "OE2" Residue "E GLU 279": "OE1" <-> "OE2" Residue "E GLU 456": "OE1" <-> "OE2" Residue "F ARG 20": "NH1" <-> "NH2" Residue "F GLU 36": "OE1" <-> "OE2" Residue "F GLU 104": "OE1" <-> "OE2" Residue "F GLU 117": "OE1" <-> "OE2" Residue "F ARG 217": "NH1" <-> "NH2" Residue "F ARG 240": "NH1" <-> "NH2" Residue "F GLU 278": "OE1" <-> "OE2" Residue "F ARG 371": "NH1" <-> "NH2" Residue "H GLU 43": "OE1" <-> "OE2" Residue "K GLU 2": "OE1" <-> "OE2" Residue "Q GLU 36": "OE1" <-> "OE2" Residue "R GLU 2": "OE1" <-> "OE2" Residue "S GLU 43": "OE1" <-> "OE2" Residue "a ARG 182": "NH1" <-> "NH2" Residue "a ARG 224": "NH1" <-> "NH2" Residue "b ARG 91": "NH1" <-> "NH2" Residue "b GLU 99": "OE1" <-> "OE2" Residue "b GLU 107": "OE1" <-> "OE2" Residue "b GLU 119": "OE1" <-> "OE2" Residue "b GLU 143": "OE1" <-> "OE2" Residue "d GLU 52": "OE1" <-> "OE2" Residue "d GLU 68": "OE1" <-> "OE2" Residue "d GLU 92": "OE1" <-> "OE2" Residue "d GLU 131": "OE1" <-> "OE2" Residue "d GLU 170": "OE1" <-> "OE2" Residue "e ARG 51": "NH1" <-> "NH2" Residue "e GLU 59": "OE1" <-> "OE2" Residue "e ARG 85": "NH1" <-> "NH2" Residue "e GLU 91": "OE1" <-> "OE2" Residue "g ARG 66": "NH1" <-> "NH2" Residue "g ARG 224": "NH1" <-> "NH2" Residue "g GLU 227": "OE1" <-> "OE2" Residue "p GLU 35": "OE1" <-> "OE2" Residue "p GLU 88": "OE1" <-> "OE2" Residue "p GLU 99": "OE1" <-> "OE2" Residue "p GLU 112": "OE1" <-> "OE2" Residue "p GLU 118": "OE1" <-> "OE2" Residue "p ARG 121": "NH1" <-> "NH2" Time to flip residues: 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/chem_data/mon_lib" Total number of atoms: 37149 Number of models: 1 Model: "" Number of chains: 26 Chain: "A" Number of atoms: 3875 Number of conformers: 1 Conformer: "" Number of residues, atoms: 512, 3875 Classifications: {'peptide': 512} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 493} Chain: "B" Number of atoms: 3863 Number of conformers: 1 Conformer: "" Number of residues, atoms: 511, 3863 Classifications: {'peptide': 511} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 492} 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: {'PTRANS': 22, 'TRANS': 440} Chain: "E" 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: "F" 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: "G" 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: "H" 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: "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: 577 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 577 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 4, 'TRANS': 74} Chain: "L" 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: "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: 585 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 585 Classifications: {'peptide': 80} Link IDs: {'PTRANS': 4, 'TRANS': 75} 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: 577 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 577 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 4, 'TRANS': 74} 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: 2105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 277, 2105 Classifications: {'peptide': 277} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 15, 'TRANS': 261} Unresolved non-hydrogen bonds: 86 Unresolved non-hydrogen angles: 113 Unresolved non-hydrogen dihedrals: 79 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: 57 Chain: "b" Number of atoms: 1146 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1146 Classifications: {'peptide': 150} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 147} 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: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 18.88, per 1000 atoms: 0.51 Number of scatterers: 37149 At special positions: 0 Unit cell: (133.45, 143.65, 240.55, 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 11 15.00 Mg 4 11.99 O 7018 8.00 N 6313 7.00 C 23656 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: 21.34 Conformation dependent library (CDL) restraints added in 7.0 seconds 9712 Ramachandran restraints generated. 4856 Oldfield, 0 Emsley, 4856 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8922 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 173 helices and 22 sheets defined 54.7% alpha, 9.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.42 Creating SS restraints... Processing helix chain 'A' and resid 4 through 14 Processing helix chain 'A' and resid 18 through 24 removed outlier: 3.728A pdb=" N THR A 22 " --> pdb=" O GLY A 18 " (cutoff:3.500A) Processing helix chain 'A' and resid 137 through 139 No H-bonds generated for 'chain 'A' and resid 137 through 139' Processing helix chain 'A' and resid 152 through 157 Processing helix chain 'A' and resid 176 through 189 removed outlier: 3.556A pdb=" N GLN A 187 " --> pdb=" O ALA A 183 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N LYS A 188 " --> pdb=" O ILE A 184 " (cutoff:3.500A) removed outlier: 5.126A pdb=" N ASN A 189 " --> pdb=" O ILE A 185 " (cutoff:3.500A) Processing helix chain 'A' and resid 203 through 215 Processing helix chain 'A' and resid 233 through 253 Proline residue: A 240 - end of helix removed outlier: 3.624A pdb=" N ARG A 253 " --> pdb=" O TYR A 249 " (cutoff:3.500A) Processing helix chain 'A' and resid 264 through 277 Processing helix chain 'A' and resid 284 through 286 No H-bonds generated for 'chain 'A' and resid 284 through 286' Processing helix chain 'A' and resid 289 through 301 removed outlier: 4.133A pdb=" N GLU A 300 " --> pdb=" O ARG A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 307 through 313 Processing helix chain 'A' and resid 341 through 349 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 403 removed outlier: 4.395A pdb=" N GLY A 392 " --> pdb=" O LYS A 388 " (cutoff:3.500A) removed outlier: 6.013A pdb=" N GLY A 393 " --> pdb=" O LYS A 389 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N ILE A 394 " --> pdb=" O LEU A 390 " (cutoff:3.500A) Processing helix chain 'A' and resid 408 through 410 No H-bonds generated for 'chain 'A' and resid 408 through 410' Processing helix chain 'A' and resid 416 through 432 Processing helix chain 'A' and resid 442 through 453 Processing helix chain 'A' and resid 465 through 479 Processing helix chain 'A' and resid 481 through 490 Processing helix chain 'A' and resid 495 through 511 Processing helix chain 'B' and resid 10 through 18 Processing helix chain 'B' and resid 24 through 27 No H-bonds generated for 'chain 'B' and resid 24 through 27' Processing helix chain 'B' and resid 102 through 104 No H-bonds generated for 'chain 'B' and resid 102 through 104' 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 Processing helix chain 'B' and resid 176 through 185 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: 3.640A pdb=" N TYR B 249 " --> pdb=" O THR B 245 " (cutoff:3.500A) removed outlier: 4.667A pdb=" N PHE B 250 " --> pdb=" O MET B 246 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N ARG B 251 " --> pdb=" O GLY B 247 " (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 289 through 301 removed outlier: 3.909A pdb=" N PHE B 292 " --> pdb=" O GLY B 289 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ARG B 297 " --> pdb=" O LEU B 294 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N GLU B 300 " --> pdb=" O ARG B 297 " (cutoff:3.500A) Processing helix chain 'B' and resid 307 through 313 Processing helix chain 'B' and resid 341 through 349 removed outlier: 3.615A 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 390 Processing helix chain 'B' and resid 394 through 410 removed outlier: 5.226A pdb=" N PHE B 410 " --> 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 454 Processing helix chain 'B' and resid 464 through 479 Processing helix chain 'B' and resid 481 through 490 Processing helix chain 'B' and resid 495 through 509 Processing helix chain 'C' and resid 7 through 19 removed outlier: 3.925A pdb=" N ASP C 19 " --> pdb=" O GLN C 15 " (cutoff:3.500A) Processing helix chain 'C' and resid 102 through 104 No H-bonds generated for 'chain 'C' and resid 102 through 104' Processing helix chain 'C' and resid 137 through 139 No H-bonds generated for 'chain 'C' and resid 137 through 139' Processing helix chain 'C' and resid 152 through 157 Processing helix chain 'C' and resid 176 through 188 removed outlier: 4.376A pdb=" N GLN C 187 " --> pdb=" O ALA C 183 " (cutoff:3.500A) removed outlier: 5.230A pdb=" N LYS C 188 " --> pdb=" O ILE C 184 " (cutoff:3.500A) Processing helix chain 'C' and resid 203 through 216 Processing helix chain 'C' and resid 233 through 252 Proline residue: C 240 - end of helix removed outlier: 3.699A pdb=" N PHE C 250 " --> pdb=" O MET C 246 " (cutoff:3.500A) Processing helix chain 'C' and resid 264 through 278 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 289 through 301 removed outlier: 3.699A pdb=" N ARG C 297 " --> pdb=" O LEU C 294 " (cutoff:3.500A) removed outlier: 4.715A pdb=" N GLU C 300 " --> pdb=" O ARG C 297 " (cutoff:3.500A) Processing helix chain 'C' and resid 307 through 314 Processing helix chain 'C' and resid 341 through 349 removed outlier: 3.962A pdb=" N SER C 348 " --> pdb=" O THR C 344 " (cutoff:3.500A) removed outlier: 4.108A 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 407 removed outlier: 5.118A pdb=" N GLY C 392 " --> pdb=" O LYS C 388 " (cutoff:3.500A) removed outlier: 5.610A pdb=" N GLY C 393 " --> pdb=" O LYS C 389 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N ILE C 394 " --> pdb=" O LEU C 390 " (cutoff:3.500A) removed outlier: 5.943A pdb=" N ALA C 406 " --> pdb=" O ARG C 402 " (cutoff:3.500A) removed outlier: 7.010A pdb=" N PHE C 407 " --> pdb=" O GLU C 403 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 432 removed outlier: 3.862A pdb=" N MET C 432 " --> pdb=" O VAL C 428 " (cutoff:3.500A) Processing helix chain 'C' and resid 442 through 453 Processing helix chain 'C' and resid 462 through 479 removed outlier: 5.143A pdb=" N VAL C 466 " --> pdb=" O LYS C 463 " (cutoff:3.500A) Processing helix chain 'C' and resid 481 through 490 Processing helix chain 'C' and resid 495 through 510 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 115 through 117 No H-bonds generated for 'chain 'D' and resid 115 through 117' Processing helix chain 'D' and resid 130 through 135 Processing helix chain 'D' and resid 154 through 168 Processing helix chain 'D' and resid 182 through 194 Processing helix chain 'D' and resid 212 through 231 removed outlier: 4.678A pdb=" N ALA D 219 " --> pdb=" O ARG D 215 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N LEU D 220 " --> pdb=" O LEU D 216 " (cutoff:3.500A) Processing helix chain 'D' and resid 249 through 259 removed outlier: 3.714A pdb=" N GLY D 256 " --> pdb=" O TYR D 252 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N VAL D 259 " --> pdb=" O ALA D 255 " (cutoff:3.500A) Processing helix chain 'D' and resid 274 through 285 removed outlier: 4.287A pdb=" N ALA D 277 " --> pdb=" O PRO D 274 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N GLU D 285 " --> 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 317 removed outlier: 4.178A pdb=" N THR D 316 " --> pdb=" O SER D 312 " (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: 3.534A pdb=" N LYS D 376 " --> pdb=" O TYR D 372 " (cutoff:3.500A) removed outlier: 4.747A pdb=" N ASP D 377 " --> pdb=" O LYS D 373 " (cutoff:3.500A) removed outlier: 5.168A pdb=" N ILE D 378 " --> pdb=" O GLU D 374 " (cutoff:3.500A) Processing helix chain 'D' and resid 392 through 405 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 115 through 117 No H-bonds generated for 'chain 'E' and resid 115 through 117' Processing helix chain 'E' and resid 154 through 167 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: 4.274A pdb=" N ALA E 219 " --> pdb=" O ARG E 215 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N LEU E 220 " --> pdb=" O LEU E 216 " (cutoff:3.500A) Processing helix chain 'E' and resid 249 through 262 Processing helix chain 'E' and resid 276 through 285 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 Processing helix chain 'E' and resid 329 through 332 No H-bonds generated for 'chain 'E' and resid 329 through 332' Processing helix chain 'E' and resid 356 through 381 removed outlier: 4.238A pdb=" N ASP E 377 " --> pdb=" O LYS E 373 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N ILE E 378 " --> pdb=" O GLU E 374 " (cutoff:3.500A) Processing helix chain 'E' and resid 389 through 405 Processing helix chain 'E' and resid 410 through 416 removed outlier: 4.544A pdb=" N VAL E 414 " --> pdb=" O HIS E 410 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N PHE E 415 " --> pdb=" O VAL E 411 " (cutoff:3.500A) Processing helix chain 'E' and resid 428 through 436 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 130 through 135 Processing helix chain 'F' and resid 154 through 165 Processing helix chain 'F' and resid 182 through 194 Processing helix chain 'F' and resid 212 through 216 Processing helix chain 'F' and resid 219 through 231 Processing helix chain 'F' and resid 249 through 260 removed outlier: 3.748A pdb=" N THR F 253 " --> pdb=" O ILE F 249 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N VAL F 259 " --> pdb=" O ALA F 255 " (cutoff:3.500A) Processing helix chain 'F' and resid 276 through 287 removed outlier: 3.742A pdb=" N ARG F 286 " --> pdb=" O VAL F 282 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N ILE F 287 " --> pdb=" O LEU F 283 " (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 319 removed outlier: 3.814A pdb=" N ALA F 318 " --> pdb=" O ALA F 314 " (cutoff:3.500A) removed outlier: 4.909A pdb=" N HIS F 319 " --> pdb=" O THR F 315 " (cutoff:3.500A) Processing helix chain 'F' and resid 328 through 332 Processing helix chain 'F' and resid 351 through 354 No H-bonds generated for 'chain 'F' and resid 351 through 354' Processing helix chain 'F' and resid 356 through 381 removed outlier: 4.525A pdb=" N ASP F 377 " --> pdb=" O LYS F 373 " (cutoff:3.500A) removed outlier: 4.977A pdb=" N ILE F 378 " --> pdb=" O GLU F 374 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N ILE F 379 " --> pdb=" O LEU F 375 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ALA F 380 " --> pdb=" O LYS F 376 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ILE F 381 " --> pdb=" O ASP F 377 " (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 405 Processing helix chain 'F' and resid 412 through 414 No H-bonds generated for 'chain 'F' and resid 412 through 414' Processing helix chain 'F' and resid 425 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 2 through 40 removed outlier: 3.636A pdb=" N ARG G 33 " --> pdb=" O LEU G 29 " (cutoff:3.500A) Processing helix chain 'G' and resid 45 through 59 Processing helix chain 'G' and resid 61 through 76 Processing helix chain 'H' and resid 2 through 40 removed outlier: 3.714A pdb=" N ARG H 33 " --> pdb=" O LEU H 29 " (cutoff:3.500A) Processing helix chain 'H' and resid 43 through 59 Proline residue: H 46 - end of helix removed outlier: 4.409A pdb=" N GLY H 57 " --> pdb=" O LEU H 54 " (cutoff:3.500A) Processing helix chain 'H' and resid 61 through 75 Processing helix chain 'J' and resid 2 through 40 removed outlier: 3.758A pdb=" N ILE J 16 " --> pdb=" O SER J 12 " (cutoff:3.500A) Processing helix chain 'J' and resid 45 through 59 Processing helix chain 'J' and resid 61 through 75 Processing helix chain 'K' and resid 3 through 40 removed outlier: 3.831A pdb=" N ARG K 33 " --> pdb=" O LEU K 29 " (cutoff:3.500A) Processing helix chain 'K' and resid 44 through 75 removed outlier: 4.270A pdb=" N GLY K 57 " --> pdb=" O LEU K 54 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N ASP K 60 " --> pdb=" O GLY K 57 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N ALA K 61 " --> pdb=" O LEU K 58 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N VAL K 62 " --> pdb=" O LEU K 59 " (cutoff:3.500A) Proline residue: K 63 - end of helix Processing helix chain 'L' and resid 3 through 40 removed outlier: 3.715A 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 Processing helix chain 'L' and resid 61 through 74 Processing helix chain 'O' and resid 2 through 40 removed outlier: 3.671A pdb=" N GLY O 19 " --> pdb=" O LEU O 15 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ARG O 33 " --> pdb=" O LEU O 29 " (cutoff:3.500A) Processing helix chain 'O' and resid 45 through 59 Processing helix chain 'O' and resid 61 through 75 Processing helix chain 'P' and resid 2 through 40 removed outlier: 4.007A pdb=" N GLY P 28 " --> pdb=" O ALA P 24 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N ARG P 33 " --> pdb=" O LEU P 29 " (cutoff:3.500A) Processing helix chain 'P' and resid 42 through 59 removed outlier: 3.784A pdb=" N ALA P 45 " --> pdb=" O PRO P 42 " (cutoff:3.500A) Proline residue: P 46 - end of helix Processing helix chain 'P' and resid 61 through 75 removed outlier: 3.979A pdb=" N ILE P 65 " --> pdb=" O ALA P 61 " (cutoff:3.500A) Processing helix chain 'Q' and resid 3 through 40 removed outlier: 4.171A pdb=" N GLY Q 19 " --> pdb=" O LEU Q 15 " (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 75 Processing helix chain 'R' and resid 3 through 40 removed outlier: 4.052A pdb=" N GLY R 19 " --> pdb=" O LEU R 15 " (cutoff:3.500A) Processing helix chain 'R' and resid 42 through 59 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 Processing helix chain 'S' and resid 42 through 59 Proline residue: S 46 - end of helix removed outlier: 4.069A pdb=" N GLY S 57 " --> pdb=" O LEU S 54 " (cutoff:3.500A) Processing helix chain 'S' and resid 61 through 76 Processing helix chain 'a' and resid 16 through 25 Processing helix chain 'a' and resid 53 through 72 removed outlier: 3.831A pdb=" N PHE a 63 " --> pdb=" O LEU a 59 " (cutoff:3.500A) removed outlier: 3.824A 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: 5.662A pdb=" N ASP a 126 " --> pdb=" O MET a 122 " (cutoff:3.500A) removed outlier: 5.175A pdb=" N LEU a 127 " --> pdb=" O ASN a 123 " (cutoff:3.500A) Processing helix chain 'a' and resid 130 through 143 Proline residue: a 134 - end of helix removed outlier: 5.669A pdb=" N PHE a 139 " --> pdb=" O GLN a 135 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N VAL a 140 " --> pdb=" O VAL a 136 " (cutoff:3.500A) Processing helix chain 'a' and resid 148 through 153 Processing helix chain 'a' and resid 163 through 182 Processing helix chain 'a' and resid 186 through 190 Processing helix chain 'a' and resid 202 through 247 removed outlier: 4.697A pdb=" N ILE a 210 " --> pdb=" O LYS a 206 " (cutoff:3.500A) Proline residue: a 211 - end of helix removed outlier: 3.755A pdb=" N THR a 220 " --> pdb=" O LEU a 216 " (cutoff:3.500A) removed outlier: 5.522A pdb=" N PHE a 221 " --> pdb=" O GLU a 217 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N LEU a 222 " --> pdb=" O LEU a 218 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N ARG a 224 " --> pdb=" O THR a 220 " (cutoff:3.500A) Proline residue: a 225 - end of helix Processing helix chain 'a' and resid 258 through 287 removed outlier: 3.802A pdb=" N THR a 270 " --> pdb=" O ILE a 266 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N LEU a 271 " --> pdb=" O LEU a 267 " (cutoff:3.500A) Processing helix chain 'b' and resid 8 through 138 removed outlier: 3.658A pdb=" N VAL b 18 " --> pdb=" O PHE b 14 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ALA b 19 " --> pdb=" O ALA b 15 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N PHE b 20 " --> pdb=" O PHE b 16 " (cutoff:3.500A) removed outlier: 4.796A pdb=" N TRP b 26 " --> pdb=" O MET b 22 " (cutoff:3.500A) Proline residue: b 27 - end of helix removed outlier: 3.958A pdb=" N GLU b 35 " --> pdb=" O ASN b 31 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N ARG b 36 " --> pdb=" O ALA b 32 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N GLN b 37 " --> pdb=" O ILE b 33 " (cutoff:3.500A) removed outlier: 4.695A pdb=" N ARG b 38 " --> pdb=" O SER b 34 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N ASP b 42 " --> pdb=" O ARG b 38 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N GLY b 43 " --> pdb=" O LYS b 39 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N GLN b 60 " --> pdb=" O ASP b 56 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N VAL b 61 " --> pdb=" O ALA b 57 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N LYS b 62 " --> pdb=" O GLN b 58 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLN b 63 " --> pdb=" O ALA b 59 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ALA b 84 " --> pdb=" O ASN b 80 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N GLN b 85 " --> pdb=" O ARG b 81 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N GLU b 118 " --> pdb=" O ASN b 114 " (cutoff:3.500A) removed outlier: 5.170A pdb=" N GLU b 119 " --> pdb=" O SER b 115 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N LEU b 120 " --> pdb=" O ALA b 116 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N GLU b 133 " --> pdb=" O VAL b 129 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N LYS b 134 " --> pdb=" O THR b 130 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N ILE b 135 " --> pdb=" O GLY b 131 " (cutoff:3.500A) removed outlier: 4.808A pdb=" N LEU b 136 " --> pdb=" O ALA b 132 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ASN b 137 " --> pdb=" O GLU b 133 " (cutoff:3.500A) Processing helix chain 'd' and resid 4 through 22 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 84 Processing helix chain 'd' and resid 86 through 104 removed outlier: 3.506A pdb=" N LEU d 89 " --> pdb=" O ARG d 86 " (cutoff:3.500A) Proline residue: d 91 - end of helix Processing helix chain 'd' and resid 120 through 132 Processing helix chain 'd' and resid 165 through 175 Processing helix chain 'e' and resid 89 through 124 removed outlier: 4.775A pdb=" N GLU e 96 " --> pdb=" O ALA e 93 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N LYS e 109 " --> pdb=" O ALA e 106 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N LEU e 112 " --> pdb=" O LYS e 109 " (cutoff:3.500A) removed outlier: 5.360A pdb=" N SER e 114 " --> pdb=" O ASP e 111 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ALA e 117 " --> pdb=" O SER e 114 " (cutoff:3.500A) removed outlier: 4.891A pdb=" N LEU e 118 " --> pdb=" O ALA e 115 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ALA e 119 " --> pdb=" O ALA e 116 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N LEU e 121 " --> pdb=" O LEU e 118 " (cutoff:3.500A) Processing helix chain 'e' and resid 128 through 134 removed outlier: 4.016A pdb=" N LYS e 133 " --> pdb=" O THR e 130 " (cutoff:3.500A) Processing helix chain 'g' and resid 4 through 59 removed outlier: 4.024A pdb=" N ALA g 40 " --> pdb=" O GLN g 36 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N GLN g 41 " --> pdb=" O GLU g 37 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N GLY g 42 " --> pdb=" O ARG g 38 " (cutoff:3.500A) removed outlier: 4.353A 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 109 removed outlier: 3.798A pdb=" N GLN g 109 " --> pdb=" O ALA g 105 " (cutoff:3.500A) Processing helix chain 'g' and resid 120 through 129 removed outlier: 3.800A pdb=" N TYR g 129 " --> pdb=" O PHE g 125 " (cutoff:3.500A) Processing helix chain 'g' and resid 146 through 161 removed outlier: 4.002A pdb=" N GLY g 151 " --> pdb=" O GLU g 147 " (cutoff:3.500A) removed outlier: 4.865A pdb=" N SER g 152 " --> pdb=" O GLN g 148 " (cutoff:3.500A) Processing helix chain 'g' and resid 214 through 287 Processing helix chain 'p' and resid 3 through 138 removed outlier: 3.745A pdb=" N TRP p 26 " --> pdb=" O MET p 22 " (cutoff:3.500A) Proline residue: p 27 - end of helix removed outlier: 4.146A pdb=" N ALA p 67 " --> pdb=" O GLN p 63 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N ARG p 121 " --> pdb=" O ARG p 117 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N GLN p 122 " --> pdb=" O GLU p 118 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N GLN p 123 " --> pdb=" O GLU p 119 " (cutoff:3.500A) Processing helix chain 'p' and resid 142 through 155 Processing sheet with id= A, first strand: chain 'A' and resid 30 through 36 removed outlier: 6.404A pdb=" N ARG A 41 " --> pdb=" O VAL A 33 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N VAL A 35 " --> pdb=" O ILE A 39 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N ILE A 39 " --> pdb=" O VAL A 35 " (cutoff:3.500A) removed outlier: 7.371A pdb=" N VAL A 75 " --> pdb=" O ALA A 64 " (cutoff:3.500A) removed outlier: 5.939A pdb=" N ALA A 64 " --> pdb=" O VAL A 75 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 97 through 100 removed outlier: 4.017A pdb=" N LEU A 126 " --> pdb=" O VAL A 100 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 107 through 109 removed outlier: 4.424A pdb=" N ARG A 107 " --> pdb=" O THR A 222 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N VAL A 224 " --> pdb=" O ARG A 107 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N CYS A 194 " --> pdb=" O THR A 223 " (cutoff:3.500A) removed outlier: 8.508A pdb=" N VAL A 225 " --> pdb=" O CYS A 194 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N TYR A 196 " --> pdb=" O VAL A 225 " (cutoff:3.500A) removed outlier: 7.916A pdb=" N ALA A 227 " --> pdb=" O TYR A 196 " (cutoff:3.500A) removed outlier: 5.960A pdb=" N ALA A 198 " --> pdb=" O ALA A 227 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N LYS A 193 " --> pdb=" O ASP A 256 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N VAL A 197 " --> pdb=" O ILE A 260 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N SER A 324 " --> pdb=" O ALA A 257 " (cutoff:3.500A) removed outlier: 8.340A pdb=" N ILE A 259 " --> pdb=" O SER A 324 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N THR A 326 " --> pdb=" O ILE A 259 " (cutoff:3.500A) removed outlier: 7.770A pdb=" N TYR A 261 " --> pdb=" O THR A 326 " (cutoff:3.500A) removed outlier: 6.041A pdb=" N LEU A 328 " --> pdb=" O TYR A 261 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N GLU A 166 " --> pdb=" O ALA A 327 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N GLY A 352 " --> pdb=" O LEU A 167 " (cutoff:3.500A) removed outlier: 7.742A pdb=" N ILE A 169 " --> pdb=" O GLY A 352 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N ILE A 354 " --> pdb=" O ILE A 169 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 29 through 31 removed outlier: 4.217A pdb=" N PHE B 61 " --> pdb=" O LEU B 77 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N GLY B 73 " --> pdb=" O LEU B 65 " (cutoff:3.500A) removed outlier: 5.709A pdb=" N HIS B 43 " --> pdb=" O ILE B 32 " (cutoff:3.500A) removed outlier: 5.357A pdb=" N ILE B 32 " --> pdb=" O HIS B 43 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 97 through 100 removed outlier: 4.271A pdb=" N LEU B 126 " --> pdb=" O VAL B 100 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 374 through 376 removed outlier: 6.330A pdb=" N ARG B 165 " --> pdb=" O GLY B 352 " (cutoff:3.500A) removed outlier: 7.785A pdb=" N ILE B 354 " --> pdb=" O ARG B 165 " (cutoff:3.500A) removed outlier: 5.904A pdb=" N LEU B 167 " --> pdb=" O ILE B 354 " (cutoff:3.500A) removed outlier: 7.301A pdb=" N ALA B 327 " --> pdb=" O GLU B 166 " (cutoff:3.500A) removed outlier: 7.842A pdb=" N ILE B 168 " --> pdb=" O ALA B 327 " (cutoff:3.500A) removed outlier: 8.277A pdb=" N GLY B 170 " --> pdb=" O PRO B 329 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N ILE B 331 " --> pdb=" O GLY B 170 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N LYS B 193 " --> pdb=" O LEU B 258 " (cutoff:3.500A) removed outlier: 8.423A pdb=" N ILE B 260 " --> pdb=" O LYS B 193 " (cutoff:3.500A) removed outlier: 7.449A pdb=" N VAL B 195 " --> pdb=" O ILE B 260 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'C' and resid 30 through 36 removed outlier: 6.428A pdb=" N ARG C 41 " --> pdb=" O VAL C 33 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N VAL C 35 " --> pdb=" O ILE C 39 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N ILE C 39 " --> pdb=" O VAL C 35 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N VAL C 75 " --> pdb=" O ALA C 64 " (cutoff:3.500A) removed outlier: 5.656A pdb=" N ALA C 64 " --> pdb=" O VAL C 75 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'C' and resid 97 through 100 removed outlier: 4.013A pdb=" N LEU C 126 " --> pdb=" O VAL C 100 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'C' and resid 353 through 356 removed outlier: 8.431A pdb=" N ILE C 354 " --> pdb=" O ARG C 165 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N LEU C 167 " --> pdb=" O ILE C 354 " (cutoff:3.500A) removed outlier: 7.650A pdb=" N LEU C 356 " --> pdb=" O LEU C 167 " (cutoff:3.500A) removed outlier: 7.256A pdb=" N ILE C 169 " --> pdb=" O LEU C 356 " (cutoff:3.500A) removed outlier: 8.409A pdb=" N GLU C 166 " --> pdb=" O LEU C 325 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N ALA C 327 " --> pdb=" O GLU C 166 " (cutoff:3.500A) removed outlier: 7.131A pdb=" N ILE C 168 " --> pdb=" O ALA C 327 " (cutoff:3.500A) removed outlier: 8.368A pdb=" N GLY C 170 " --> pdb=" O PRO C 329 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N ILE C 331 " --> pdb=" O GLY C 170 " (cutoff:3.500A) removed outlier: 6.220A pdb=" N LYS C 193 " --> pdb=" O LEU C 258 " (cutoff:3.500A) removed outlier: 8.267A pdb=" N ILE C 260 " --> pdb=" O LYS C 193 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N VAL C 195 " --> pdb=" O ILE C 260 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'D' and resid 5 through 10 removed outlier: 3.577A pdb=" N ARG D 5 " --> pdb=" O GLU D 17 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N GLU D 17 " --> pdb=" O ARG D 5 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N ASP D 15 " --> pdb=" O ILE D 7 " (cutoff:3.500A) removed outlier: 4.746A pdb=" N ILE D 9 " --> pdb=" O VAL D 13 " (cutoff:3.500A) removed outlier: 7.050A pdb=" N VAL D 13 " --> pdb=" O ILE D 9 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N GLN D 43 " --> pdb=" O ARG D 51 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N ILE D 53 " --> pdb=" O VAL D 41 " (cutoff:3.500A) removed outlier: 5.953A pdb=" N VAL D 41 " --> pdb=" O ILE D 53 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N MET D 55 " --> pdb=" O LEU D 39 " (cutoff:3.500A) removed outlier: 5.452A pdb=" N LEU D 39 " --> pdb=" O MET D 55 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'D' and resid 75 through 77 Processing sheet with id= L, first strand: chain 'D' and resid 322 through 325 removed outlier: 9.330A pdb=" N VAL D 144 " --> pdb=" O ILE D 295 " (cutoff:3.500A) removed outlier: 7.135A pdb=" N SER D 297 " --> pdb=" O VAL D 144 " (cutoff:3.500A) removed outlier: 8.560A pdb=" N LEU D 146 " --> pdb=" O SER D 297 " (cutoff:3.500A) removed outlier: 7.211A pdb=" N GLN D 299 " --> pdb=" O LEU D 146 " (cutoff:3.500A) removed outlier: 6.095A pdb=" N VAL D 242 " --> pdb=" O THR D 296 " (cutoff:3.500A) removed outlier: 7.924A pdb=" N ILE D 298 " --> pdb=" O VAL D 242 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N LEU D 244 " --> pdb=" O ILE D 298 " (cutoff:3.500A) removed outlier: 7.563A pdb=" N ALA D 300 " --> pdb=" O LEU D 244 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N VAL D 246 " --> pdb=" O ALA D 300 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'E' and resid 5 through 10 removed outlier: 3.569A pdb=" N ARG E 5 " --> pdb=" O GLU E 17 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N ASP E 15 " --> pdb=" O ILE E 7 " (cutoff:3.500A) removed outlier: 5.132A pdb=" N ILE E 9 " --> pdb=" O VAL E 13 " (cutoff:3.500A) removed outlier: 7.451A pdb=" N VAL E 13 " --> pdb=" O ILE E 9 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N GLN E 43 " --> pdb=" O ARG E 51 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N ILE E 53 " --> pdb=" O VAL E 41 " (cutoff:3.500A) removed outlier: 5.774A pdb=" N VAL E 41 " --> pdb=" O ILE E 53 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'E' and resid 75 through 77 Processing sheet with id= O, first strand: chain 'E' and resid 85 through 87 removed outlier: 4.438A pdb=" N ARG E 85 " --> pdb=" O VAL E 201 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N TYR E 205 " --> pdb=" O MET E 87 " (cutoff:3.500A) removed outlier: 7.020A pdb=" N SER E 173 " --> pdb=" O ALA E 202 " (cutoff:3.500A) removed outlier: 8.499A pdb=" N VAL E 204 " --> pdb=" O SER E 173 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N PHE E 175 " --> pdb=" O VAL E 204 " (cutoff:3.500A) removed outlier: 9.103A pdb=" N VAL E 174 " --> pdb=" O ASP E 241 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N LEU E 243 " --> pdb=" O VAL E 174 " (cutoff:3.500A) removed outlier: 8.252A pdb=" N ALA E 176 " --> pdb=" O LEU E 243 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N PHE E 245 " --> pdb=" O ALA E 176 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N SER E 294 " --> pdb=" O VAL E 242 " (cutoff:3.500A) removed outlier: 8.115A pdb=" N LEU E 244 " --> pdb=" O SER E 294 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N THR E 296 " --> pdb=" O LEU E 244 " (cutoff:3.500A) removed outlier: 8.049A pdb=" N VAL E 246 " --> pdb=" O THR E 296 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N ILE E 298 " --> pdb=" O VAL E 246 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N GLN E 299 " --> pdb=" O VAL E 144 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N LEU E 146 " --> pdb=" O GLN E 299 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N ALA E 322 " --> pdb=" O GLY E 145 " (cutoff:3.500A) removed outlier: 8.118A pdb=" N PHE E 147 " --> pdb=" O ALA E 322 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N VAL E 324 " --> pdb=" O PHE E 147 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'F' and resid 3 through 5 removed outlier: 6.577A pdb=" N ARG F 51 " --> pdb=" O GLN F 42 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'F' and resid 75 through 77 Processing sheet with id= R, first strand: chain 'F' and resid 322 through 325 removed outlier: 7.608A pdb=" N VAL F 144 " --> pdb=" O ILE F 295 " (cutoff:3.500A) removed outlier: 5.850A pdb=" N SER F 297 " --> pdb=" O VAL F 144 " (cutoff:3.500A) removed outlier: 7.414A pdb=" N LEU F 146 " --> pdb=" O SER F 297 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N GLN F 299 " --> pdb=" O LEU F 146 " (cutoff:3.500A) removed outlier: 7.553A pdb=" N GLY F 148 " --> pdb=" O GLN F 299 " (cutoff:3.500A) removed outlier: 5.645A pdb=" N VAL F 301 " --> pdb=" O GLY F 148 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N VAL F 242 " --> pdb=" O THR F 296 " (cutoff:3.500A) removed outlier: 7.910A pdb=" N ILE F 298 " --> pdb=" O VAL F 242 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N LEU F 244 " --> pdb=" O ILE F 298 " (cutoff:3.500A) removed outlier: 8.554A pdb=" N ALA F 300 " --> pdb=" O LEU F 244 " (cutoff:3.500A) removed outlier: 7.227A pdb=" N VAL F 246 " --> pdb=" O ALA F 300 " (cutoff:3.500A) removed outlier: 8.739A pdb=" N TYR F 302 " --> pdb=" O VAL F 246 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N VAL F 174 " --> pdb=" O PHE F 245 " (cutoff:3.500A) removed outlier: 8.534A pdb=" N ASP F 247 " --> pdb=" O VAL F 174 " (cutoff:3.500A) removed outlier: 7.337A pdb=" N ALA F 176 " --> pdb=" O ASP F 247 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'd' and resid 137 through 144 Processing sheet with id= T, first strand: chain 'e' and resid 41 through 44 removed outlier: 5.999A pdb=" N GLN e 5 " --> pdb=" O VAL e 76 " (cutoff:3.500A) removed outlier: 8.046A pdb=" N VAL e 78 " --> pdb=" O GLN e 5 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N ASP e 7 " --> pdb=" O VAL e 78 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N ALA e 80 " --> pdb=" O ASP e 7 " (cutoff:3.500A) removed outlier: 6.967A pdb=" N VAL e 9 " --> pdb=" O ALA e 80 " (cutoff:3.500A) removed outlier: 5.483A pdb=" N SER e 10 " --> pdb=" O SER e 14 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N SER e 14 " --> pdb=" O SER e 10 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'e' and resid 31 through 34 removed outlier: 5.326A pdb=" N LYS e 26 " --> pdb=" O PRO e 49 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'g' and resid 182 through 187 removed outlier: 7.509A pdb=" N ARG g 75 " --> pdb=" O ASP g 166 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N ILE g 168 " --> pdb=" O ARG g 75 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N GLY g 77 " --> pdb=" O ILE g 168 " (cutoff:3.500A) removed outlier: 5.939A pdb=" N LEU g 170 " --> pdb=" O GLY g 77 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N ILE g 79 " --> pdb=" O LEU g 170 " (cutoff:3.500A) removed outlier: 4.879A pdb=" N SER g 172 " --> pdb=" O ILE g 79 " (cutoff:3.500A) removed outlier: 7.071A pdb=" N VAL g 81 " --> pdb=" O SER g 172 " (cutoff:3.500A) removed outlier: 9.236A pdb=" N GLY g 174 " --> pdb=" O VAL g 81 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N GLU g 112 " --> pdb=" O VAL g 76 " (cutoff:3.500A) removed outlier: 7.781A pdb=" N TYR g 78 " --> pdb=" O GLU g 112 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N GLN g 114 " --> pdb=" O TYR g 78 " (cutoff:3.500A) removed outlier: 7.738A pdb=" N ILE g 80 " --> pdb=" O GLN g 114 " (cutoff:3.500A) removed outlier: 7.007A pdb=" N ALA g 116 " --> pdb=" O ILE g 80 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N LYS g 132 " --> pdb=" O PHE g 115 " (cutoff:3.500A) removed outlier: 8.311A pdb=" N LEU g 117 " --> pdb=" O LYS g 132 " (cutoff:3.500A) removed outlier: 8.466A pdb=" N LEU g 134 " --> pdb=" O LEU g 117 " (cutoff:3.500A) 2032 hydrogen bonds defined for protein. 5493 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: 17.87 Time building geometry restraints manager: 22.12 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 7060 1.32 - 1.45: 8530 1.45 - 1.57: 21850 1.57 - 1.69: 18 1.69 - 1.81: 277 Bond restraints: 37735 Sorted by residual: bond pdb=" C4 ATP C 601 " pdb=" C5 ATP C 601 " ideal model delta sigma weight residual 1.388 1.471 -0.083 1.00e-02 1.00e+04 6.92e+01 bond pdb=" C4 ATP B 601 " pdb=" C5 ATP B 601 " ideal model delta sigma weight residual 1.388 1.470 -0.082 1.00e-02 1.00e+04 6.80e+01 bond pdb=" C4 ATP A 601 " pdb=" C5 ATP A 601 " ideal model delta sigma weight residual 1.388 1.470 -0.082 1.00e-02 1.00e+04 6.78e+01 bond pdb=" C5 ATP B 601 " pdb=" C6 ATP B 601 " ideal model delta sigma weight residual 1.409 1.482 -0.073 1.00e-02 1.00e+04 5.36e+01 bond pdb=" C5 ATP A 601 " pdb=" C6 ATP A 601 " ideal model delta sigma weight residual 1.409 1.482 -0.073 1.00e-02 1.00e+04 5.31e+01 ... (remaining 37730 not shown) Histogram of bond angle deviations from ideal: 95.53 - 103.67: 557 103.67 - 111.81: 18325 111.81 - 119.95: 15196 119.95 - 128.09: 16926 128.09 - 136.23: 154 Bond angle restraints: 51158 Sorted by residual: angle pdb=" PB ATP C 601 " pdb=" O3B ATP C 601 " pdb=" PG ATP C 601 " ideal model delta sigma weight residual 139.87 120.37 19.50 1.00e+00 1.00e+00 3.80e+02 angle pdb=" PB ATP A 601 " pdb=" O3B ATP A 601 " pdb=" PG ATP A 601 " ideal model delta sigma weight residual 139.87 121.74 18.13 1.00e+00 1.00e+00 3.29e+02 angle pdb=" PA ATP A 601 " pdb=" O3A ATP A 601 " pdb=" PB ATP A 601 " ideal model delta sigma weight residual 136.83 119.11 17.72 1.00e+00 1.00e+00 3.14e+02 angle pdb=" PA ATP B 601 " pdb=" O3A ATP B 601 " pdb=" PB ATP B 601 " ideal model delta sigma weight residual 136.83 120.06 16.77 1.00e+00 1.00e+00 2.81e+02 angle pdb=" PB ATP B 601 " pdb=" O3B ATP B 601 " pdb=" PG ATP B 601 " ideal model delta sigma weight residual 139.87 123.13 16.74 1.00e+00 1.00e+00 2.80e+02 ... (remaining 51153 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.06: 20951 18.06 - 36.12: 1414 36.12 - 54.18: 235 54.18 - 72.23: 89 72.23 - 90.29: 56 Dihedral angle restraints: 22745 sinusoidal: 8813 harmonic: 13932 Sorted by residual: dihedral pdb=" N VAL D 414 " pdb=" C VAL D 414 " pdb=" CA VAL D 414 " pdb=" CB VAL D 414 " ideal model delta harmonic sigma weight residual 123.40 141.17 -17.77 0 2.50e+00 1.60e-01 5.05e+01 dihedral pdb=" CA TYR F 205 " pdb=" C TYR F 205 " pdb=" N GLY F 206 " pdb=" CA GLY F 206 " ideal model delta harmonic sigma weight residual 180.00 151.57 28.43 0 5.00e+00 4.00e-02 3.23e+01 dihedral pdb=" C VAL D 414 " pdb=" N VAL D 414 " pdb=" CA VAL D 414 " pdb=" CB VAL D 414 " ideal model delta harmonic sigma weight residual -122.00 -135.68 13.68 0 2.50e+00 1.60e-01 3.00e+01 ... (remaining 22742 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.147: 5964 0.147 - 0.293: 26 0.293 - 0.440: 3 0.440 - 0.587: 0 0.587 - 0.734: 1 Chirality restraints: 5994 Sorted by residual: chirality pdb=" CA VAL D 414 " pdb=" N VAL D 414 " pdb=" C VAL D 414 " pdb=" CB VAL D 414 " both_signs ideal model delta sigma weight residual False 2.44 1.71 0.73 2.00e-01 2.50e+01 1.35e+01 chirality pdb=" CB ILE O 14 " pdb=" CA ILE O 14 " pdb=" CG1 ILE O 14 " pdb=" CG2 ILE O 14 " both_signs ideal model delta sigma weight residual False 2.64 2.29 0.36 2.00e-01 2.50e+01 3.20e+00 chirality pdb=" CA GLU D 413 " pdb=" N GLU D 413 " pdb=" C GLU D 413 " pdb=" CB GLU D 413 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.50e+00 ... (remaining 5991 not shown) Planarity restraints: 6634 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE Q 18 " -0.047 2.00e-02 2.50e+03 3.51e-02 2.16e+01 pdb=" CG PHE Q 18 " 0.078 2.00e-02 2.50e+03 pdb=" CD1 PHE Q 18 " -0.005 2.00e-02 2.50e+03 pdb=" CD2 PHE Q 18 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE Q 18 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE Q 18 " -0.006 2.00e-02 2.50e+03 pdb=" CZ PHE Q 18 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE R 18 " -0.041 2.00e-02 2.50e+03 3.10e-02 1.69e+01 pdb=" CG PHE R 18 " 0.067 2.00e-02 2.50e+03 pdb=" CD1 PHE R 18 " 0.010 2.00e-02 2.50e+03 pdb=" CD2 PHE R 18 " -0.012 2.00e-02 2.50e+03 pdb=" CE1 PHE R 18 " -0.014 2.00e-02 2.50e+03 pdb=" CE2 PHE R 18 " 0.005 2.00e-02 2.50e+03 pdb=" CZ PHE R 18 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA B 89 " 0.017 2.00e-02 2.50e+03 3.42e-02 1.17e+01 pdb=" C ALA B 89 " -0.059 2.00e-02 2.50e+03 pdb=" O ALA B 89 " 0.022 2.00e-02 2.50e+03 pdb=" N ARG B 90 " 0.020 2.00e-02 2.50e+03 ... (remaining 6631 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.64: 886 2.64 - 3.20: 41532 3.20 - 3.77: 62353 3.77 - 4.33: 84707 4.33 - 4.90: 126997 Nonbonded interactions: 316475 Sorted by model distance: nonbonded pdb=" OG1 THR C 177 " pdb="MG MG C 602 " model vdw 2.074 2.170 nonbonded pdb=" OG1 THR A 177 " pdb="MG MG A 602 " model vdw 2.099 2.170 nonbonded pdb=" OG1 THR B 177 " pdb="MG MG B 602 " model vdw 2.099 2.170 nonbonded pdb=" O2G ATP B 601 " pdb="MG MG B 602 " model vdw 2.131 2.170 nonbonded pdb=" OD1 ASP D 88 " pdb=" N VAL D 89 " model vdw 2.151 2.520 ... (remaining 316470 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 or resid 601 through 602)) selection = (chain 'B' and (resid 6 through 511 or resid 601 through 602)) selection = (chain 'C' and (resid 6 through 511 or resid 601 through 602)) } ncs_group { reference = chain 'D' selection = (chain 'E' and resid 2 through 464) selection = (chain 'F' and resid 2 through 464) } ncs_group { reference = (chain 'G' and resid 2 through 80) selection = (chain 'H' and resid 2 through 80) selection = (chain 'J' and resid 2 through 80) selection = chain 'K' selection = chain 'L' selection = (chain 'O' and resid 2 through 80) selection = (chain 'P' and resid 2 through 80) selection = chain 'Q' selection = chain 'R' selection = (chain 'S' and resid 2 through 80) } ncs_group { reference = chain 'b' selection = (chain 'p' and resid 7 through 156) } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.410 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: 21.960 Check model and map are aligned: 0.620 Set scattering table: 0.370 Process input model: 108.160 Find NCS groups from input model: 2.960 Set up NCS constraints: 0.250 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: 0.010 Load rotamer database and sin/cos tables:3.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 141.910 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8578 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 : 0.006 0.083 37735 Z= 0.368 Angle : 0.867 19.501 51158 Z= 0.529 Chirality : 0.047 0.734 5994 Planarity : 0.005 0.057 6634 Dihedral : 13.876 90.293 13823 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 27.29 Ramachandran Plot: Outliers : 0.02 % Allowed : 6.28 % Favored : 93.70 % Rotamer Outliers : 0.05 % Cbeta Deviations : 0.07 % 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: -0.91 (0.12), residues: 4856 helix: 0.19 (0.10), residues: 2628 sheet: -0.86 (0.20), residues: 575 loop : -1.67 (0.15), residues: 1653 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9712 Ramachandran restraints generated. 4856 Oldfield, 0 Emsley, 4856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9712 Ramachandran restraints generated. 4856 Oldfield, 0 Emsley, 4856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 425 residues out of total 3854 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 423 time to evaluate : 4.607 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 0 residues processed: 425 average time/residue: 0.4817 time to fit residues: 334.3646 Evaluate side-chains 281 residues out of total 3854 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 281 time to evaluate : 3.492 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.5760 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 481 random chunks: chunk 406 optimal weight: 20.0000 chunk 364 optimal weight: 8.9990 chunk 202 optimal weight: 3.9990 chunk 124 optimal weight: 20.0000 chunk 245 optimal weight: 4.9990 chunk 194 optimal weight: 5.9990 chunk 377 optimal weight: 0.2980 chunk 145 optimal weight: 6.9990 chunk 229 optimal weight: 2.9990 chunk 280 optimal weight: 10.0000 chunk 436 optimal weight: 5.9990 overall best weight: 3.6588 ------------------------------------------------------------------------------- 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: