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/7p3n_13181/05_2023/7p3n_13181_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p3n_13181/05_2023/7p3n_13181.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p3n_13181/05_2023/7p3n_13181.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p3n_13181/05_2023/7p3n_13181.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p3n_13181/05_2023/7p3n_13181_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p3n_13181/05_2023/7p3n_13181_updated.pdb" } resolution = 4.6 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= 0.007 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 23633 2.51 5 N 6307 2.21 5 O 7012 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 52": "OE1" <-> "OE2" Residue "A GLU 85": "OE1" <-> "OE2" Residue "A GLU 300": "OE1" <-> "OE2" Residue "A GLU 308": "OE1" <-> "OE2" Residue "A GLU 416": "OE1" <-> "OE2" Residue "A ARG 477": "NH1" <-> "NH2" Residue "B GLU 8": "OE1" <-> "OE2" Residue "B GLU 103": "OE1" <-> "OE2" Residue "B GLU 166": "OE1" <-> "OE2" Residue "B GLU 214": "OE1" <-> "OE2" Residue "B GLU 255": "OE1" <-> "OE2" Residue "B GLU 285": "OE1" <-> "OE2" Residue "B GLU 403": "OE1" <-> "OE2" Residue "B GLU 461": "OE1" <-> "OE2" Residue "B ARG 477": "NH1" <-> "NH2" Residue "B GLU 498": "OE1" <-> "OE2" Residue "C GLU 166": "OE1" <-> "OE2" Residue "C GLU 332": "OE1" <-> "OE2" Residue "C GLU 423": "OE1" <-> "OE2" Residue "C GLU 461": "OE1" <-> "OE2" Residue "C GLU 479": "OE1" <-> "OE2" Residue "D ARG 5": "NH1" <-> "NH2" Residue "D ARG 20": "NH1" <-> "NH2" Residue "D GLU 96": "OE1" <-> "OE2" Residue "D ARG 181": "NH1" <-> "NH2" Residue "D GLU 191": "OE1" <-> "OE2" Residue "D GLU 210": "OE1" <-> "OE2" Residue "D GLU 227": "OE1" <-> "OE2" Residue "D GLU 278": "OE1" <-> "OE2" Residue "D GLU 357": "OE1" <-> "OE2" Residue "D GLU 386": "OE1" <-> "OE2" Residue "D GLU 427": "OE1" <-> "OE2" Residue "E ARG 20": "NH1" <-> "NH2" Residue "E GLU 180": "OE1" <-> "OE2" Residue "E ARG 217": "NH1" <-> "NH2" Residue "E GLU 227": "OE1" <-> "OE2" Residue "E GLU 232": "OE1" <-> "OE2" Residue "E ARG 240": "NH1" <-> "NH2" Residue "E TYR 252": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 258": "OE1" <-> "OE2" Residue "E ARG 371": "NH1" <-> "NH2" Residue "E GLU 427": "OE1" <-> "OE2" Residue "E GLU 439": "OE1" <-> "OE2" Residue "F GLU 59": "OE1" <-> "OE2" Residue "F GLU 126": "OE1" <-> "OE2" Residue "F GLU 232": "OE1" <-> "OE2" Residue "F ARG 251": "NH1" <-> "NH2" Residue "F GLU 285": "OE1" <-> "OE2" Residue "F ARG 363": "NH1" <-> "NH2" Residue "F GLU 374": "OE1" <-> "OE2" Residue "F GLU 389": "OE1" <-> "OE2" Residue "F GLU 413": "OE1" <-> "OE2" Residue "H GLU 36": "OE1" <-> "OE2" Residue "O GLU 43": "OE1" <-> "OE2" Residue "O PHE 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P GLU 43": "OE1" <-> "OE2" Residue "Q GLU 36": "OE1" <-> "OE2" Residue "S GLU 2": "OE1" <-> "OE2" Residue "a GLU 87": "OE1" <-> "OE2" Residue "a ARG 182": "NH1" <-> "NH2" Residue "a ARG 224": "NH1" <-> "NH2" Residue "a GLU 240": "OE1" <-> "OE2" Residue "b ARG 38": "NH1" <-> "NH2" Residue "b ARG 91": "NH1" <-> "NH2" Residue "b GLU 97": "OE1" <-> "OE2" Residue "b GLU 112": "OE1" <-> "OE2" Residue "b GLU 143": "OE1" <-> "OE2" Residue "d GLU 98": "OE1" <-> "OE2" Residue "d GLU 121": "OE1" <-> "OE2" Residue "d GLU 131": "OE1" <-> "OE2" Residue "e ARG 51": "NH1" <-> "NH2" Residue "e GLU 60": "OE1" <-> "OE2" Residue "e ARG 85": "NH1" <-> "NH2" Residue "g GLU 62": "OE1" <-> "OE2" Residue "g ARG 66": "NH1" <-> "NH2" Residue "g GLU 108": "OE1" <-> "OE2" Residue "g GLU 164": "OE1" <-> "OE2" Residue "g GLU 196": "OE1" <-> "OE2" Residue "g ARG 224": "NH1" <-> "NH2" Residue "g GLU 227": "OE1" <-> "OE2" Residue "g GLU 281": "OE1" <-> "OE2" Residue "p GLU 77": "OE1" <-> "OE2" Residue "p ARG 121": "NH1" <-> "NH2" Time to flip residues: 0.15s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/chem_data/mon_lib" Total number of atoms: 37114 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: 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: 3821 Number of conformers: 1 Conformer: "" Number of residues, atoms: 506, 3821 Classifications: {'peptide': 506} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 488} Chain: "D" 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: "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: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 440} 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: {'PTRANS': 22, 'TRANS': 440} 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: 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: 585 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 585 Classifications: {'peptide': 80} Link IDs: {'PTRANS': 4, 'TRANS': 75} 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: 577 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 577 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 4, 'TRANS': 74} 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: 1112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 1112 Classifications: {'peptide': 145} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 142} 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: "E" 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: 19.64, per 1000 atoms: 0.53 Number of scatterers: 37114 At special positions: 0 Unit cell: (135.15, 138.55, 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 11 15.00 Mg 4 11.99 O 7012 8.00 N 6307 7.00 C 23633 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 17.99 Conformation dependent library (CDL) restraints added in 6.3 seconds 9702 Ramachandran restraints generated. 4851 Oldfield, 0 Emsley, 4851 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8914 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 178 helices and 25 sheets defined 54.6% alpha, 9.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.41 Creating SS restraints... Processing helix chain 'A' and resid 4 through 14 Processing helix chain 'A' and resid 18 through 25 removed outlier: 3.660A pdb=" N THR A 25 " --> pdb=" O ASP A 21 " (cutoff:3.500A) 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 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 187 removed outlier: 3.705A pdb=" N ASP A 182 " --> pdb=" O ALA A 178 " (cutoff:3.500A) Processing helix chain 'A' and resid 203 through 216 Processing helix chain 'A' and resid 233 through 252 Proline residue: A 240 - end of helix removed outlier: 3.727A pdb=" N PHE A 250 " --> pdb=" O MET A 246 " (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: 4.093A 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 removed outlier: 3.841A pdb=" N SER A 348 " --> pdb=" O THR A 344 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ILE A 349 " --> pdb=" O ASN A 345 " (cutoff:3.500A) Processing helix chain 'A' and resid 358 through 362 Processing helix chain 'A' and resid 380 through 382 No H-bonds generated for 'chain 'A' and resid 380 through 382' Processing helix chain 'A' and resid 385 through 403 removed outlier: 4.720A pdb=" N GLY A 392 " --> pdb=" O LYS A 388 " (cutoff:3.500A) removed outlier: 5.669A pdb=" N GLY A 393 " --> pdb=" O LYS A 389 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N ILE A 394 " --> pdb=" O LEU A 390 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 409 removed outlier: 3.953A pdb=" N GLN A 409 " --> pdb=" O ALA A 406 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 432 Processing helix chain 'A' and resid 442 through 453 Processing helix chain 'A' and resid 463 through 479 removed outlier: 3.666A pdb=" N VAL A 466 " --> pdb=" O LYS A 463 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ASP A 467 " --> pdb=" O LYS A 464 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ARG A 477 " --> pdb=" O ALA A 474 " (cutoff:3.500A) Processing helix chain 'A' and resid 481 through 490 Processing helix chain 'A' and resid 495 through 510 Processing helix chain 'B' and resid 10 through 18 Processing helix chain 'B' and resid 23 through 27 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 154 through 157 No H-bonds generated for 'chain 'B' and resid 154 through 157' Processing helix chain 'B' and resid 176 through 190 removed outlier: 3.530A pdb=" N ALA B 180 " --> pdb=" O LYS B 176 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N LYS B 188 " --> pdb=" O ILE B 184 " (cutoff:3.500A) removed outlier: 5.080A pdb=" N ASN B 189 " --> pdb=" O ILE B 185 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N SER B 190 " --> pdb=" O ALA B 186 " (cutoff:3.500A) Processing helix chain 'B' and resid 203 through 216 Processing helix chain 'B' and resid 233 through 253 Proline residue: B 240 - end of helix removed outlier: 3.657A pdb=" N PHE B 250 " --> pdb=" O MET B 246 " (cutoff:3.500A) Processing helix chain 'B' and resid 264 through 277 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: 3.600A pdb=" N PHE B 292 " --> pdb=" O GLY B 289 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ARG B 297 " --> pdb=" O LEU B 294 " (cutoff:3.500A) removed outlier: 4.253A 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 347 Processing helix chain 'B' and resid 358 through 361 No H-bonds generated for 'chain 'B' and resid 358 through 361' Processing helix chain 'B' and resid 380 through 382 No H-bonds generated for 'chain 'B' and resid 380 through 382' Processing helix chain 'B' and resid 385 through 407 removed outlier: 4.110A pdb=" N GLY B 392 " --> pdb=" O LYS B 388 " (cutoff:3.500A) removed outlier: 4.950A pdb=" N GLY B 393 " --> pdb=" O LYS B 389 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N ILE B 394 " --> pdb=" O LEU B 390 " (cutoff:3.500A) removed outlier: 4.682A pdb=" N ALA B 406 " --> pdb=" O ARG B 402 " (cutoff:3.500A) removed outlier: 5.926A pdb=" N PHE B 407 " --> pdb=" O GLU B 403 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 429 Processing helix chain 'B' and resid 442 through 453 Processing helix chain 'B' and resid 462 through 479 removed outlier: 4.868A pdb=" N VAL B 466 " --> pdb=" O LYS B 463 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ALA B 471 " --> pdb=" O PHE B 468 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N TYR B 475 " --> pdb=" O LEU B 472 " (cutoff:3.500A) Processing helix chain 'B' and resid 481 through 490 Processing helix chain 'B' and resid 495 through 511 Processing helix chain 'C' and resid 7 through 17 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 153 through 157 Processing helix chain 'C' and resid 177 through 190 removed outlier: 3.636A pdb=" N LYS C 188 " --> pdb=" O ILE C 184 " (cutoff:3.500A) removed outlier: 4.978A pdb=" N ASN C 189 " --> pdb=" O ILE C 185 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N SER C 190 " --> pdb=" O ALA C 186 " (cutoff:3.500A) Processing helix chain 'C' and resid 203 through 216 Processing helix chain 'C' and resid 233 through 253 Proline residue: C 240 - end of helix removed outlier: 3.589A pdb=" N TYR C 249 " --> pdb=" O THR C 245 " (cutoff:3.500A) removed outlier: 4.569A pdb=" N PHE C 250 " --> pdb=" O MET C 246 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N ARG C 251 " --> pdb=" O GLY C 247 " (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 289 through 301 removed outlier: 4.255A pdb=" N ARG C 297 " --> pdb=" O LEU C 294 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLU C 300 " --> pdb=" O ARG C 297 " (cutoff:3.500A) Processing helix chain 'C' and resid 307 through 313 Processing helix chain 'C' and resid 334 through 336 No H-bonds generated for 'chain 'C' and resid 334 through 336' Processing helix chain 'C' and resid 341 through 347 Processing helix chain 'C' and resid 358 through 362 Processing helix chain 'C' and resid 371 through 373 No H-bonds generated for 'chain 'C' and resid 371 through 373' Processing helix chain 'C' and resid 385 through 390 Processing helix chain 'C' and resid 394 through 409 removed outlier: 3.730A pdb=" N GLN C 409 " --> pdb=" O ALA C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 431 Processing helix chain 'C' and resid 442 through 453 Processing helix chain 'C' and resid 463 through 479 removed outlier: 3.797A pdb=" N VAL C 466 " --> pdb=" O LYS C 463 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ALA C 471 " --> pdb=" O PHE C 468 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N SER C 478 " --> pdb=" O TYR C 475 " (cutoff:3.500A) Processing helix chain 'C' and resid 481 through 490 Processing helix chain 'C' and resid 495 through 509 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 168 Processing helix chain 'D' and resid 182 through 194 Processing helix chain 'D' and resid 196 through 200 Processing helix chain 'D' and resid 212 through 231 removed outlier: 4.733A pdb=" N ALA D 219 " --> pdb=" O ARG D 215 " (cutoff:3.500A) removed outlier: 4.726A pdb=" N LEU D 220 " --> pdb=" O LEU D 216 " (cutoff:3.500A) Processing helix chain 'D' and resid 249 through 262 Processing helix chain 'D' and resid 274 through 285 removed outlier: 4.231A pdb=" N ALA D 277 " --> pdb=" O PRO D 274 " (cutoff:3.500A) removed outlier: 4.511A 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 318 removed outlier: 3.614A pdb=" N ALA D 318 " --> pdb=" O ALA D 314 " (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 382 removed outlier: 4.119A pdb=" N ASP D 377 " --> pdb=" O LYS D 373 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N ILE D 378 " --> pdb=" O GLU D 374 " (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 405 Processing helix chain 'D' and resid 410 through 415 removed outlier: 3.514A pdb=" N VAL D 414 " --> pdb=" O HIS D 410 " (cutoff:3.500A) Processing helix chain 'D' and resid 428 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 130 through 135 Processing helix chain 'E' and resid 154 through 168 removed outlier: 3.568A pdb=" N MET E 158 " --> pdb=" O LYS E 154 " (cutoff:3.500A) Processing helix chain 'E' and resid 182 through 194 Processing helix chain 'E' and resid 212 through 216 Processing helix chain 'E' and resid 219 through 231 Processing helix chain 'E' and resid 249 through 260 Processing helix chain 'E' and resid 274 through 285 removed outlier: 4.074A pdb=" N ALA E 277 " --> pdb=" O PRO E 274 " (cutoff:3.500A) 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 319 removed outlier: 3.796A pdb=" N ALA E 318 " --> pdb=" O ALA E 314 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N HIS E 319 " --> pdb=" O THR E 315 " (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 381 removed outlier: 4.368A pdb=" N ASP E 377 " --> pdb=" O LYS E 373 " (cutoff:3.500A) removed outlier: 4.800A pdb=" N ILE E 378 " --> pdb=" O GLU E 374 " (cutoff:3.500A) Processing helix chain 'E' and resid 384 through 386 No H-bonds generated for 'chain 'E' and resid 384 through 386' Processing helix chain 'E' and resid 389 through 405 Processing helix chain 'E' and resid 412 through 414 No H-bonds generated for 'chain 'E' and resid 412 through 414' Processing helix chain 'E' and resid 425 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 168 Processing helix chain 'F' and resid 182 through 195 Processing helix chain 'F' and resid 197 through 200 Processing helix chain 'F' and resid 212 through 231 removed outlier: 4.917A pdb=" N ALA F 219 " --> pdb=" O ARG F 215 " (cutoff:3.500A) removed outlier: 4.697A pdb=" N LEU F 220 " --> pdb=" O LEU F 216 " (cutoff:3.500A) Processing helix chain 'F' and resid 249 through 263 removed outlier: 4.078A pdb=" N ALA F 261 " --> pdb=" O THR F 257 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N LEU F 262 " --> pdb=" O GLU F 258 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N LEU F 263 " --> pdb=" O VAL F 259 " (cutoff:3.500A) Processing helix chain 'F' and resid 276 through 285 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 317 Processing helix chain 'F' and resid 328 through 332 Processing helix chain 'F' and resid 356 through 382 removed outlier: 4.325A pdb=" N ASP F 377 " --> pdb=" O LYS F 373 " (cutoff:3.500A) removed outlier: 4.883A pdb=" N ILE F 378 " --> pdb=" O GLU F 374 " (cutoff:3.500A) Processing helix chain 'F' and resid 392 through 404 Processing helix chain 'F' and resid 425 through 437 Processing helix chain 'F' and resid 445 through 448 No H-bonds generated for '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: 3.690A pdb=" N ARG G 33 " --> pdb=" O LEU G 29 " (cutoff:3.500A) Processing helix chain 'G' and resid 44 through 57 removed outlier: 3.627A pdb=" N LEU G 48 " --> pdb=" O ALA G 45 " (cutoff:3.500A) Processing helix chain 'G' and resid 61 through 75 Processing helix chain 'H' and resid 2 through 40 removed outlier: 3.840A pdb=" N ARG H 40 " --> pdb=" O GLU H 36 " (cutoff:3.500A) Processing helix chain 'H' and resid 42 through 59 Proline residue: H 46 - end of helix removed outlier: 3.980A 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: 3.619A pdb=" N GLY J 28 " --> pdb=" O ALA J 24 " (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 38 Processing helix chain 'K' and resid 42 through 59 Proline residue: K 46 - end of helix Processing helix chain 'K' and resid 61 through 75 Processing helix chain 'L' and resid 3 through 40 Processing helix chain 'L' and resid 45 through 57 Processing helix chain 'L' and resid 61 through 76 Processing helix chain 'O' and resid 2 through 40 removed outlier: 3.677A pdb=" N GLY O 19 " --> pdb=" O LEU O 15 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ARG O 33 " --> pdb=" O LEU O 29 " (cutoff:3.500A) Processing helix chain 'O' and resid 42 through 59 Proline residue: O 46 - end of helix removed outlier: 3.804A pdb=" N GLY O 57 " --> pdb=" O LEU O 54 " (cutoff:3.500A) Processing helix chain 'O' and resid 61 through 74 Processing helix chain 'P' and resid 2 through 40 removed outlier: 3.850A pdb=" N ARG P 33 " --> pdb=" O LEU P 29 " (cutoff:3.500A) Processing helix chain 'P' and resid 45 through 59 Processing helix chain 'P' and resid 61 through 76 Processing helix chain 'Q' and resid 2 through 40 removed outlier: 3.982A pdb=" N ARG Q 33 " --> pdb=" O LEU Q 29 " (cutoff:3.500A) Processing helix chain 'Q' and resid 45 through 76 removed outlier: 3.575A pdb=" N GLY Q 57 " --> pdb=" O PHE Q 53 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N LEU Q 58 " --> pdb=" O LEU Q 54 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ASP Q 60 " --> pdb=" O ALA Q 56 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ALA Q 61 " --> pdb=" O GLY Q 57 " (cutoff:3.500A) removed outlier: 5.465A pdb=" N VAL Q 62 " --> pdb=" O LEU Q 58 " (cutoff:3.500A) Proline residue: Q 63 - end of helix Processing helix chain 'R' and resid 2 through 40 Processing helix chain 'R' and resid 42 through 57 Proline residue: R 46 - end of helix Processing helix chain 'R' and resid 61 through 75 Processing helix chain 'S' and resid 3 through 40 Processing helix chain 'S' and resid 43 through 57 Proline residue: S 46 - end of helix removed outlier: 3.506A pdb=" N ALA S 56 " --> pdb=" O PHE S 53 " (cutoff:3.500A) Processing helix chain 'S' and resid 61 through 75 Processing helix chain 'a' and resid 16 through 26 removed outlier: 4.211A pdb=" N LYS a 25 " --> pdb=" O MET a 21 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N MET a 26 " --> pdb=" O THR a 22 " (cutoff:3.500A) Processing helix chain 'a' and resid 53 through 71 removed outlier: 4.056A 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 109 through 127 removed outlier: 4.080A pdb=" N ASP a 126 " --> pdb=" O MET a 122 " (cutoff:3.500A) removed outlier: 4.667A 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: 4.127A pdb=" N PHE a 139 " --> pdb=" O GLN a 135 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N VAL a 140 " --> pdb=" O VAL a 136 " (cutoff:3.500A) Processing helix chain 'a' and resid 148 through 153 removed outlier: 4.351A pdb=" N TYR a 153 " --> pdb=" O PRO a 149 " (cutoff:3.500A) Processing helix chain 'a' and resid 162 through 180 Processing helix chain 'a' and resid 186 through 190 Processing helix chain 'a' and resid 203 through 209 Processing helix chain 'a' and resid 211 through 219 Processing helix chain 'a' and resid 222 through 246 removed outlier: 4.039A pdb=" N ILE a 226 " --> pdb=" O LEU a 222 " (cutoff:3.500A) Processing helix chain 'a' and resid 257 through 288 removed outlier: 4.668A pdb=" N TRP a 261 " --> pdb=" O LEU a 257 " (cutoff:3.500A) Processing helix chain 'b' and resid 13 through 138 removed outlier: 4.079A pdb=" N PHE b 24 " --> pdb=" O PHE b 20 " (cutoff:3.500A) removed outlier: 4.871A pdb=" N TRP b 26 " --> pdb=" O MET b 22 " (cutoff:3.500A) Proline residue: b 27 - end of helix removed outlier: 3.777A pdb=" N ILE b 33 " --> pdb=" O LEU b 29 " (cutoff:3.500A) removed outlier: 4.627A pdb=" N SER b 34 " --> pdb=" O ILE b 30 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N GLU b 35 " --> pdb=" O ASN b 31 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N ALA b 52 " --> pdb=" O GLU b 48 " (cutoff:3.500A) removed outlier: 4.728A pdb=" N ASP b 53 " --> pdb=" O LYS b 49 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N LEU b 54 " --> pdb=" O ALA b 50 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N GLN b 58 " --> pdb=" O LEU b 54 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ALA b 59 " --> pdb=" O ALA b 55 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N GLN b 60 " --> pdb=" O ASP b 56 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N ALA b 67 " --> pdb=" O GLN b 63 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N ALA b 68 " --> pdb=" O GLU b 64 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N LYS b 69 " --> pdb=" O LEU b 65 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N GLU b 112 " --> pdb=" O ALA b 108 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLU b 119 " --> pdb=" O SER b 115 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N GLU b 133 " --> pdb=" O VAL b 129 " (cutoff:3.500A) removed outlier: 5.461A pdb=" N LYS b 134 " --> pdb=" O THR b 130 " (cutoff:3.500A) removed outlier: 5.423A pdb=" N ILE b 135 " --> pdb=" O GLY b 131 " (cutoff:3.500A) removed outlier: 5.336A pdb=" N LEU b 136 " --> pdb=" O ALA b 132 " (cutoff:3.500A) removed outlier: 4.124A 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 83 Processing helix chain 'd' and resid 88 through 104 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 91 through 125 removed outlier: 3.722A pdb=" N LEU e 95 " --> pdb=" O ALA e 92 " (cutoff:3.500A) removed outlier: 4.925A pdb=" N GLU e 96 " --> pdb=" O ALA e 93 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LEU e 112 " --> pdb=" O LYS e 109 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N ASP e 113 " --> pdb=" O SER e 110 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N ALA e 115 " --> pdb=" O LEU e 112 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N ALA e 116 " --> pdb=" O ASP e 113 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ALA e 117 " --> pdb=" O SER e 114 " (cutoff:3.500A) removed outlier: 4.794A pdb=" N LEU e 118 " --> pdb=" O ALA e 115 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N ALA e 119 " --> pdb=" O ALA e 116 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N THR e 124 " --> pdb=" O LEU e 121 " (cutoff:3.500A) Processing helix chain 'e' and resid 128 through 135 removed outlier: 3.815A pdb=" N ILE e 134 " --> pdb=" O THR e 130 " (cutoff:3.500A) Processing helix chain 'g' and resid 4 through 59 removed outlier: 4.366A pdb=" N ALA g 40 " --> pdb=" O GLN g 36 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N GLN g 41 " --> pdb=" O GLU g 37 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N GLY g 42 " --> pdb=" O ARG g 38 " (cutoff:3.500A) removed outlier: 4.401A 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: 3.567A pdb=" N GLU g 108 " --> pdb=" O LYS g 104 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N GLN g 109 " --> pdb=" O ALA g 105 " (cutoff:3.500A) Processing helix chain 'g' and resid 120 through 129 Processing helix chain 'g' and resid 146 through 161 removed outlier: 4.235A pdb=" N GLY g 151 " --> pdb=" O GLU g 147 " (cutoff:3.500A) removed outlier: 4.874A pdb=" N SER g 152 " --> pdb=" O GLN g 148 " (cutoff:3.500A) Processing helix chain 'g' and resid 214 through 286 Processing helix chain 'p' and resid 3 through 138 Proline residue: p 27 - end of helix removed outlier: 4.320A pdb=" N ARG p 121 " --> pdb=" O ARG p 117 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N GLN p 122 " --> pdb=" O GLU p 118 " (cutoff:3.500A) removed outlier: 3.838A 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 29 through 31 removed outlier: 7.198A pdb=" N GLY A 73 " --> pdb=" O LEU A 65 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N HIS A 43 " --> pdb=" O ILE A 32 " (cutoff:3.500A) removed outlier: 6.017A pdb=" N ILE A 32 " --> pdb=" O HIS A 43 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 97 through 100 removed outlier: 4.301A 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 110 removed outlier: 4.021A pdb=" N ARG A 107 " --> pdb=" O THR A 222 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N VAL A 224 " --> pdb=" O ARG A 107 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N VAL A 109 " --> pdb=" O VAL A 224 " (cutoff:3.500A) removed outlier: 7.097A pdb=" N CYS A 194 " --> pdb=" O THR A 223 " (cutoff:3.500A) removed outlier: 8.885A pdb=" N VAL A 225 " --> pdb=" O CYS A 194 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N TYR A 196 " --> pdb=" O VAL A 225 " (cutoff:3.500A) removed outlier: 7.938A pdb=" N ALA A 227 " --> pdb=" O TYR A 196 " (cutoff:3.500A) removed outlier: 6.266A pdb=" N ALA A 198 " --> pdb=" O ALA A 227 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LYS A 193 " --> pdb=" O ASP A 256 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ILE A 260 " --> pdb=" O VAL A 195 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N VAL A 197 " --> pdb=" O ILE A 260 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N SER A 324 " --> pdb=" O ALA A 257 " (cutoff:3.500A) removed outlier: 7.695A pdb=" N ILE A 259 " --> pdb=" O SER A 324 " (cutoff:3.500A) removed outlier: 6.022A pdb=" N THR A 326 " --> pdb=" O ILE A 259 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 353 through 355 removed outlier: 6.310A pdb=" N LEU A 167 " --> pdb=" O ILE A 354 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ILE A 331 " --> pdb=" O ILE A 168 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 29 through 31 removed outlier: 3.525A pdb=" N ALA B 89 " --> pdb=" O GLY B 30 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N GLY B 73 " --> pdb=" O LEU B 65 " (cutoff:3.500A) removed outlier: 4.882A pdb=" N LEU B 67 " --> pdb=" O SER B 71 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N SER B 71 " --> pdb=" O LEU B 67 " (cutoff:3.500A) removed outlier: 5.592A pdb=" N HIS B 43 " --> pdb=" O ILE B 32 " (cutoff:3.500A) removed outlier: 5.644A 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: 3.752A pdb=" N LEU B 126 " --> pdb=" O VAL B 100 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 107 through 110 removed outlier: 6.695A pdb=" N CYS B 194 " --> pdb=" O THR B 223 " (cutoff:3.500A) removed outlier: 8.641A pdb=" N VAL B 225 " --> pdb=" O CYS B 194 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N TYR B 196 " --> pdb=" O VAL B 225 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N THR B 326 " --> pdb=" O ILE B 259 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N GLU B 166 " --> pdb=" O ALA B 327 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ILE B 168 " --> pdb=" O PRO B 329 " (cutoff:3.500A) removed outlier: 6.994A pdb=" N GLY B 352 " --> pdb=" O LEU B 167 " (cutoff:3.500A) removed outlier: 8.409A pdb=" N ILE B 169 " --> pdb=" O GLY B 352 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N ILE B 354 " --> pdb=" O ILE B 169 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'C' and resid 31 through 36 removed outlier: 6.362A pdb=" N ARG C 41 " --> pdb=" O VAL C 33 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N VAL C 35 " --> pdb=" O ILE C 39 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N ILE C 39 " --> pdb=" O VAL C 35 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N GLY C 73 " --> pdb=" O ASN C 66 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N VAL C 75 " --> pdb=" O ALA C 64 " (cutoff:3.500A) removed outlier: 5.921A pdb=" N ALA C 64 " --> pdb=" O VAL C 75 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ALA C 64 " --> pdb=" O GLU C 52 " (cutoff:3.500A) removed outlier: 5.004A pdb=" N GLU C 52 " --> pdb=" O ALA C 64 " (cutoff:3.500A) removed outlier: 4.861A pdb=" N ARG C 94 " --> pdb=" O MET C 53 " (cutoff:3.500A) removed outlier: 7.656A pdb=" N GLU C 55 " --> pdb=" O THR C 92 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N THR C 92 " --> pdb=" O GLU C 55 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'C' and resid 97 through 100 removed outlier: 4.037A pdb=" N LEU C 126 " --> pdb=" O VAL C 100 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'C' and resid 107 through 109 removed outlier: 4.144A pdb=" N ARG C 107 " --> pdb=" O THR C 222 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N VAL C 109 " --> pdb=" O VAL C 224 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N ALA C 226 " --> pdb=" O VAL C 109 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N CYS C 194 " --> pdb=" O THR C 223 " (cutoff:3.500A) removed outlier: 8.914A pdb=" N VAL C 225 " --> pdb=" O CYS C 194 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N TYR C 196 " --> pdb=" O VAL C 225 " (cutoff:3.500A) removed outlier: 8.084A pdb=" N ALA C 227 " --> pdb=" O TYR C 196 " (cutoff:3.500A) removed outlier: 6.158A pdb=" N ALA C 198 " --> pdb=" O ALA C 227 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N SER C 324 " --> pdb=" O ALA C 257 " (cutoff:3.500A) removed outlier: 7.883A pdb=" N ILE C 259 " --> pdb=" O SER C 324 " (cutoff:3.500A) removed outlier: 6.045A pdb=" N THR C 326 " --> pdb=" O ILE C 259 " (cutoff:3.500A) removed outlier: 7.261A pdb=" N TYR C 261 " --> pdb=" O THR C 326 " (cutoff:3.500A) removed outlier: 6.005A pdb=" N LEU C 328 " --> pdb=" O TYR C 261 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'C' and resid 353 through 355 removed outlier: 6.200A pdb=" N LEU C 167 " --> pdb=" O ILE C 354 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N GLY C 170 " --> pdb=" O ILE C 331 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'D' and resid 3 through 5 removed outlier: 3.918A pdb=" N THR D 38 " --> pdb=" O MET D 55 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ILE D 53 " --> pdb=" O GLU D 40 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N ARG D 51 " --> pdb=" O GLN D 42 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N VAL D 16 " --> pdb=" O VAL D 50 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N GLU D 17 " --> pdb=" O ILE D 6 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N ILE D 6 " --> pdb=" O GLU D 17 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'D' and resid 75 through 77 Processing sheet with id= N, first strand: chain 'D' and resid 322 through 325 removed outlier: 3.565A pdb=" N ALA D 322 " --> pdb=" O LYS D 143 " (cutoff:3.500A) removed outlier: 9.426A pdb=" N VAL D 144 " --> pdb=" O ILE D 295 " (cutoff:3.500A) removed outlier: 7.346A pdb=" N SER D 297 " --> pdb=" O VAL D 144 " (cutoff:3.500A) removed outlier: 8.337A pdb=" N LEU D 146 " --> pdb=" O SER D 297 " (cutoff:3.500A) removed outlier: 7.265A pdb=" N GLN D 299 " --> pdb=" O LEU D 146 " (cutoff:3.500A) removed outlier: 6.210A pdb=" N VAL D 242 " --> pdb=" O THR D 296 " (cutoff:3.500A) removed outlier: 7.888A pdb=" N ILE D 298 " --> pdb=" O VAL D 242 " (cutoff:3.500A) removed outlier: 6.100A pdb=" N LEU D 244 " --> pdb=" O ILE D 298 " (cutoff:3.500A) removed outlier: 7.466A pdb=" N ALA D 300 " --> pdb=" O LEU D 244 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N VAL D 246 " --> pdb=" O ALA D 300 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N LEU D 172 " --> pdb=" O LEU D 243 " (cutoff:3.500A) removed outlier: 7.860A pdb=" N PHE D 245 " --> pdb=" O LEU D 172 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N VAL D 174 " --> pdb=" O PHE D 245 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'E' and resid 3 through 5 removed outlier: 3.877A pdb=" N THR E 38 " --> pdb=" O MET E 55 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N ARG E 51 " --> pdb=" O GLN E 42 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ILE E 10 " --> pdb=" O VAL E 13 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N ASP E 15 " --> pdb=" O GLN E 8 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N GLN E 8 " --> pdb=" O ASP E 15 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N GLU E 17 " --> pdb=" O ILE E 6 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N ILE E 6 " --> pdb=" O GLU E 17 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'E' and resid 75 through 77 Processing sheet with id= Q, first strand: chain 'E' and resid 322 through 325 removed outlier: 8.197A pdb=" N VAL E 144 " --> pdb=" O ILE E 295 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N SER E 297 " --> pdb=" O VAL E 144 " (cutoff:3.500A) removed outlier: 8.278A pdb=" N LEU E 146 " --> pdb=" O SER E 297 " (cutoff:3.500A) removed outlier: 7.490A pdb=" N GLN E 299 " --> pdb=" O LEU E 146 " (cutoff:3.500A) removed outlier: 7.741A pdb=" N GLY E 148 " --> pdb=" O GLN E 299 " (cutoff:3.500A) removed outlier: 5.949A pdb=" N VAL E 301 " --> pdb=" O GLY E 148 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'E' and resid 175 through 178 Processing sheet with id= S, first strand: chain 'F' and resid 3 through 5 removed outlier: 3.529A pdb=" N THR F 38 " --> pdb=" O MET F 55 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ILE F 53 " --> pdb=" O GLU F 40 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N ARG F 51 " --> pdb=" O GLN F 42 " (cutoff:3.500A) removed outlier: 5.824A pdb=" N GLU F 17 " --> pdb=" O ILE F 6 " (cutoff:3.500A) removed outlier: 6.134A pdb=" N ILE F 6 " --> pdb=" O GLU F 17 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'F' and resid 75 through 77 Processing sheet with id= U, first strand: chain 'F' and resid 322 through 324 removed outlier: 9.351A pdb=" N VAL F 144 " --> pdb=" O ILE F 295 " (cutoff:3.500A) removed outlier: 7.346A pdb=" N SER F 297 " --> pdb=" O VAL F 144 " (cutoff:3.500A) removed outlier: 8.424A pdb=" N LEU F 146 " --> pdb=" O SER F 297 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N GLN F 299 " --> pdb=" O LEU F 146 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'd' and resid 110 through 113 Processing sheet with id= W, first strand: chain 'e' and resid 41 through 45 removed outlier: 4.038A pdb=" N GLY e 67 " --> pdb=" O LEU e 45 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N GLN e 5 " --> pdb=" O VAL e 76 " (cutoff:3.500A) removed outlier: 8.010A pdb=" N VAL e 78 " --> pdb=" O GLN e 5 " (cutoff:3.500A) removed outlier: 7.095A pdb=" N ASP e 7 " --> pdb=" O VAL e 78 " (cutoff:3.500A) removed outlier: 7.379A pdb=" N ALA e 80 " --> pdb=" O ASP e 7 " (cutoff:3.500A) removed outlier: 6.218A pdb=" N VAL e 9 " --> pdb=" O ALA e 80 " (cutoff:3.500A) removed outlier: 5.563A pdb=" N SER e 10 " --> pdb=" O SER e 14 " (cutoff:3.500A) removed outlier: 4.553A 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: 6.037A pdb=" N LYS e 26 " --> pdb=" O PRO e 49 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N THR e 82 " --> pdb=" O SER e 65 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'g' and resid 181 through 187 removed outlier: 7.736A pdb=" N ARG g 75 " --> pdb=" O ASP g 166 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N ILE g 168 " --> pdb=" O ARG g 75 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N GLY g 77 " --> pdb=" O ILE g 168 " (cutoff:3.500A) removed outlier: 5.528A pdb=" N LEU g 170 " --> pdb=" O GLY g 77 " (cutoff:3.500A) removed outlier: 5.361A pdb=" N ILE g 79 " --> pdb=" O LEU g 170 " (cutoff:3.500A) removed outlier: 4.923A pdb=" N SER g 172 " --> pdb=" O ILE g 79 " (cutoff:3.500A) removed outlier: 7.201A pdb=" N VAL g 81 " --> pdb=" O SER g 172 " (cutoff:3.500A) removed outlier: 9.743A pdb=" N GLY g 174 " --> pdb=" O VAL g 81 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N GLU g 112 " --> pdb=" O VAL g 76 " (cutoff:3.500A) removed outlier: 8.246A pdb=" N TYR g 78 " --> pdb=" O GLU g 112 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N GLN g 114 " --> pdb=" O TYR g 78 " (cutoff:3.500A) removed outlier: 7.535A pdb=" N ILE g 80 " --> pdb=" O GLN g 114 " (cutoff:3.500A) removed outlier: 6.150A pdb=" N ALA g 116 " --> pdb=" O ILE g 80 " (cutoff:3.500A) removed outlier: 7.824A pdb=" N LYS g 132 " --> pdb=" O PHE g 115 " (cutoff:3.500A) removed outlier: 8.757A pdb=" N LEU g 117 " --> pdb=" O LYS g 132 " (cutoff:3.500A) removed outlier: 8.736A pdb=" N LEU g 134 " --> pdb=" O LEU g 117 " (cutoff:3.500A) 2039 hydrogen bonds defined for protein. 5508 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: 14.24 Time building geometry restraints manager: 18.80 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 11040 1.33 - 1.45: 5110 1.45 - 1.57: 21254 1.57 - 1.69: 19 1.69 - 1.81: 277 Bond restraints: 37700 Sorted by residual: bond pdb=" C1' ADP E 601 " pdb=" N9 ADP E 601 " ideal model delta sigma weight residual 1.485 1.339 0.146 2.00e-02 2.50e+03 5.32e+01 bond pdb=" O3A ATP C 601 " pdb=" PB ATP C 601 " 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 4.19e+01 bond pdb=" O3A ATP B 601 " pdb=" PB ATP B 601 " ideal model delta sigma weight residual 1.592 1.663 -0.071 1.10e-02 8.26e+03 4.15e+01 bond pdb=" C5 ATP B 601 " pdb=" N7 ATP B 601 " ideal model delta sigma weight residual 1.387 1.336 0.051 1.00e-02 1.00e+04 2.65e+01 ... (remaining 37695 not shown) Histogram of bond angle deviations from ideal: 93.64 - 102.61: 178 102.61 - 111.58: 17881 111.58 - 120.54: 19015 120.54 - 129.51: 13915 129.51 - 138.47: 122 Bond angle restraints: 51111 Sorted by residual: angle pdb=" N ALA b 57 " pdb=" CA ALA b 57 " pdb=" C ALA b 57 " ideal model delta sigma weight residual 111.07 122.09 -11.02 1.07e+00 8.73e-01 1.06e+02 angle pdb=" N LYS b 51 " pdb=" CA LYS b 51 " pdb=" C LYS b 51 " ideal model delta sigma weight residual 111.07 120.88 -9.81 1.07e+00 8.73e-01 8.41e+01 angle pdb=" C ALA b 57 " pdb=" N GLN b 58 " pdb=" CA GLN b 58 " ideal model delta sigma weight residual 120.38 131.05 -10.67 1.37e+00 5.33e-01 6.06e+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 601 " pdb=" C4 ATP C 601 " pdb=" N3 ATP C 601 " ideal model delta sigma weight residual 126.80 119.33 7.47 1.00e+00 1.00e+00 5.58e+01 ... (remaining 51106 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.20: 21804 25.20 - 50.41: 779 50.41 - 75.61: 105 75.61 - 100.82: 35 100.82 - 126.02: 1 Dihedral angle restraints: 22724 sinusoidal: 8805 harmonic: 13919 Sorted by residual: dihedral pdb=" C THR B 513 " pdb=" N THR B 513 " pdb=" CA THR B 513 " pdb=" CB THR B 513 " ideal model delta harmonic sigma weight residual -122.00 -139.85 17.85 0 2.50e+00 1.60e-01 5.10e+01 dihedral pdb=" O2A ADP E 601 " pdb=" O3A ADP E 601 " pdb=" PA ADP E 601 " pdb=" PB ADP E 601 " ideal model delta sinusoidal sigma weight residual -60.00 66.03 -126.02 1 2.00e+01 2.50e-03 3.81e+01 dihedral pdb=" CA MET B 49 " pdb=" C MET B 49 " pdb=" N TYR B 50 " pdb=" CA TYR B 50 " ideal model delta harmonic sigma weight residual 180.00 150.66 29.34 0 5.00e+00 4.00e-02 3.44e+01 ... (remaining 22721 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.138: 5954 0.138 - 0.275: 32 0.275 - 0.413: 1 0.413 - 0.551: 0 0.551 - 0.688: 1 Chirality restraints: 5988 Sorted by residual: chirality pdb=" CA THR B 513 " pdb=" N THR B 513 " pdb=" C THR B 513 " pdb=" CB THR B 513 " both_signs ideal model delta sigma weight residual False 2.53 1.84 0.69 2.00e-01 2.50e+01 1.18e+01 chirality pdb=" CA ILE b 40 " pdb=" N ILE b 40 " pdb=" C ILE b 40 " pdb=" CB ILE b 40 " both_signs ideal model delta sigma weight residual False 2.43 2.75 -0.31 2.00e-01 2.50e+01 2.45e+00 chirality pdb=" C1' ADP E 601 " pdb=" C2' ADP E 601 " pdb=" N9 ADP E 601 " pdb=" O4' ADP E 601 " both_signs ideal model delta sigma weight residual False 2.48 2.21 0.27 2.00e-01 2.50e+01 1.83e+00 ... (remaining 5985 not shown) Planarity restraints: 6628 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE J 18 " 0.036 2.00e-02 2.50e+03 2.63e-02 1.21e+01 pdb=" CG PHE J 18 " -0.058 2.00e-02 2.50e+03 pdb=" CD1 PHE J 18 " 0.002 2.00e-02 2.50e+03 pdb=" CD2 PHE J 18 " -0.002 2.00e-02 2.50e+03 pdb=" CE1 PHE J 18 " 0.004 2.00e-02 2.50e+03 pdb=" CE2 PHE J 18 " 0.008 2.00e-02 2.50e+03 pdb=" CZ PHE J 18 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE H 18 " 0.024 2.00e-02 2.50e+03 2.49e-02 1.08e+01 pdb=" CG PHE H 18 " -0.058 2.00e-02 2.50e+03 pdb=" CD1 PHE H 18 " 0.016 2.00e-02 2.50e+03 pdb=" CD2 PHE H 18 " 0.008 2.00e-02 2.50e+03 pdb=" CE1 PHE H 18 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE H 18 " 0.008 2.00e-02 2.50e+03 pdb=" CZ PHE H 18 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE Q 18 " 0.035 2.00e-02 2.50e+03 2.48e-02 1.08e+01 pdb=" CG PHE Q 18 " -0.052 2.00e-02 2.50e+03 pdb=" CD1 PHE Q 18 " 0.002 2.00e-02 2.50e+03 pdb=" CD2 PHE Q 18 " -0.005 2.00e-02 2.50e+03 pdb=" CE1 PHE Q 18 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 PHE Q 18 " 0.005 2.00e-02 2.50e+03 pdb=" CZ PHE Q 18 " 0.018 2.00e-02 2.50e+03 ... (remaining 6625 not shown) Histogram of nonbonded interaction distances: 1.78 - 2.40: 308 2.40 - 3.03: 27133 3.03 - 3.65: 63935 3.65 - 4.28: 90820 4.28 - 4.90: 139251 Nonbonded interactions: 321447 Sorted by model distance: nonbonded pdb=" O2B ATP A 601 " pdb="MG MG A 602 " model vdw 1.777 2.170 nonbonded pdb=" O2G ATP C 601 " pdb="MG MG C 602 " model vdw 1.958 2.170 nonbonded pdb=" O PRO E 267 " pdb=" O SER E 268 " model vdw 2.061 3.040 nonbonded pdb=" OD1 ASP E 88 " pdb=" N VAL E 89 " model vdw 2.129 2.520 nonbonded pdb=" OD1 ASP D 88 " pdb=" N VAL D 89 " model vdw 2.172 2.520 ... (remaining 321442 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' } ncs_group { reference = (chain 'D' and resid 2 through 464) selection = (chain 'E' and resid 2 through 464) selection = chain 'F' } ncs_group { reference = chain 'G' 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' and resid 2 through 80) selection = (chain 'R' and resid 2 through 80) selection = chain 'S' } ncs_group { reference = chain 'b' selection = (chain 'p' and resid 12 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: 5.880 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.040 Extract box with map and model: 21.950 Check model and map are aligned: 0.630 Set scattering table: 0.370 Process input model: 101.790 Find NCS groups from input model: 2.790 Set up NCS constraints: 0.230 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:3.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 136.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8365 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 : 0.005 0.146 37700 Z= 0.342 Angle : 0.851 17.193 51111 Z= 0.499 Chirality : 0.046 0.688 5988 Planarity : 0.005 0.050 6628 Dihedral : 13.736 126.024 13810 Min Nonbonded Distance : 1.777 Molprobity Statistics. All-atom Clashscore : 31.13 Ramachandran Plot: Outliers : 0.12 % Allowed : 7.44 % Favored : 92.43 % Rotamer Outliers : 0.21 % Cbeta Deviations : 0.02 % 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: -1.16 (0.12), residues: 4851 helix: 0.11 (0.10), residues: 2567 sheet: -1.12 (0.21), residues: 551 loop : -1.91 (0.15), residues: 1733 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9702 Ramachandran restraints generated. 4851 Oldfield, 0 Emsley, 4851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9702 Ramachandran restraints generated. 4851 Oldfield, 0 Emsley, 4851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 362 residues out of total 3851 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 354 time to evaluate : 4.461 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 revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 2 residues processed: 361 average time/residue: 0.4547 time to fit residues: 262.4266 Evaluate side-chains 246 residues out of total 3851 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 244 time to evaluate : 3.416 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.3091 time to fit residues: 5.5993 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 405 optimal weight: 7.9990 chunk 363 optimal weight: 0.7980 chunk 201 optimal weight: 7.9990 chunk 124 optimal weight: 20.0000 chunk 245 optimal weight: 8.9990 chunk 194 optimal weight: 8.9990 chunk 376 optimal weight: 10.0000 chunk 145 optimal weight: 6.9990 chunk 228 optimal weight: 7.9990 chunk 280 optimal weight: 2.9990 chunk 435 optimal weight: 5.9990 overall best weight: 4.9588 ------------------------------------------------------------------------------- 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: