Starting phenix.real_space_refine (version: dev) on Thu Dec 15 00:41:22 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7njs_12417/12_2022/7njs_12417_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7njs_12417/12_2022/7njs_12417.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.46 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7njs_12417/12_2022/7njs_12417.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7njs_12417/12_2022/7njs_12417.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7njs_12417/12_2022/7njs_12417_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7njs_12417/12_2022/7njs_12417_trim_updated.pdb" } resolution = 2.46 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= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "A GLU 86": "OE1" <-> "OE2" Residue "A GLU 224": "OE1" <-> "OE2" Residue "C TYR 18": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ASP 412": "OD1" <-> "OD2" Residue "D ASP 199": "OD1" <-> "OD2" Residue "F ASP 384": "OD1" <-> "OD2" Residue "G GLU 189": "OE1" <-> "OE2" Residue "G PHE 190": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G GLU 213": "OE1" <-> "OE2" Residue "H ASP 91": "OD1" <-> "OD2" Residue "L GLU 65": "OE1" <-> "OE2" Residue "M ASP 32": "OD1" <-> "OD2" Residue "M GLU 65": "OE1" <-> "OE2" Residue "P GLU 65": "OE1" <-> "OE2" Residue "Q PHE 69": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "R GLU 48": "OE1" <-> "OE2" Residue "R GLU 65": "OE1" <-> "OE2" Residue "R TYR 68": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "S GLU 65": "OE1" <-> "OE2" Residue "T ASP 32": "OD1" <-> "OD2" Residue "a GLU 67": "OE1" <-> "OE2" Residue "a PHE 142": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "a GLU 177": "OE1" <-> "OE2" Residue "a TYR 209": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "b GLU 61": "OE1" <-> "OE2" Residue "d GLU 68": "OE1" <-> "OE2" Residue "d PHE 187": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "d ASP 425": "OD1" <-> "OD2" Residue "d GLU 426": "OE1" <-> "OE2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/chem_data/mon_lib" Total number of atoms: 74642 Number of models: 1 Model: "" Number of chains: 31 Chain: "A" Number of atoms: 7808 Number of conformers: 1 Conformer: "" Number of residues, atoms: 517, 7808 Classifications: {'peptide': 517} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 19, 'TRANS': 495} Chain: "B" Number of atoms: 7623 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 503, 7602 Classifications: {'peptide': 503} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 19, 'TRANS': 481} Chain breaks: 2 Conformer: "B" Number of residues, atoms: 503, 7602 Classifications: {'peptide': 503} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 19, 'TRANS': 481} Chain breaks: 2 bond proxies already assigned to first conformer: 7635 Chain: "C" Number of atoms: 7942 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 521, 7900 Classifications: {'peptide': 521} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 22, 'TRANS': 496} Chain breaks: 2 Conformer: "B" Number of residues, atoms: 521, 7900 Classifications: {'peptide': 521} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 22, 'TRANS': 496} Chain breaks: 2 bond proxies already assigned to first conformer: 7916 Chain: "D" Number of atoms: 7162 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 468, 7144 Classifications: {'peptide': 468} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 22, 'TRANS': 443} Conformer: "B" Number of residues, atoms: 468, 7144 Classifications: {'peptide': 468} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 22, 'TRANS': 443} bond proxies already assigned to first conformer: 7190 Chain: "E" Number of atoms: 7087 Number of conformers: 1 Conformer: "" Number of residues, atoms: 464, 7087 Classifications: {'peptide': 464} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 22, 'TRANS': 439} Chain: "F" Number of atoms: 7144 Number of conformers: 1 Conformer: "" Number of residues, atoms: 468, 7144 Classifications: {'peptide': 468} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 22, 'TRANS': 443} Chain: "G" Number of atoms: 4567 Number of conformers: 1 Conformer: "" Number of residues, atoms: 297, 4567 Classifications: {'peptide': 297} Link IDs: {'PCIS': 2, 'PTRANS': 7, 'TRANS': 287} Chain breaks: 1 Chain: "H" Number of atoms: 1802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 1802 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 3, 'TRANS': 114} Chain: "L" Number of atoms: 1192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 1192 Classifications: {'peptide': 84} Link IDs: {'PTRANS': 4, 'TRANS': 79} Chain: "M" Number of atoms: 1192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 1192 Classifications: {'peptide': 84} Link IDs: {'PTRANS': 4, 'TRANS': 79} Chain: "N" Number of atoms: 1192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 1192 Classifications: {'peptide': 84} Link IDs: {'PTRANS': 4, 'TRANS': 79} Chain: "O" Number of atoms: 1192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 1192 Classifications: {'peptide': 84} Link IDs: {'PTRANS': 4, 'TRANS': 79} Chain: "P" Number of atoms: 1192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 1192 Classifications: {'peptide': 84} Link IDs: {'PTRANS': 4, 'TRANS': 79} Chain: "Q" Number of atoms: 1192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 1192 Classifications: {'peptide': 84} Link IDs: {'PTRANS': 4, 'TRANS': 79} Chain: "R" Number of atoms: 1192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 1192 Classifications: {'peptide': 84} Link IDs: {'PTRANS': 4, 'TRANS': 79} Chain: "S" Number of atoms: 1192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 1192 Classifications: {'peptide': 84} Link IDs: {'PTRANS': 4, 'TRANS': 79} Chain: "T" Number of atoms: 1204 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 1204 Classifications: {'peptide': 85} Link IDs: {'PTRANS': 4, 'TRANS': 80} Chain: "a" Number of atoms: 3767 Number of conformers: 1 Conformer: "" Number of residues, atoms: 238, 3767 Classifications: {'peptide': 238} Link IDs: {'PTRANS': 10, 'TRANS': 227} Chain: "b" Number of atoms: 2161 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 2161 Classifications: {'peptide': 144} Link IDs: {'PTRANS': 3, 'TRANS': 140} Chain: "d" Number of atoms: 6640 Number of conformers: 1 Conformer: "" Number of residues, atoms: 437, 6640 Classifications: {'peptide': 437} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 12, 'TRANS': 424} Chain breaks: 1 Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "F" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Residues with excluded nonbonded symmetry interactions: 3 residue: pdb=" N APHE B 354 " occ=0.80 ... (38 atoms not shown) pdb=" HZ BPHE B 354 " occ=0.20 residue: pdb=" N APHE C 354 " occ=0.70 ... (38 atoms not shown) pdb=" HZ BPHE C 354 " occ=0.30 residue: pdb=" N AGLN D 453 " occ=0.50 ... (32 atoms not shown) pdb="HE22BGLN D 453 " occ=0.50 Time building chain proxies: 31.52, per 1000 atoms: 0.42 Number of scatterers: 74642 At special positions: 0 Unit cell: (139.44, 126.16, 250.66, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) S 107 16.00 P 16 15.00 Mg 5 11.99 O 7180 8.00 N 6405 7.00 C 23583 6.00 H 37346 1.00 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: 53.63 Conformation dependent library (CDL) restraints added in 6.4 seconds 9780 Ramachandran restraints generated. 4890 Oldfield, 0 Emsley, 4890 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8886 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 184 helices and 27 sheets defined 55.3% alpha, 9.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.30 Creating SS restraints... Processing helix chain 'A' and resid 8 through 20 Processing helix chain 'A' and resid 82 through 84 No H-bonds generated for 'chain 'A' and resid 82 through 84' Processing helix chain 'A' and resid 104 through 106 No H-bonds generated for 'chain 'A' and resid 104 through 106' Processing helix chain 'A' and resid 154 through 159 Processing helix chain 'A' and resid 178 through 195 removed outlier: 4.134A pdb=" N ARG A 190 " --> pdb=" O ILE A 186 " (cutoff:3.500A) removed outlier: 4.953A pdb=" N GLU A 191 " --> pdb=" O LEU A 187 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N ALA A 192 " --> pdb=" O ASN A 188 " (cutoff:3.500A) Processing helix chain 'A' and resid 213 through 225 Processing helix chain 'A' and resid 228 through 230 No H-bonds generated for 'chain 'A' and resid 228 through 230' Processing helix chain 'A' and resid 243 through 263 Proline residue: A 250 - end of helix removed outlier: 3.612A pdb=" N ASN A 263 " --> pdb=" O HIS A 259 " (cutoff:3.500A) Processing helix chain 'A' and resid 274 through 287 Processing helix chain 'A' and resid 294 through 296 No H-bonds generated for 'chain 'A' and resid 294 through 296' Processing helix chain 'A' and resid 301 through 311 removed outlier: 4.004A pdb=" N ARG A 311 " --> pdb=" O ARG A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 317 through 319 No H-bonds generated for 'chain 'A' and resid 317 through 319' Processing helix chain 'A' and resid 340 through 348 Processing helix chain 'A' and resid 357 through 361 Processing helix chain 'A' and resid 378 through 381 Processing helix chain 'A' and resid 384 through 389 Processing helix chain 'A' and resid 393 through 406 removed outlier: 4.861A pdb=" N ALA A 405 " --> pdb=" O ARG A 401 " (cutoff:3.500A) removed outlier: 5.549A pdb=" N PHE A 406 " --> pdb=" O GLU A 402 " (cutoff:3.500A) Processing helix chain 'A' and resid 415 through 431 Processing helix chain 'A' and resid 441 through 452 Processing helix chain 'A' and resid 461 through 478 removed outlier: 5.154A pdb=" N GLN A 465 " --> pdb=" O GLU A 462 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N VAL A 475 " --> pdb=" O LEU A 472 " (cutoff:3.500A) Processing helix chain 'A' and resid 481 through 489 Processing helix chain 'A' and resid 494 through 510 Processing helix chain 'B' and resid 9 through 19 removed outlier: 3.533A pdb=" N VAL B 19 " --> pdb=" O GLU B 16 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 84 No H-bonds generated for 'chain 'B' and resid 82 through 84' Processing helix chain 'B' and resid 104 through 106 No H-bonds generated for 'chain 'B' and resid 104 through 106' Processing helix chain 'B' and resid 154 through 159 Processing helix chain 'B' and resid 178 through 195 removed outlier: 3.852A pdb=" N GLN B 189 " --> pdb=" O THR B 185 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N ARG B 190 " --> pdb=" O ILE B 186 " (cutoff:3.500A) removed outlier: 5.355A pdb=" N GLU B 191 " --> pdb=" O LEU B 187 " (cutoff:3.500A) removed outlier: 5.017A pdb=" N ALA B 192 " --> pdb=" O ASN B 188 " (cutoff:3.500A) Processing helix chain 'B' and resid 213 through 225 Processing helix chain 'B' and resid 229 through 231 No H-bonds generated for 'chain 'B' and resid 229 through 231' Processing helix chain 'B' and resid 243 through 263 Proline residue: B 250 - end of helix removed outlier: 3.727A pdb=" N TRP B 260 " --> pdb=" O ILE B 256 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ASN B 263 " --> pdb=" O HIS B 259 " (cutoff:3.500A) Processing helix chain 'B' and resid 274 through 287 Processing helix chain 'B' and resid 294 through 296 No H-bonds generated for 'chain 'B' and resid 294 through 296' Processing helix chain 'B' and resid 301 through 309 removed outlier: 3.574A pdb=" N LEU B 308 " --> pdb=" O LEU B 304 " (cutoff:3.500A) Processing helix chain 'B' and resid 317 through 319 No H-bonds generated for 'chain 'B' and resid 317 through 319' Processing helix chain 'B' and resid 340 through 348 Processing helix chain 'B' and resid 357 through 361 Processing helix chain 'B' and resid 384 through 406 removed outlier: 4.912A pdb=" N SER B 392 " --> pdb=" O GLU B 388 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N LEU B 393 " --> pdb=" O VAL B 389 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N GLU B 402 " --> pdb=" O SER B 398 " (cutoff:3.500A) Processing helix chain 'B' and resid 415 through 431 Processing helix chain 'B' and resid 441 through 452 Processing helix chain 'B' and resid 461 through 477 removed outlier: 4.863A pdb=" N GLN B 465 " --> pdb=" O GLU B 462 " (cutoff:3.500A) Processing helix chain 'B' and resid 481 through 489 Processing helix chain 'B' and resid 494 through 510 removed outlier: 3.685A pdb=" N GLY B 510 " --> pdb=" O GLU B 506 " (cutoff:3.500A) Processing helix chain 'C' and resid 10 through 21 Processing helix chain 'C' and resid 82 through 84 No H-bonds generated for 'chain 'C' and resid 82 through 84' Processing helix chain 'C' and resid 104 through 106 No H-bonds generated for 'chain 'C' and resid 104 through 106' Processing helix chain 'C' and resid 139 through 141 No H-bonds generated for 'chain 'C' and resid 139 through 141' Processing helix chain 'C' and resid 154 through 159 Processing helix chain 'C' and resid 178 through 195 removed outlier: 3.787A pdb=" N GLN C 189 " --> pdb=" O THR C 185 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N ARG C 190 " --> pdb=" O ILE C 186 " (cutoff:3.500A) removed outlier: 5.223A pdb=" N GLU C 191 " --> pdb=" O LEU C 187 " (cutoff:3.500A) removed outlier: 4.932A pdb=" N ALA C 192 " --> pdb=" O ASN C 188 " (cutoff:3.500A) Processing helix chain 'C' and resid 213 through 225 Processing helix chain 'C' and resid 229 through 231 No H-bonds generated for 'chain 'C' and resid 229 through 231' Processing helix chain 'C' and resid 243 through 263 Proline residue: C 250 - end of helix removed outlier: 3.703A pdb=" N TRP C 260 " --> pdb=" O ILE C 256 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ASN C 263 " --> pdb=" O HIS C 259 " (cutoff:3.500A) Processing helix chain 'C' and resid 274 through 287 Processing helix chain 'C' and resid 294 through 296 No H-bonds generated for 'chain 'C' and resid 294 through 296' Processing helix chain 'C' and resid 301 through 309 removed outlier: 3.522A pdb=" N LEU C 308 " --> pdb=" O LEU C 304 " (cutoff:3.500A) Processing helix chain 'C' and resid 317 through 319 No H-bonds generated for 'chain 'C' and resid 317 through 319' Processing helix chain 'C' and resid 340 through 348 Processing helix chain 'C' and resid 357 through 361 Processing helix chain 'C' and resid 378 through 381 Processing helix chain 'C' and resid 384 through 389 Processing helix chain 'C' and resid 393 through 406 Processing helix chain 'C' and resid 415 through 431 Processing helix chain 'C' and resid 441 through 452 Processing helix chain 'C' and resid 461 through 478 removed outlier: 4.898A pdb=" N GLN C 465 " --> pdb=" O GLU C 462 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N SER C 478 " --> pdb=" O VAL C 475 " (cutoff:3.500A) Processing helix chain 'C' and resid 480 through 489 Processing helix chain 'C' and resid 494 through 510 Processing helix chain 'D' and resid 92 through 94 No H-bonds generated for 'chain 'D' and resid 92 through 94' Processing helix chain 'D' and resid 127 through 129 No H-bonds generated for 'chain 'D' and resid 127 through 129' Processing helix chain 'D' and resid 142 through 147 Processing helix chain 'D' and resid 166 through 177 Processing helix chain 'D' and resid 194 through 207 Processing helix chain 'D' and resid 210 through 212 No H-bonds generated for 'chain 'D' and resid 210 through 212' Processing helix chain 'D' and resid 224 through 243 removed outlier: 4.865A pdb=" N ALA D 231 " --> pdb=" O ARG D 227 " (cutoff:3.500A) removed outlier: 4.599A pdb=" N LEU D 232 " --> pdb=" O MET D 228 " (cutoff:3.500A) Processing helix chain 'D' and resid 256 through 267 Processing helix chain 'D' and resid 276 through 278 No H-bonds generated for 'chain 'D' and resid 276 through 278' Processing helix chain 'D' and resid 283 through 293 Processing helix chain 'D' and resid 311 through 313 No H-bonds generated for 'chain 'D' and resid 311 through 313' Processing helix chain 'D' and resid 318 through 326 removed outlier: 4.319A pdb=" N ALA D 325 " --> pdb=" O ALA D 321 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N HIS D 326 " --> pdb=" O THR D 322 " (cutoff:3.500A) Processing helix chain 'D' and resid 335 through 339 Processing helix chain 'D' and resid 358 through 361 No H-bonds generated for 'chain 'D' and resid 358 through 361' Processing helix chain 'D' and resid 363 through 389 removed outlier: 4.689A pdb=" N ASP D 384 " --> pdb=" O LYS D 380 " (cutoff:3.500A) removed outlier: 4.895A pdb=" N ILE D 385 " --> pdb=" O ASP D 381 " (cutoff:3.500A) Processing helix chain 'D' and resid 391 through 393 No H-bonds generated for 'chain 'D' and resid 391 through 393' Processing helix chain 'D' and resid 396 through 412 Processing helix chain 'D' and resid 417 through 423 removed outlier: 3.674A pdb=" N GLU D 420 " --> pdb=" O MET D 417 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N GLN D 421 " --> pdb=" O ALA D 418 " (cutoff:3.500A) Processing helix chain 'D' and resid 432 through 443 Processing helix chain 'D' and resid 452 through 455 Processing helix chain 'D' and resid 461 through 470 Processing helix chain 'E' and resid 92 through 94 No H-bonds generated for 'chain 'E' and resid 92 through 94' Processing helix chain 'E' and resid 127 through 129 No H-bonds generated for 'chain 'E' and resid 127 through 129' Processing helix chain 'E' and resid 142 through 147 Processing helix chain 'E' and resid 166 through 179 Processing helix chain 'E' and resid 194 through 207 Processing helix chain 'E' and resid 210 through 212 No H-bonds generated for 'chain 'E' and resid 210 through 212' Processing helix chain 'E' and resid 224 through 243 removed outlier: 4.899A pdb=" N ALA E 231 " --> pdb=" O ARG E 227 " (cutoff:3.500A) removed outlier: 4.679A pdb=" N LEU E 232 " --> pdb=" O MET E 228 " (cutoff:3.500A) Processing helix chain 'E' and resid 256 through 269 Processing helix chain 'E' and resid 276 through 278 No H-bonds generated for 'chain 'E' and resid 276 through 278' Processing helix chain 'E' and resid 283 through 293 removed outlier: 4.030A pdb=" N ARG E 293 " --> pdb=" O GLU E 289 " (cutoff:3.500A) Processing helix chain 'E' and resid 311 through 313 No H-bonds generated for 'chain 'E' and resid 311 through 313' Processing helix chain 'E' and resid 318 through 324 Processing helix chain 'E' and resid 335 through 339 Processing helix chain 'E' and resid 358 through 361 No H-bonds generated for 'chain 'E' and resid 358 through 361' Processing helix chain 'E' and resid 363 through 389 removed outlier: 4.302A pdb=" N ASP E 384 " --> pdb=" O LYS E 380 " (cutoff:3.500A) removed outlier: 4.700A pdb=" N ILE E 385 " --> pdb=" O ASP E 381 " (cutoff:3.500A) Processing helix chain 'E' and resid 391 through 393 No H-bonds generated for 'chain 'E' and resid 391 through 393' Processing helix chain 'E' and resid 396 through 411 Processing helix chain 'E' and resid 418 through 421 removed outlier: 3.592A pdb=" N GLN E 421 " --> pdb=" O ALA E 418 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 418 through 421' Processing helix chain 'E' and resid 432 through 443 Processing helix chain 'E' and resid 452 through 455 Processing helix chain 'E' and resid 461 through 469 Processing helix chain 'F' and resid 92 through 94 No H-bonds generated for 'chain 'F' and resid 92 through 94' Processing helix chain 'F' and resid 127 through 129 No H-bonds generated for 'chain 'F' and resid 127 through 129' Processing helix chain 'F' and resid 142 through 147 Processing helix chain 'F' and resid 166 through 177 Processing helix chain 'F' and resid 194 through 206 Processing helix chain 'F' and resid 210 through 212 No H-bonds generated for 'chain 'F' and resid 210 through 212' Processing helix chain 'F' and resid 224 through 243 removed outlier: 4.848A pdb=" N ALA F 231 " --> pdb=" O ARG F 227 " (cutoff:3.500A) removed outlier: 4.861A pdb=" N LEU F 232 " --> pdb=" O MET F 228 " (cutoff:3.500A) Processing helix chain 'F' and resid 256 through 269 Processing helix chain 'F' and resid 276 through 278 No H-bonds generated for 'chain 'F' and resid 276 through 278' Processing helix chain 'F' and resid 283 through 293 Processing helix chain 'F' and resid 311 through 313 No H-bonds generated for 'chain 'F' and resid 311 through 313' Processing helix chain 'F' and resid 318 through 326 removed outlier: 4.427A pdb=" N ALA F 325 " --> pdb=" O ALA F 321 " (cutoff:3.500A) removed outlier: 4.719A pdb=" N HIS F 326 " --> pdb=" O THR F 322 " (cutoff:3.500A) Processing helix chain 'F' and resid 335 through 340 removed outlier: 3.603A pdb=" N LYS F 340 " --> pdb=" O ALA F 336 " (cutoff:3.500A) Processing helix chain 'F' and resid 358 through 361 No H-bonds generated for 'chain 'F' and resid 358 through 361' Processing helix chain 'F' and resid 363 through 389 removed outlier: 4.552A pdb=" N ASP F 384 " --> pdb=" O LYS F 380 " (cutoff:3.500A) removed outlier: 5.000A pdb=" N ILE F 385 " --> pdb=" O ASP F 381 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ILE F 388 " --> pdb=" O ASP F 384 " (cutoff:3.500A) Processing helix chain 'F' and resid 391 through 393 No H-bonds generated for 'chain 'F' and resid 391 through 393' Processing helix chain 'F' and resid 396 through 411 Processing helix chain 'F' and resid 420 through 423 No H-bonds generated for 'chain 'F' and resid 420 through 423' Processing helix chain 'F' and resid 432 through 444 Processing helix chain 'F' and resid 452 through 455 Processing helix chain 'F' and resid 461 through 471 Processing helix chain 'G' and resid 4 through 59 Proline residue: G 45 - end of helix Processing helix chain 'G' and resid 66 through 68 No H-bonds generated for 'chain 'G' and resid 66 through 68' Processing helix chain 'G' and resid 92 through 109 Processing helix chain 'G' and resid 121 through 130 Processing helix chain 'G' and resid 147 through 163 Processing helix chain 'G' and resid 173 through 175 No H-bonds generated for 'chain 'G' and resid 173 through 175' Processing helix chain 'G' and resid 228 through 303 Proline residue: G 237 - end of helix Processing helix chain 'H' and resid 92 through 98 Processing helix chain 'H' and resid 104 through 117 Processing helix chain 'L' and resid 5 through 45 Processing helix chain 'L' and resid 47 through 49 No H-bonds generated for 'chain 'L' and resid 47 through 49' Processing helix chain 'L' and resid 51 through 79 removed outlier: 4.045A pdb=" N THR L 55 " --> pdb=" O ARG L 52 " (cutoff:3.500A) Proline residue: L 56 - end of helix removed outlier: 4.307A pdb=" N ALA L 66 " --> pdb=" O LEU L 63 " (cutoff:3.500A) Processing helix chain 'M' and resid 5 through 45 Processing helix chain 'M' and resid 47 through 80 removed outlier: 3.822A pdb=" N GLN M 50 " --> pdb=" O PRO M 47 " (cutoff:3.500A) removed outlier: 4.718A pdb=" N GLY M 51 " --> pdb=" O GLU M 48 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N PHE M 54 " --> pdb=" O GLY M 51 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N THR M 55 " --> pdb=" O ARG M 52 " (cutoff:3.500A) Proline residue: M 56 - end of helix removed outlier: 3.756A pdb=" N ALA M 67 " --> pdb=" O VAL M 64 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N PHE M 80 " --> pdb=" O LEU M 77 " (cutoff:3.500A) Processing helix chain 'N' and resid 5 through 45 Processing helix chain 'N' and resid 47 through 79 removed outlier: 3.935A pdb=" N GLY N 51 " --> pdb=" O GLU N 48 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N PHE N 54 " --> pdb=" O GLY N 51 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N THR N 55 " --> pdb=" O ARG N 52 " (cutoff:3.500A) Proline residue: N 56 - end of helix removed outlier: 3.586A pdb=" N GLU N 65 " --> pdb=" O GLY N 62 " (cutoff:3.500A) Processing helix chain 'O' and resid 5 through 45 Processing helix chain 'O' and resid 47 through 80 removed outlier: 4.033A pdb=" N GLY O 51 " --> pdb=" O GLU O 48 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N PHE O 54 " --> pdb=" O GLY O 51 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N THR O 55 " --> pdb=" O ARG O 52 " (cutoff:3.500A) Proline residue: O 56 - end of helix removed outlier: 3.963A pdb=" N ALA O 66 " --> pdb=" O LEU O 63 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N VAL O 79 " --> pdb=" O ALA O 76 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N PHE O 80 " --> pdb=" O LEU O 77 " (cutoff:3.500A) Processing helix chain 'P' and resid 5 through 45 Processing helix chain 'P' and resid 50 through 80 removed outlier: 3.950A pdb=" N THR P 55 " --> pdb=" O GLY P 51 " (cutoff:3.500A) Proline residue: P 56 - end of helix Processing helix chain 'Q' and resid 5 through 45 Processing helix chain 'Q' and resid 47 through 80 removed outlier: 3.842A pdb=" N GLN Q 50 " --> pdb=" O PRO Q 47 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N GLY Q 51 " --> pdb=" O GLU Q 48 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N LEU Q 53 " --> pdb=" O GLN Q 50 " (cutoff:3.500A) removed outlier: 4.849A pdb=" N PHE Q 54 " --> pdb=" O GLY Q 51 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N THR Q 55 " --> pdb=" O ARG Q 52 " (cutoff:3.500A) Proline residue: Q 56 - end of helix removed outlier: 3.514A pdb=" N GLU Q 65 " --> pdb=" O GLY Q 62 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N PHE Q 80 " --> pdb=" O LEU Q 77 " (cutoff:3.500A) Processing helix chain 'R' and resid 5 through 45 Processing helix chain 'R' and resid 47 through 80 removed outlier: 4.124A pdb=" N GLY R 51 " --> pdb=" O GLU R 48 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N LEU R 53 " --> pdb=" O GLN R 50 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N PHE R 54 " --> pdb=" O GLY R 51 " (cutoff:3.500A) Proline residue: R 56 - end of helix removed outlier: 4.167A pdb=" N ALA R 66 " --> pdb=" O LEU R 63 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N PHE R 80 " --> pdb=" O LEU R 77 " (cutoff:3.500A) Processing helix chain 'S' and resid 5 through 45 Processing helix chain 'S' and resid 50 through 80 Proline residue: S 56 - end of helix removed outlier: 3.539A pdb=" N ALA S 67 " --> pdb=" O LEU S 63 " (cutoff:3.500A) Processing helix chain 'T' and resid 5 through 45 Processing helix chain 'T' and resid 47 through 79 removed outlier: 4.702A pdb=" N GLY T 51 " --> pdb=" O GLU T 48 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N THR T 55 " --> pdb=" O ARG T 52 " (cutoff:3.500A) Proline residue: T 56 - end of helix removed outlier: 3.883A pdb=" N ALA T 66 " --> pdb=" O LEU T 63 " (cutoff:3.500A) Processing helix chain 'a' and resid 29 through 51 Processing helix chain 'a' and resid 61 through 80 Processing helix chain 'a' and resid 88 through 108 removed outlier: 3.921A pdb=" N ALA a 107 " --> pdb=" O SER a 103 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N VAL a 108 " --> pdb=" O ASN a 104 " (cutoff:3.500A) Processing helix chain 'a' and resid 127 through 129 No H-bonds generated for 'chain 'a' and resid 127 through 129' Processing helix chain 'a' and resid 131 through 153 Processing helix chain 'a' and resid 157 through 164 Processing helix chain 'a' and resid 168 through 205 Proline residue: a 172 - end of helix removed outlier: 4.535A pdb=" N LYS a 181 " --> pdb=" O GLU a 178 " (cutoff:3.500A) Proline residue: a 182 - end of helix removed outlier: 4.128A pdb=" N LEU a 187 " --> pdb=" O SER a 184 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N ARG a 188 " --> pdb=" O LEU a 185 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N ALA a 195 " --> pdb=" O ASN a 192 " (cutoff:3.500A) removed outlier: 4.929A pdb=" N VAL a 200 " --> pdb=" O GLY a 197 " (cutoff:3.500A) Processing helix chain 'a' and resid 208 through 244 removed outlier: 5.824A pdb=" N PHE a 213 " --> pdb=" O TYR a 209 " (cutoff:3.500A) Proline residue: a 214 - end of helix removed outlier: 3.860A pdb=" N PHE a 224 " --> pdb=" O THR a 220 " (cutoff:3.500A) Processing helix chain 'b' and resid 29 through 47 Processing helix chain 'b' and resid 50 through 146 removed outlier: 3.890A pdb=" N GLN b 82 " --> pdb=" O VAL b 78 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N GLU b 145 " --> pdb=" O ARG b 141 " (cutoff:3.500A) removed outlier: 5.176A pdb=" N SER b 146 " --> pdb=" O SER b 142 " (cutoff:3.500A) Processing helix chain 'b' and resid 148 through 160 Processing helix chain 'd' and resid 2 through 21 Processing helix chain 'd' and resid 23 through 136 Processing helix chain 'd' and resid 140 through 156 Processing helix chain 'd' and resid 174 through 190 Processing helix chain 'd' and resid 196 through 215 Processing helix chain 'd' and resid 217 through 224 Processing helix chain 'd' and resid 231 through 241 Processing helix chain 'd' and resid 247 through 258 Processing helix chain 'd' and resid 264 through 286 removed outlier: 3.944A pdb=" N ILE d 268 " --> pdb=" O GLU d 264 " (cutoff:3.500A) Processing helix chain 'd' and resid 289 through 304 Processing helix chain 'd' and resid 307 through 314 Processing helix chain 'd' and resid 320 through 330 Processing helix chain 'd' and resid 339 through 350 Processing helix chain 'd' and resid 357 through 372 removed outlier: 4.033A pdb=" N ARG d 372 " --> pdb=" O ALA d 368 " (cutoff:3.500A) Processing helix chain 'd' and resid 387 through 401 Processing helix chain 'd' and resid 413 through 415 No H-bonds generated for 'chain 'd' and resid 413 through 415' Processing helix chain 'd' and resid 432 through 442 Processing sheet with id= A, first strand: chain 'A' and resid 31 through 33 removed outlier: 6.370A pdb=" N GLY A 75 " --> pdb=" O LEU A 67 " (cutoff:3.500A) removed outlier: 6.097A pdb=" N GLU A 45 " --> pdb=" O VAL A 34 " (cutoff:3.500A) removed outlier: 5.488A pdb=" N VAL A 34 " --> pdb=" O GLU A 45 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 99 through 102 Processing sheet with id= C, first strand: chain 'A' and resid 351 through 355 Processing sheet with id= D, first strand: chain 'A' and resid 232 through 237 removed outlier: 8.504A pdb=" N THR A 233 " --> pdb=" O VAL A 202 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N CYS A 204 " --> pdb=" O THR A 233 " (cutoff:3.500A) removed outlier: 7.732A pdb=" N VAL A 235 " --> pdb=" O CYS A 204 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N TYR A 206 " --> pdb=" O VAL A 235 " (cutoff:3.500A) removed outlier: 7.509A pdb=" N ALA A 237 " --> pdb=" O TYR A 206 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N ALA A 208 " --> pdb=" O ALA A 237 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N HIS A 266 " --> pdb=" O ARG A 203 " (cutoff:3.500A) removed outlier: 8.050A pdb=" N VAL A 205 " --> pdb=" O HIS A 266 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N LEU A 268 " --> pdb=" O VAL A 205 " (cutoff:3.500A) removed outlier: 7.565A pdb=" N VAL A 207 " --> pdb=" O LEU A 268 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N VAL A 270 " --> pdb=" O VAL A 207 " (cutoff:3.500A) removed outlier: 7.380A pdb=" N ILE A 209 " --> pdb=" O VAL A 270 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N ASP A 272 " --> pdb=" O ILE A 209 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N SER A 323 " --> pdb=" O VAL A 267 " (cutoff:3.500A) removed outlier: 7.704A pdb=" N ILE A 269 " --> pdb=" O SER A 323 " (cutoff:3.500A) removed outlier: 6.120A pdb=" N THR A 325 " --> pdb=" O ILE A 269 " (cutoff:3.500A) removed outlier: 7.535A pdb=" N PHE A 271 " --> pdb=" O THR A 325 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N LEU A 327 " --> pdb=" O PHE A 271 " (cutoff:3.500A) No H-bonds generated for sheet with id= D Processing sheet with id= E, first strand: chain 'B' and resid 31 through 33 removed outlier: 4.115A pdb=" N LEU B 63 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N GLY B 75 " --> pdb=" O LEU B 67 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ASP B 36 " --> pdb=" O HIS B 43 " (cutoff:3.500A) removed outlier: 6.129A pdb=" N GLU B 45 " --> pdb=" O VAL B 34 " (cutoff:3.500A) removed outlier: 5.667A pdb=" N VAL B 34 " --> pdb=" O GLU B 45 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 99 through 102 Processing sheet with id= G, first strand: chain 'B' and resid 352 through 355 removed outlier: 6.550A pdb=" N LEU B 169 " --> pdb=" O CYS B 353 " (cutoff:3.500A) removed outlier: 7.225A pdb=" N LEU B 355 " --> pdb=" O LEU B 169 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N ILE B 171 " --> pdb=" O LEU B 355 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 232 through 237 removed outlier: 6.504A pdb=" N CYS B 204 " --> pdb=" O THR B 233 " (cutoff:3.500A) removed outlier: 7.772A pdb=" N VAL B 235 " --> pdb=" O CYS B 204 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N TYR B 206 " --> pdb=" O VAL B 235 " (cutoff:3.500A) removed outlier: 7.453A pdb=" N ALA B 237 " --> pdb=" O TYR B 206 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N ALA B 208 " --> pdb=" O ALA B 237 " (cutoff:3.500A) removed outlier: 6.218A pdb=" N SER B 323 " --> pdb=" O VAL B 267 " (cutoff:3.500A) removed outlier: 7.612A pdb=" N ILE B 269 " --> pdb=" O SER B 323 " (cutoff:3.500A) removed outlier: 6.067A pdb=" N THR B 325 " --> pdb=" O ILE B 269 " (cutoff:3.500A) removed outlier: 7.513A pdb=" N PHE B 271 " --> pdb=" O THR B 325 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N LEU B 327 " --> pdb=" O PHE B 271 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'C' and resid 31 through 33 removed outlier: 6.500A pdb=" N GLY C 75 " --> pdb=" O LEU C 67 " (cutoff:3.500A) removed outlier: 6.097A pdb=" N GLU C 45 " --> pdb=" O VAL C 34 " (cutoff:3.500A) removed outlier: 5.508A pdb=" N VAL C 34 " --> pdb=" O GLU C 45 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'C' and resid 99 through 102 Processing sheet with id= K, first strand: chain 'C' and resid 352 through 355 removed outlier: 6.574A pdb=" N LEU C 169 " --> pdb=" O CYS C 353 " (cutoff:3.500A) removed outlier: 7.253A pdb=" N LEU C 355 " --> pdb=" O LEU C 169 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N ILE C 171 " --> pdb=" O LEU C 355 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'C' and resid 232 through 237 removed outlier: 8.600A pdb=" N THR C 233 " --> pdb=" O VAL C 202 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N CYS C 204 " --> pdb=" O THR C 233 " (cutoff:3.500A) removed outlier: 7.722A pdb=" N VAL C 235 " --> pdb=" O CYS C 204 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N TYR C 206 " --> pdb=" O VAL C 235 " (cutoff:3.500A) removed outlier: 7.462A pdb=" N ALA C 237 " --> pdb=" O TYR C 206 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N ALA C 208 " --> pdb=" O ALA C 237 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N HIS C 266 " --> pdb=" O ARG C 203 " (cutoff:3.500A) removed outlier: 8.058A pdb=" N VAL C 205 " --> pdb=" O HIS C 266 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N LEU C 268 " --> pdb=" O VAL C 205 " (cutoff:3.500A) removed outlier: 7.467A pdb=" N VAL C 207 " --> pdb=" O LEU C 268 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N VAL C 270 " --> pdb=" O VAL C 207 " (cutoff:3.500A) removed outlier: 7.322A pdb=" N ILE C 209 " --> pdb=" O VAL C 270 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N ASP C 272 " --> pdb=" O ILE C 209 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N SER C 323 " --> pdb=" O VAL C 267 " (cutoff:3.500A) removed outlier: 7.725A pdb=" N ILE C 269 " --> pdb=" O SER C 323 " (cutoff:3.500A) removed outlier: 6.220A pdb=" N THR C 325 " --> pdb=" O ILE C 269 " (cutoff:3.500A) removed outlier: 7.624A pdb=" N PHE C 271 " --> pdb=" O THR C 325 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N LEU C 327 " --> pdb=" O PHE C 271 " (cutoff:3.500A) No H-bonds generated for sheet with id= L Processing sheet with id= M, first strand: chain 'D' and resid 11 through 16 removed outlier: 6.631A pdb=" N ASP D 21 " --> pdb=" O VAL D 13 " (cutoff:3.500A) removed outlier: 4.807A pdb=" N ILE D 15 " --> pdb=" O VAL D 19 " (cutoff:3.500A) removed outlier: 7.254A pdb=" N VAL D 19 " --> pdb=" O ILE D 15 " (cutoff:3.500A) removed outlier: 6.198A pdb=" N ILE D 65 " --> pdb=" O VAL D 53 " (cutoff:3.500A) removed outlier: 5.667A pdb=" N VAL D 53 " --> pdb=" O ILE D 65 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'D' and resid 87 through 89 Processing sheet with id= O, first strand: chain 'D' and resid 329 through 332 removed outlier: 7.367A pdb=" N ILE D 156 " --> pdb=" O ILE D 302 " (cutoff:3.500A) removed outlier: 6.048A pdb=" N SER D 304 " --> pdb=" O ILE D 156 " (cutoff:3.500A) removed outlier: 7.759A pdb=" N LEU D 158 " --> pdb=" O SER D 304 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N GLN D 306 " --> pdb=" O LEU D 158 " (cutoff:3.500A) removed outlier: 7.870A pdb=" N GLY D 160 " --> pdb=" O GLN D 306 " (cutoff:3.500A) removed outlier: 6.136A pdb=" N VAL D 308 " --> pdb=" O GLY D 160 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N VAL D 249 " --> pdb=" O THR D 303 " (cutoff:3.500A) removed outlier: 7.718A pdb=" N MET D 305 " --> pdb=" O VAL D 249 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N LEU D 251 " --> pdb=" O MET D 305 " (cutoff:3.500A) removed outlier: 7.873A pdb=" N ALA D 307 " --> pdb=" O LEU D 251 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N ILE D 253 " --> pdb=" O ALA D 307 " (cutoff:3.500A) removed outlier: 8.166A pdb=" N TYR D 309 " --> pdb=" O ILE D 253 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N THR D 184 " --> pdb=" O LEU D 250 " (cutoff:3.500A) removed outlier: 7.990A pdb=" N PHE D 252 " --> pdb=" O THR D 184 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N VAL D 186 " --> pdb=" O PHE D 252 " (cutoff:3.500A) removed outlier: 8.019A pdb=" N ASP D 254 " --> pdb=" O VAL D 186 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N ALA D 188 " --> pdb=" O ASP D 254 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'E' and resid 11 through 16 removed outlier: 6.548A pdb=" N ASP E 21 " --> pdb=" O VAL E 13 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N ILE E 15 " --> pdb=" O VAL E 19 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N VAL E 19 " --> pdb=" O ILE E 15 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N ILE E 65 " --> pdb=" O VAL E 53 " (cutoff:3.500A) removed outlier: 5.803A pdb=" N VAL E 53 " --> pdb=" O ILE E 65 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'E' and resid 87 through 89 Processing sheet with id= R, first strand: chain 'E' and resid 329 through 332 removed outlier: 8.455A pdb=" N ILE E 156 " --> pdb=" O ILE E 302 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N SER E 304 " --> pdb=" O ILE E 156 " (cutoff:3.500A) removed outlier: 7.568A pdb=" N LEU E 158 " --> pdb=" O SER E 304 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N GLN E 306 " --> pdb=" O LEU E 158 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N VAL E 249 " --> pdb=" O THR E 303 " (cutoff:3.500A) removed outlier: 7.870A pdb=" N MET E 305 " --> pdb=" O VAL E 249 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N LEU E 251 " --> pdb=" O MET E 305 " (cutoff:3.500A) removed outlier: 7.755A pdb=" N ALA E 307 " --> pdb=" O LEU E 251 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N ILE E 253 " --> pdb=" O ALA E 307 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N THR E 184 " --> pdb=" O LEU E 250 " (cutoff:3.500A) removed outlier: 7.983A pdb=" N PHE E 252 " --> pdb=" O THR E 184 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N VAL E 186 " --> pdb=" O PHE E 252 " (cutoff:3.500A) removed outlier: 8.032A pdb=" N ASP E 254 " --> pdb=" O VAL E 186 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N ALA E 188 " --> pdb=" O ASP E 254 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'F' and resid 11 through 16 removed outlier: 6.635A pdb=" N ASP F 21 " --> pdb=" O VAL F 13 " (cutoff:3.500A) removed outlier: 4.709A pdb=" N ILE F 15 " --> pdb=" O VAL F 19 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N VAL F 19 " --> pdb=" O ILE F 15 " (cutoff:3.500A) removed outlier: 6.130A pdb=" N ILE F 65 " --> pdb=" O VAL F 53 " (cutoff:3.500A) removed outlier: 5.748A pdb=" N VAL F 53 " --> pdb=" O ILE F 65 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'F' and resid 87 through 89 Processing sheet with id= U, first strand: chain 'F' and resid 329 through 332 removed outlier: 7.582A pdb=" N ILE F 156 " --> pdb=" O ILE F 302 " (cutoff:3.500A) removed outlier: 6.183A pdb=" N SER F 304 " --> pdb=" O ILE F 156 " (cutoff:3.500A) removed outlier: 7.851A pdb=" N LEU F 158 " --> pdb=" O SER F 304 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N GLN F 306 " --> pdb=" O LEU F 158 " (cutoff:3.500A) removed outlier: 7.997A pdb=" N GLY F 160 " --> pdb=" O GLN F 306 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N VAL F 308 " --> pdb=" O GLY F 160 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N VAL F 249 " --> pdb=" O THR F 303 " (cutoff:3.500A) removed outlier: 7.701A pdb=" N MET F 305 " --> pdb=" O VAL F 249 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N LEU F 251 " --> pdb=" O MET F 305 " (cutoff:3.500A) removed outlier: 7.682A pdb=" N ALA F 307 " --> pdb=" O LEU F 251 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N ILE F 253 " --> pdb=" O ALA F 307 " (cutoff:3.500A) removed outlier: 8.094A pdb=" N TYR F 309 " --> pdb=" O ILE F 253 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N THR F 184 " --> pdb=" O LEU F 250 " (cutoff:3.500A) removed outlier: 8.160A pdb=" N PHE F 252 " --> pdb=" O THR F 184 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N VAL F 186 " --> pdb=" O PHE F 252 " (cutoff:3.500A) removed outlier: 8.095A pdb=" N ASP F 254 " --> pdb=" O VAL F 186 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N ALA F 188 " --> pdb=" O ASP F 254 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'G' and resid 197 through 204 removed outlier: 6.408A pdb=" N LEU G 183 " --> pdb=" O ALA G 203 " (cutoff:3.500A) removed outlier: 8.618A pdb=" N HIS G 184 " --> pdb=" O ARG G 76 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N GLY G 78 " --> pdb=" O HIS G 184 " (cutoff:3.500A) removed outlier: 7.819A pdb=" N VAL G 186 " --> pdb=" O GLY G 78 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N LEU G 80 " --> pdb=" O VAL G 186 " (cutoff:3.500A) removed outlier: 8.453A pdb=" N THR G 188 " --> pdb=" O LEU G 80 " (cutoff:3.500A) removed outlier: 9.012A pdb=" N VAL G 82 " --> pdb=" O THR G 188 " (cutoff:3.500A) removed outlier: 6.061A pdb=" N ASP G 113 " --> pdb=" O ALA G 77 " (cutoff:3.500A) removed outlier: 7.036A pdb=" N VAL G 79 " --> pdb=" O ASP G 113 " (cutoff:3.500A) removed outlier: 6.094A pdb=" N VAL G 115 " --> pdb=" O VAL G 79 " (cutoff:3.500A) removed outlier: 7.474A pdb=" N VAL G 81 " --> pdb=" O VAL G 115 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N TYR G 117 " --> pdb=" O VAL G 81 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N GLU G 136 " --> pdb=" O VAL G 118 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'H' and resid 41 through 44 removed outlier: 6.249A pdb=" N ASN H 5 " --> pdb=" O VAL H 77 " (cutoff:3.500A) removed outlier: 7.636A pdb=" N ILE H 79 " --> pdb=" O ASN H 5 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N GLU H 7 " --> pdb=" O ILE H 79 " (cutoff:3.500A) removed outlier: 7.179A pdb=" N VAL H 81 " --> pdb=" O GLU H 7 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N VAL H 9 " --> pdb=" O VAL H 81 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N LEU H 4 " --> pdb=" O ALA H 20 " (cutoff:3.500A) removed outlier: 5.987A pdb=" N ALA H 10 " --> pdb=" O GLU H 14 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N GLU H 14 " --> pdb=" O ALA H 10 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'H' and resid 31 through 34 removed outlier: 3.951A pdb=" N ARG H 26 " --> pdb=" O MET H 50 " (cutoff:3.500A) removed outlier: 5.517A pdb=" N MET H 50 " --> pdb=" O ARG H 26 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'a' and resid 20 through 22 Processing sheet with id= Z, first strand: chain 'a' and resid 112 through 114 Processing sheet with id= AA, first strand: chain 'd' and resid 405 through 411 removed outlier: 6.207A pdb=" N VAL d 375 " --> pdb=" O SER d 406 " (cutoff:3.500A) removed outlier: 7.356A pdb=" N GLN d 408 " --> pdb=" O VAL d 375 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N ALA d 377 " --> pdb=" O GLN d 408 " (cutoff:3.500A) removed outlier: 7.416A pdb=" N HIS d 410 " --> pdb=" O ALA d 377 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N VAL d 379 " --> pdb=" O HIS d 410 " (cutoff:3.500A) 2113 hydrogen bonds defined for protein. 5475 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: 28.13 Time building geometry restraints manager: 56.17 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 37326 1.03 - 1.23: 558 1.23 - 1.43: 14817 1.43 - 1.62: 22347 1.62 - 1.82: 194 Bond restraints: 75242 Sorted by residual: bond pdb=" C4 ADP D 600 " pdb=" C5 ADP D 600 " ideal model delta sigma weight residual 1.490 1.466 0.024 2.00e-02 2.50e+03 1.43e+00 bond pdb=" C LEU C 47 " pdb=" O LEU C 47 " ideal model delta sigma weight residual 1.235 1.240 -0.005 4.70e-03 4.53e+04 1.20e+00 bond pdb=" C4 ADP E 600 " pdb=" C5 ADP E 600 " ideal model delta sigma weight residual 1.490 1.468 0.022 2.00e-02 2.50e+03 1.20e+00 bond pdb=" CG PRO F 344 " pdb=" CD PRO F 344 " ideal model delta sigma weight residual 1.512 1.485 0.027 2.70e-02 1.37e+03 9.65e-01 bond pdb=" CB MET d 109 " pdb=" CG MET d 109 " ideal model delta sigma weight residual 1.520 1.547 -0.027 3.00e-02 1.11e+03 8.27e-01 ... (remaining 75237 not shown) Histogram of bond angle deviations from ideal: 99.85 - 107.87: 8840 107.87 - 115.90: 89356 115.90 - 123.93: 32954 123.93 - 131.95: 5132 131.95 - 139.98: 43 Bond angle restraints: 136325 Sorted by residual: angle pdb=" CB MET d 109 " pdb=" CG MET d 109 " pdb=" SD MET d 109 " ideal model delta sigma weight residual 112.70 122.68 -9.98 3.00e+00 1.11e-01 1.11e+01 angle pdb=" CB MET R 21 " pdb=" CG MET R 21 " pdb=" SD MET R 21 " ideal model delta sigma weight residual 112.70 120.95 -8.25 3.00e+00 1.11e-01 7.56e+00 angle pdb=" CG LYS B 384 " pdb=" CD LYS B 384 " pdb=" CE LYS B 384 " ideal model delta sigma weight residual 111.30 117.29 -5.99 2.30e+00 1.89e-01 6.77e+00 angle pdb=" N GLY E 218 " pdb=" CA GLY E 218 " pdb=" C GLY E 218 " ideal model delta sigma weight residual 113.18 107.13 6.05 2.37e+00 1.78e-01 6.52e+00 angle pdb=" CA TYR a 145 " pdb=" CB TYR a 145 " pdb=" CG TYR a 145 " ideal model delta sigma weight residual 113.90 118.40 -4.50 1.80e+00 3.09e-01 6.24e+00 ... (remaining 136320 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.33: 27754 24.33 - 48.65: 1473 48.65 - 72.98: 229 72.98 - 97.30: 57 97.30 - 121.63: 1 Dihedral angle restraints: 29514 sinusoidal: 13818 harmonic: 15696 Sorted by residual: dihedral pdb=" O2A ADP E 600 " pdb=" O3A ADP E 600 " pdb=" PA ADP E 600 " pdb=" PB ADP E 600 " ideal model delta sinusoidal sigma weight residual 300.00 178.37 121.63 1 2.00e+01 2.50e-03 3.66e+01 dihedral pdb=" C5' ADP D 600 " pdb=" O5' ADP D 600 " pdb=" PA ADP D 600 " pdb=" O2A ADP D 600 " ideal model delta sinusoidal sigma weight residual -60.00 -134.69 74.69 1 2.00e+01 2.50e-03 1.77e+01 dihedral pdb=" CA GLY F 218 " pdb=" C GLY F 218 " pdb=" N GLN F 219 " pdb=" CA GLN F 219 " ideal model delta harmonic sigma weight residual -180.00 -159.74 -20.26 0 5.00e+00 4.00e-02 1.64e+01 ... (remaining 29511 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.058: 5189 0.058 - 0.116: 689 0.116 - 0.175: 74 0.175 - 0.233: 3 0.233 - 0.291: 9 Chirality restraints: 5964 Sorted by residual: chirality pdb=" C2' ATP B 600 " pdb=" C1' ATP B 600 " pdb=" C3' ATP B 600 " pdb=" O2' ATP B 600 " both_signs ideal model delta sigma weight residual False -2.68 -2.97 0.29 2.00e-01 2.50e+01 2.12e+00 chirality pdb=" C2' ATP F 600 " pdb=" C1' ATP F 600 " pdb=" C3' ATP F 600 " pdb=" O2' ATP F 600 " both_signs ideal model delta sigma weight residual False -2.68 -2.97 0.29 2.00e-01 2.50e+01 2.11e+00 chirality pdb=" C2' ATP C 600 " pdb=" C1' ATP C 600 " pdb=" C3' ATP C 600 " pdb=" O2' ATP C 600 " both_signs ideal model delta sigma weight residual False -2.68 -2.97 0.29 2.00e-01 2.50e+01 2.07e+00 ... (remaining 5961 not shown) Planarity restraints: 11437 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU H 35 " 0.028 5.00e-02 4.00e+02 4.23e-02 2.87e+00 pdb=" N PRO H 36 " -0.073 5.00e-02 4.00e+02 pdb=" CA PRO H 36 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO H 36 " 0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL d 23 " -0.025 5.00e-02 4.00e+02 3.72e-02 2.21e+00 pdb=" N PRO d 24 " 0.064 5.00e-02 4.00e+02 pdb=" CA PRO d 24 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO d 24 " -0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ILE b 37 " 0.007 2.00e-02 2.50e+03 1.49e-02 2.21e+00 pdb=" C ILE b 37 " -0.026 2.00e-02 2.50e+03 pdb=" O ILE b 37 " 0.010 2.00e-02 2.50e+03 pdb=" N PHE b 38 " 0.009 2.00e-02 2.50e+03 ... (remaining 11434 not shown) Histogram of nonbonded interaction distances: 1.55 - 2.16: 3412 2.16 - 2.77: 148377 2.77 - 3.38: 227006 3.38 - 3.99: 296268 3.99 - 4.60: 462576 Nonbonded interactions: 1137639 Sorted by model distance: nonbonded pdb=" O ALA B 339 " pdb=" HG1 THR B 343 " model vdw 1.550 1.850 nonbonded pdb=" OE1 GLU Q 48 " pdb=" H GLU Q 48 " model vdw 1.587 1.850 nonbonded pdb=" O PRO a 207 " pdb=" H GLN a 211 " model vdw 1.590 1.850 nonbonded pdb=" O ALA B 192 " pdb=" HG1 THR B 195 " model vdw 1.597 1.850 nonbonded pdb=" O LEU a 187 " pdb=" H GLY a 191 " model vdw 1.599 1.850 ... (remaining 1137634 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 7 and (name N or name CA or name C or name O or name CB o \ r name OG or name HA or name HB2 or name HB3 or name HG )) or resid 8 through 21 \ or (resid 30 and (name N or name CA or name C or name O or name CB or name CG o \ r name CD or name OE1 or name OE2 or name HA or name HB2 or name HB3 or name HG2 \ or name HG3)) or resid 31 through 173 or resid 175 through 353 or resid 356 thr \ ough 407 or (resid 414 and (name N or name CA or name C or name O or name CB or \ name CG or name OD1 or name OD2 or name HA or name HB2 or name HB3)) or resid 41 \ 5 through 515 or resid 518 through 519 or resid 600 through 601)) selection = (chain 'B' and ((resid 7 and (name N or name CA or name C or name O or name CB o \ r name OG or name HA or name HB2 or name HB3 or name HG )) or resid 8 through 21 \ or (resid 30 and (name N or name CA or name C or name O or name CB or name CG o \ r name CD or name OE1 or name OE2 or name HA or name HB2 or name HB3 or name HG2 \ or name HG3)) or resid 31 through 173 or resid 175 through 353 or resid 356 thr \ ough 515 or resid 518 through 519 or resid 600 through 601)) selection = (chain 'C' and (resid 7 through 21 or resid 30 through 173 or resid 175 through \ 353 or resid 356 through 407 or (resid 414 and (name N or name CA or name C or n \ ame O or name CB or name CG or name OD1 or name OD2 or name HA or name HB2 or na \ me HB3)) or resid 415 through 514 or resid 532 or resid 537 through 538 or resid \ 600 through 601)) } ncs_group { reference = (chain 'D' and (resid 8 through 452 or resid 455 through 471)) selection = (chain 'E' and (resid 8 through 166 or (resid 167 and (name N or name CA or name \ C or name O or name CB or name OG1 or name CG2 or name H or name HA or name HB \ or name HG21 or name HG22 or name HG23)) or resid 168 through 452 or resid 455 t \ hrough 471)) selection = (chain 'F' and (resid 8 through 452 or resid 455 through 471)) } ncs_group { reference = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = (chain 'T' and ((resid 3 and (name N or name CA or name C or name O or name CB o \ r name CG or name CD1 or name CD2 or name HA or name HB2 or name HB3 or name HG \ or name HD11 or name HD12 or name HD13 or name HD21 or name HD22 or name HD23)) \ or resid 4 through 86)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians P 16 5.49 5 Mg 5 5.21 5 S 107 5.16 5 C 23583 2.51 5 N 6405 2.21 5 O 7180 1.98 5 H 37346 0.53 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.20 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.680 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: 0.870 Extract box with map and model: 28.940 Check model and map are aligned: 0.850 Convert atoms to be neutral: 0.480 Process input model: 200.340 Find NCS groups from input model: 2.800 Set up NCS constraints: 0.400 Set refine NCS operators: 0.000 Set scattering table: 0.030 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:12.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 253.030 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8767 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 : 0.002 0.029 37896 Z= 0.163 Angle : 0.495 9.975 51405 Z= 0.257 Chirality : 0.041 0.291 5964 Planarity : 0.003 0.045 6729 Dihedral : 16.678 121.626 13749 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 4.15 Ramachandran Plot: Outliers : 0.02 % Allowed : 1.68 % Favored : 98.30 % Rotamer Outliers : 1.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.90 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.22 (0.12), residues: 4890 helix: 2.36 (0.10), residues: 2659 sheet: -0.12 (0.21), residues: 536 loop : 0.70 (0.16), residues: 1695 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9780 Ramachandran restraints generated. 4890 Oldfield, 0 Emsley, 4890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9780 Ramachandran restraints generated. 4890 Oldfield, 0 Emsley, 4890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 179 is missing expected H atoms. Skipping. Residue THR 179 is missing expected H atoms. Skipping. Residue THR 179 is missing expected H atoms. Skipping. Residue THR 167 is missing expected H atoms. Skipping. Residue THR 167 is missing expected H atoms. Skipping. Evaluate side-chains 305 residues out of total 3833 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 258 time to evaluate : 4.565 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 47 outliers final: 39 residues processed: 302 average time/residue: 2.4664 time to fit residues: 923.3044 Evaluate side-chains 262 residues out of total 3833 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 223 time to evaluate : 4.415 Switching outliers to nearest non-outliers outliers start: 39 outliers final: 39 residues processed: 1 average time/residue: 0.7440 time to fit residues: 6.6985 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 483 random chunks: chunk 407 optimal weight: 3.9990 chunk 366 optimal weight: 2.9990 chunk 203 optimal weight: 0.6980 chunk 125 optimal weight: 2.9990 chunk 246 optimal weight: 0.8980 chunk 195 optimal weight: 1.9990 chunk 378 optimal weight: 1.9990 chunk 146 optimal weight: 2.9990 chunk 230 optimal weight: 0.9990 chunk 281 optimal weight: 1.9990 chunk 438 optimal weight: 4.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 335 ASN F 425 GLN G 25 GLN N 50 GLN ** O 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 50 GLN a 174 ASN ** b 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 131 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8780 moved from start: 0.0304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.041 37896 Z= 0.239 Angle : 0.495 7.852 51405 Z= 0.260 Chirality : 0.039 0.151 5964 Planarity : 0.004 0.041 6729 Dihedral : 4.939 120.714 5289 Min Nonbonded Distance : 1.809 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.02 % Allowed : 1.97 % Favored : 98.01 % Rotamer Outliers : 2.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.90 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.03 (0.12), residues: 4890 helix: 2.14 (0.10), residues: 2661 sheet: -0.09 (0.21), residues: 536 loop : 0.69 (0.16), residues: 1693 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9780 Ramachandran restraints generated. 4890 Oldfield, 0 Emsley, 4890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9780 Ramachandran restraints generated. 4890 Oldfield, 0 Emsley, 4890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 179 is missing expected H atoms. Skipping. Residue THR 179 is missing expected H atoms. Skipping. Residue THR 179 is missing expected H atoms. Skipping. Residue THR 167 is missing expected H atoms. Skipping. Residue THR 167 is missing expected H atoms. Skipping. Evaluate side-chains 304 residues out of total 3833 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 225 time to evaluate : 4.529 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 79 outliers final: 48 residues processed: 288 average time/residue: 2.4051 time to fit residues: 865.9752 Evaluate side-chains 268 residues out of total 3833 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 220 time to evaluate : 4.554 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 48 outliers final: 44 residues processed: 6 average time/residue: 1.3283 time to fit residues: 16.9666 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 483 random chunks: chunk 243 optimal weight: 5.9990 chunk 136 optimal weight: 2.9990 chunk 365 optimal weight: 3.9990 chunk 298 optimal weight: 3.9990 chunk 120 optimal weight: 1.9990 chunk 439 optimal weight: 3.9990 chunk 474 optimal weight: 4.9990 chunk 391 optimal weight: 3.9990 chunk 435 optimal weight: 0.9990 chunk 149 optimal weight: 2.9990 chunk 352 optimal weight: 0.7980 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 425 GLN ** O 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 50 GLN b 131 GLN d 410 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8798 moved from start: 0.0500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.057 37896 Z= 0.334 Angle : 0.526 8.702 51405 Z= 0.277 Chirality : 0.041 0.162 5964 Planarity : 0.004 0.046 6729 Dihedral : 5.237 120.146 5289 Min Nonbonded Distance : 1.698 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.48 % Favored : 97.50 % Rotamer Outliers : 2.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.90 % Cis-general : 0.13 % 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: 1.80 (0.12), residues: 4890 helix: 1.94 (0.10), residues: 2654 sheet: -0.10 (0.21), residues: 536 loop : 0.59 (0.16), residues: 1700 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9780 Ramachandran restraints generated. 4890 Oldfield, 0 Emsley, 4890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9780 Ramachandran restraints generated. 4890 Oldfield, 0 Emsley, 4890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 179 is missing expected H atoms. Skipping. Residue THR 179 is missing expected H atoms. Skipping. Residue THR 179 is missing expected H atoms. Skipping. Residue THR 167 is missing expected H atoms. Skipping. Residue THR 167 is missing expected H atoms. Skipping. Evaluate side-chains 314 residues out of total 3833 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 223 time to evaluate : 4.462 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 91 outliers final: 57 residues processed: 295 average time/residue: 2.4698 time to fit residues: 909.4676 Evaluate side-chains 271 residues out of total 3833 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 214 time to evaluate : 4.440 Switching outliers to nearest non-outliers outliers start: 57 outliers final: 48 residues processed: 10 average time/residue: 1.3546 time to fit residues: 24.7323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 483 random chunks: chunk 434 optimal weight: 5.9990 chunk 330 optimal weight: 4.9990 chunk 228 optimal weight: 2.9990 chunk 48 optimal weight: 2.9990 chunk 209 optimal weight: 2.9990 chunk 295 optimal weight: 1.9990 chunk 440 optimal weight: 1.9990 chunk 466 optimal weight: 3.9990 chunk 230 optimal weight: 0.7980 chunk 417 optimal weight: 0.5980 chunk 125 optimal weight: 2.9990 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 425 GLN N 50 GLN ** O 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 50 GLN a 174 ASN b 131 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8794 moved from start: 0.0521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.043 37896 Z= 0.287 Angle : 0.513 8.551 51405 Z= 0.268 Chirality : 0.040 0.154 5964 Planarity : 0.004 0.045 6729 Dihedral : 5.229 120.368 5289 Min Nonbonded Distance : 1.706 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.36 % Favored : 97.62 % Rotamer Outliers : 2.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.90 % Cis-general : 0.13 % 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: 1.76 (0.12), residues: 4890 helix: 1.90 (0.10), residues: 2655 sheet: -0.11 (0.21), residues: 536 loop : 0.59 (0.16), residues: 1699 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9780 Ramachandran restraints generated. 4890 Oldfield, 0 Emsley, 4890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9780 Ramachandran restraints generated. 4890 Oldfield, 0 Emsley, 4890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 179 is missing expected H atoms. Skipping. Residue THR 179 is missing expected H atoms. Skipping. Residue THR 179 is missing expected H atoms. Skipping. Residue THR 167 is missing expected H atoms. Skipping. Residue THR 167 is missing expected H atoms. Skipping. Evaluate side-chains 302 residues out of total 3833 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 220 time to evaluate : 4.537 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 82 outliers final: 58 residues processed: 288 average time/residue: 2.4201 time to fit residues: 876.9863 Evaluate side-chains 271 residues out of total 3833 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 213 time to evaluate : 4.433 Switching outliers to nearest non-outliers outliers start: 58 outliers final: 52 residues processed: 8 average time/residue: 1.0448 time to fit residues: 18.4057 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 483 random chunks: chunk 388 optimal weight: 3.9990 chunk 265 optimal weight: 1.9990 chunk 6 optimal weight: 1.9990 chunk 347 optimal weight: 2.9990 chunk 192 optimal weight: 2.9990 chunk 398 optimal weight: 2.9990 chunk 322 optimal weight: 2.9990 chunk 0 optimal weight: 7.9990 chunk 238 optimal weight: 3.9990 chunk 419 optimal weight: 0.7980 chunk 117 optimal weight: 1.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 425 GLN ** O 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 50 GLN b 131 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8801 moved from start: 0.0599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.056 37896 Z= 0.335 Angle : 0.528 8.746 51405 Z= 0.277 Chirality : 0.041 0.162 5964 Planarity : 0.004 0.047 6729 Dihedral : 5.338 120.800 5289 Min Nonbonded Distance : 1.686 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.64 % Favored : 97.34 % Rotamer Outliers : 2.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.90 % Cis-general : 0.13 % 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: 1.69 (0.12), residues: 4890 helix: 1.84 (0.10), residues: 2655 sheet: -0.12 (0.21), residues: 536 loop : 0.55 (0.16), residues: 1699 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9780 Ramachandran restraints generated. 4890 Oldfield, 0 Emsley, 4890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9780 Ramachandran restraints generated. 4890 Oldfield, 0 Emsley, 4890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 179 is missing expected H atoms. Skipping. Residue THR 179 is missing expected H atoms. Skipping. Residue THR 179 is missing expected H atoms. Skipping. Residue THR 167 is missing expected H atoms. Skipping. Residue THR 167 is missing expected H atoms. Skipping. Evaluate side-chains 306 residues out of total 3833 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 222 time to evaluate : 4.552 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 84 outliers final: 56 residues processed: 293 average time/residue: 2.4342 time to fit residues: 888.6482 Evaluate side-chains 266 residues out of total 3833 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 210 time to evaluate : 4.443 Switching outliers to nearest non-outliers outliers start: 56 outliers final: 51 residues processed: 6 average time/residue: 1.1847 time to fit residues: 15.9396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 483 random chunks: chunk 157 optimal weight: 1.9990 chunk 420 optimal weight: 3.9990 chunk 92 optimal weight: 1.9990 chunk 274 optimal weight: 3.9990 chunk 115 optimal weight: 0.9980 chunk 467 optimal weight: 4.9990 chunk 387 optimal weight: 2.9990 chunk 216 optimal weight: 2.9990 chunk 38 optimal weight: 2.9990 chunk 154 optimal weight: 0.4980 chunk 245 optimal weight: 1.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 425 GLN F 425 GLN N 50 GLN ** O 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 174 ASN b 131 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8794 moved from start: 0.0588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.039 37896 Z= 0.268 Angle : 0.512 8.542 51405 Z= 0.267 Chirality : 0.040 0.157 5964 Planarity : 0.004 0.045 6729 Dihedral : 5.263 121.112 5289 Min Nonbonded Distance : 1.692 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.44 % Favored : 97.54 % Rotamer Outliers : 2.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.90 % Cis-general : 0.13 % 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: 1.74 (0.12), residues: 4890 helix: 1.87 (0.10), residues: 2656 sheet: -0.12 (0.21), residues: 536 loop : 0.59 (0.16), residues: 1698 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9780 Ramachandran restraints generated. 4890 Oldfield, 0 Emsley, 4890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9780 Ramachandran restraints generated. 4890 Oldfield, 0 Emsley, 4890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 179 is missing expected H atoms. Skipping. Residue THR 179 is missing expected H atoms. Skipping. Residue THR 179 is missing expected H atoms. Skipping. Residue THR 167 is missing expected H atoms. Skipping. Residue THR 167 is missing expected H atoms. Skipping. Evaluate side-chains 297 residues out of total 3833 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 215 time to evaluate : 4.559 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 82 outliers final: 57 residues processed: 284 average time/residue: 2.6284 time to fit residues: 925.9341 Evaluate side-chains 259 residues out of total 3833 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 202 time to evaluate : 4.412 Switching outliers to nearest non-outliers outliers start: 57 outliers final: 52 residues processed: 7 average time/residue: 1.2970 time to fit residues: 18.5085 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 483 random chunks: chunk 450 optimal weight: 2.9990 chunk 52 optimal weight: 6.9990 chunk 266 optimal weight: 2.9990 chunk 341 optimal weight: 3.9990 chunk 264 optimal weight: 0.9990 chunk 393 optimal weight: 1.9990 chunk 260 optimal weight: 0.9980 chunk 465 optimal weight: 6.9990 chunk 291 optimal weight: 2.9990 chunk 283 optimal weight: 1.9990 chunk 214 optimal weight: 3.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 425 GLN ** O 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8799 moved from start: 0.0636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.051 37896 Z= 0.311 Angle : 0.525 8.767 51405 Z= 0.274 Chirality : 0.040 0.160 5964 Planarity : 0.004 0.059 6729 Dihedral : 5.322 121.378 5289 Min Nonbonded Distance : 1.672 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.64 % Favored : 97.34 % Rotamer Outliers : 2.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.90 % Cis-general : 0.13 % 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: 1.69 (0.12), residues: 4890 helix: 1.83 (0.10), residues: 2656 sheet: -0.13 (0.21), residues: 536 loop : 0.56 (0.16), residues: 1698 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9780 Ramachandran restraints generated. 4890 Oldfield, 0 Emsley, 4890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9780 Ramachandran restraints generated. 4890 Oldfield, 0 Emsley, 4890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 179 is missing expected H atoms. Skipping. Residue THR 179 is missing expected H atoms. Skipping. Residue THR 179 is missing expected H atoms. Skipping. Residue THR 167 is missing expected H atoms. Skipping. Residue THR 167 is missing expected H atoms. Skipping. Evaluate side-chains 292 residues out of total 3833 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 211 time to evaluate : 4.628 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 81 outliers final: 56 residues processed: 280 average time/residue: 2.5502 time to fit residues: 892.5389 Evaluate side-chains 265 residues out of total 3833 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 209 time to evaluate : 4.465 Switching outliers to nearest non-outliers outliers start: 56 outliers final: 52 residues processed: 5 average time/residue: 1.3558 time to fit residues: 15.2716 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 483 random chunks: chunk 288 optimal weight: 1.9990 chunk 185 optimal weight: 2.9990 chunk 278 optimal weight: 0.9990 chunk 140 optimal weight: 2.9990 chunk 91 optimal weight: 4.9990 chunk 90 optimal weight: 1.9990 chunk 295 optimal weight: 0.6980 chunk 317 optimal weight: 2.9990 chunk 230 optimal weight: 1.9990 chunk 43 optimal weight: 0.7980 chunk 365 optimal weight: 4.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 425 GLN ** O 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8790 moved from start: 0.0606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.035 37896 Z= 0.239 Angle : 0.507 8.990 51405 Z= 0.263 Chirality : 0.039 0.158 5964 Planarity : 0.004 0.044 6729 Dihedral : 5.222 121.481 5289 Min Nonbonded Distance : 1.698 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.34 % Favored : 97.64 % Rotamer Outliers : 1.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.90 % Cis-general : 0.13 % 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: 1.77 (0.12), residues: 4890 helix: 1.91 (0.10), residues: 2654 sheet: -0.11 (0.21), residues: 536 loop : 0.61 (0.16), residues: 1700 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9780 Ramachandran restraints generated. 4890 Oldfield, 0 Emsley, 4890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9780 Ramachandran restraints generated. 4890 Oldfield, 0 Emsley, 4890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 179 is missing expected H atoms. Skipping. Residue THR 179 is missing expected H atoms. Skipping. Residue THR 179 is missing expected H atoms. Skipping. Residue THR 167 is missing expected H atoms. Skipping. Residue THR 167 is missing expected H atoms. Skipping. Evaluate side-chains 282 residues out of total 3833 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 214 time to evaluate : 4.585 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 68 outliers final: 59 residues processed: 273 average time/residue: 2.5597 time to fit residues: 870.7321 Evaluate side-chains 265 residues out of total 3833 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 206 time to evaluate : 4.470 Switching outliers to nearest non-outliers outliers start: 59 outliers final: 55 residues processed: 6 average time/residue: 1.2103 time to fit residues: 16.3212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 483 random chunks: chunk 423 optimal weight: 0.4980 chunk 445 optimal weight: 5.9990 chunk 406 optimal weight: 3.9990 chunk 433 optimal weight: 4.9990 chunk 261 optimal weight: 0.7980 chunk 188 optimal weight: 0.9980 chunk 340 optimal weight: 2.9990 chunk 133 optimal weight: 1.9990 chunk 392 optimal weight: 0.7980 chunk 410 optimal weight: 0.5980 chunk 432 optimal weight: 0.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 425 GLN a 174 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8775 moved from start: 0.0505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.037 37896 Z= 0.164 Angle : 0.486 10.204 51405 Z= 0.250 Chirality : 0.039 0.153 5964 Planarity : 0.003 0.042 6729 Dihedral : 5.006 121.065 5289 Min Nonbonded Distance : 1.759 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.13 % Favored : 97.85 % Rotamer Outliers : 1.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.90 % Cis-general : 0.13 % 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: 1.92 (0.12), residues: 4890 helix: 2.03 (0.10), residues: 2653 sheet: -0.10 (0.21), residues: 536 loop : 0.69 (0.16), residues: 1701 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9780 Ramachandran restraints generated. 4890 Oldfield, 0 Emsley, 4890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9780 Ramachandran restraints generated. 4890 Oldfield, 0 Emsley, 4890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 179 is missing expected H atoms. Skipping. Residue THR 179 is missing expected H atoms. Skipping. Residue THR 179 is missing expected H atoms. Skipping. Residue THR 167 is missing expected H atoms. Skipping. Residue THR 167 is missing expected H atoms. Skipping. Evaluate side-chains 277 residues out of total 3833 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 219 time to evaluate : 4.549 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 outliers start: 58 outliers final: 54 residues processed: 274 average time/residue: 2.6002 time to fit residues: 890.0996 Evaluate side-chains 265 residues out of total 3833 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 211 time to evaluate : 4.581 Switching outliers to nearest non-outliers outliers start: 54 outliers final: 53 residues processed: 1 average time/residue: 0.7631 time to fit residues: 6.9026 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 483 random chunks: chunk 284 optimal weight: 1.9990 chunk 458 optimal weight: 5.9990 chunk 279 optimal weight: 2.9990 chunk 217 optimal weight: 3.9990 chunk 318 optimal weight: 1.9990 chunk 481 optimal weight: 2.9990 chunk 442 optimal weight: 0.0070 chunk 383 optimal weight: 2.9990 chunk 39 optimal weight: 0.9980 chunk 295 optimal weight: 0.5980 chunk 234 optimal weight: 1.9990 overall best weight: 1.1202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 425 GLN ** O 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8782 moved from start: 0.0557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.035 37896 Z= 0.219 Angle : 0.498 10.935 51405 Z= 0.257 Chirality : 0.039 0.142 5964 Planarity : 0.004 0.067 6729 Dihedral : 5.023 120.195 5289 Min Nonbonded Distance : 1.728 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.19 % Favored : 97.79 % Rotamer Outliers : 1.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.90 % Cis-general : 0.13 % 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: 1.93 (0.12), residues: 4890 helix: 2.03 (0.10), residues: 2661 sheet: -0.06 (0.21), residues: 536 loop : 0.69 (0.16), residues: 1693 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9780 Ramachandran restraints generated. 4890 Oldfield, 0 Emsley, 4890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9780 Ramachandran restraints generated. 4890 Oldfield, 0 Emsley, 4890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 179 is missing expected H atoms. Skipping. Residue THR 179 is missing expected H atoms. Skipping. Residue THR 179 is missing expected H atoms. Skipping. Residue THR 167 is missing expected H atoms. Skipping. Residue THR 167 is missing expected H atoms. Skipping. Evaluate side-chains 277 residues out of total 3833 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 215 time to evaluate : 4.503 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 62 outliers final: 57 residues processed: 273 average time/residue: 2.5245 time to fit residues: 857.5372 Evaluate side-chains 266 residues out of total 3833 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 209 time to evaluate : 4.456 Switching outliers to nearest non-outliers outliers start: 57 outliers final: 55 residues processed: 3 average time/residue: 1.2118 time to fit residues: 10.8726 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 483 random chunks: chunk 304 optimal weight: 3.9990 chunk 408 optimal weight: 3.9990 chunk 117 optimal weight: 1.9990 chunk 353 optimal weight: 0.7980 chunk 56 optimal weight: 2.9990 chunk 106 optimal weight: 2.9990 chunk 383 optimal weight: 2.9990 chunk 160 optimal weight: 1.9990 chunk 394 optimal weight: 1.9990 chunk 48 optimal weight: 2.9990 chunk 70 optimal weight: 2.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 425 GLN ** O 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.074614 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2886 r_free = 0.2886 target = 0.055427 restraints weight = 271226.668| |-----------------------------------------------------------------------------| r_work (start): 0.2869 rms_B_bonded: 1.64 r_work: 0.2781 rms_B_bonded: 1.79 restraints_weight: 0.5000 r_work: 0.2678 rms_B_bonded: 3.10 restraints_weight: 0.2500 r_work (final): 0.2678 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3338 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3338 r_free = 0.3338 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3338 r_free = 0.3338 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3338 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8979 moved from start: 0.0663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.054 37896 Z= 0.328 Angle : 0.528 10.980 51405 Z= 0.275 Chirality : 0.040 0.163 5964 Planarity : 0.004 0.058 6729 Dihedral : 5.243 120.134 5289 Min Nonbonded Distance : 1.664 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.50 % Favored : 97.48 % Rotamer Outliers : 1.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.90 % Cis-general : 0.13 % 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: 1.80 (0.12), residues: 4890 helix: 1.92 (0.10), residues: 2659 sheet: -0.07 (0.21), residues: 536 loop : 0.60 (0.16), residues: 1695 =============================================================================== Job complete usr+sys time: 16501.68 seconds wall clock time: 285 minutes 8.01 seconds (17108.01 seconds total)