Starting phenix.real_space_refine (version: dev) on Thu Dec 15 03:21:49 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7njl_12382/12_2022/7njl_12382_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7njl_12382/12_2022/7njl_12382.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.71 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7njl_12382/12_2022/7njl_12382.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7njl_12382/12_2022/7njl_12382.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7njl_12382/12_2022/7njl_12382_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7njl_12382/12_2022/7njl_12382_trim_updated.pdb" } resolution = 2.71 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= 0.002 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 "B GLU 81": "OE1" <-> "OE2" Residue "B TYR 400": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 436": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 467": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D GLU 393": "OE1" <-> "OE2" Residue "D GLU 469": "OE1" <-> "OE2" Residue "E PHE 456": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F ASP 363": "OD1" <-> "OD2" Residue "G PHE 161": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G GLU 255": "OE1" <-> "OE2" Residue "M PHE 69": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "O GLU 48": "OE1" <-> "OE2" Residue "P ASP 32": "OD1" <-> "OD2" Residue "P PHE 58": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "Q ASP 32": "OD1" <-> "OD2" Residue "R PHE 78": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "a TYR 145": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "a TYR 240": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "b ASP 70": "OD1" <-> "OD2" Residue "b GLU 88": "OE1" <-> "OE2" Residue "d GLU 185": "OE1" <-> "OE2" Time to flip residues: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/chem_data/mon_lib" Total number of atoms: 74775 Number of models: 1 Model: "" Number of chains: 31 Chain: "A" Number of atoms: 7704 Number of conformers: 1 Conformer: "" Number of residues, atoms: 509, 7704 Classifications: {'peptide': 509} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 19, 'TRANS': 487} Chain breaks: 2 Chain: "B" Number of atoms: 7639 Number of conformers: 1 Conformer: "" Number of residues, atoms: 505, 7639 Classifications: {'peptide': 505} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 19, 'TRANS': 483} Chain breaks: 2 Chain: "C" Number of atoms: 8067 Number of conformers: 1 Conformer: "" Number of residues, atoms: 533, 8067 Classifications: {'peptide': 533} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 22, 'TRANS': 508} Chain breaks: 2 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: 7166 Number of conformers: 1 Conformer: "" Number of residues, atoms: 469, 7166 Classifications: {'peptide': 469} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 22, 'TRANS': 444} Chain: "G" Number of atoms: 4590 Number of conformers: 1 Conformer: "" Number of residues, atoms: 298, 4590 Classifications: {'peptide': 298} Link IDs: {'PCIS': 2, 'PTRANS': 8, '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: 1204 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 1204 Classifications: {'peptide': 85} Link IDs: {'PTRANS': 4, 'TRANS': 80} 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: 1204 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 1204 Classifications: {'peptide': 85} Link IDs: {'PTRANS': 4, 'TRANS': 80} 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: 1192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 1192 Classifications: {'peptide': 84} Link IDs: {'PTRANS': 4, 'TRANS': 79} 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: 2172 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 2172 Classifications: {'peptide': 145} Link IDs: {'PTRANS': 3, 'TRANS': 141} Chain: "d" Number of atoms: 6668 Number of conformers: 1 Conformer: "" Number of residues, atoms: 439, 6668 Classifications: {'peptide': 439} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 12, 'TRANS': 426} 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: 1 residue: pdb=" N AGLN D 453 " occ=0.50 ... (32 atoms not shown) pdb="HE22BGLN D 453 " occ=0.50 Time building chain proxies: 28.48, per 1000 atoms: 0.38 Number of scatterers: 74775 At special positions: 0 Unit cell: (136.12, 129.48, 252.32, 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 7199 8.00 N 6419 7.00 C 23615 6.00 H 37414 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: 54.01 Conformation dependent library (CDL) restraints added in 6.5 seconds 9782 Ramachandran restraints generated. 4891 Oldfield, 0 Emsley, 4891 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8902 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 182 helices and 26 sheets defined 55.0% alpha, 9.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.31 Creating SS restraints... Processing helix chain 'A' and resid 9 through 21 removed outlier: 3.951A pdb=" N VAL A 19 " --> pdb=" O GLU A 16 " (cutoff:3.500A) 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 194 removed outlier: 3.723A pdb=" N GLN A 189 " --> pdb=" O THR A 185 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N ARG A 190 " --> pdb=" O ILE A 186 " (cutoff:3.500A) removed outlier: 5.172A pdb=" N GLU A 191 " --> pdb=" O LEU A 187 " (cutoff:3.500A) removed outlier: 4.835A 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 243 through 263 Proline residue: A 250 - end of helix removed outlier: 3.696A pdb=" N TRP A 260 " --> pdb=" O ILE A 256 " (cutoff:3.500A) removed outlier: 3.565A 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 310 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 362 Processing helix chain 'A' and resid 378 through 381 Processing helix chain 'A' and resid 384 through 390 Processing helix chain 'A' and resid 393 through 406 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: 4.722A pdb=" N GLN A 465 " --> pdb=" O GLU A 462 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N SER A 478 " --> pdb=" O VAL A 475 " (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 8 through 22 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 139 through 141 No H-bonds generated for 'chain 'B' and resid 139 through 141' Processing helix chain 'B' and resid 154 through 159 Processing helix chain 'B' and resid 178 through 195 removed outlier: 3.839A pdb=" N GLN B 189 " --> pdb=" O THR B 185 " (cutoff:3.500A) removed outlier: 4.633A pdb=" N ARG B 190 " --> pdb=" O ILE B 186 " (cutoff:3.500A) removed outlier: 5.351A pdb=" N GLU B 191 " --> pdb=" O LEU B 187 " (cutoff:3.500A) removed outlier: 4.914A 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: 3.690A 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 310 removed outlier: 3.545A 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 362 Processing helix chain 'B' and resid 384 through 405 removed outlier: 4.596A pdb=" N SER B 392 " --> pdb=" O GLU B 388 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N LEU B 393 " --> pdb=" O VAL B 389 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N LEU B 395 " --> pdb=" O GLY B 391 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N GLU B 402 " --> pdb=" O SER B 398 " (cutoff:3.500A) removed outlier: 4.992A pdb=" N ALA B 405 " --> pdb=" O ARG B 401 " (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: 5.070A pdb=" N GLN B 465 " --> pdb=" O GLU B 462 " (cutoff:3.500A) Processing helix chain 'B' and resid 481 through 488 Processing helix chain 'B' and resid 494 through 509 Processing helix chain 'C' and resid 8 through 21 removed outlier: 3.788A pdb=" N ILE C 15 " --> pdb=" O ILE C 11 " (cutoff:3.500A) Processing helix chain 'C' and resid 59 through 61 No H-bonds generated for 'chain 'C' and resid 59 through 61' 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: 3.762A pdb=" N GLN C 189 " --> pdb=" O THR C 185 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N ARG C 190 " --> pdb=" O ILE C 186 " (cutoff:3.500A) removed outlier: 5.411A pdb=" N GLU C 191 " --> pdb=" O LEU C 187 " (cutoff:3.500A) removed outlier: 5.160A 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 262 Proline residue: C 250 - end of helix removed outlier: 3.725A pdb=" N TRP C 260 " --> pdb=" O ILE C 256 " (cutoff:3.500A) Processing helix chain 'C' and resid 274 through 288 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 311 removed outlier: 3.631A pdb=" N LEU C 308 " --> pdb=" O LEU C 304 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N ARG C 311 " --> pdb=" O ARG C 307 " (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 430 Processing helix chain 'C' and resid 441 through 452 Processing helix chain 'C' and resid 461 through 477 removed outlier: 4.563A pdb=" N GLN C 465 " --> pdb=" O GLU C 462 " (cutoff:3.500A) Processing helix chain 'C' and resid 481 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 206 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: 4.881A pdb=" N ALA D 231 " --> pdb=" O ARG D 227 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N LEU D 232 " --> pdb=" O MET D 228 " (cutoff:3.500A) Processing helix chain 'D' and resid 256 through 265 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: 4.274A pdb=" N ALA D 325 " --> pdb=" O ALA D 321 " (cutoff:3.500A) removed outlier: 4.579A 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 388 removed outlier: 4.531A pdb=" N ASP D 384 " --> pdb=" O LYS D 380 " (cutoff:3.500A) removed outlier: 4.826A 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 420 through 423 No H-bonds generated for 'chain 'D' and resid 420 through 423' 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 146 Processing helix chain 'E' and resid 166 through 180 Processing helix chain 'E' and resid 194 through 206 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: 5.163A pdb=" N ALA E 231 " --> pdb=" O ARG E 227 " (cutoff:3.500A) removed outlier: 4.723A 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: 4.204A 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 340 removed outlier: 3.542A pdb=" N LYS E 340 " --> pdb=" O ALA E 336 " (cutoff:3.500A) 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: 4.274A pdb=" N ASP E 384 " --> pdb=" O LYS E 380 " (cutoff:3.500A) removed outlier: 4.701A 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 417 through 421 removed outlier: 3.740A pdb=" N GLN E 421 " --> pdb=" O ALA E 418 " (cutoff:3.500A) Processing helix chain 'E' and resid 432 through 444 Processing helix chain 'E' and resid 452 through 455 Processing helix chain 'E' and resid 461 through 470 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 244 removed outlier: 5.027A pdb=" N ALA F 231 " --> pdb=" O ARG F 227 " (cutoff:3.500A) removed outlier: 4.952A 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: 4.445A pdb=" N ALA F 325 " --> pdb=" O ALA F 321 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N HIS F 326 " --> pdb=" O THR F 322 " (cutoff:3.500A) Processing helix chain 'F' and resid 335 through 339 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: 4.524A pdb=" N ASP F 384 " --> pdb=" O LYS F 380 " (cutoff:3.500A) removed outlier: 4.952A pdb=" N ILE F 385 " --> pdb=" O ASP F 381 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N ILE F 388 " --> pdb=" O ASP F 384 " (cutoff:3.500A) 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 443 Processing helix chain 'F' and resid 452 through 455 Processing helix chain 'F' and resid 461 through 470 Processing helix chain 'G' and resid 4 through 42 Processing helix chain 'G' and resid 44 through 59 removed outlier: 3.610A pdb=" N ASN G 52 " --> pdb=" O ALA G 48 " (cutoff:3.500A) Processing helix chain 'G' and resid 92 through 109 removed outlier: 3.948A pdb=" N LEU G 106 " --> pdb=" O GLU G 102 " (cutoff:3.500A) Processing helix chain 'G' and resid 122 through 130 Processing helix chain 'G' and resid 147 through 165 removed outlier: 3.608A pdb=" N GLY G 164 " --> pdb=" O ALA G 160 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N ALA G 165 " --> pdb=" O PHE G 161 " (cutoff:3.500A) Processing helix chain 'G' and resid 228 through 303 Proline residue: G 237 - end of helix Processing helix chain 'H' and resid 87 through 89 No H-bonds generated for 'chain 'H' and resid 87 through 89' Processing helix chain 'H' and resid 92 through 100 removed outlier: 4.052A pdb=" N ALA H 100 " --> pdb=" O LYS H 96 " (cutoff:3.500A) 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 79 removed outlier: 4.264A pdb=" N GLY L 51 " --> pdb=" O GLU L 48 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N PHE L 54 " --> pdb=" O GLY L 51 " (cutoff:3.500A) Proline residue: L 56 - end of helix removed outlier: 3.941A pdb=" N VAL L 61 " --> pdb=" O PHE L 58 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N GLY L 62 " --> pdb=" O ILE L 59 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N GLU L 65 " --> pdb=" O GLY L 62 " (cutoff:3.500A) Processing helix chain 'M' and resid 5 through 45 Processing helix chain 'M' and resid 47 through 79 removed outlier: 3.995A pdb=" N GLY M 51 " --> pdb=" O GLU M 48 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N PHE M 54 " --> pdb=" O GLY M 51 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N THR M 55 " --> pdb=" O ARG M 52 " (cutoff:3.500A) Proline residue: M 56 - end of helix removed outlier: 3.938A pdb=" N VAL M 61 " --> pdb=" O PHE M 58 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N VAL M 64 " --> pdb=" O VAL M 61 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N GLU M 65 " --> pdb=" O GLY M 62 " (cutoff:3.500A) Processing helix chain 'N' and resid 5 through 45 Processing helix chain 'N' and resid 48 through 79 removed outlier: 3.803A pdb=" N GLY N 51 " --> pdb=" O GLU N 48 " (cutoff:3.500A) Proline residue: N 56 - end of helix removed outlier: 4.020A pdb=" N TYR N 68 " --> pdb=" O GLU N 65 " (cutoff:3.500A) Processing helix chain 'O' and resid 5 through 45 Processing helix chain 'O' and resid 47 through 79 removed outlier: 4.885A pdb=" N GLY O 51 " --> pdb=" O GLU O 48 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N THR O 55 " --> pdb=" O ARG O 52 " (cutoff:3.500A) Proline residue: O 56 - end of helix removed outlier: 3.662A pdb=" N VAL O 61 " --> pdb=" O PHE O 58 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N GLU O 65 " --> pdb=" O GLY O 62 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N ALA O 66 " --> pdb=" O LEU O 63 " (cutoff:3.500A) Processing helix chain 'P' and resid 5 through 45 Processing helix chain 'P' and resid 48 through 80 removed outlier: 3.912A pdb=" N GLY P 51 " --> pdb=" O GLU P 48 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N LEU P 53 " --> pdb=" O GLN P 50 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N PHE P 54 " --> pdb=" O GLY P 51 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N THR P 55 " --> pdb=" O ARG P 52 " (cutoff:3.500A) Proline residue: P 56 - end of helix removed outlier: 3.764A pdb=" N GLU P 65 " --> pdb=" O GLY P 62 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N ALA P 66 " --> pdb=" O LEU P 63 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N VAL P 79 " --> pdb=" O ALA P 76 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N PHE P 80 " --> pdb=" O LEU P 77 " (cutoff:3.500A) Processing helix chain 'Q' and resid 5 through 45 removed outlier: 3.606A pdb=" N ARG Q 45 " --> pdb=" O SER Q 41 " (cutoff:3.500A) Processing helix chain 'Q' and resid 47 through 50 Processing helix chain 'Q' and resid 53 through 79 Processing helix chain 'R' and resid 5 through 45 Processing helix chain 'R' and resid 47 through 79 removed outlier: 5.190A pdb=" N GLY R 51 " --> pdb=" O GLU R 48 " (cutoff:3.500A) Proline residue: R 56 - end of helix removed outlier: 3.556A pdb=" N VAL R 61 " --> pdb=" O PHE R 58 " (cutoff:3.500A) removed outlier: 4.838A pdb=" N GLU R 65 " --> pdb=" O GLY R 62 " (cutoff:3.500A) Processing helix chain 'S' and resid 5 through 45 Processing helix chain 'S' and resid 47 through 79 removed outlier: 4.379A pdb=" N GLY S 51 " --> pdb=" O GLU S 48 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N PHE S 54 " --> pdb=" O GLY S 51 " (cutoff:3.500A) Proline residue: S 56 - end of helix removed outlier: 4.141A pdb=" N GLY S 62 " --> pdb=" O ILE S 59 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N GLU S 65 " --> pdb=" O GLY S 62 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N PHE S 69 " --> pdb=" O ALA S 66 " (cutoff:3.500A) Processing helix chain 'T' and resid 5 through 45 Processing helix chain 'T' and resid 50 through 80 Proline residue: T 56 - end of helix removed outlier: 3.719A pdb=" N ASN T 71 " --> pdb=" O ALA T 67 " (cutoff:3.500A) Processing helix chain 'a' and resid 29 through 52 Processing helix chain 'a' and resid 61 through 80 Processing helix chain 'a' and resid 89 through 108 removed outlier: 3.976A pdb=" N ALA a 107 " --> pdb=" O SER a 103 " (cutoff:3.500A) removed outlier: 4.485A 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 155 through 164 Proline residue: a 159 - end of helix Processing helix chain 'a' and resid 171 through 205 Proline residue: a 182 - end of helix removed outlier: 4.256A pdb=" N LEU a 189 " --> pdb=" O LEU a 185 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N MET a 205 " --> pdb=" O ALA a 201 " (cutoff:3.500A) Processing helix chain 'a' and resid 208 through 244 removed outlier: 5.928A pdb=" N PHE a 213 " --> pdb=" O TYR a 209 " (cutoff:3.500A) Proline residue: a 214 - end of helix removed outlier: 3.850A pdb=" N PHE a 224 " --> pdb=" O THR a 220 " (cutoff:3.500A) Processing helix chain 'b' and resid 29 through 47 removed outlier: 3.985A pdb=" N VAL b 34 " --> pdb=" O PHE b 31 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ILE b 37 " --> pdb=" O VAL b 34 " (cutoff:3.500A) Processing helix chain 'b' and resid 50 through 160 removed outlier: 4.092A pdb=" N SER b 142 " --> pdb=" O ASP b 138 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N GLY b 143 " --> pdb=" O GLN b 139 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N SER b 146 " --> pdb=" O SER b 142 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N SER b 147 " --> pdb=" O GLY b 143 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N VAL b 148 " --> pdb=" O LEU b 144 " (cutoff:3.500A) removed outlier: 4.725A pdb=" N ASP b 149 " --> pdb=" O GLU b 145 " (cutoff:3.500A) removed outlier: 5.606A pdb=" N GLY b 150 " --> pdb=" O SER b 146 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N LEU b 151 " --> pdb=" O SER b 147 " (cutoff:3.500A) Processing helix chain 'd' and resid 2 through 138 removed outlier: 4.387A pdb=" N VAL d 23 " --> pdb=" O VAL d 19 " (cutoff:3.500A) Proline residue: d 24 - end of helix removed outlier: 3.578A pdb=" N GLU d 131 " --> pdb=" O ASN d 127 " (cutoff:3.500A) Processing helix chain 'd' and resid 140 through 155 Processing helix chain 'd' and resid 174 through 191 Processing helix chain 'd' and resid 196 through 215 Processing helix chain 'd' and resid 219 through 224 Processing helix chain 'd' and resid 231 through 240 Processing helix chain 'd' and resid 247 through 258 Processing helix chain 'd' and resid 264 through 286 removed outlier: 3.509A pdb=" N ILE d 285 " --> pdb=" O ARG d 282 " (cutoff:3.500A) Processing helix chain 'd' and resid 289 through 305 Processing helix chain 'd' and resid 307 through 313 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: 3.807A 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 441 Processing sheet with id= A, first strand: chain 'A' and resid 90 through 92 removed outlier: 6.859A pdb=" N HIS A 43 " --> pdb=" O ILE A 35 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N ALA A 37 " --> pdb=" O ILE A 41 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N ILE A 41 " --> pdb=" O ALA A 37 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N VAL A 77 " --> pdb=" O ALA A 66 " (cutoff:3.500A) removed outlier: 5.822A pdb=" N ALA A 66 " --> pdb=" O VAL A 77 " (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: 6.711A pdb=" N CYS A 204 " --> pdb=" O THR A 233 " (cutoff:3.500A) removed outlier: 7.883A pdb=" N VAL A 235 " --> pdb=" O CYS A 204 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N TYR A 206 " --> pdb=" O VAL A 235 " (cutoff:3.500A) removed outlier: 7.613A pdb=" N ALA A 237 " --> pdb=" O TYR A 206 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N ALA A 208 " --> pdb=" O ALA A 237 " (cutoff:3.500A) removed outlier: 6.192A pdb=" N SER A 323 " --> pdb=" O VAL A 267 " (cutoff:3.500A) removed outlier: 7.513A pdb=" N ILE A 269 " --> pdb=" O SER A 323 " (cutoff:3.500A) removed outlier: 6.038A pdb=" N THR A 325 " --> pdb=" O ILE A 269 " (cutoff:3.500A) removed outlier: 7.582A pdb=" N PHE A 271 " --> pdb=" O THR A 325 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N LEU A 327 " --> pdb=" O PHE A 271 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 90 through 92 removed outlier: 6.778A pdb=" N HIS B 43 " --> pdb=" O ILE B 35 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N ALA B 37 " --> pdb=" O ILE B 41 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N ILE B 41 " --> pdb=" O ALA B 37 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N VAL B 77 " --> pdb=" O ALA B 66 " (cutoff:3.500A) removed outlier: 5.754A pdb=" N ALA B 66 " --> pdb=" O VAL B 77 " (cutoff:3.500A) removed outlier: 6.145A pdb=" N LEU B 79 " --> pdb=" O GLY B 64 " (cutoff:3.500A) removed outlier: 5.515A pdb=" N GLY B 64 " --> pdb=" O LEU B 79 " (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: 6.380A pdb=" N LEU B 169 " --> pdb=" O CYS B 353 " (cutoff:3.500A) removed outlier: 7.164A pdb=" N LEU B 355 " --> pdb=" O LEU B 169 " (cutoff:3.500A) removed outlier: 6.675A 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: 6.541A pdb=" N CYS B 204 " --> pdb=" O THR B 233 " (cutoff:3.500A) removed outlier: 7.767A pdb=" N VAL B 235 " --> pdb=" O CYS B 204 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N TYR B 206 " --> pdb=" O VAL B 235 " (cutoff:3.500A) removed outlier: 7.597A pdb=" N ALA B 237 " --> pdb=" O TYR B 206 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N ALA B 208 " --> pdb=" O ALA B 237 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N SER B 323 " --> pdb=" O VAL B 267 " (cutoff:3.500A) removed outlier: 7.639A pdb=" N ILE B 269 " --> pdb=" O SER B 323 " (cutoff:3.500A) removed outlier: 6.093A pdb=" N THR B 325 " --> pdb=" O ILE B 269 " (cutoff:3.500A) removed outlier: 7.512A pdb=" N PHE B 271 " --> pdb=" O THR B 325 " (cutoff:3.500A) removed outlier: 6.753A 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: 6.394A pdb=" N GLY C 75 " --> pdb=" O LEU C 67 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ASP C 36 " --> pdb=" O HIS C 43 " (cutoff:3.500A) removed outlier: 6.190A pdb=" N GLU C 45 " --> pdb=" O VAL C 34 " (cutoff:3.500A) removed outlier: 5.654A 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: 6.573A pdb=" N LEU C 169 " --> pdb=" O CYS C 353 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N LEU C 355 " --> pdb=" O LEU C 169 " (cutoff:3.500A) removed outlier: 6.551A 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: 6.616A pdb=" N CYS C 204 " --> pdb=" O THR C 233 " (cutoff:3.500A) removed outlier: 7.797A pdb=" N VAL C 235 " --> pdb=" O CYS C 204 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N TYR C 206 " --> pdb=" O VAL C 235 " (cutoff:3.500A) removed outlier: 7.410A pdb=" N ALA C 237 " --> pdb=" O TYR C 206 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N ALA C 208 " --> pdb=" O ALA C 237 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N SER C 323 " --> pdb=" O VAL C 267 " (cutoff:3.500A) removed outlier: 7.756A pdb=" N ILE C 269 " --> pdb=" O SER C 323 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N THR C 325 " --> pdb=" O ILE C 269 " (cutoff:3.500A) removed outlier: 7.675A pdb=" N PHE C 271 " --> pdb=" O THR C 325 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N LEU C 327 " --> pdb=" O PHE C 271 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'D' and resid 11 through 16 removed outlier: 6.599A pdb=" N ASP D 21 " --> pdb=" O VAL D 13 " (cutoff:3.500A) removed outlier: 4.751A pdb=" N ILE D 15 " --> pdb=" O VAL D 19 " (cutoff:3.500A) removed outlier: 7.186A pdb=" N VAL D 19 " --> pdb=" O ILE D 15 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N ILE D 65 " --> pdb=" O VAL D 53 " (cutoff:3.500A) removed outlier: 5.596A 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: 7.351A pdb=" N ILE D 156 " --> pdb=" O ILE D 302 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N SER D 304 " --> pdb=" O ILE D 156 " (cutoff:3.500A) removed outlier: 7.917A pdb=" N LEU D 158 " --> pdb=" O SER D 304 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N GLN D 306 " --> pdb=" O LEU D 158 " (cutoff:3.500A) removed outlier: 7.978A pdb=" N GLY D 160 " --> pdb=" O GLN D 306 " (cutoff:3.500A) removed outlier: 6.135A pdb=" N VAL D 308 " --> pdb=" O GLY D 160 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N VAL D 249 " --> pdb=" O THR D 303 " (cutoff:3.500A) removed outlier: 7.786A pdb=" N MET D 305 " --> pdb=" O VAL D 249 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N LEU D 251 " --> pdb=" O MET D 305 " (cutoff:3.500A) removed outlier: 7.800A pdb=" N ALA D 307 " --> pdb=" O LEU D 251 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N ILE D 253 " --> pdb=" O ALA D 307 " (cutoff:3.500A) removed outlier: 8.270A pdb=" N TYR D 309 " --> pdb=" O ILE D 253 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N THR D 184 " --> pdb=" O LEU D 250 " (cutoff:3.500A) removed outlier: 7.986A pdb=" N PHE D 252 " --> pdb=" O THR D 184 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N VAL D 186 " --> pdb=" O PHE D 252 " (cutoff:3.500A) removed outlier: 8.003A pdb=" N ASP D 254 " --> pdb=" O VAL D 186 " (cutoff:3.500A) removed outlier: 6.240A 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: 6.616A pdb=" N ASP E 21 " --> pdb=" O VAL E 13 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N ILE E 15 " --> pdb=" O VAL E 19 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N VAL E 19 " --> pdb=" O ILE E 15 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N ILE E 65 " --> pdb=" O VAL E 53 " (cutoff:3.500A) removed outlier: 5.801A 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: 8.494A pdb=" N ILE E 156 " --> pdb=" O ILE E 302 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N SER E 304 " --> pdb=" O ILE E 156 " (cutoff:3.500A) removed outlier: 7.492A pdb=" N LEU E 158 " --> pdb=" O SER E 304 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N GLN E 306 " --> pdb=" O LEU E 158 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N VAL E 249 " --> pdb=" O THR E 303 " (cutoff:3.500A) removed outlier: 7.771A pdb=" N MET E 305 " --> pdb=" O VAL E 249 " (cutoff:3.500A) removed outlier: 6.206A pdb=" N LEU E 251 " --> pdb=" O MET E 305 " (cutoff:3.500A) removed outlier: 7.589A pdb=" N ALA E 307 " --> pdb=" O LEU E 251 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N ILE E 253 " --> pdb=" O ALA E 307 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N THR E 184 " --> pdb=" O LEU E 250 " (cutoff:3.500A) removed outlier: 7.924A pdb=" N PHE E 252 " --> pdb=" O THR E 184 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N VAL E 186 " --> pdb=" O PHE E 252 " (cutoff:3.500A) removed outlier: 7.977A pdb=" N ASP E 254 " --> pdb=" O VAL E 186 " (cutoff:3.500A) removed outlier: 6.346A 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: 6.598A pdb=" N ASP F 21 " --> pdb=" O VAL F 13 " (cutoff:3.500A) removed outlier: 4.784A pdb=" N ILE F 15 " --> pdb=" O VAL F 19 " (cutoff:3.500A) removed outlier: 7.185A pdb=" N VAL F 19 " --> pdb=" O ILE F 15 " (cutoff:3.500A) removed outlier: 6.016A pdb=" N ILE F 65 " --> pdb=" O VAL F 53 " (cutoff:3.500A) removed outlier: 5.549A 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: 7.302A pdb=" N ILE F 156 " --> pdb=" O ILE F 302 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N SER F 304 " --> pdb=" O ILE F 156 " (cutoff:3.500A) removed outlier: 7.966A pdb=" N LEU F 158 " --> pdb=" O SER F 304 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N GLN F 306 " --> pdb=" O LEU F 158 " (cutoff:3.500A) removed outlier: 8.086A pdb=" N GLY F 160 " --> pdb=" O GLN F 306 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N VAL F 308 " --> pdb=" O GLY F 160 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N VAL F 249 " --> pdb=" O THR F 303 " (cutoff:3.500A) removed outlier: 7.645A pdb=" N MET F 305 " --> pdb=" O VAL F 249 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N LEU F 251 " --> pdb=" O MET F 305 " (cutoff:3.500A) removed outlier: 7.746A pdb=" N ALA F 307 " --> pdb=" O LEU F 251 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N ILE F 253 " --> pdb=" O ALA F 307 " (cutoff:3.500A) removed outlier: 8.240A pdb=" N TYR F 309 " --> pdb=" O ILE F 253 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N THR F 184 " --> pdb=" O LEU F 250 " (cutoff:3.500A) removed outlier: 7.940A pdb=" N PHE F 252 " --> pdb=" O THR F 184 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N VAL F 186 " --> pdb=" O PHE F 252 " (cutoff:3.500A) removed outlier: 7.933A pdb=" N ASP F 254 " --> pdb=" O VAL F 186 " (cutoff:3.500A) removed outlier: 6.172A pdb=" N ALA F 188 " --> pdb=" O ASP F 254 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'G' and resid 136 through 138 removed outlier: 3.888A pdb=" N GLU G 136 " --> pdb=" O LEU G 116 " (cutoff:3.500A) removed outlier: 5.881A pdb=" N GLU G 182 " --> pdb=" O GLY G 78 " (cutoff:3.500A) removed outlier: 7.483A pdb=" N LEU G 80 " --> pdb=" O GLU G 182 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N HIS G 184 " --> pdb=" O LEU G 80 " (cutoff:3.500A) removed outlier: 7.571A pdb=" N VAL G 82 " --> pdb=" O HIS G 184 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N VAL G 186 " --> pdb=" O VAL G 82 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N ILE G 185 " --> pdb=" O ARG G 202 " (cutoff:3.500A) removed outlier: 5.173A pdb=" N ARG G 202 " --> pdb=" O ILE G 185 " (cutoff:3.500A) removed outlier: 7.125A pdb=" N PHE G 187 " --> pdb=" O ALA G 200 " (cutoff:3.500A) removed outlier: 5.259A pdb=" N ALA G 200 " --> pdb=" O PHE G 187 " (cutoff:3.500A) removed outlier: 5.985A pdb=" N GLU G 189 " --> pdb=" O ALA G 198 " (cutoff:3.500A) removed outlier: 5.897A pdb=" N ALA G 198 " --> pdb=" O GLU G 189 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'H' and resid 41 through 44 removed outlier: 6.488A pdb=" N ASN H 5 " --> pdb=" O VAL H 77 " (cutoff:3.500A) removed outlier: 7.959A pdb=" N ILE H 79 " --> pdb=" O ASN H 5 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N GLU H 7 " --> pdb=" O ILE H 79 " (cutoff:3.500A) removed outlier: 7.414A pdb=" N VAL H 81 " --> pdb=" O GLU H 7 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N VAL H 9 " --> pdb=" O VAL H 81 " (cutoff:3.500A) removed outlier: 5.964A pdb=" N ALA H 10 " --> pdb=" O GLU H 14 " (cutoff:3.500A) removed outlier: 4.498A 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 35 removed outlier: 4.137A pdb=" N ARG H 26 " --> pdb=" O MET H 50 " (cutoff:3.500A) removed outlier: 5.805A pdb=" N MET H 50 " --> pdb=" O ARG H 26 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ASN H 83 " --> pdb=" O ASP H 66 " (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 'd' and resid 406 through 411 removed outlier: 3.576A pdb=" N ALA d 377 " --> pdb=" O SER d 406 " (cutoff:3.500A) 2109 hydrogen bonds defined for protein. 5490 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: 32.44 Time building geometry restraints manager: 56.52 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: 37394 1.03 - 1.23: 21 1.23 - 1.42: 15359 1.42 - 1.62: 22400 1.62 - 1.81: 194 Bond restraints: 75368 Sorted by residual: bond pdb=" C4 ADP D 600 " pdb=" C5 ADP D 600 " ideal model delta sigma weight residual 1.490 1.465 0.025 2.00e-02 2.50e+03 1.53e+00 bond pdb=" CG1 ILE T 20 " pdb=" CD1 ILE T 20 " ideal model delta sigma weight residual 1.513 1.468 0.045 3.90e-02 6.57e+02 1.36e+00 bond pdb=" CG LEU a 179 " pdb=" CD2 LEU a 179 " ideal model delta sigma weight residual 1.521 1.483 0.038 3.30e-02 9.18e+02 1.33e+00 bond pdb=" CB MET R 21 " pdb=" CG MET R 21 " ideal model delta sigma weight residual 1.520 1.486 0.034 3.00e-02 1.11e+03 1.32e+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 1.24e+00 ... (remaining 75363 not shown) Histogram of bond angle deviations from ideal: 98.99 - 107.20: 1864 107.20 - 115.40: 96105 115.40 - 123.60: 32848 123.60 - 131.80: 5694 131.80 - 140.00: 43 Bond angle restraints: 136554 Sorted by residual: angle pdb=" N ILE a 11 " pdb=" CA ILE a 11 " pdb=" C ILE a 11 " ideal model delta sigma weight residual 113.53 109.51 4.02 9.80e-01 1.04e+00 1.68e+01 angle pdb=" N ILE A 35 " pdb=" CA ILE A 35 " pdb=" C ILE A 35 " ideal model delta sigma weight residual 112.96 109.19 3.77 1.00e+00 1.00e+00 1.42e+01 angle pdb=" N VAL E 164 " pdb=" CA VAL E 164 " pdb=" C VAL E 164 " ideal model delta sigma weight residual 113.20 109.91 3.29 9.60e-01 1.09e+00 1.17e+01 angle pdb=" N GLU G 41 " pdb=" CA GLU G 41 " pdb=" CB GLU G 41 " ideal model delta sigma weight residual 110.16 114.38 -4.22 1.48e+00 4.57e-01 8.14e+00 angle pdb=" N GLN d 116 " pdb=" CA GLN d 116 " pdb=" CB GLN d 116 " ideal model delta sigma weight residual 110.12 114.28 -4.16 1.47e+00 4.63e-01 8.03e+00 ... (remaining 136549 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.29: 28902 32.29 - 64.58: 578 64.58 - 96.86: 70 96.86 - 129.15: 3 129.15 - 161.44: 1 Dihedral angle restraints: 29554 sinusoidal: 13853 harmonic: 15701 Sorted by residual: 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 -60.00 101.44 -161.44 1 2.00e+01 2.50e-03 4.68e+01 dihedral pdb=" C5' ADP E 600 " pdb=" O5' ADP E 600 " pdb=" PA ADP E 600 " pdb=" O2A ADP E 600 " ideal model delta sinusoidal sigma weight residual 300.00 178.75 121.26 1 2.00e+01 2.50e-03 3.65e+01 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 -60.00 47.84 -107.84 1 2.00e+01 2.50e-03 3.14e+01 ... (remaining 29551 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 5165 0.059 - 0.118: 724 0.118 - 0.176: 75 0.176 - 0.235: 3 0.235 - 0.294: 10 Chirality restraints: 5977 Sorted by residual: 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 2.16e+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 2.09e+00 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 2.07e+00 ... (remaining 5974 not shown) Planarity restraints: 11448 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA MET R 21 " 0.009 2.00e-02 2.50e+03 1.79e-02 3.21e+00 pdb=" C MET R 21 " -0.031 2.00e-02 2.50e+03 pdb=" O MET R 21 " 0.011 2.00e-02 2.50e+03 pdb=" N GLY R 22 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY F 17 " 0.027 5.00e-02 4.00e+02 4.15e-02 2.76e+00 pdb=" N PRO F 18 " -0.072 5.00e-02 4.00e+02 pdb=" CA PRO F 18 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO F 18 " 0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA MET Q 21 " 0.007 2.00e-02 2.50e+03 1.49e-02 2.21e+00 pdb=" C MET Q 21 " -0.026 2.00e-02 2.50e+03 pdb=" O MET Q 21 " 0.009 2.00e-02 2.50e+03 pdb=" N GLY Q 22 " 0.009 2.00e-02 2.50e+03 ... (remaining 11445 not shown) Histogram of nonbonded interaction distances: 1.51 - 2.13: 2252 2.13 - 2.74: 140995 2.74 - 3.36: 230138 3.36 - 3.98: 295296 3.98 - 4.60: 464897 Nonbonded interactions: 1133578 Sorted by model distance: nonbonded pdb="HE21 GLN C 399 " pdb=" O LYS D 340 " model vdw 1.507 1.850 nonbonded pdb=" O PHE C 22 " pdb=" HE ARG b 158 " model vdw 1.511 1.850 nonbonded pdb=" OE1 GLU T 48 " pdb=" H GLU T 48 " model vdw 1.540 1.850 nonbonded pdb=" O GLU L 65 " pdb=" H PHE L 69 " model vdw 1.575 1.850 nonbonded pdb=" H ILE G 185 " pdb=" O ARG G 201 " model vdw 1.586 1.850 ... (remaining 1133573 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and ((resid 6 and (name N or name CA or name C or name O or name CB o \ r name CG1 or name CG2 or name CD1 or name HA or name HB or name HG12 or name HG \ 13 or name HG21 or name HG22 or name HG23 or name HD11 or name HD12 or name HD13 \ )) or resid 7 through 22 or (resid 29 and (name N or name CA or name C or name O \ or name CB or name CG or 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 30 through 406 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 nam \ e OD2 or name HA or name HB2 or name HB3)) or resid 415 through 521 or resid 600 \ through 601)) selection = (chain 'B' and ((resid 6 and (name N or name CA or name C or name O or name CB o \ r name CG1 or name CG2 or name CD1 or name HA or name HB or name HG12 or name HG \ 13 or name HG21 or name HG22 or name HG23 or name HD11 or name HD12 or name HD13 \ )) or resid 7 through 22 or resid 29 through 521 or resid 600 through 601)) selection = (chain 'C' and (resid 6 through 22 or (resid 29 and (name N or name CA or name C \ or name O or name CB or name CG or name CD or name OE1 or name OE2 or name HA o \ r name HB2 or name HB3 or name HG2 or name HG3)) or resid 30 through 406 or (res \ id 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 415 through 521 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 and (name N or name CA or name C or name O or name CB o \ r name OG1 or name CG2 or name HA or name HB or name HG1 or name HG21 or name HG \ 22 or name HG23)) or resid 9 through 452 or resid 455 through 471)) } ncs_group { reference = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = (chain 'P' 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)) selection = chain 'Q' selection = (chain 'R' 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)) selection = chain 'S' selection = chain 'T' } 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 23615 2.51 5 N 6419 2.21 5 O 7199 1.98 5 H 37414 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=0.50 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: 7.990 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.910 Extract box with map and model: 29.620 Check model and map are aligned: 0.870 Convert atoms to be neutral: 0.510 Process input model: 206.250 Find NCS groups from input model: 3.320 Set up NCS constraints: 0.380 Set refine NCS operators: 0.000 Set scattering table: 0.040 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:12.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 262.690 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8583 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 : 0.003 0.045 37954 Z= 0.174 Angle : 0.506 7.279 51475 Z= 0.268 Chirality : 0.042 0.294 5977 Planarity : 0.003 0.044 6735 Dihedral : 14.710 161.437 13775 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.35 % Favored : 97.61 % Rotamer Outliers : 0.00 % 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: 1.54 (0.12), residues: 4891 helix: 1.74 (0.10), residues: 2616 sheet: -0.16 (0.21), residues: 540 loop : 0.47 (0.16), residues: 1735 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9782 Ramachandran restraints generated. 4891 Oldfield, 0 Emsley, 4891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9782 Ramachandran restraints generated. 4891 Oldfield, 0 Emsley, 4891 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 422 residues out of total 3852 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 422 time to evaluate : 4.866 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 1 residues processed: 422 average time/residue: 2.4144 time to fit residues: 1272.2392 Evaluate side-chains 298 residues out of total 3852 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 297 time to evaluate : 4.793 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 1 residues processed: 1 average time/residue: 0.6961 time to fit residues: 6.9080 ------------------------------------------------------------------------------- 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: 0.0070 chunk 366 optimal weight: 4.9990 chunk 203 optimal weight: 1.9990 chunk 125 optimal weight: 2.9990 chunk 246 optimal weight: 1.9990 chunk 195 optimal weight: 0.9990 chunk 378 optimal weight: 3.9990 chunk 146 optimal weight: 0.9980 chunk 230 optimal weight: 1.9990 chunk 281 optimal weight: 1.9990 chunk 438 optimal weight: 8.9990 overall best weight: 1.2004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 50 GLN R 71 ASN S 71 ASN a 104 ASN b 82 GLN ** d 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8608 moved from start: 0.0605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.054 37954 Z= 0.235 Angle : 0.517 8.017 51475 Z= 0.267 Chirality : 0.040 0.188 5977 Planarity : 0.004 0.061 6735 Dihedral : 5.582 146.185 5294 Min Nonbonded Distance : 1.714 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.45 % Favored : 97.50 % Rotamer Outliers : 0.83 % 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: 1.49 (0.12), residues: 4891 helix: 1.70 (0.10), residues: 2603 sheet: -0.14 (0.21), residues: 549 loop : 0.45 (0.16), residues: 1739 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9782 Ramachandran restraints generated. 4891 Oldfield, 0 Emsley, 4891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9782 Ramachandran restraints generated. 4891 Oldfield, 0 Emsley, 4891 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 346 residues out of total 3852 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 314 time to evaluate : 4.894 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 32 outliers final: 12 residues processed: 337 average time/residue: 2.2322 time to fit residues: 951.4393 Evaluate side-chains 305 residues out of total 3852 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 293 time to evaluate : 4.796 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 8 residues processed: 4 average time/residue: 1.1491 time to fit residues: 12.6284 ------------------------------------------------------------------------------- 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: 3.9990 chunk 136 optimal weight: 2.9990 chunk 365 optimal weight: 4.9990 chunk 298 optimal weight: 0.6980 chunk 120 optimal weight: 2.9990 chunk 439 optimal weight: 6.9990 chunk 474 optimal weight: 6.9990 chunk 391 optimal weight: 4.9990 chunk 435 optimal weight: 2.9990 chunk 149 optimal weight: 2.9990 chunk 352 optimal weight: 0.7980 overall best weight: 2.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 335 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 50 GLN b 82 GLN ** d 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8632 moved from start: 0.0833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.087 37954 Z= 0.360 Angle : 0.553 8.946 51475 Z= 0.288 Chirality : 0.042 0.180 5977 Planarity : 0.004 0.058 6735 Dihedral : 5.658 131.701 5294 Min Nonbonded Distance : 1.639 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.74 % Favored : 97.22 % Rotamer Outliers : 1.04 % 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: 1.29 (0.12), residues: 4891 helix: 1.53 (0.10), residues: 2605 sheet: -0.15 (0.21), residues: 557 loop : 0.33 (0.16), residues: 1729 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9782 Ramachandran restraints generated. 4891 Oldfield, 0 Emsley, 4891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9782 Ramachandran restraints generated. 4891 Oldfield, 0 Emsley, 4891 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 345 residues out of total 3852 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 305 time to evaluate : 4.925 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 40 outliers final: 17 residues processed: 331 average time/residue: 2.1758 time to fit residues: 918.8515 Evaluate side-chains 309 residues out of total 3852 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 292 time to evaluate : 4.808 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 12 residues processed: 5 average time/residue: 0.7133 time to fit residues: 12.0777 ------------------------------------------------------------------------------- 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: 4.9990 chunk 330 optimal weight: 2.9990 chunk 228 optimal weight: 1.9990 chunk 48 optimal weight: 0.3980 chunk 209 optimal weight: 3.9990 chunk 295 optimal weight: 1.9990 chunk 440 optimal weight: 5.9990 chunk 466 optimal weight: 1.9990 chunk 230 optimal weight: 1.9990 chunk 417 optimal weight: 4.9990 chunk 125 optimal weight: 2.9990 overall best weight: 1.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 50 GLN b 82 GLN ** d 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8626 moved from start: 0.0873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.066 37954 Z= 0.290 Angle : 0.533 8.602 51475 Z= 0.275 Chirality : 0.041 0.179 5977 Planarity : 0.004 0.051 6735 Dihedral : 5.585 125.787 5294 Min Nonbonded Distance : 1.703 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.68 % Favored : 97.28 % Rotamer Outliers : 1.12 % 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: 1.30 (0.12), residues: 4891 helix: 1.54 (0.10), residues: 2598 sheet: -0.16 (0.21), residues: 559 loop : 0.35 (0.16), residues: 1734 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9782 Ramachandran restraints generated. 4891 Oldfield, 0 Emsley, 4891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9782 Ramachandran restraints generated. 4891 Oldfield, 0 Emsley, 4891 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 338 residues out of total 3852 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 295 time to evaluate : 4.969 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 43 outliers final: 21 residues processed: 322 average time/residue: 2.2971 time to fit residues: 936.1244 Evaluate side-chains 308 residues out of total 3852 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 287 time to evaluate : 4.768 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 13 residues processed: 8 average time/residue: 0.9737 time to fit residues: 18.0753 ------------------------------------------------------------------------------- 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: 1.9990 chunk 398 optimal weight: 3.9990 chunk 322 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 238 optimal weight: 3.9990 chunk 419 optimal weight: 4.9990 chunk 117 optimal weight: 1.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 50 GLN ** d 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8639 moved from start: 0.0997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.089 37954 Z= 0.372 Angle : 0.560 9.504 51475 Z= 0.291 Chirality : 0.042 0.182 5977 Planarity : 0.004 0.056 6735 Dihedral : 5.703 139.345 5294 Min Nonbonded Distance : 1.670 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.07 % Favored : 96.89 % Rotamer Outliers : 1.19 % 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: 1.19 (0.12), residues: 4891 helix: 1.44 (0.10), residues: 2607 sheet: -0.18 (0.21), residues: 556 loop : 0.28 (0.16), residues: 1728 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9782 Ramachandran restraints generated. 4891 Oldfield, 0 Emsley, 4891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9782 Ramachandran restraints generated. 4891 Oldfield, 0 Emsley, 4891 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 336 residues out of total 3852 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 290 time to evaluate : 4.858 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 46 outliers final: 22 residues processed: 324 average time/residue: 2.2638 time to fit residues: 929.6319 Evaluate side-chains 305 residues out of total 3852 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 283 time to evaluate : 4.849 Switching outliers to nearest non-outliers outliers start: 22 outliers final: 17 residues processed: 5 average time/residue: 0.7615 time to fit residues: 12.4473 ------------------------------------------------------------------------------- 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: 2.9990 chunk 92 optimal weight: 0.9990 chunk 274 optimal weight: 3.9990 chunk 115 optimal weight: 1.9990 chunk 467 optimal weight: 5.9990 chunk 387 optimal weight: 2.9990 chunk 216 optimal weight: 3.9990 chunk 38 optimal weight: 1.9990 chunk 154 optimal weight: 1.9990 chunk 245 optimal weight: 1.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 420 GLN R 50 GLN ** d 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8633 moved from start: 0.1015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.071 37954 Z= 0.308 Angle : 0.543 8.746 51475 Z= 0.281 Chirality : 0.041 0.181 5977 Planarity : 0.004 0.061 6735 Dihedral : 5.684 147.053 5294 Min Nonbonded Distance : 1.691 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.74 % Favored : 97.22 % Rotamer Outliers : 1.01 % 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: 1.24 (0.12), residues: 4891 helix: 1.49 (0.10), residues: 2603 sheet: -0.17 (0.21), residues: 556 loop : 0.31 (0.16), residues: 1732 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9782 Ramachandran restraints generated. 4891 Oldfield, 0 Emsley, 4891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9782 Ramachandran restraints generated. 4891 Oldfield, 0 Emsley, 4891 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 327 residues out of total 3852 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 288 time to evaluate : 4.872 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 39 outliers final: 22 residues processed: 317 average time/residue: 2.2499 time to fit residues: 912.5132 Evaluate side-chains 307 residues out of total 3852 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 285 time to evaluate : 4.837 Switching outliers to nearest non-outliers outliers start: 22 outliers final: 18 residues processed: 4 average time/residue: 0.7998 time to fit residues: 11.4958 ------------------------------------------------------------------------------- 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: 6.9990 chunk 52 optimal weight: 3.9990 chunk 266 optimal weight: 0.7980 chunk 341 optimal weight: 5.9990 chunk 264 optimal weight: 1.9990 chunk 393 optimal weight: 4.9990 chunk 260 optimal weight: 2.9990 chunk 465 optimal weight: 8.9990 chunk 291 optimal weight: 2.9990 chunk 283 optimal weight: 2.9990 chunk 214 optimal weight: 3.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 245 GLN ** G 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 50 GLN ** d 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8643 moved from start: 0.1104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.090 37954 Z= 0.389 Angle : 0.570 9.407 51475 Z= 0.296 Chirality : 0.042 0.183 5977 Planarity : 0.004 0.069 6735 Dihedral : 5.815 163.490 5294 Min Nonbonded Distance : 1.667 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.09 % Favored : 96.87 % Rotamer Outliers : 0.96 % 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: 1.12 (0.12), residues: 4891 helix: 1.40 (0.10), residues: 2605 sheet: -0.19 (0.21), residues: 556 loop : 0.24 (0.16), residues: 1730 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9782 Ramachandran restraints generated. 4891 Oldfield, 0 Emsley, 4891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9782 Ramachandran restraints generated. 4891 Oldfield, 0 Emsley, 4891 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 323 residues out of total 3852 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 286 time to evaluate : 4.829 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 37 outliers final: 23 residues processed: 315 average time/residue: 2.2989 time to fit residues: 916.3292 Evaluate side-chains 305 residues out of total 3852 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 282 time to evaluate : 4.807 Switching outliers to nearest non-outliers outliers start: 23 outliers final: 19 residues processed: 4 average time/residue: 0.7265 time to fit residues: 10.8728 ------------------------------------------------------------------------------- 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: 0.9980 chunk 185 optimal weight: 0.6980 chunk 278 optimal weight: 0.6980 chunk 140 optimal weight: 3.9990 chunk 91 optimal weight: 1.9990 chunk 90 optimal weight: 0.9980 chunk 295 optimal weight: 1.9990 chunk 317 optimal weight: 2.9990 chunk 230 optimal weight: 0.7980 chunk 43 optimal weight: 1.9990 chunk 365 optimal weight: 2.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** N 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 50 GLN a 243 GLN ** d 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8616 moved from start: 0.0993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.047 37954 Z= 0.191 Angle : 0.517 8.311 51475 Z= 0.264 Chirality : 0.040 0.183 5977 Planarity : 0.004 0.079 6735 Dihedral : 5.655 174.687 5294 Min Nonbonded Distance : 1.748 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.39 % Favored : 97.57 % Rotamer Outliers : 0.91 % 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: 1.42 (0.12), residues: 4891 helix: 1.64 (0.10), residues: 2601 sheet: -0.16 (0.21), residues: 547 loop : 0.41 (0.16), residues: 1743 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9782 Ramachandran restraints generated. 4891 Oldfield, 0 Emsley, 4891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9782 Ramachandran restraints generated. 4891 Oldfield, 0 Emsley, 4891 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 332 residues out of total 3852 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 297 time to evaluate : 4.988 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 35 outliers final: 21 residues processed: 323 average time/residue: 2.2871 time to fit residues: 936.5068 Evaluate side-chains 303 residues out of total 3852 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 282 time to evaluate : 4.854 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 17 residues processed: 4 average time/residue: 1.1187 time to fit residues: 12.5905 ------------------------------------------------------------------------------- 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: 3.9990 chunk 445 optimal weight: 6.9990 chunk 406 optimal weight: 3.9990 chunk 433 optimal weight: 4.9990 chunk 261 optimal weight: 1.9990 chunk 188 optimal weight: 0.9980 chunk 340 optimal weight: 3.9990 chunk 133 optimal weight: 2.9990 chunk 392 optimal weight: 3.9990 chunk 410 optimal weight: 0.4980 chunk 432 optimal weight: 0.9980 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** N 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 50 GLN ** d 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8627 moved from start: 0.1045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.066 37954 Z= 0.275 Angle : 0.539 9.533 51475 Z= 0.277 Chirality : 0.041 0.176 5977 Planarity : 0.004 0.083 6735 Dihedral : 5.636 168.063 5294 Min Nonbonded Distance : 1.721 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.86 % Favored : 97.09 % Rotamer Outliers : 0.78 % 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: 1.38 (0.12), residues: 4891 helix: 1.61 (0.10), residues: 2600 sheet: -0.13 (0.21), residues: 547 loop : 0.38 (0.16), residues: 1744 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9782 Ramachandran restraints generated. 4891 Oldfield, 0 Emsley, 4891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9782 Ramachandran restraints generated. 4891 Oldfield, 0 Emsley, 4891 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 315 residues out of total 3852 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 285 time to evaluate : 4.889 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 30 outliers final: 16 residues processed: 309 average time/residue: 2.3173 time to fit residues: 914.2702 Evaluate side-chains 297 residues out of total 3852 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 281 time to evaluate : 4.842 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 16 residues processed: 0 time to fit residues: 5.5906 ------------------------------------------------------------------------------- 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: 2.9990 chunk 458 optimal weight: 6.9990 chunk 279 optimal weight: 0.9980 chunk 217 optimal weight: 2.9990 chunk 318 optimal weight: 2.9990 chunk 481 optimal weight: 4.9990 chunk 442 optimal weight: 0.9980 chunk 383 optimal weight: 0.8980 chunk 39 optimal weight: 2.9990 chunk 295 optimal weight: 0.8980 chunk 234 optimal weight: 0.3980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** N 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 50 GLN ** d 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8611 moved from start: 0.1012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.056 37954 Z= 0.185 Angle : 0.516 10.712 51475 Z= 0.263 Chirality : 0.040 0.182 5977 Planarity : 0.004 0.089 6735 Dihedral : 5.404 147.261 5294 Min Nonbonded Distance : 1.769 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.52 % Favored : 97.44 % Rotamer Outliers : 0.62 % 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: 1.51 (0.12), residues: 4891 helix: 1.72 (0.10), residues: 2601 sheet: -0.13 (0.21), residues: 559 loop : 0.45 (0.16), residues: 1731 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9782 Ramachandran restraints generated. 4891 Oldfield, 0 Emsley, 4891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9782 Ramachandran restraints generated. 4891 Oldfield, 0 Emsley, 4891 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 313 residues out of total 3852 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 289 time to evaluate : 5.329 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 24 outliers final: 18 residues processed: 307 average time/residue: 2.3423 time to fit residues: 918.3205 Evaluate side-chains 300 residues out of total 3852 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 282 time to evaluate : 4.870 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 16 residues processed: 2 average time/residue: 1.5100 time to fit residues: 9.8930 ------------------------------------------------------------------------------- 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: 0.1980 chunk 408 optimal weight: 0.2980 chunk 117 optimal weight: 2.9990 chunk 353 optimal weight: 0.9990 chunk 56 optimal weight: 1.9990 chunk 106 optimal weight: 1.9990 chunk 383 optimal weight: 1.9990 chunk 160 optimal weight: 2.9990 chunk 394 optimal weight: 1.9990 chunk 48 optimal weight: 2.9990 chunk 70 optimal weight: 0.7980 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** N 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 71 ASN R 50 GLN ** d 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.079482 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2978 r_free = 0.2978 target = 0.059442 restraints weight = 271860.577| |-----------------------------------------------------------------------------| r_work (start): 0.2955 rms_B_bonded: 1.62 r_work: 0.2875 rms_B_bonded: 1.78 restraints_weight: 0.5000 r_work: 0.2775 rms_B_bonded: 3.11 restraints_weight: 0.2500 r_work (final): 0.2775 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3432 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3432 r_free = 0.3432 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3432 r_free = 0.3432 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3432 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8787 moved from start: 0.1023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.049 37954 Z= 0.191 Angle : 0.512 10.456 51475 Z= 0.261 Chirality : 0.040 0.176 5977 Planarity : 0.003 0.087 6735 Dihedral : 5.233 126.625 5294 Min Nonbonded Distance : 1.774 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.64 % Favored : 97.32 % Rotamer Outliers : 0.62 % 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: 1.58 (0.12), residues: 4891 helix: 1.77 (0.10), residues: 2607 sheet: -0.08 (0.21), residues: 552 loop : 0.49 (0.16), residues: 1732 =============================================================================== Job complete usr+sys time: 16734.39 seconds wall clock time: 289 minutes 7.33 seconds (17347.33 seconds total)