Starting phenix.real_space_refine on Sat Mar 16 16:09:36 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7njo_12397/03_2024/7njo_12397_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7njo_12397/03_2024/7njo_12397.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.92 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7njo_12397/03_2024/7njo_12397.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7njo_12397/03_2024/7njo_12397.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7njo_12397/03_2024/7njo_12397_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7njo_12397/03_2024/7njo_12397_trim_updated.pdb" } resolution = 2.92 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned 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 23579 2.51 5 N 6404 2.21 5 O 7185 1.98 5 H 37345 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 86": "OE1" <-> "OE2" Residue "A ASP 273": "OD1" <-> "OD2" Residue "A ASP 484": "OD1" <-> "OD2" Residue "A GLU 488": "OE1" <-> "OE2" Residue "B GLU 30": "OE1" <-> "OE2" Residue "B ASP 184": "OD1" <-> "OD2" Residue "B TYR 436": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C GLU 83": "OE1" <-> "OE2" Residue "D ASP 206": "OD1" <-> "OD2" Residue "D GLU 437": "OE1" <-> "OE2" Residue "D GLU 469": "OE1" <-> "OE2" Residue "M PHE 58": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "M PHE 78": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "a TYR 113": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "a TYR 145": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "a GLU 177": "OE1" <-> "OE2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 74641 Number of models: 1 Model: "" Number of chains: 31 Chain: "A" Number of atoms: 7684 Number of conformers: 1 Conformer: "" Number of residues, atoms: 507, 7684 Classifications: {'peptide': 507} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 19, 'TRANS': 485} 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: 8087 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 533, 8070 Classifications: {'peptide': 533} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 22, 'TRANS': 508} Chain breaks: 2 Conformer: "B" Number of residues, atoms: 533, 8070 Classifications: {'peptide': 533} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 22, 'TRANS': 508} Chain breaks: 2 bond proxies already assigned to first conformer: 8111 Chain: "D" Number of atoms: 7158 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: 7194 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: 4551 Number of conformers: 1 Conformer: "" Number of residues, atoms: 296, 4551 Classifications: {'peptide': 296} Link IDs: {'PCIS': 2, 'PTRANS': 7, 'TRANS': 286} Chain breaks: 1 Chain: "H" Number of atoms: 1801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 1801 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: 1173 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 1173 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 4, 'TRANS': 78} 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: 1204 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 1204 Classifications: {'peptide': 85} Link IDs: {'PTRANS': 4, 'TRANS': 80} 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: 1173 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 1173 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 4, 'TRANS': 78} 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: 2120 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 2120 Classifications: {'peptide': 141} Link IDs: {'PTRANS': 3, 'TRANS': 137} Chain: "d" Number of atoms: 6656 Number of conformers: 1 Conformer: "" Number of residues, atoms: 438, 6656 Classifications: {'peptide': 438} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 12, 'TRANS': 425} 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} Time building chain proxies: 29.41, per 1000 atoms: 0.39 Number of scatterers: 74641 At special positions: 0 Unit cell: (135.29, 129.48, 249.83, 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 7185 8.00 N 6404 7.00 C 23579 6.00 H 37345 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 53.03 Conformation dependent library (CDL) restraints added in 7.3 seconds 9760 Ramachandran restraints generated. 4880 Oldfield, 0 Emsley, 4880 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8884 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 184 helices and 26 sheets defined 54.9% alpha, 9.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 9.81 Creating SS restraints... Processing helix chain 'A' and resid 9 through 21 removed outlier: 3.947A 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 195 removed outlier: 3.735A pdb=" N GLN A 189 " --> pdb=" O THR A 185 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N ARG A 190 " --> pdb=" O ILE A 186 " (cutoff:3.500A) removed outlier: 5.075A pdb=" N GLU A 191 " --> pdb=" O LEU A 187 " (cutoff:3.500A) removed outlier: 4.771A 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: 3.613A pdb=" N TRP A 260 " --> pdb=" O ILE A 256 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ASN A 263 " --> pdb=" O HIS A 259 " (cutoff:3.500A) Processing helix chain 'A' and resid 274 through 287 Processing helix chain 'A' and resid 294 through 296 No H-bonds generated for 'chain 'A' and resid 294 through 296' Processing helix chain 'A' and resid 301 through 311 removed outlier: 4.095A pdb=" N ARG A 311 " --> pdb=" O ARG A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 317 through 319 No H-bonds generated for 'chain 'A' and resid 317 through 319' Processing helix chain 'A' and resid 340 through 348 Processing helix chain 'A' and resid 357 through 362 Processing helix chain 'A' and resid 378 through 381 Processing helix chain 'A' and resid 384 through 389 Processing helix chain 'A' and resid 393 through 402 Processing helix chain 'A' and resid 415 through 431 Processing helix chain 'A' and resid 441 through 452 Processing helix chain 'A' and resid 464 through 478 Processing helix chain 'A' and resid 481 through 489 Processing helix chain 'A' and resid 494 through 509 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: 3.829A pdb=" N GLN B 189 " --> pdb=" O THR B 185 " (cutoff:3.500A) removed outlier: 4.642A pdb=" N ARG B 190 " --> pdb=" O ILE B 186 " (cutoff:3.500A) removed outlier: 5.468A pdb=" N GLU B 191 " --> pdb=" O LEU B 187 " (cutoff:3.500A) removed outlier: 5.099A 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 228 through 231 Processing helix chain 'B' and resid 243 through 263 Proline residue: B 250 - end of helix removed outlier: 3.763A pdb=" N TRP B 260 " --> pdb=" O ILE B 256 " (cutoff:3.500A) removed outlier: 3.590A 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 311 removed outlier: 4.240A pdb=" N ARG B 311 " --> pdb=" O ARG B 307 " (cutoff:3.500A) Processing helix chain 'B' and resid 317 through 319 No H-bonds generated for 'chain 'B' and resid 317 through 319' Processing helix chain 'B' and resid 340 through 348 Processing helix chain 'B' and resid 357 through 361 Processing helix chain 'B' and resid 384 through 405 removed outlier: 4.683A pdb=" N SER B 392 " --> pdb=" O GLU B 388 " (cutoff:3.500A) removed outlier: 4.813A pdb=" N LEU B 393 " --> pdb=" O VAL B 389 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N LEU B 395 " --> pdb=" O GLY B 391 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ASP B 396 " --> pdb=" O SER B 392 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N LEU B 397 " --> pdb=" O LEU B 393 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N SER B 398 " --> pdb=" O ARG B 394 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N GLU B 402 " --> pdb=" O SER B 398 " (cutoff:3.500A) removed outlier: 3.776A 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 removed outlier: 3.538A pdb=" N GLY B 451 " --> pdb=" O ALA B 447 " (cutoff:3.500A) Processing helix chain 'B' and resid 461 through 477 removed outlier: 5.112A pdb=" N GLN B 465 " --> pdb=" O GLU B 462 " (cutoff:3.500A) Processing helix chain 'B' and resid 481 through 489 Processing helix chain 'B' and resid 494 through 510 removed outlier: 3.991A pdb=" N LYS B 509 " --> pdb=" O ASN B 505 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N GLY B 510 " --> pdb=" O GLU B 506 " (cutoff:3.500A) Processing helix chain 'C' and resid 8 through 21 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 154 through 159 Processing helix chain 'C' and resid 178 through 195 removed outlier: 4.174A pdb=" N ARG C 190 " --> pdb=" O ILE C 186 " (cutoff:3.500A) removed outlier: 5.027A pdb=" N GLU C 191 " --> pdb=" O LEU C 187 " (cutoff:3.500A) removed outlier: 4.797A pdb=" N ALA C 192 " --> pdb=" O ASN C 188 " (cutoff:3.500A) Processing helix chain 'C' and resid 213 through 226 Processing helix chain 'C' and resid 228 through 230 No H-bonds generated for 'chain 'C' and resid 228 through 230' Processing helix chain 'C' and resid 243 through 263 Proline residue: C 250 - end of helix removed outlier: 3.640A pdb=" N TRP C 260 " --> pdb=" O ILE C 256 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N ASN C 263 " --> pdb=" O HIS C 259 " (cutoff:3.500A) Processing helix chain 'C' and resid 274 through 287 Processing helix chain 'C' and resid 294 through 296 No H-bonds generated for 'chain 'C' and resid 294 through 296' Processing helix chain 'C' and resid 301 through 309 Processing helix chain 'C' and resid 317 through 319 No H-bonds generated for 'chain 'C' and resid 317 through 319' Processing helix chain 'C' and resid 340 through 348 Processing helix chain 'C' and resid 357 through 361 Processing helix chain 'C' and resid 378 through 381 Processing helix chain 'C' and resid 384 through 389 Processing helix chain 'C' and resid 393 through 406 Processing helix chain 'C' and resid 415 through 431 Processing helix chain 'C' and resid 441 through 452 Processing helix chain 'C' and resid 461 through 477 removed outlier: 4.440A pdb=" N GLN C 465 " --> pdb=" O GLU C 462 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N GLU C 468 " --> pdb=" O GLN C 465 " (cutoff:3.500A) Processing helix chain 'C' and resid 481 through 489 Processing helix chain 'C' and resid 494 through 510 removed outlier: 3.505A pdb=" N GLY C 510 " --> pdb=" O GLU C 506 " (cutoff:3.500A) Processing helix chain 'C' and resid 530 through 532 No H-bonds generated for 'chain 'C' and resid 530 through 532' Processing helix chain 'D' and resid 43 through 45 No H-bonds generated for 'chain 'D' and resid 43 through 45' 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 176 Processing helix chain 'D' and resid 178 through 180 No H-bonds generated for 'chain 'D' and resid 178 through 180' Processing helix chain 'D' and resid 194 through 207 Processing helix chain 'D' and resid 210 through 212 No H-bonds generated for 'chain 'D' and resid 210 through 212' Processing helix chain 'D' and resid 224 through 243 removed outlier: 5.249A pdb=" N ALA D 231 " --> pdb=" O ARG D 227 " (cutoff:3.500A) removed outlier: 4.656A pdb=" N LEU D 232 " --> pdb=" O MET D 228 " (cutoff:3.500A) Processing helix chain 'D' and resid 256 through 265 removed outlier: 3.675A pdb=" N THR D 260 " --> pdb=" O ILE D 256 " (cutoff:3.500A) 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: 4.520A pdb=" N ALA D 325 " --> pdb=" O ALA D 321 " (cutoff:3.500A) removed outlier: 4.707A pdb=" N HIS D 326 " --> pdb=" O THR D 322 " (cutoff:3.500A) Processing helix chain 'D' and resid 335 through 340 removed outlier: 3.608A pdb=" N LYS D 340 " --> pdb=" O ALA D 336 " (cutoff:3.500A) 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: 4.661A pdb=" N ASP D 384 " --> pdb=" O LYS D 380 " (cutoff:3.500A) removed outlier: 4.937A 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 471 Processing helix chain 'E' and resid 92 through 94 No H-bonds generated for 'chain 'E' and resid 92 through 94' Processing helix chain 'E' and resid 127 through 129 No H-bonds generated for 'chain 'E' and resid 127 through 129' Processing helix chain 'E' and resid 142 through 147 Processing helix chain 'E' and resid 166 through 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: 5.028A pdb=" N ALA E 231 " --> pdb=" O ARG E 227 " (cutoff:3.500A) removed outlier: 4.750A pdb=" N LEU E 232 " --> pdb=" O MET E 228 " (cutoff:3.500A) Processing helix chain 'E' and resid 256 through 270 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: 4.168A 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 325 Processing helix chain 'E' and resid 335 through 339 Processing helix chain 'E' and resid 358 through 361 No H-bonds generated for 'chain 'E' and resid 358 through 361' Processing helix chain 'E' and resid 363 through 389 removed outlier: 4.618A pdb=" N ASP E 384 " --> pdb=" O LYS E 380 " (cutoff:3.500A) removed outlier: 4.612A 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 419 No H-bonds generated for 'chain 'E' and resid 417 through 419' 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 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 207 Processing helix chain 'F' and resid 209 through 212 Processing helix chain 'F' and resid 224 through 243 removed outlier: 4.626A pdb=" N ALA F 231 " --> pdb=" O ARG F 227 " (cutoff:3.500A) removed outlier: 4.873A 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: 4.424A pdb=" N ALA F 325 " --> pdb=" O ALA F 321 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N HIS F 326 " --> pdb=" O THR F 322 " (cutoff:3.500A) Processing helix chain 'F' and resid 335 through 340 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 381 Processing helix chain 'F' and resid 383 through 386 No H-bonds generated for 'chain 'F' and resid 383 through 386' Processing helix chain 'F' and resid 391 through 393 No H-bonds generated for 'chain 'F' and resid 391 through 393' Processing helix chain 'F' and resid 396 through 411 Processing helix chain 'F' and resid 420 through 423 No H-bonds generated for 'chain 'F' and resid 420 through 423' Processing helix chain 'F' and resid 432 through 444 Processing helix chain 'F' and resid 452 through 455 Processing helix chain 'F' and resid 461 through 471 Processing helix chain 'G' and resid 4 through 59 Proline residue: G 45 - end of helix Processing helix chain 'G' and resid 92 through 109 Processing helix chain 'G' and resid 121 through 130 Processing helix chain 'G' and resid 147 through 164 Processing helix chain 'G' and resid 173 through 175 No H-bonds generated for 'chain 'G' and resid 173 through 175' Processing helix chain 'G' and resid 228 through 303 Proline residue: G 237 - end of helix Processing helix chain 'H' and resid 87 through 89 No H-bonds generated for 'chain 'H' and resid 87 through 89' Processing helix chain 'H' and resid 92 through 97 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 80 removed outlier: 4.213A pdb=" N GLY L 51 " --> pdb=" O GLU L 48 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N PHE L 54 " --> pdb=" O GLY L 51 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N THR L 55 " --> pdb=" O ARG L 52 " (cutoff:3.500A) Proline residue: L 56 - end of helix removed outlier: 3.720A pdb=" N GLU L 65 " --> pdb=" O GLY L 62 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ALA L 66 " --> pdb=" O LEU L 63 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N ALA L 67 " --> pdb=" O VAL L 64 " (cutoff:3.500A) Processing helix chain 'M' and resid 5 through 45 Processing helix chain 'M' and resid 47 through 78 removed outlier: 4.141A pdb=" N GLY M 51 " --> pdb=" O GLU M 48 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N THR M 55 " --> pdb=" O ARG M 52 " (cutoff:3.500A) Proline residue: M 56 - end of helix removed outlier: 3.966A pdb=" N ALA M 67 " --> pdb=" O VAL M 64 " (cutoff:3.500A) Processing helix chain 'N' and resid 5 through 45 Processing helix chain 'N' and resid 47 through 79 removed outlier: 3.762A pdb=" N GLN N 50 " --> pdb=" O PRO N 47 " (cutoff:3.500A) removed outlier: 4.701A pdb=" N GLY N 51 " --> pdb=" O GLU N 48 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N PHE N 54 " --> pdb=" O GLY N 51 " (cutoff:3.500A) Proline residue: N 56 - end of helix removed outlier: 4.860A pdb=" N GLU N 65 " --> pdb=" O GLY N 62 " (cutoff:3.500A) Processing helix chain 'O' and resid 5 through 45 Processing helix chain 'O' and resid 50 through 79 Proline residue: O 56 - end of helix removed outlier: 3.879A pdb=" N ASN O 71 " --> pdb=" O ALA O 67 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N ALA O 76 " --> pdb=" O LEU O 72 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N LEU O 77 " --> pdb=" O ALA O 73 " (cutoff:3.500A) Processing helix chain 'P' and resid 5 through 45 Processing helix chain 'P' and resid 54 through 80 Processing helix chain 'Q' and resid 5 through 45 Processing helix chain 'Q' and resid 47 through 49 No H-bonds generated for 'chain 'Q' and resid 47 through 49' Processing helix chain 'Q' and resid 54 through 79 Processing helix chain 'R' and resid 5 through 45 Processing helix chain 'R' and resid 47 through 79 removed outlier: 3.570A pdb=" N GLN R 50 " --> pdb=" O PRO R 47 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N GLY R 51 " --> pdb=" O GLU R 48 " (cutoff:3.500A) removed outlier: 4.812A pdb=" N PHE R 54 " --> pdb=" O GLY R 51 " (cutoff:3.500A) Proline residue: R 56 - end of helix removed outlier: 4.486A pdb=" N ALA R 66 " --> pdb=" O LEU R 63 " (cutoff:3.500A) Processing helix chain 'S' and resid 5 through 45 Processing helix chain 'S' and resid 47 through 78 removed outlier: 3.897A pdb=" N GLN S 50 " --> pdb=" O PRO S 47 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N GLY S 51 " --> pdb=" O GLU S 48 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N PHE S 54 " --> pdb=" O GLY S 51 " (cutoff:3.500A) Proline residue: S 56 - end of helix removed outlier: 3.655A pdb=" N VAL S 61 " --> pdb=" O PHE S 58 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N GLU S 65 " --> pdb=" O GLY S 62 " (cutoff:3.500A) removed outlier: 4.722A pdb=" N ALA S 66 " --> pdb=" O LEU S 63 " (cutoff:3.500A) Processing helix chain 'T' and resid 5 through 45 Processing helix chain 'T' and resid 47 through 78 removed outlier: 4.850A pdb=" N GLY T 51 " --> pdb=" O GLU T 48 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N THR T 55 " --> pdb=" O ARG T 52 " (cutoff:3.500A) Proline residue: T 56 - end of helix removed outlier: 4.028A pdb=" N GLU T 65 " --> pdb=" O GLY T 62 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N ALA T 66 " --> pdb=" O LEU T 63 " (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 87 through 108 Proline residue: a 91 - end of helix removed outlier: 4.944A pdb=" N VAL a 98 " --> pdb=" O THR a 95 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N LEU a 106 " --> pdb=" O SER a 103 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N ALA a 107 " --> 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 152 Processing helix chain 'a' and resid 157 through 164 Processing helix chain 'a' and resid 171 through 205 Proline residue: a 182 - end of helix removed outlier: 4.474A pdb=" N LEU a 189 " --> pdb=" O LEU a 185 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N PHE a 190 " --> pdb=" O ALA a 186 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N GLY a 196 " --> pdb=" O ASN a 192 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N MET a 205 " --> pdb=" O ALA a 201 " (cutoff:3.500A) Processing helix chain 'a' and resid 208 through 243 removed outlier: 5.799A pdb=" N PHE a 213 " --> pdb=" O TYR a 209 " (cutoff:3.500A) Proline residue: a 214 - end of helix removed outlier: 3.868A pdb=" N PHE a 224 " --> pdb=" O THR a 220 " (cutoff:3.500A) Processing helix chain 'b' and resid 29 through 47 removed outlier: 3.840A pdb=" N VAL b 34 " --> pdb=" O PHE b 31 " (cutoff:3.500A) Processing helix chain 'b' and resid 50 through 160 removed outlier: 3.620A pdb=" N GLN b 139 " --> pdb=" O ALA b 135 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N SER b 142 " --> pdb=" O ASP b 138 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N SER b 146 " --> pdb=" O SER b 142 " (cutoff:3.500A) removed outlier: 4.828A pdb=" N SER b 147 " --> pdb=" O GLY b 143 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N VAL b 148 " --> pdb=" O LEU b 144 " (cutoff:3.500A) removed outlier: 4.614A pdb=" N ASP b 149 " --> pdb=" O GLU b 145 " (cutoff:3.500A) removed outlier: 5.044A pdb=" N GLY b 150 " --> pdb=" O SER b 146 " (cutoff:3.500A) Processing helix chain 'd' and resid 2 through 21 Processing helix chain 'd' and resid 23 through 137 Processing helix chain 'd' and resid 140 through 156 Processing helix chain 'd' and resid 174 through 192 removed outlier: 3.656A pdb=" N GLY d 192 " --> pdb=" O ASP d 188 " (cutoff:3.500A) Processing helix chain 'd' and resid 198 through 215 Processing helix chain 'd' and resid 217 through 224 Processing helix chain 'd' and resid 231 through 241 Processing helix chain 'd' and resid 247 through 258 Processing helix chain 'd' and resid 264 through 286 removed outlier: 3.508A pdb=" N ILE d 268 " --> pdb=" O GLU d 264 " (cutoff:3.500A) Processing helix chain 'd' and resid 289 through 305 Processing helix chain 'd' and resid 307 through 312 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: 3.851A pdb=" N ARG d 372 " --> pdb=" O ALA d 368 " (cutoff:3.500A) Processing helix chain 'd' and resid 387 through 401 Processing helix chain 'd' and resid 413 through 415 No H-bonds generated for 'chain 'd' and resid 413 through 415' Processing helix chain 'd' and resid 432 through 442 Processing sheet with id= A, first strand: chain 'A' and resid 31 through 33 removed outlier: 6.288A pdb=" N GLY A 75 " --> pdb=" O LEU A 67 " (cutoff:3.500A) removed outlier: 6.120A pdb=" N GLU A 45 " --> pdb=" O VAL A 34 " (cutoff:3.500A) removed outlier: 5.477A pdb=" N VAL A 34 " --> pdb=" O GLU A 45 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 99 through 102 Processing sheet with id= C, first strand: chain 'A' and resid 352 through 355 removed outlier: 6.298A pdb=" N LEU A 169 " --> pdb=" O CYS A 353 " (cutoff:3.500A) removed outlier: 7.085A pdb=" N LEU A 355 " --> pdb=" O LEU A 169 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N ILE A 171 " --> pdb=" O LEU A 355 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 232 through 237 removed outlier: 8.602A pdb=" N THR A 233 " --> pdb=" O VAL A 202 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N CYS A 204 " --> pdb=" O THR A 233 " (cutoff:3.500A) removed outlier: 7.919A pdb=" N VAL A 235 " --> pdb=" O CYS A 204 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N TYR A 206 " --> pdb=" O VAL A 235 " (cutoff:3.500A) removed outlier: 7.470A pdb=" N ALA A 237 " --> pdb=" O TYR A 206 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N ALA A 208 " --> pdb=" O ALA A 237 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N HIS A 266 " --> pdb=" O ARG A 203 " (cutoff:3.500A) removed outlier: 7.955A pdb=" N VAL A 205 " --> pdb=" O HIS A 266 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N LEU A 268 " --> pdb=" O VAL A 205 " (cutoff:3.500A) removed outlier: 7.665A pdb=" N VAL A 207 " --> pdb=" O LEU A 268 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N VAL A 270 " --> pdb=" O VAL A 207 " (cutoff:3.500A) removed outlier: 7.376A pdb=" N ILE A 209 " --> pdb=" O VAL A 270 " (cutoff:3.500A) removed outlier: 6.225A pdb=" N ASP A 272 " --> pdb=" O ILE A 209 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N SER A 323 " --> pdb=" O VAL A 267 " (cutoff:3.500A) removed outlier: 7.696A pdb=" N ILE A 269 " --> pdb=" O SER A 323 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N THR A 325 " --> pdb=" O ILE A 269 " (cutoff:3.500A) removed outlier: 7.710A pdb=" N PHE A 271 " --> pdb=" O THR A 325 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N LEU A 327 " --> pdb=" O PHE A 271 " (cutoff:3.500A) No H-bonds generated for sheet with id= D Processing sheet with id= E, first strand: chain 'B' and resid 31 through 33 removed outlier: 4.021A pdb=" N LEU B 63 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N GLY B 75 " --> pdb=" O LEU B 67 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ASP B 36 " --> pdb=" O HIS B 43 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N GLU B 45 " --> pdb=" O VAL B 34 " (cutoff:3.500A) removed outlier: 5.654A pdb=" N VAL B 34 " --> pdb=" O GLU B 45 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 99 through 102 Processing sheet with id= G, first strand: chain 'B' and resid 352 through 355 removed outlier: 6.887A pdb=" N LEU B 169 " --> pdb=" O CYS B 353 " (cutoff:3.500A) removed outlier: 7.304A pdb=" N LEU B 355 " --> pdb=" O LEU B 169 " (cutoff:3.500A) removed outlier: 6.880A 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: 6.668A pdb=" N CYS B 204 " --> pdb=" O THR B 233 " (cutoff:3.500A) removed outlier: 7.907A pdb=" N VAL B 235 " --> pdb=" O CYS B 204 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N TYR B 206 " --> pdb=" O VAL B 235 " (cutoff:3.500A) removed outlier: 7.429A pdb=" N ALA B 237 " --> pdb=" O TYR B 206 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N ALA B 208 " --> pdb=" O ALA B 237 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N SER B 323 " --> pdb=" O VAL B 267 " (cutoff:3.500A) removed outlier: 7.702A pdb=" N ILE B 269 " --> pdb=" O SER B 323 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N THR B 325 " --> pdb=" O ILE B 269 " (cutoff:3.500A) removed outlier: 7.605A pdb=" N PHE B 271 " --> pdb=" O THR B 325 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'C' and resid 31 through 33 removed outlier: 6.378A pdb=" N GLY C 75 " --> pdb=" O LEU C 67 " (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: 6.524A pdb=" N LEU C 169 " --> pdb=" O CYS C 353 " (cutoff:3.500A) removed outlier: 7.072A pdb=" N LEU C 355 " --> pdb=" O LEU C 169 " (cutoff:3.500A) removed outlier: 6.463A 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: 6.666A pdb=" N CYS C 204 " --> pdb=" O THR C 233 " (cutoff:3.500A) removed outlier: 7.880A pdb=" N VAL C 235 " --> pdb=" O CYS C 204 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N TYR C 206 " --> pdb=" O VAL C 235 " (cutoff:3.500A) removed outlier: 7.291A pdb=" N ALA C 237 " --> pdb=" O TYR C 206 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N ALA C 208 " --> pdb=" O ALA C 237 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N SER C 323 " --> pdb=" O VAL C 267 " (cutoff:3.500A) removed outlier: 7.773A pdb=" N ILE C 269 " --> pdb=" O SER C 323 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N THR C 325 " --> pdb=" O ILE C 269 " (cutoff:3.500A) removed outlier: 7.548A pdb=" N PHE C 271 " --> pdb=" O THR C 325 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'D' and resid 11 through 16 removed outlier: 6.815A pdb=" N ASP D 21 " --> pdb=" O VAL D 13 " (cutoff:3.500A) removed outlier: 4.842A pdb=" N ILE D 15 " --> pdb=" O VAL D 19 " (cutoff:3.500A) removed outlier: 7.222A pdb=" N VAL D 19 " --> pdb=" O ILE D 15 " (cutoff:3.500A) removed outlier: 6.052A pdb=" N ILE D 65 " --> pdb=" O VAL D 53 " (cutoff:3.500A) removed outlier: 5.765A 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: 7.501A pdb=" N ILE D 156 " --> pdb=" O ILE D 302 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N SER D 304 " --> pdb=" O ILE D 156 " (cutoff:3.500A) removed outlier: 7.993A pdb=" N LEU D 158 " --> pdb=" O SER D 304 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N GLN D 306 " --> pdb=" O LEU D 158 " (cutoff:3.500A) removed outlier: 8.380A pdb=" N GLY D 160 " --> pdb=" O GLN D 306 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N VAL D 308 " --> pdb=" O GLY D 160 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N VAL D 249 " --> pdb=" O THR D 303 " (cutoff:3.500A) removed outlier: 7.666A pdb=" N MET D 305 " --> pdb=" O VAL D 249 " (cutoff:3.500A) removed outlier: 5.988A pdb=" N LEU D 251 " --> pdb=" O MET D 305 " (cutoff:3.500A) removed outlier: 7.818A pdb=" N ALA D 307 " --> pdb=" O LEU D 251 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N ILE D 253 " --> pdb=" O ALA D 307 " (cutoff:3.500A) removed outlier: 8.224A pdb=" N TYR D 309 " --> pdb=" O ILE D 253 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N THR D 184 " --> pdb=" O LEU D 250 " (cutoff:3.500A) removed outlier: 7.944A pdb=" N PHE D 252 " --> pdb=" O THR D 184 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N VAL D 186 " --> pdb=" O PHE D 252 " (cutoff:3.500A) removed outlier: 8.000A pdb=" N ASP D 254 " --> pdb=" O VAL D 186 " (cutoff:3.500A) removed outlier: 6.197A 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: 6.537A pdb=" N ASP E 21 " --> pdb=" O VAL E 13 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N ILE E 15 " --> pdb=" O VAL E 19 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N VAL E 19 " --> pdb=" O ILE E 15 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N ILE E 65 " --> pdb=" O VAL E 53 " (cutoff:3.500A) removed outlier: 5.784A 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: 8.384A pdb=" N ILE E 156 " --> pdb=" O ILE E 302 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N SER E 304 " --> pdb=" O ILE E 156 " (cutoff:3.500A) removed outlier: 7.504A pdb=" N LEU E 158 " --> pdb=" O SER E 304 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N GLN E 306 " --> pdb=" O LEU E 158 " (cutoff:3.500A) removed outlier: 6.158A pdb=" N VAL E 249 " --> pdb=" O THR E 303 " (cutoff:3.500A) removed outlier: 7.439A pdb=" N MET E 305 " --> pdb=" O VAL E 249 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N LEU E 251 " --> pdb=" O MET E 305 " (cutoff:3.500A) removed outlier: 7.417A pdb=" N ALA E 307 " --> pdb=" O LEU E 251 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N ILE E 253 " --> pdb=" O ALA E 307 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N THR E 184 " --> pdb=" O LEU E 250 " (cutoff:3.500A) removed outlier: 7.807A pdb=" N PHE E 252 " --> pdb=" O THR E 184 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N VAL E 186 " --> pdb=" O PHE E 252 " (cutoff:3.500A) removed outlier: 7.938A pdb=" N ASP E 254 " --> pdb=" O VAL E 186 " (cutoff:3.500A) removed outlier: 6.329A 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: 6.648A pdb=" N ASP F 21 " --> pdb=" O VAL F 13 " (cutoff:3.500A) removed outlier: 4.752A pdb=" N ILE F 15 " --> pdb=" O VAL F 19 " (cutoff:3.500A) removed outlier: 7.081A pdb=" N VAL F 19 " --> pdb=" O ILE F 15 " (cutoff:3.500A) removed outlier: 6.190A pdb=" N ILE F 65 " --> pdb=" O VAL F 53 " (cutoff:3.500A) removed outlier: 5.690A 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 333 removed outlier: 7.643A pdb=" N ILE F 156 " --> pdb=" O ILE F 302 " (cutoff:3.500A) removed outlier: 6.115A pdb=" N SER F 304 " --> pdb=" O ILE F 156 " (cutoff:3.500A) removed outlier: 7.762A pdb=" N LEU F 158 " --> pdb=" O SER F 304 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N GLN F 306 " --> pdb=" O LEU F 158 " (cutoff:3.500A) removed outlier: 7.903A pdb=" N GLY F 160 " --> pdb=" O GLN F 306 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N VAL F 308 " --> pdb=" O GLY F 160 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N VAL F 249 " --> pdb=" O THR F 303 " (cutoff:3.500A) removed outlier: 7.693A pdb=" N MET F 305 " --> pdb=" O VAL F 249 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N LEU F 251 " --> pdb=" O MET F 305 " (cutoff:3.500A) removed outlier: 7.576A pdb=" N ALA F 307 " --> pdb=" O LEU F 251 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N ILE F 253 " --> pdb=" O ALA F 307 " (cutoff:3.500A) removed outlier: 8.329A pdb=" N TYR F 309 " --> pdb=" O ILE F 253 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'G' and resid 197 through 204 removed outlier: 6.166A pdb=" N LEU G 183 " --> pdb=" O ALA G 203 " (cutoff:3.500A) removed outlier: 8.957A pdb=" N HIS G 184 " --> pdb=" O ARG G 76 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N GLY G 78 " --> pdb=" O HIS G 184 " (cutoff:3.500A) removed outlier: 8.037A pdb=" N VAL G 186 " --> pdb=" O GLY G 78 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N LEU G 80 " --> pdb=" O VAL G 186 " (cutoff:3.500A) removed outlier: 8.612A pdb=" N THR G 188 " --> pdb=" O LEU G 80 " (cutoff:3.500A) removed outlier: 8.978A pdb=" N VAL G 82 " --> pdb=" O THR G 188 " (cutoff:3.500A) removed outlier: 5.836A pdb=" N ASP G 113 " --> pdb=" O ALA G 77 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N VAL G 79 " --> pdb=" O ASP G 113 " (cutoff:3.500A) removed outlier: 6.024A pdb=" N VAL G 115 " --> pdb=" O VAL G 79 " (cutoff:3.500A) removed outlier: 7.720A pdb=" N VAL G 81 " --> pdb=" O VAL G 115 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N TYR G 117 " --> pdb=" O VAL G 81 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N GLU G 136 " --> pdb=" O VAL G 118 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'H' and resid 41 through 44 removed outlier: 6.014A pdb=" N ASN H 5 " --> pdb=" O VAL H 77 " (cutoff:3.500A) removed outlier: 7.525A pdb=" N ILE H 79 " --> pdb=" O ASN H 5 " (cutoff:3.500A) removed outlier: 6.973A pdb=" N GLU H 7 " --> pdb=" O ILE H 79 " (cutoff:3.500A) removed outlier: 7.459A pdb=" N VAL H 81 " --> pdb=" O GLU H 7 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N VAL H 9 " --> pdb=" O VAL H 81 " (cutoff:3.500A) removed outlier: 5.815A pdb=" N ALA H 10 " --> pdb=" O GLU H 14 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N GLU H 14 " --> pdb=" O ALA H 10 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'H' and resid 31 through 34 removed outlier: 3.652A pdb=" N ARG H 26 " --> pdb=" O MET H 50 " (cutoff:3.500A) removed outlier: 5.276A pdb=" N MET H 50 " --> pdb=" O ARG H 26 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'a' and resid 19 through 22 Processing sheet with id= Z, first strand: chain 'd' and resid 406 through 411 2106 hydrogen bonds defined for protein. 5616 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: 27.15 Time building geometry restraints manager: 55.27 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: 37325 1.03 - 1.23: 54 1.23 - 1.42: 15304 1.42 - 1.62: 22358 1.62 - 1.81: 194 Bond restraints: 75235 Sorted by residual: bond pdb=" CB ARG C 221 " pdb=" CG ARG C 221 " ideal model delta sigma weight residual 1.520 1.474 0.046 3.00e-02 1.11e+03 2.30e+00 bond pdb=" C4 ADP D 600 " pdb=" C5 ADP D 600 " ideal model delta sigma weight residual 1.490 1.462 0.028 2.00e-02 2.50e+03 2.03e+00 bond pdb=" CB GLN C 399 " pdb=" CG GLN C 399 " ideal model delta sigma weight residual 1.520 1.478 0.042 3.00e-02 1.11e+03 1.98e+00 bond pdb=" CG1 ILE Q 30 " pdb=" CD1 ILE Q 30 " ideal model delta sigma weight residual 1.513 1.459 0.054 3.90e-02 6.57e+02 1.93e+00 bond pdb=" CG1 ILE P 30 " pdb=" CD1 ILE P 30 " ideal model delta sigma weight residual 1.513 1.460 0.053 3.90e-02 6.57e+02 1.85e+00 ... (remaining 75230 not shown) Histogram of bond angle deviations from ideal: 98.98 - 107.16: 1737 107.16 - 115.34: 95956 115.34 - 123.52: 32762 123.52 - 131.70: 5815 131.70 - 139.88: 43 Bond angle restraints: 136313 Sorted by residual: angle pdb=" C ASP F 254 " pdb=" N ASN F 255 " pdb=" CA ASN F 255 " ideal model delta sigma weight residual 121.70 127.85 -6.15 1.80e+00 3.09e-01 1.17e+01 angle pdb=" C LYS C 220 " pdb=" N ARG C 221 " pdb=" CA ARG C 221 " ideal model delta sigma weight residual 120.68 115.34 5.34 1.70e+00 3.46e-01 9.85e+00 angle pdb=" N VAL S 79 " pdb=" CA VAL S 79 " pdb=" C VAL S 79 " ideal model delta sigma weight residual 113.71 110.76 2.95 9.50e-01 1.11e+00 9.65e+00 angle pdb=" C ASP A 272 " pdb=" N ASP A 273 " pdb=" CA ASP A 273 " ideal model delta sigma weight residual 121.70 127.23 -5.53 1.80e+00 3.09e-01 9.42e+00 angle pdb=" C ASP D 254 " pdb=" N ASN D 255 " pdb=" CA ASN D 255 " ideal model delta sigma weight residual 121.70 127.18 -5.48 1.80e+00 3.09e-01 9.27e+00 ... (remaining 136308 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.48: 33929 35.48 - 70.97: 1188 70.97 - 106.45: 55 106.45 - 141.94: 3 141.94 - 177.42: 1 Dihedral angle restraints: 35176 sinusoidal: 19496 harmonic: 15680 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 -60.00 117.42 -177.42 1 2.00e+01 2.50e-03 4.80e+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 300.00 174.46 125.54 1 2.00e+01 2.50e-03 3.80e+01 dihedral pdb=" O1B ADP E 600 " pdb=" O3A ADP E 600 " pdb=" PB ADP E 600 " pdb=" PA ADP E 600 " ideal model delta sinusoidal sigma weight residual -60.00 56.58 -116.58 1 2.00e+01 2.50e-03 3.47e+01 ... (remaining 35173 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.060: 5208 0.060 - 0.120: 687 0.120 - 0.180: 59 0.180 - 0.241: 2 0.241 - 0.301: 10 Chirality restraints: 5966 Sorted by residual: chirality pdb=" C2' ATP B 600 " pdb=" C1' ATP B 600 " pdb=" C3' ATP B 600 " pdb=" O2' ATP B 600 " both_signs ideal model delta sigma weight residual False -2.68 -2.98 0.30 2.00e-01 2.50e+01 2.26e+00 chirality pdb=" C2' ATP C 600 " pdb=" C1' ATP C 600 " pdb=" C3' ATP C 600 " pdb=" O2' ATP C 600 " both_signs ideal model delta sigma weight residual False -2.68 -2.97 0.29 2.00e-01 2.50e+01 2.10e+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 2.07e+00 ... (remaining 5963 not shown) Planarity restraints: 11427 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG C 221 " 0.086 9.50e-02 1.11e+02 3.06e-02 3.65e+00 pdb=" NE ARG C 221 " -0.019 2.00e-02 2.50e+03 pdb=" CZ ARG C 221 " 0.026 2.00e-02 2.50e+03 pdb=" NH1 ARG C 221 " 0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG C 221 " -0.002 2.00e-02 2.50e+03 pdb="HH11 ARG C 221 " -0.001 2.00e-02 2.50e+03 pdb="HH12 ARG C 221 " -0.010 2.00e-02 2.50e+03 pdb="HH21 ARG C 221 " 0.000 2.00e-02 2.50e+03 pdb="HH22 ARG C 221 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE H 69 " 0.018 2.00e-02 2.50e+03 1.09e-02 3.59e+00 pdb=" CG PHE H 69 " -0.030 2.00e-02 2.50e+03 pdb=" CD1 PHE H 69 " 0.007 2.00e-02 2.50e+03 pdb=" CD2 PHE H 69 " -0.002 2.00e-02 2.50e+03 pdb=" CE1 PHE H 69 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE H 69 " 0.010 2.00e-02 2.50e+03 pdb=" CZ PHE H 69 " 0.004 2.00e-02 2.50e+03 pdb=" HD1 PHE H 69 " -0.004 2.00e-02 2.50e+03 pdb=" HD2 PHE H 69 " -0.000 2.00e-02 2.50e+03 pdb=" HE1 PHE H 69 " 0.003 2.00e-02 2.50e+03 pdb=" HE2 PHE H 69 " -0.002 2.00e-02 2.50e+03 pdb=" HZ PHE H 69 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE D 456 " -0.014 2.00e-02 2.50e+03 9.46e-03 2.68e+00 pdb=" CG PHE D 456 " 0.026 2.00e-02 2.50e+03 pdb=" CD1 PHE D 456 " -0.009 2.00e-02 2.50e+03 pdb=" CD2 PHE D 456 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE D 456 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 PHE D 456 " -0.008 2.00e-02 2.50e+03 pdb=" CZ PHE D 456 " -0.000 2.00e-02 2.50e+03 pdb=" HD1 PHE D 456 " 0.002 2.00e-02 2.50e+03 pdb=" HD2 PHE D 456 " 0.001 2.00e-02 2.50e+03 pdb=" HE1 PHE D 456 " -0.003 2.00e-02 2.50e+03 pdb=" HE2 PHE D 456 " -0.001 2.00e-02 2.50e+03 pdb=" HZ PHE D 456 " 0.002 2.00e-02 2.50e+03 ... (remaining 11424 not shown) Histogram of nonbonded interaction distances: 1.51 - 2.13: 2361 2.13 - 2.75: 143248 2.75 - 3.36: 228593 3.36 - 3.98: 292834 3.98 - 4.60: 461809 Nonbonded interactions: 1128845 Sorted by model distance: nonbonded pdb=" O PHE R 58 " pdb=" H GLY R 62 " model vdw 1.511 1.850 nonbonded pdb=" O VAL R 61 " pdb=" H GLU R 65 " model vdw 1.521 1.850 nonbonded pdb=" O VAL B 19 " pdb=" H SER B 23 " model vdw 1.529 1.850 nonbonded pdb=" H GLY D 165 " pdb=" O1B ADP D 600 " model vdw 1.547 1.850 nonbonded pdb=" H LYS G 75 " pdb=" OD2 ASP G 181 " model vdw 1.562 1.850 ... (remaining 1128840 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 5 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 353 or resi \ d 355 through 406 or resid 415 through 521 or resid 600 through 601)) selection = (chain 'B' and (resid 5 through 22 or resid 29 through 353 or resid 355 through \ 406 or resid 415 through 521 or resid 600 through 601)) selection = (chain 'C' and (resid 5 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 353 or resi \ d 355 through 406 or resid 415 through 521 or resid 600 through 601)) } ncs_group { reference = (chain 'D' and (resid 8 through 452 or resid 454 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 454 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 454 through 471)) } ncs_group { reference = (chain 'L' and ((resid 4 and (name N or name CA or name C or name O or name CB o \ r name CG or name OD1 or name OD2 or name HA or name HB2 or name HB3)) or resid \ 5 through 86)) selection = (chain 'M' and ((resid 4 and (name N or name CA or name C or name O or name CB o \ r name CG or name OD1 or name OD2 or name HA or name HB2 or name HB3)) or resid \ 5 through 86)) selection = (chain 'N' and ((resid 4 and (name N or name CA or name C or name O or name CB o \ r name CG or name OD1 or name OD2 or name HA or name HB2 or name HB3)) or resid \ 5 through 86)) selection = chain 'O' selection = (chain 'P' and ((resid 4 and (name N or name CA or name C or name O or name CB o \ r name CG or name OD1 or name OD2 or name HA or name HB2 or name HB3)) or resid \ 5 through 86)) selection = (chain 'Q' and ((resid 4 and (name N or name CA or name C or name O or name CB o \ r name CG or name OD1 or name OD2 or name HA or name HB2 or name HB3)) or resid \ 5 through 86)) selection = (chain 'R' and ((resid 4 and (name N or name CA or name C or name O or name CB o \ r name CG or name OD1 or name OD2 or name HA or name HB2 or name HB3)) or resid \ 5 through 86)) selection = chain 'S' selection = (chain 'T' and ((resid 4 and (name N or name CA or name C or name O or name CB o \ r name CG or name OD1 or name OD2 or name HA or name HB2 or name HB3)) or resid \ 5 through 86)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 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: 4.730 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: 0.890 Extract box with map and model: 26.520 Check model and map are aligned: 0.840 Set scattering table: 0.530 Process input model: 203.980 Find NCS groups from input model: 2.790 Set up NCS constraints: 0.250 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:11.480 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 252.030 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8456 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 37890 Z= 0.248 Angle : 0.531 6.676 51390 Z= 0.281 Chirality : 0.042 0.301 5966 Planarity : 0.003 0.042 6724 Dihedral : 15.212 177.420 13876 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.89 % Favored : 97.07 % Rotamer: Outliers : 0.00 % Allowed : 0.34 % Favored : 99.66 % 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: 1.46 (0.12), residues: 4880 helix: 1.80 (0.10), residues: 2604 sheet: -0.55 (0.22), residues: 531 loop : 0.34 (0.16), residues: 1745 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 193 HIS 0.005 0.001 HIS B 479 PHE 0.031 0.001 PHE H 69 TYR 0.010 0.001 TYR R 68 ARG 0.023 0.000 ARG C 221 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9760 Ramachandran restraints generated. 4880 Oldfield, 0 Emsley, 4880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9760 Ramachandran restraints generated. 4880 Oldfield, 0 Emsley, 4880 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 423 residues out of total 3843 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 423 time to evaluate : 4.547 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: B 199 LYS cc_start: 0.8198 (mmpt) cc_final: 0.7980 (mmtt) REVERT: E 408 ILE cc_start: 0.8991 (tt) cc_final: 0.8735 (pt) REVERT: N 32 ASP cc_start: 0.8363 (t70) cc_final: 0.8085 (t0) REVERT: P 50 GLN cc_start: 0.8077 (tp40) cc_final: 0.7742 (mm-40) REVERT: P 75 MET cc_start: 0.8618 (tmm) cc_final: 0.8391 (tmm) REVERT: R 80 PHE cc_start: 0.5667 (m-10) cc_final: 0.5435 (t80) REVERT: a 111 LEU cc_start: 0.7570 (mp) cc_final: 0.7208 (mp) outliers start: 0 outliers final: 1 residues processed: 423 average time/residue: 2.8018 time to fit residues: 1434.5602 Evaluate side-chains 259 residues out of total 3843 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 258 time to evaluate : 4.722 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain d residue 30 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 483 random chunks: chunk 407 optimal weight: 4.9990 chunk 366 optimal weight: 3.9990 chunk 203 optimal weight: 1.9990 chunk 125 optimal weight: 2.9990 chunk 246 optimal weight: 0.7980 chunk 195 optimal weight: 2.9990 chunk 378 optimal weight: 4.9990 chunk 146 optimal weight: 0.9980 chunk 230 optimal weight: 2.9990 chunk 281 optimal weight: 1.9990 chunk 438 optimal weight: 3.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 208 ASN G 288 GLN G 291 GLN ** O 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 71 ASN R 46 GLN a 72 GLN ** b 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8489 moved from start: 0.0691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 37890 Z= 0.303 Angle : 0.539 6.514 51390 Z= 0.280 Chirality : 0.041 0.155 5966 Planarity : 0.004 0.079 6724 Dihedral : 7.477 157.621 5412 Min Nonbonded Distance : 1.622 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.89 % Favored : 97.09 % Rotamer: Outliers : 0.70 % Allowed : 7.93 % Favored : 91.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.90 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.40 (0.12), residues: 4880 helix: 1.76 (0.10), residues: 2603 sheet: -0.55 (0.22), residues: 527 loop : 0.29 (0.16), residues: 1750 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 247 HIS 0.004 0.001 HIS D 449 PHE 0.023 0.001 PHE d 187 TYR 0.027 0.001 TYR a 145 ARG 0.005 0.000 ARG F 406 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9760 Ramachandran restraints generated. 4880 Oldfield, 0 Emsley, 4880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9760 Ramachandran restraints generated. 4880 Oldfield, 0 Emsley, 4880 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 301 residues out of total 3843 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 274 time to evaluate : 4.505 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 468 GLU cc_start: 0.8401 (OUTLIER) cc_final: 0.8100 (pt0) REVERT: D 138 GLU cc_start: 0.7710 (OUTLIER) cc_final: 0.7024 (tm-30) REVERT: E 408 ILE cc_start: 0.9000 (tt) cc_final: 0.8733 (pt) REVERT: G 143 GLU cc_start: 0.8027 (OUTLIER) cc_final: 0.7642 (pm20) REVERT: M 32 ASP cc_start: 0.8436 (m-30) cc_final: 0.8100 (m-30) REVERT: N 32 ASP cc_start: 0.8336 (t70) cc_final: 0.8053 (t0) REVERT: P 50 GLN cc_start: 0.8083 (tp40) cc_final: 0.7763 (mm-40) REVERT: P 75 MET cc_start: 0.8669 (tmm) cc_final: 0.8397 (tmm) REVERT: R 80 PHE cc_start: 0.5729 (m-10) cc_final: 0.5384 (t80) outliers start: 27 outliers final: 8 residues processed: 291 average time/residue: 2.5392 time to fit residues: 913.9081 Evaluate side-chains 266 residues out of total 3843 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 255 time to evaluate : 4.550 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 498 GLU Chi-restraints excluded: chain C residue 358 ASP Chi-restraints excluded: chain C residue 468 GLU Chi-restraints excluded: chain C residue 529 ASP Chi-restraints excluded: chain D residue 138 GLU Chi-restraints excluded: chain E residue 416 MET Chi-restraints excluded: chain F residue 148 THR Chi-restraints excluded: chain F residue 334 SER Chi-restraints excluded: chain F residue 442 LEU Chi-restraints excluded: chain G residue 143 GLU Chi-restraints excluded: chain G residue 162 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 483 random chunks: chunk 243 optimal weight: 4.9990 chunk 136 optimal weight: 0.5980 chunk 365 optimal weight: 5.9990 chunk 298 optimal weight: 1.9990 chunk 120 optimal weight: 0.6980 chunk 439 optimal weight: 9.9990 chunk 474 optimal weight: 6.9990 chunk 391 optimal weight: 4.9990 chunk 435 optimal weight: 0.8980 chunk 149 optimal weight: 2.9990 chunk 352 optimal weight: 0.8980 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 208 ASN G 288 GLN Q 46 GLN ** b 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 32 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8475 moved from start: 0.0770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 37890 Z= 0.210 Angle : 0.508 6.800 51390 Z= 0.261 Chirality : 0.040 0.150 5966 Planarity : 0.003 0.054 6724 Dihedral : 7.205 143.508 5409 Min Nonbonded Distance : 1.728 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.64 % Favored : 97.33 % Rotamer: Outliers : 0.60 % Allowed : 9.46 % Favored : 89.94 % 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: 1.57 (0.12), residues: 4880 helix: 1.90 (0.10), residues: 2607 sheet: -0.46 (0.22), residues: 525 loop : 0.35 (0.16), residues: 1748 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 193 HIS 0.003 0.001 HIS F 97 PHE 0.015 0.001 PHE D 456 TYR 0.020 0.001 TYR a 145 ARG 0.004 0.000 ARG F 406 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9760 Ramachandran restraints generated. 4880 Oldfield, 0 Emsley, 4880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9760 Ramachandran restraints generated. 4880 Oldfield, 0 Emsley, 4880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 179 is missing expected H atoms. Skipping. Residue THR 179 is missing expected H atoms. Skipping. Residue THR 179 is missing expected H atoms. Skipping. Residue THR 167 is missing expected H atoms. Skipping. Residue THR 167 is missing expected H atoms. Skipping. Evaluate side-chains 297 residues out of total 3843 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 274 time to evaluate : 4.642 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: B 420 GLN cc_start: 0.7786 (OUTLIER) cc_final: 0.7470 (tt0) REVERT: E 408 ILE cc_start: 0.8997 (tt) cc_final: 0.8746 (pt) REVERT: G 143 GLU cc_start: 0.8033 (OUTLIER) cc_final: 0.7624 (pm20) REVERT: M 32 ASP cc_start: 0.8379 (m-30) cc_final: 0.8076 (m-30) REVERT: N 32 ASP cc_start: 0.8306 (t70) cc_final: 0.8040 (t0) REVERT: P 21 MET cc_start: 0.9008 (mmm) cc_final: 0.8043 (mpm) REVERT: P 50 GLN cc_start: 0.8059 (tp40) cc_final: 0.7755 (mm-40) REVERT: R 80 PHE cc_start: 0.5709 (m-10) cc_final: 0.5370 (t80) outliers start: 23 outliers final: 11 residues processed: 290 average time/residue: 2.5884 time to fit residues: 939.3558 Evaluate side-chains 267 residues out of total 3843 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 254 time to evaluate : 5.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 498 GLU Chi-restraints excluded: chain B residue 420 GLN Chi-restraints excluded: chain C residue 358 ASP Chi-restraints excluded: chain C residue 529 ASP Chi-restraints excluded: chain F residue 148 THR Chi-restraints excluded: chain F residue 334 SER Chi-restraints excluded: chain F residue 442 LEU Chi-restraints excluded: chain G residue 53 MET Chi-restraints excluded: chain G residue 143 GLU Chi-restraints excluded: chain O residue 26 ILE Chi-restraints excluded: chain T residue 55 THR Chi-restraints excluded: chain a residue 211 GLN Chi-restraints excluded: chain d residue 376 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 483 random chunks: chunk 434 optimal weight: 9.9990 chunk 330 optimal weight: 10.0000 chunk 228 optimal weight: 3.9990 chunk 48 optimal weight: 2.9990 chunk 209 optimal weight: 0.0870 chunk 295 optimal weight: 2.9990 chunk 440 optimal weight: 5.9990 chunk 466 optimal weight: 3.9990 chunk 230 optimal weight: 2.9990 chunk 417 optimal weight: 7.9990 chunk 125 optimal weight: 2.9990 overall best weight: 2.4166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 208 ASN G 288 GLN ** b 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8512 moved from start: 0.0983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.075 37890 Z= 0.404 Angle : 0.570 7.395 51390 Z= 0.298 Chirality : 0.042 0.160 5966 Planarity : 0.004 0.102 6724 Dihedral : 7.347 129.926 5409 Min Nonbonded Distance : 1.627 Molprobity Statistics. All-atom Clashscore : 9.04 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.14 % Favored : 96.84 % Rotamer: Outliers : 1.12 % Allowed : 10.71 % Favored : 88.17 % 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: 1.27 (0.12), residues: 4880 helix: 1.67 (0.10), residues: 2603 sheet: -0.56 (0.22), residues: 533 loop : 0.18 (0.16), residues: 1744 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 247 HIS 0.005 0.001 HIS D 449 PHE 0.018 0.001 PHE D 456 TYR 0.020 0.002 TYR a 145 ARG 0.007 0.000 ARG F 406 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9760 Ramachandran restraints generated. 4880 Oldfield, 0 Emsley, 4880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9760 Ramachandran restraints generated. 4880 Oldfield, 0 Emsley, 4880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 179 is missing expected H atoms. Skipping. Residue THR 179 is missing expected H atoms. Skipping. Residue THR 179 is missing expected H atoms. Skipping. Residue THR 167 is missing expected H atoms. Skipping. Residue THR 167 is missing expected H atoms. Skipping. Evaluate side-chains 306 residues out of total 3843 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 263 time to evaluate : 4.591 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 270 VAL cc_start: 0.9160 (OUTLIER) cc_final: 0.8823 (p) REVERT: C 468 GLU cc_start: 0.8490 (OUTLIER) cc_final: 0.8238 (pt0) REVERT: D 138 GLU cc_start: 0.7720 (OUTLIER) cc_final: 0.7067 (tm-30) REVERT: G 130 ARG cc_start: 0.7699 (OUTLIER) cc_final: 0.6542 (mmt90) REVERT: M 32 ASP cc_start: 0.8477 (m-30) cc_final: 0.8183 (m-30) REVERT: N 32 ASP cc_start: 0.8388 (t70) cc_final: 0.8086 (t0) REVERT: P 50 GLN cc_start: 0.8142 (tp40) cc_final: 0.7830 (mm-40) REVERT: R 80 PHE cc_start: 0.5761 (m-10) cc_final: 0.5396 (t80) outliers start: 43 outliers final: 17 residues processed: 297 average time/residue: 2.4451 time to fit residues: 905.2959 Evaluate side-chains 272 residues out of total 3843 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 251 time to evaluate : 4.475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 498 GLU Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain B residue 479 HIS Chi-restraints excluded: chain C residue 358 ASP Chi-restraints excluded: chain C residue 468 GLU Chi-restraints excluded: chain C residue 529 ASP Chi-restraints excluded: chain D residue 138 GLU Chi-restraints excluded: chain F residue 148 THR Chi-restraints excluded: chain F residue 334 SER Chi-restraints excluded: chain F residue 363 ASP Chi-restraints excluded: chain F residue 442 LEU Chi-restraints excluded: chain G residue 130 ARG Chi-restraints excluded: chain G residue 143 GLU Chi-restraints excluded: chain H residue 91 ASP Chi-restraints excluded: chain N residue 50 GLN Chi-restraints excluded: chain O residue 26 ILE Chi-restraints excluded: chain S residue 15 ILE Chi-restraints excluded: chain T residue 55 THR Chi-restraints excluded: chain a residue 211 GLN Chi-restraints excluded: chain d residue 276 ARG Chi-restraints excluded: chain d residue 376 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 483 random chunks: chunk 388 optimal weight: 5.9990 chunk 265 optimal weight: 1.9990 chunk 6 optimal weight: 0.9990 chunk 347 optimal weight: 0.7980 chunk 192 optimal weight: 1.9990 chunk 398 optimal weight: 3.9990 chunk 322 optimal weight: 5.9990 chunk 0 optimal weight: 8.9990 chunk 238 optimal weight: 4.9990 chunk 419 optimal weight: 3.9990 chunk 117 optimal weight: 1.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 505 ASN B 399 GLN F 208 ASN G 288 GLN ** b 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 32 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8496 moved from start: 0.0990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 37890 Z= 0.267 Angle : 0.530 7.261 51390 Z= 0.273 Chirality : 0.040 0.153 5966 Planarity : 0.004 0.074 6724 Dihedral : 7.143 123.490 5409 Min Nonbonded Distance : 1.682 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.64 % Favored : 97.33 % Rotamer: Outliers : 1.09 % Allowed : 11.75 % Favored : 87.16 % 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: 1.41 (0.12), residues: 4880 helix: 1.79 (0.10), residues: 2602 sheet: -0.51 (0.22), residues: 532 loop : 0.24 (0.16), residues: 1746 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 193 HIS 0.003 0.001 HIS F 97 PHE 0.020 0.001 PHE O 69 TYR 0.020 0.001 TYR a 145 ARG 0.006 0.000 ARG D 26 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9760 Ramachandran restraints generated. 4880 Oldfield, 0 Emsley, 4880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9760 Ramachandran restraints generated. 4880 Oldfield, 0 Emsley, 4880 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 308 residues out of total 3843 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 266 time to evaluate : 4.577 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 270 VAL cc_start: 0.9152 (OUTLIER) cc_final: 0.8806 (p) REVERT: D 138 GLU cc_start: 0.7671 (OUTLIER) cc_final: 0.7034 (tm-30) REVERT: G 108 ARG cc_start: 0.7876 (OUTLIER) cc_final: 0.7529 (mtm110) REVERT: G 130 ARG cc_start: 0.7654 (OUTLIER) cc_final: 0.6556 (mmt90) REVERT: M 32 ASP cc_start: 0.8447 (m-30) cc_final: 0.8144 (m-30) REVERT: N 32 ASP cc_start: 0.8347 (t70) cc_final: 0.8074 (t0) REVERT: P 21 MET cc_start: 0.8861 (OUTLIER) cc_final: 0.8074 (mpm) REVERT: P 50 GLN cc_start: 0.8044 (tp40) cc_final: 0.7742 (mm-40) REVERT: R 80 PHE cc_start: 0.5736 (m-10) cc_final: 0.5357 (t80) outliers start: 42 outliers final: 20 residues processed: 296 average time/residue: 2.5519 time to fit residues: 937.3489 Evaluate side-chains 273 residues out of total 3843 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 248 time to evaluate : 4.556 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 ASP Chi-restraints excluded: chain A residue 498 GLU Chi-restraints excluded: chain B residue 70 ASP Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain B residue 479 HIS Chi-restraints excluded: chain C residue 358 ASP Chi-restraints excluded: chain C residue 529 ASP Chi-restraints excluded: chain D residue 138 GLU Chi-restraints excluded: chain E residue 71 ASP Chi-restraints excluded: chain F residue 148 THR Chi-restraints excluded: chain F residue 334 SER Chi-restraints excluded: chain F residue 363 ASP Chi-restraints excluded: chain G residue 108 ARG Chi-restraints excluded: chain G residue 130 ARG Chi-restraints excluded: chain G residue 143 GLU Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain H residue 91 ASP Chi-restraints excluded: chain N residue 50 GLN Chi-restraints excluded: chain O residue 26 ILE Chi-restraints excluded: chain P residue 21 MET Chi-restraints excluded: chain S residue 15 ILE Chi-restraints excluded: chain T residue 55 THR Chi-restraints excluded: chain d residue 30 MET Chi-restraints excluded: chain d residue 276 ARG Chi-restraints excluded: chain d residue 376 VAL 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: 2.9990 chunk 274 optimal weight: 3.9990 chunk 115 optimal weight: 0.9990 chunk 467 optimal weight: 7.9990 chunk 387 optimal weight: 5.9990 chunk 216 optimal weight: 2.9990 chunk 38 optimal weight: 2.9990 chunk 154 optimal weight: 0.5980 chunk 245 optimal weight: 1.9990 overall best weight: 1.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 505 ASN ** B 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 420 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 208 ASN G 288 GLN ** b 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8501 moved from start: 0.1063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 37890 Z= 0.298 Angle : 0.538 7.844 51390 Z= 0.278 Chirality : 0.040 0.154 5966 Planarity : 0.004 0.084 6724 Dihedral : 7.104 117.949 5409 Min Nonbonded Distance : 1.681 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.93 % Favored : 97.05 % Rotamer: Outliers : 1.04 % Allowed : 12.63 % Favored : 86.33 % 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: 1.41 (0.12), residues: 4880 helix: 1.80 (0.10), residues: 2603 sheet: -0.52 (0.22), residues: 531 loop : 0.22 (0.16), residues: 1746 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 193 HIS 0.003 0.001 HIS F 97 PHE 0.019 0.001 PHE O 69 TYR 0.019 0.001 TYR a 145 ARG 0.008 0.000 ARG D 26 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9760 Ramachandran restraints generated. 4880 Oldfield, 0 Emsley, 4880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9760 Ramachandran restraints generated. 4880 Oldfield, 0 Emsley, 4880 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 296 residues out of total 3843 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 256 time to evaluate : 4.784 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: B 270 VAL cc_start: 0.9167 (OUTLIER) cc_final: 0.8819 (p) REVERT: D 138 GLU cc_start: 0.7688 (OUTLIER) cc_final: 0.7045 (tm-30) REVERT: G 108 ARG cc_start: 0.7873 (OUTLIER) cc_final: 0.7497 (mtm110) REVERT: G 130 ARG cc_start: 0.7634 (OUTLIER) cc_final: 0.6501 (mmt90) REVERT: N 32 ASP cc_start: 0.8354 (t70) cc_final: 0.8085 (t0) REVERT: P 21 MET cc_start: 0.8814 (OUTLIER) cc_final: 0.8111 (mpm) REVERT: P 50 GLN cc_start: 0.8036 (tp40) cc_final: 0.7733 (mm-40) REVERT: R 65 GLU cc_start: 0.7166 (tm-30) cc_final: 0.6944 (tm-30) REVERT: R 80 PHE cc_start: 0.5742 (m-10) cc_final: 0.5358 (t80) REVERT: b 101 ASP cc_start: 0.8608 (m-30) cc_final: 0.8358 (m-30) outliers start: 40 outliers final: 22 residues processed: 288 average time/residue: 2.5341 time to fit residues: 911.0372 Evaluate side-chains 274 residues out of total 3843 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 247 time to evaluate : 4.499 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 ASP Chi-restraints excluded: chain A residue 498 GLU Chi-restraints excluded: chain B residue 70 ASP Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain B residue 479 HIS Chi-restraints excluded: chain C residue 358 ASP Chi-restraints excluded: chain C residue 529 ASP Chi-restraints excluded: chain D residue 138 GLU Chi-restraints excluded: chain E residue 71 ASP Chi-restraints excluded: chain F residue 148 THR Chi-restraints excluded: chain F residue 334 SER Chi-restraints excluded: chain F residue 363 ASP Chi-restraints excluded: chain G residue 108 ARG Chi-restraints excluded: chain G residue 130 ARG Chi-restraints excluded: chain G residue 143 GLU Chi-restraints excluded: chain H residue 25 THR Chi-restraints excluded: chain H residue 91 ASP Chi-restraints excluded: chain N residue 50 GLN Chi-restraints excluded: chain O residue 26 ILE Chi-restraints excluded: chain P residue 21 MET Chi-restraints excluded: chain S residue 15 ILE Chi-restraints excluded: chain S residue 55 THR Chi-restraints excluded: chain T residue 55 THR Chi-restraints excluded: chain a residue 211 GLN Chi-restraints excluded: chain d residue 14 ILE Chi-restraints excluded: chain d residue 276 ARG Chi-restraints excluded: chain d residue 376 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 483 random chunks: chunk 450 optimal weight: 3.9990 chunk 52 optimal weight: 0.9990 chunk 266 optimal weight: 1.9990 chunk 341 optimal weight: 3.9990 chunk 264 optimal weight: 1.9990 chunk 393 optimal weight: 0.4980 chunk 260 optimal weight: 1.9990 chunk 465 optimal weight: 6.9990 chunk 291 optimal weight: 3.9990 chunk 283 optimal weight: 2.9990 chunk 214 optimal weight: 3.9990 overall best weight: 1.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 208 ASN G 288 GLN ** b 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 32 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8496 moved from start: 0.1085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 37890 Z= 0.265 Angle : 0.532 8.036 51390 Z= 0.274 Chirality : 0.040 0.151 5966 Planarity : 0.004 0.063 6724 Dihedral : 7.015 116.403 5409 Min Nonbonded Distance : 1.694 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.69 % Favored : 97.29 % Rotamer: Outliers : 0.96 % Allowed : 13.13 % Favored : 85.91 % 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: 1.47 (0.12), residues: 4880 helix: 1.84 (0.10), residues: 2604 sheet: -0.50 (0.22), residues: 531 loop : 0.26 (0.16), residues: 1745 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 193 HIS 0.003 0.001 HIS F 97 PHE 0.020 0.001 PHE d 16 TYR 0.019 0.001 TYR a 145 ARG 0.014 0.000 ARG C 221 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9760 Ramachandran restraints generated. 4880 Oldfield, 0 Emsley, 4880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9760 Ramachandran restraints generated. 4880 Oldfield, 0 Emsley, 4880 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 290 residues out of total 3843 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 253 time to evaluate : 4.571 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 270 VAL cc_start: 0.9164 (OUTLIER) cc_final: 0.8812 (p) REVERT: D 138 GLU cc_start: 0.7668 (OUTLIER) cc_final: 0.7023 (tm-30) REVERT: G 108 ARG cc_start: 0.7857 (OUTLIER) cc_final: 0.7491 (mtm110) REVERT: G 130 ARG cc_start: 0.7637 (OUTLIER) cc_final: 0.6543 (mmt90) REVERT: M 21 MET cc_start: 0.8502 (mmm) cc_final: 0.8268 (mmm) REVERT: M 32 ASP cc_start: 0.8373 (m-30) cc_final: 0.8147 (m-30) REVERT: N 32 ASP cc_start: 0.8336 (t70) cc_final: 0.8073 (t0) REVERT: P 21 MET cc_start: 0.8823 (OUTLIER) cc_final: 0.8131 (mpm) REVERT: P 50 GLN cc_start: 0.8032 (tp40) cc_final: 0.7733 (mm-40) REVERT: R 65 GLU cc_start: 0.7122 (OUTLIER) cc_final: 0.6884 (tm-30) REVERT: R 80 PHE cc_start: 0.5757 (m-10) cc_final: 0.5367 (t80) outliers start: 37 outliers final: 23 residues processed: 283 average time/residue: 2.5026 time to fit residues: 885.4062 Evaluate side-chains 273 residues out of total 3843 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 244 time to evaluate : 4.554 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 ASP Chi-restraints excluded: chain A residue 498 GLU Chi-restraints excluded: chain B residue 70 ASP Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain B residue 479 HIS Chi-restraints excluded: chain C residue 358 ASP Chi-restraints excluded: chain C residue 529 ASP Chi-restraints excluded: chain D residue 138 GLU Chi-restraints excluded: chain E residue 59 ASP Chi-restraints excluded: chain E residue 64 CYS Chi-restraints excluded: chain F residue 148 THR Chi-restraints excluded: chain F residue 334 SER Chi-restraints excluded: chain F residue 363 ASP Chi-restraints excluded: chain G residue 108 ARG Chi-restraints excluded: chain G residue 130 ARG Chi-restraints excluded: chain G residue 143 GLU Chi-restraints excluded: chain G residue 193 MET Chi-restraints excluded: chain H residue 25 THR Chi-restraints excluded: chain O residue 26 ILE Chi-restraints excluded: chain P residue 21 MET Chi-restraints excluded: chain R residue 65 GLU Chi-restraints excluded: chain S residue 15 ILE Chi-restraints excluded: chain S residue 55 THR Chi-restraints excluded: chain T residue 55 THR Chi-restraints excluded: chain a residue 187 LEU Chi-restraints excluded: chain a residue 211 GLN Chi-restraints excluded: chain d residue 14 ILE Chi-restraints excluded: chain d residue 276 ARG Chi-restraints excluded: chain d residue 376 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 483 random chunks: chunk 288 optimal weight: 1.9990 chunk 185 optimal weight: 2.9990 chunk 278 optimal weight: 0.0470 chunk 140 optimal weight: 4.9990 chunk 91 optimal weight: 2.9990 chunk 90 optimal weight: 2.9990 chunk 295 optimal weight: 2.9990 chunk 317 optimal weight: 1.9990 chunk 230 optimal weight: 2.9990 chunk 43 optimal weight: 1.9990 chunk 365 optimal weight: 3.9990 overall best weight: 1.8086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 505 ASN F 208 ASN G 288 GLN ** b 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8503 moved from start: 0.1136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 37890 Z= 0.309 Angle : 0.546 8.589 51390 Z= 0.281 Chirality : 0.041 0.153 5966 Planarity : 0.004 0.059 6724 Dihedral : 7.028 115.777 5409 Min Nonbonded Distance : 1.681 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.93 % Favored : 97.05 % Rotamer: Outliers : 1.09 % Allowed : 13.28 % Favored : 85.63 % 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: 1.41 (0.12), residues: 4880 helix: 1.80 (0.10), residues: 2602 sheet: -0.51 (0.22), residues: 531 loop : 0.22 (0.16), residues: 1747 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 247 HIS 0.003 0.001 HIS F 97 PHE 0.039 0.001 PHE Q 57 TYR 0.018 0.001 TYR a 145 ARG 0.011 0.000 ARG C 221 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9760 Ramachandran restraints generated. 4880 Oldfield, 0 Emsley, 4880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9760 Ramachandran restraints generated. 4880 Oldfield, 0 Emsley, 4880 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 294 residues out of total 3843 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 252 time to evaluate : 4.553 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 270 VAL cc_start: 0.9175 (OUTLIER) cc_final: 0.8823 (p) REVERT: D 138 GLU cc_start: 0.7686 (OUTLIER) cc_final: 0.7059 (tm-30) REVERT: G 108 ARG cc_start: 0.7831 (OUTLIER) cc_final: 0.7484 (mtm110) REVERT: G 130 ARG cc_start: 0.7631 (OUTLIER) cc_final: 0.6499 (mmt90) REVERT: H 69 PHE cc_start: 0.8089 (OUTLIER) cc_final: 0.7806 (t80) REVERT: L 30 ILE cc_start: 0.8947 (OUTLIER) cc_final: 0.8723 (pt) REVERT: N 32 ASP cc_start: 0.8362 (t70) cc_final: 0.8097 (t0) REVERT: P 21 MET cc_start: 0.8827 (OUTLIER) cc_final: 0.8037 (mpm) REVERT: P 50 GLN cc_start: 0.8026 (tp40) cc_final: 0.7734 (mm-40) REVERT: Q 74 PHE cc_start: 0.8944 (m-80) cc_final: 0.8677 (m-80) REVERT: R 80 PHE cc_start: 0.5768 (m-10) cc_final: 0.5372 (t80) REVERT: b 53 ILE cc_start: 0.9376 (mm) cc_final: 0.8965 (tp) outliers start: 42 outliers final: 25 residues processed: 287 average time/residue: 2.4728 time to fit residues: 895.1601 Evaluate side-chains 278 residues out of total 3843 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 246 time to evaluate : 4.540 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 ASP Chi-restraints excluded: chain A residue 498 GLU Chi-restraints excluded: chain B residue 70 ASP Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain B residue 479 HIS Chi-restraints excluded: chain C residue 358 ASP Chi-restraints excluded: chain D residue 138 GLU Chi-restraints excluded: chain E residue 59 ASP Chi-restraints excluded: chain E residue 64 CYS Chi-restraints excluded: chain E residue 71 ASP Chi-restraints excluded: chain F residue 148 THR Chi-restraints excluded: chain F residue 334 SER Chi-restraints excluded: chain F residue 363 ASP Chi-restraints excluded: chain G residue 108 ARG Chi-restraints excluded: chain G residue 130 ARG Chi-restraints excluded: chain G residue 143 GLU Chi-restraints excluded: chain H residue 25 THR Chi-restraints excluded: chain H residue 69 PHE Chi-restraints excluded: chain L residue 30 ILE Chi-restraints excluded: chain O residue 26 ILE Chi-restraints excluded: chain O residue 59 ILE Chi-restraints excluded: chain P residue 21 MET Chi-restraints excluded: chain S residue 15 ILE Chi-restraints excluded: chain S residue 55 THR Chi-restraints excluded: chain T residue 55 THR Chi-restraints excluded: chain a residue 111 LEU Chi-restraints excluded: chain a residue 187 LEU Chi-restraints excluded: chain a residue 211 GLN Chi-restraints excluded: chain d residue 14 ILE Chi-restraints excluded: chain d residue 30 MET Chi-restraints excluded: chain d residue 276 ARG Chi-restraints excluded: chain d residue 376 VAL 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: 6.9990 chunk 261 optimal weight: 1.9990 chunk 188 optimal weight: 0.3980 chunk 340 optimal weight: 5.9990 chunk 133 optimal weight: 0.7980 chunk 392 optimal weight: 4.9990 chunk 410 optimal weight: 0.7980 chunk 432 optimal weight: 4.9990 overall best weight: 1.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 208 ASN G 288 GLN ** b 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8499 moved from start: 0.1154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 37890 Z= 0.279 Angle : 0.545 8.515 51390 Z= 0.279 Chirality : 0.040 0.154 5966 Planarity : 0.004 0.060 6724 Dihedral : 6.972 114.730 5409 Min Nonbonded Distance : 1.695 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.75 % Favored : 97.23 % Rotamer: Outliers : 0.99 % Allowed : 13.62 % Favored : 85.39 % 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: 1.45 (0.12), residues: 4880 helix: 1.83 (0.10), residues: 2603 sheet: -0.50 (0.22), residues: 531 loop : 0.25 (0.16), residues: 1746 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP a 218 HIS 0.003 0.001 HIS F 97 PHE 0.026 0.001 PHE d 16 TYR 0.018 0.001 TYR a 145 ARG 0.015 0.000 ARG C 221 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9760 Ramachandran restraints generated. 4880 Oldfield, 0 Emsley, 4880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9760 Ramachandran restraints generated. 4880 Oldfield, 0 Emsley, 4880 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 293 residues out of total 3843 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 255 time to evaluate : 4.619 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 270 VAL cc_start: 0.9171 (OUTLIER) cc_final: 0.8817 (p) REVERT: D 138 GLU cc_start: 0.7678 (OUTLIER) cc_final: 0.7053 (tm-30) REVERT: G 108 ARG cc_start: 0.7849 (OUTLIER) cc_final: 0.7504 (mtm110) REVERT: G 130 ARG cc_start: 0.7680 (OUTLIER) cc_final: 0.6552 (mmt90) REVERT: N 32 ASP cc_start: 0.8355 (t70) cc_final: 0.8097 (t0) REVERT: P 21 MET cc_start: 0.8835 (OUTLIER) cc_final: 0.8139 (mpm) REVERT: P 50 GLN cc_start: 0.8020 (tp40) cc_final: 0.7730 (mm-40) REVERT: P 75 MET cc_start: 0.8383 (tmt) cc_final: 0.8102 (tmt) REVERT: Q 19 LEU cc_start: 0.9079 (mp) cc_final: 0.8830 (mp) REVERT: Q 74 PHE cc_start: 0.8966 (m-80) cc_final: 0.8709 (m-80) REVERT: R 65 GLU cc_start: 0.7097 (tm-30) cc_final: 0.6864 (tm-30) REVERT: R 80 PHE cc_start: 0.5762 (m-10) cc_final: 0.5364 (t80) REVERT: b 53 ILE cc_start: 0.9362 (mm) cc_final: 0.8952 (tp) outliers start: 38 outliers final: 24 residues processed: 288 average time/residue: 2.4853 time to fit residues: 891.1997 Evaluate side-chains 274 residues out of total 3843 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 245 time to evaluate : 4.543 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 ASP Chi-restraints excluded: chain A residue 498 GLU Chi-restraints excluded: chain B residue 70 ASP Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain C residue 358 ASP Chi-restraints excluded: chain D residue 138 GLU Chi-restraints excluded: chain E residue 59 ASP Chi-restraints excluded: chain E residue 64 CYS Chi-restraints excluded: chain E residue 71 ASP Chi-restraints excluded: chain F residue 148 THR Chi-restraints excluded: chain F residue 334 SER Chi-restraints excluded: chain F residue 363 ASP Chi-restraints excluded: chain G residue 108 ARG Chi-restraints excluded: chain G residue 130 ARG Chi-restraints excluded: chain G residue 143 GLU Chi-restraints excluded: chain H residue 25 THR Chi-restraints excluded: chain O residue 26 ILE Chi-restraints excluded: chain O residue 59 ILE Chi-restraints excluded: chain P residue 21 MET Chi-restraints excluded: chain S residue 15 ILE Chi-restraints excluded: chain S residue 55 THR Chi-restraints excluded: chain T residue 55 THR Chi-restraints excluded: chain a residue 111 LEU Chi-restraints excluded: chain a residue 187 LEU Chi-restraints excluded: chain a residue 211 GLN Chi-restraints excluded: chain d residue 14 ILE Chi-restraints excluded: chain d residue 264 GLU Chi-restraints excluded: chain d residue 276 ARG Chi-restraints excluded: chain d residue 376 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 483 random chunks: chunk 284 optimal weight: 1.9990 chunk 458 optimal weight: 6.9990 chunk 279 optimal weight: 2.9990 chunk 217 optimal weight: 1.9990 chunk 318 optimal weight: 2.9990 chunk 481 optimal weight: 4.9990 chunk 442 optimal weight: 0.4980 chunk 383 optimal weight: 0.0770 chunk 39 optimal weight: 2.9990 chunk 295 optimal weight: 0.9980 chunk 234 optimal weight: 0.0970 overall best weight: 0.7338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 505 ASN F 208 ASN G 288 GLN ** b 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8475 moved from start: 0.1173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 37890 Z= 0.179 Angle : 0.529 9.863 51390 Z= 0.266 Chirality : 0.040 0.146 5966 Planarity : 0.004 0.081 6724 Dihedral : 6.741 111.306 5409 Min Nonbonded Distance : 1.745 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.60 % Favored : 97.38 % Rotamer: Outliers : 0.75 % Allowed : 13.91 % Favored : 85.34 % 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: 1.68 (0.12), residues: 4880 helix: 2.01 (0.10), residues: 2595 sheet: -0.43 (0.22), residues: 531 loop : 0.39 (0.16), residues: 1754 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 193 HIS 0.002 0.001 HIS F 97 PHE 0.020 0.001 PHE O 69 TYR 0.018 0.001 TYR a 145 ARG 0.014 0.000 ARG C 221 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9760 Ramachandran restraints generated. 4880 Oldfield, 0 Emsley, 4880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9760 Ramachandran restraints generated. 4880 Oldfield, 0 Emsley, 4880 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 295 residues out of total 3843 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 266 time to evaluate : 4.585 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash 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: B 270 VAL cc_start: 0.9133 (OUTLIER) cc_final: 0.8775 (p) REVERT: D 138 GLU cc_start: 0.7597 (OUTLIER) cc_final: 0.7032 (tm-30) REVERT: E 335 ARG cc_start: 0.7837 (mmm160) cc_final: 0.7585 (mmm-85) REVERT: G 108 ARG cc_start: 0.7875 (OUTLIER) cc_final: 0.7520 (mtm110) REVERT: G 143 GLU cc_start: 0.8001 (OUTLIER) cc_final: 0.7640 (pm20) REVERT: N 32 ASP cc_start: 0.8305 (t70) cc_final: 0.8060 (t0) REVERT: P 21 MET cc_start: 0.8818 (OUTLIER) cc_final: 0.8027 (mpm) REVERT: P 50 GLN cc_start: 0.7992 (tp40) cc_final: 0.7698 (mm-40) REVERT: P 75 MET cc_start: 0.8352 (tmt) cc_final: 0.8063 (tmt) REVERT: Q 58 PHE cc_start: 0.7072 (t80) cc_final: 0.6800 (t80) REVERT: R 65 GLU cc_start: 0.7079 (tm-30) cc_final: 0.6861 (tm-30) REVERT: R 80 PHE cc_start: 0.5557 (m-10) cc_final: 0.5235 (t80) REVERT: b 53 ILE cc_start: 0.9345 (mm) cc_final: 0.8960 (tp) REVERT: b 101 ASP cc_start: 0.8595 (m-30) cc_final: 0.8340 (m-30) outliers start: 29 outliers final: 20 residues processed: 288 average time/residue: 2.4115 time to fit residues: 872.8319 Evaluate side-chains 282 residues out of total 3843 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 257 time to evaluate : 4.465 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 ASP Chi-restraints excluded: chain A residue 498 GLU Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain C residue 358 ASP Chi-restraints excluded: chain D residue 138 GLU Chi-restraints excluded: chain E residue 59 ASP Chi-restraints excluded: chain E residue 64 CYS Chi-restraints excluded: chain F residue 148 THR Chi-restraints excluded: chain G residue 108 ARG Chi-restraints excluded: chain G residue 143 GLU Chi-restraints excluded: chain G residue 193 MET Chi-restraints excluded: chain H residue 25 THR Chi-restraints excluded: chain O residue 26 ILE Chi-restraints excluded: chain O residue 59 ILE Chi-restraints excluded: chain P residue 21 MET Chi-restraints excluded: chain S residue 15 ILE Chi-restraints excluded: chain S residue 55 THR Chi-restraints excluded: chain T residue 55 THR Chi-restraints excluded: chain a residue 111 LEU Chi-restraints excluded: chain a residue 187 LEU Chi-restraints excluded: chain a residue 211 GLN Chi-restraints excluded: chain b residue 70 ASP Chi-restraints excluded: chain d residue 14 ILE Chi-restraints excluded: chain d residue 276 ARG Chi-restraints excluded: chain d residue 376 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 483 random chunks: chunk 304 optimal weight: 3.9990 chunk 408 optimal weight: 0.7980 chunk 117 optimal weight: 1.9990 chunk 353 optimal weight: 2.9990 chunk 56 optimal weight: 1.9990 chunk 106 optimal weight: 1.9990 chunk 383 optimal weight: 4.9990 chunk 160 optimal weight: 2.9990 chunk 394 optimal weight: 0.9990 chunk 48 optimal weight: 2.9990 chunk 70 optimal weight: 3.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 505 ASN F 208 ASN G 288 GLN ** b 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.079410 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2917 r_free = 0.2917 target = 0.056326 restraints weight = 297670.631| |-----------------------------------------------------------------------------| r_work (start): 0.2898 rms_B_bonded: 1.78 r_work: 0.2816 rms_B_bonded: 1.89 restraints_weight: 0.5000 r_work: 0.2711 rms_B_bonded: 3.29 restraints_weight: 0.2500 r_work (final): 0.2711 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2710 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2710 r_free = 0.2710 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2710 r_free = 0.2710 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2710 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8710 moved from start: 0.1185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 37890 Z= 0.280 Angle : 0.552 9.455 51390 Z= 0.280 Chirality : 0.040 0.153 5966 Planarity : 0.004 0.065 6724 Dihedral : 6.844 112.590 5409 Min Nonbonded Distance : 1.711 Molprobity Statistics. All-atom Clashscore : 9.06 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.69 % Favored : 97.29 % Rotamer: Outliers : 0.81 % Allowed : 14.06 % Favored : 85.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.90 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.58 (0.12), residues: 4880 helix: 1.92 (0.10), residues: 2605 sheet: -0.44 (0.22), residues: 531 loop : 0.33 (0.16), residues: 1744 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 193 HIS 0.003 0.001 HIS D 121 PHE 0.032 0.001 PHE Q 57 TYR 0.018 0.001 TYR a 145 ARG 0.020 0.000 ARG C 221 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 17338.82 seconds wall clock time: 300 minutes 21.23 seconds (18021.23 seconds total)