Starting phenix.real_space_refine on Sun Feb 18 18:55:39 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7njk_12377/02_2024/7njk_12377_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7njk_12377/02_2024/7njk_12377.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.52 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7njk_12377/02_2024/7njk_12377.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7njk_12377/02_2024/7njk_12377.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7njk_12377/02_2024/7njk_12377_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7njk_12377/02_2024/7njk_12377_trim_updated.pdb" } resolution = 2.52 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 23577 2.51 5 N 6406 2.21 5 O 7180 1.98 5 H 37359 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "D ASP 71": "OD1" <-> "OD2" Residue "D TYR 111": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D ASP 199": "OD1" <-> "OD2" Residue "E PHE 456": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F GLU 52": "OE1" <-> "OE2" Residue "F GLU 78": "OE1" <-> "OE2" Residue "F ASP 199": "OD1" <-> "OD2" Residue "F ASP 384": "OD1" <-> "OD2" Residue "F GLU 437": "OE1" <-> "OE2" Residue "G TYR 92": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G TYR 222": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G GLU 225": "OE1" <-> "OE2" Residue "H PHE 86": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H ASP 102": "OD1" <-> "OD2" Residue "L ASP 32": "OD1" <-> "OD2" Residue "O GLU 48": "OE1" <-> "OE2" Residue "P ASP 32": "OD1" <-> "OD2" Residue "P PHE 74": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "Q PHE 69": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "R ASP 32": "OD1" <-> "OD2" Residue "a TYR 145": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "a TYR 209": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 74650 Number of models: 1 Model: "" Number of chains: 31 Chain: "A" Number of atoms: 7691 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 507, 7670 Classifications: {'peptide': 507} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 19, 'TRANS': 485} Chain breaks: 2 Conformer: "B" Number of residues, atoms: 507, 7670 Classifications: {'peptide': 507} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 19, 'TRANS': 485} Chain breaks: 2 bond proxies already assigned to first conformer: 7705 Chain: "B" Number of atoms: 7628 Number of conformers: 1 Conformer: "" Number of residues, atoms: 504, 7628 Classifications: {'peptide': 504} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 19, 'TRANS': 482} Chain breaks: 2 Chain: "C" Number of atoms: 8041 Number of conformers: 1 Conformer: "" Number of residues, atoms: 531, 8041 Classifications: {'peptide': 531} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 22, 'TRANS': 506} Chain breaks: 2 Chain: "D" Number of atoms: 7162 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 468, 7144 Classifications: {'peptide': 468} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 22, 'TRANS': 443} Conformer: "B" Number of residues, atoms: 468, 7144 Classifications: {'peptide': 468} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 22, 'TRANS': 443} bond proxies already assigned to first conformer: 7190 Chain: "E" Number of atoms: 7087 Number of conformers: 1 Conformer: "" Number of residues, atoms: 464, 7087 Classifications: {'peptide': 464} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 22, 'TRANS': 439} Chain: "F" Number of atoms: 7166 Number of conformers: 1 Conformer: "" Number of residues, atoms: 469, 7166 Classifications: {'peptide': 469} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 22, 'TRANS': 444} Chain: "G" Number of atoms: 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: 1802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 1802 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 3, 'TRANS': 114} Chain: "L" Number of atoms: 1192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 1192 Classifications: {'peptide': 84} Link IDs: {'PTRANS': 4, 'TRANS': 79} Chain: "M" Number of atoms: 1192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 1192 Classifications: {'peptide': 84} Link IDs: {'PTRANS': 4, 'TRANS': 79} Chain: "N" Number of atoms: 1192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 1192 Classifications: {'peptide': 84} Link IDs: {'PTRANS': 4, 'TRANS': 79} Chain: "O" Number of atoms: 1192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 1192 Classifications: {'peptide': 84} Link IDs: {'PTRANS': 4, 'TRANS': 79} Chain: "P" Number of atoms: 1192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 1192 Classifications: {'peptide': 84} Link IDs: {'PTRANS': 4, 'TRANS': 79} Chain: "Q" Number of atoms: 1192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 1192 Classifications: {'peptide': 84} Link IDs: {'PTRANS': 4, 'TRANS': 79} Chain: "R" Number of atoms: 1192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 1192 Classifications: {'peptide': 84} Link IDs: {'PTRANS': 4, 'TRANS': 79} Chain: "S" Number of atoms: 1192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 1192 Classifications: {'peptide': 84} Link IDs: {'PTRANS': 4, 'TRANS': 79} Chain: "T" Number of atoms: 1192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 1192 Classifications: {'peptide': 84} Link IDs: {'PTRANS': 4, 'TRANS': 79} Chain: "a" Number of atoms: 3767 Number of conformers: 1 Conformer: "" Number of residues, atoms: 238, 3767 Classifications: {'peptide': 238} Link IDs: {'PTRANS': 10, 'TRANS': 227} Chain: "b" Number of atoms: 2172 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 2172 Classifications: {'peptide': 145} Link IDs: {'PTRANS': 3, 'TRANS': 141} Chain: "d" Number of atoms: 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} Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N AGLN D 453 " occ=0.50 ... (32 atoms not shown) pdb="HE22BGLN D 453 " occ=0.50 Time building chain proxies: 28.48, per 1000 atoms: 0.38 Number of scatterers: 74650 At special positions: 0 Unit cell: (136.95, 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 7180 8.00 N 6406 7.00 C 23577 6.00 H 37359 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: 51.37 Conformation dependent library (CDL) restraints added in 6.9 seconds 9764 Ramachandran restraints generated. 4882 Oldfield, 0 Emsley, 4882 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: 185 helices and 27 sheets defined 55.3% alpha, 9.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 8.98 Creating SS restraints... Processing helix chain 'A' and resid 9 through 19 removed outlier: 3.763A pdb=" N ILE A 15 " --> pdb=" O GLU A 12 " (cutoff:3.500A) removed outlier: 4.632A pdb=" N GLU A 16 " --> pdb=" O GLY A 13 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N VAL A 19 " --> pdb=" O GLU A 16 " (cutoff:3.500A) Processing helix chain 'A' and resid 82 through 84 No H-bonds generated for 'chain 'A' and resid 82 through 84' Processing helix chain 'A' and resid 104 through 106 No H-bonds generated for 'chain 'A' and resid 104 through 106' Processing helix chain 'A' and resid 154 through 159 Processing helix chain 'A' and resid 178 through 194 removed outlier: 3.674A pdb=" N GLN A 189 " --> pdb=" O THR A 185 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N ARG A 190 " --> pdb=" O ILE A 186 " (cutoff:3.500A) removed outlier: 5.041A pdb=" N GLU A 191 " --> pdb=" O LEU A 187 " (cutoff:3.500A) removed outlier: 4.677A 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: 3.656A pdb=" N TRP A 260 " --> pdb=" O ILE A 256 " (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: 3.644A pdb=" N LEU A 308 " --> pdb=" O LEU A 304 " (cutoff:3.500A) removed outlier: 3.839A 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 403 Processing helix chain 'A' and resid 415 through 431 Processing helix chain 'A' and resid 441 through 452 Processing helix chain 'A' and resid 461 through 477 removed outlier: 4.922A pdb=" N GLN A 465 " --> pdb=" O GLU A 462 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N LEU A 472 " --> pdb=" O SER A 469 " (cutoff:3.500A) Processing helix chain 'A' and resid 481 through 489 Processing helix chain 'A' and resid 494 through 508 Processing helix chain 'B' and resid 10 through 21 removed outlier: 3.913A pdb=" N ASP B 17 " --> pdb=" O GLY B 13 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 84 No H-bonds generated for 'chain 'B' and resid 82 through 84' Processing helix chain 'B' and resid 104 through 106 No H-bonds generated for 'chain 'B' and resid 104 through 106' Processing helix chain 'B' and resid 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: 3.889A pdb=" N GLN B 189 " --> pdb=" O THR B 185 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N ARG B 190 " --> pdb=" O ILE B 186 " (cutoff:3.500A) removed outlier: 5.350A pdb=" N GLU B 191 " --> pdb=" O LEU B 187 " (cutoff:3.500A) removed outlier: 4.926A 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: 3.677A pdb=" N TRP B 260 " --> pdb=" O ILE B 256 " (cutoff:3.500A) removed outlier: 3.552A 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: 3.653A pdb=" N LEU B 308 " --> pdb=" O LEU B 304 " (cutoff:3.500A) removed outlier: 3.705A 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 346 Processing helix chain 'B' and resid 357 through 361 Processing helix chain 'B' and resid 384 through 389 Processing helix chain 'B' and resid 393 through 405 removed outlier: 3.661A pdb=" N GLU B 402 " --> pdb=" O SER B 398 " (cutoff:3.500A) Processing helix chain 'B' and resid 415 through 431 Processing helix chain 'B' and resid 441 through 453 Processing helix chain 'B' and resid 461 through 477 removed outlier: 5.113A pdb=" N GLN B 465 " --> pdb=" O GLU B 462 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N LEU B 472 " --> pdb=" O SER B 469 " (cutoff:3.500A) Processing helix chain 'B' and resid 481 through 489 Processing helix chain 'B' and resid 494 through 510 Processing helix chain 'C' and resid 8 through 21 Processing helix chain 'C' and resid 82 through 84 No H-bonds generated for 'chain 'C' and resid 82 through 84' Processing helix chain 'C' and resid 104 through 106 No H-bonds generated for 'chain 'C' and resid 104 through 106' Processing helix chain 'C' and resid 139 through 141 No H-bonds generated for 'chain 'C' and resid 139 through 141' Processing helix chain 'C' and resid 154 through 159 removed outlier: 3.615A pdb=" N MET C 159 " --> pdb=" O ALA C 155 " (cutoff:3.500A) Processing helix chain 'C' and resid 178 through 195 removed outlier: 3.725A pdb=" N GLN C 189 " --> pdb=" O THR C 185 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N ARG C 190 " --> pdb=" O ILE C 186 " (cutoff:3.500A) removed outlier: 5.354A pdb=" N GLU C 191 " --> pdb=" O LEU C 187 " (cutoff:3.500A) removed outlier: 5.009A pdb=" N ALA C 192 " --> pdb=" O ASN C 188 " (cutoff:3.500A) Processing helix chain 'C' and resid 213 through 225 Processing helix chain 'C' and resid 228 through 231 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: 3.609A pdb=" N ASN C 263 " --> pdb=" O HIS C 259 " (cutoff:3.500A) Processing helix chain 'C' and resid 274 through 287 Processing helix chain 'C' and resid 294 through 296 No H-bonds generated for 'chain 'C' and resid 294 through 296' Processing helix chain 'C' and resid 301 through 309 removed outlier: 3.590A pdb=" N HIS C 305 " --> pdb=" O VAL C 301 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N LEU C 308 " --> pdb=" O LEU C 304 " (cutoff:3.500A) Processing helix chain 'C' and resid 317 through 319 No H-bonds generated for 'chain 'C' and resid 317 through 319' Processing helix chain 'C' and resid 340 through 346 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: 4.832A pdb=" N GLN C 465 " --> pdb=" O GLU C 462 " (cutoff:3.500A) Processing helix chain 'C' and resid 481 through 489 Processing helix chain 'C' and resid 494 through 510 removed outlier: 3.793A pdb=" N LYS C 509 " --> pdb=" O ASN C 505 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N GLY C 510 " --> pdb=" O GLU C 506 " (cutoff:3.500A) Processing helix chain 'D' and resid 92 through 94 No H-bonds generated for 'chain 'D' and resid 92 through 94' Processing helix chain 'D' and resid 127 through 129 No H-bonds generated for 'chain 'D' and resid 127 through 129' Processing helix chain 'D' and resid 142 through 147 Processing helix chain 'D' and resid 166 through 177 Processing helix chain 'D' and resid 194 through 207 Processing helix chain 'D' and resid 210 through 212 No H-bonds generated for 'chain 'D' and resid 210 through 212' Processing helix chain 'D' and resid 224 through 243 removed outlier: 4.821A pdb=" N ALA D 231 " --> pdb=" O ARG D 227 " (cutoff:3.500A) removed outlier: 4.749A pdb=" N LEU D 232 " --> pdb=" O MET D 228 " (cutoff:3.500A) Processing helix chain 'D' and resid 256 through 265 Processing helix chain 'D' and resid 276 through 278 No H-bonds generated for 'chain 'D' and resid 276 through 278' Processing helix chain 'D' and resid 283 through 291 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: 4.367A pdb=" N ALA D 325 " --> pdb=" O ALA D 321 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N HIS D 326 " --> pdb=" O THR D 322 " (cutoff:3.500A) Processing helix chain 'D' and resid 335 through 340 Processing helix chain 'D' and resid 358 through 361 No H-bonds generated for 'chain 'D' and resid 358 through 361' Processing helix chain 'D' and resid 363 through 389 removed outlier: 4.707A pdb=" N ASP D 384 " --> pdb=" O LYS D 380 " (cutoff:3.500A) removed outlier: 4.797A pdb=" N ILE D 385 " --> pdb=" O ASP D 381 " (cutoff:3.500A) Processing helix chain 'D' and resid 391 through 393 No H-bonds generated for 'chain 'D' and resid 391 through 393' Processing helix chain 'D' and resid 396 through 412 Processing helix chain 'D' and resid 417 through 423 removed outlier: 3.653A pdb=" N GLU D 420 " --> pdb=" O MET D 417 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N GLN D 421 " --> pdb=" O ALA D 418 " (cutoff:3.500A) Processing helix chain 'D' and resid 432 through 444 Processing helix chain 'D' and resid 452 through 455 Processing helix chain 'D' and resid 461 through 470 Processing helix chain 'E' and resid 26 through 28 No H-bonds generated for 'chain 'E' and resid 26 through 28' 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 207 Processing helix chain 'E' and resid 210 through 212 No H-bonds generated for 'chain 'E' and resid 210 through 212' Processing helix chain 'E' and resid 224 through 243 removed outlier: 4.953A pdb=" N ALA E 231 " --> pdb=" O ARG E 227 " (cutoff:3.500A) removed outlier: 4.866A pdb=" N LEU E 232 " --> pdb=" O MET E 228 " (cutoff:3.500A) Processing helix chain 'E' and resid 256 through 269 Processing helix chain 'E' and resid 276 through 278 No H-bonds generated for 'chain 'E' and resid 276 through 278' Processing helix chain 'E' and resid 283 through 293 removed outlier: 4.024A pdb=" N ARG E 293 " --> pdb=" O GLU E 289 " (cutoff:3.500A) Processing helix chain 'E' and resid 311 through 313 No H-bonds generated for 'chain 'E' and resid 311 through 313' Processing helix chain 'E' and resid 318 through 324 Processing helix chain 'E' and resid 335 through 340 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: 4.333A pdb=" N ASP E 384 " --> pdb=" O LYS E 380 " (cutoff:3.500A) removed outlier: 4.693A 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 412 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 92 through 94 No H-bonds generated for 'chain 'F' and resid 92 through 94' Processing helix chain 'F' and resid 127 through 129 No H-bonds generated for 'chain 'F' and resid 127 through 129' Processing helix chain 'F' and resid 142 through 147 Processing helix chain 'F' and resid 166 through 177 Processing helix chain 'F' and resid 194 through 207 Processing helix chain 'F' and resid 210 through 212 No H-bonds generated for 'chain 'F' and resid 210 through 212' Processing helix chain 'F' and resid 224 through 243 removed outlier: 5.126A pdb=" N ALA F 231 " --> pdb=" O ARG F 227 " (cutoff:3.500A) removed outlier: 4.937A 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 removed outlier: 3.987A pdb=" N ARG F 293 " --> pdb=" O GLU F 289 " (cutoff:3.500A) 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: 4.520A pdb=" N ALA F 325 " --> pdb=" O ALA F 321 " (cutoff:3.500A) removed outlier: 4.640A pdb=" N HIS F 326 " --> pdb=" O THR F 322 " (cutoff:3.500A) Processing helix chain 'F' and resid 335 through 339 Processing helix chain 'F' and resid 358 through 361 No H-bonds generated for 'chain 'F' and resid 358 through 361' Processing helix chain 'F' and resid 363 through 389 removed outlier: 4.531A pdb=" N ASP F 384 " --> pdb=" O LYS F 380 " (cutoff:3.500A) removed outlier: 4.924A pdb=" N ILE F 385 " --> pdb=" O ASP F 381 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N ILE F 388 " --> pdb=" O ASP F 384 " (cutoff:3.500A) Processing helix chain 'F' and resid 396 through 412 Processing helix chain 'F' and resid 417 through 423 removed outlier: 4.197A pdb=" N GLN F 421 " --> pdb=" O ALA F 418 " (cutoff:3.500A) Processing helix chain 'F' and resid 432 through 443 Processing helix chain 'F' and resid 452 through 455 Processing helix chain 'F' and resid 461 through 471 Processing helix chain 'G' and resid 4 through 60 removed outlier: 3.594A pdb=" N ALA G 34 " --> pdb=" O THR G 30 " (cutoff:3.500A) Proline residue: G 45 - end of helix Processing helix chain 'G' and resid 66 through 68 No H-bonds generated for 'chain 'G' and resid 66 through 68' Processing helix chain 'G' and resid 92 through 109 Processing helix chain 'G' and resid 121 through 129 Processing helix chain 'G' and resid 147 through 163 Processing helix chain 'G' and resid 173 through 175 No H-bonds generated for 'chain 'G' and resid 173 through 175' Processing helix chain 'G' and resid 228 through 302 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 98 Processing helix chain 'H' and resid 104 through 117 Processing helix chain 'L' and resid 5 through 45 Processing helix chain 'L' and resid 47 through 80 removed outlier: 3.966A pdb=" N GLN L 50 " --> pdb=" O PRO L 47 " (cutoff:3.500A) removed outlier: 5.571A pdb=" N GLY L 51 " --> pdb=" O GLU L 48 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N THR L 55 " --> pdb=" O ARG L 52 " (cutoff:3.500A) Proline residue: L 56 - end of helix removed outlier: 3.672A pdb=" N VAL L 61 " --> pdb=" O PHE L 58 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N GLY L 62 " --> pdb=" O ILE L 59 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N ALA L 66 " --> pdb=" O LEU L 63 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N PHE L 69 " --> pdb=" O ALA L 66 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N PHE L 74 " --> pdb=" O ASN L 71 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N VAL L 79 " --> pdb=" O ALA L 76 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N PHE L 80 " --> pdb=" O LEU L 77 " (cutoff:3.500A) Processing helix chain 'M' and resid 5 through 45 Processing helix chain 'M' and resid 47 through 80 removed outlier: 3.873A pdb=" N GLN M 50 " --> pdb=" O PRO M 47 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N GLY M 51 " --> pdb=" O GLU M 48 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N PHE M 54 " --> pdb=" O GLY M 51 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N THR M 55 " --> pdb=" O ARG M 52 " (cutoff:3.500A) Proline residue: M 56 - end of helix removed outlier: 3.722A pdb=" N VAL M 61 " --> pdb=" O PHE M 58 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N LEU M 63 " --> pdb=" O THR M 60 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N ALA M 67 " --> pdb=" O VAL M 64 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N ILE M 70 " --> pdb=" O ALA M 67 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N VAL M 79 " --> pdb=" O ALA M 76 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N PHE M 80 " --> pdb=" O LEU M 77 " (cutoff:3.500A) Processing helix chain 'N' and resid 5 through 45 Processing helix chain 'N' and resid 47 through 49 No H-bonds generated for 'chain 'N' and resid 47 through 49' Processing helix chain 'N' and resid 52 through 79 removed outlier: 3.713A pdb=" N THR N 55 " --> pdb=" O ARG N 52 " (cutoff:3.500A) Proline residue: N 56 - end of helix removed outlier: 4.120A pdb=" N GLY N 62 " --> pdb=" O ILE N 59 " (cutoff:3.500A) removed outlier: 4.624A pdb=" N GLU N 65 " --> pdb=" O GLY N 62 " (cutoff:3.500A) Processing helix chain 'O' and resid 5 through 45 Processing helix chain 'O' and resid 47 through 79 removed outlier: 4.085A pdb=" N LEU O 53 " --> pdb=" O GLN O 50 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N PHE O 54 " --> pdb=" O GLY O 51 " (cutoff:3.500A) Proline residue: O 56 - end of helix removed outlier: 4.001A pdb=" N VAL O 61 " --> pdb=" O PHE O 58 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N VAL O 64 " --> pdb=" O VAL O 61 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N GLU O 65 " --> pdb=" O GLY O 62 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ALA O 66 " --> pdb=" O LEU O 63 " (cutoff:3.500A) Processing helix chain 'P' and resid 5 through 45 Processing helix chain 'P' and resid 47 through 79 removed outlier: 3.860A pdb=" N GLY P 51 " --> pdb=" O GLU P 48 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N LEU P 53 " --> pdb=" O GLN P 50 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N PHE P 54 " --> pdb=" O GLY P 51 " (cutoff:3.500A) Proline residue: P 56 - end of helix removed outlier: 3.728A pdb=" N VAL P 64 " --> pdb=" O VAL P 61 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N GLU P 65 " --> pdb=" O GLY P 62 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N ALA P 66 " --> pdb=" O LEU P 63 " (cutoff:3.500A) Processing helix chain 'Q' and resid 6 through 45 Processing helix chain 'Q' and resid 47 through 79 removed outlier: 4.472A pdb=" N GLY Q 51 " --> pdb=" O GLU Q 48 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N PHE Q 54 " --> pdb=" O GLY Q 51 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N THR Q 55 " --> pdb=" O ARG Q 52 " (cutoff:3.500A) Proline residue: Q 56 - end of helix removed outlier: 4.046A pdb=" N VAL Q 61 " --> pdb=" O PHE Q 58 " (cutoff:3.500A) Processing helix chain 'R' and resid 5 through 45 Processing helix chain 'R' and resid 47 through 80 removed outlier: 3.682A pdb=" N GLN R 50 " --> pdb=" O PRO R 47 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N GLY R 51 " --> pdb=" O GLU R 48 " (cutoff:3.500A) Proline residue: R 56 - end of helix removed outlier: 3.537A pdb=" N VAL R 79 " --> pdb=" O ALA R 76 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N PHE R 80 " --> pdb=" O LEU R 77 " (cutoff:3.500A) Processing helix chain 'S' and resid 5 through 45 Processing helix chain 'S' and resid 47 through 79 removed outlier: 3.835A pdb=" N GLN S 50 " --> pdb=" O PRO S 47 " (cutoff:3.500A) removed outlier: 4.859A pdb=" N GLY S 51 " --> pdb=" O GLU S 48 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N THR S 55 " --> pdb=" O ARG S 52 " (cutoff:3.500A) Proline residue: S 56 - end of helix removed outlier: 4.000A pdb=" N GLU S 65 " --> pdb=" O GLY S 62 " (cutoff:3.500A) removed outlier: 4.938A 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 80 removed outlier: 4.705A pdb=" N GLY T 51 " --> pdb=" O GLU T 48 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N THR T 55 " --> pdb=" O ARG T 52 " (cutoff:3.500A) Proline residue: T 56 - end of helix removed outlier: 3.914A pdb=" N GLY T 62 " --> pdb=" O ILE T 59 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N GLU T 65 " --> pdb=" O GLY T 62 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N ALA T 66 " --> pdb=" O LEU T 63 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N PHE T 80 " --> pdb=" O LEU T 77 " (cutoff:3.500A) Processing helix chain 'a' and resid 29 through 50 Processing helix chain 'a' and resid 61 through 80 Processing helix chain 'a' and resid 88 through 108 removed outlier: 4.046A pdb=" N ALA a 107 " --> pdb=" O SER a 103 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N VAL a 108 " --> pdb=" O ASN a 104 " (cutoff:3.500A) Processing helix chain 'a' and resid 127 through 129 No H-bonds generated for 'chain 'a' and resid 127 through 129' Processing helix chain 'a' and resid 131 through 153 Processing helix chain 'a' and resid 155 through 164 Proline residue: a 159 - end of helix Processing helix chain 'a' and resid 168 through 205 Proline residue: a 172 - end of helix removed outlier: 3.840A pdb=" N ILE a 175 " --> pdb=" O PRO a 172 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N LYS a 181 " --> pdb=" O GLU a 178 " (cutoff:3.500A) Proline residue: a 182 - end of helix removed outlier: 3.882A pdb=" N LEU a 187 " --> pdb=" O SER a 184 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N ARG a 188 " --> pdb=" O LEU a 185 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N GLY a 191 " --> pdb=" O ARG a 188 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N ALA a 195 " --> pdb=" O ASN a 192 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N LEU a 199 " --> pdb=" O GLY a 196 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N VAL a 200 " --> pdb=" O GLY a 197 " (cutoff:3.500A) Processing helix chain 'a' and resid 208 through 244 removed outlier: 3.806A pdb=" N TRP a 212 " --> pdb=" O TRP a 208 " (cutoff:3.500A) removed outlier: 5.997A pdb=" N PHE a 213 " --> pdb=" O TYR a 209 " (cutoff:3.500A) Proline residue: a 214 - end of helix removed outlier: 3.713A pdb=" N PHE a 224 " --> pdb=" O THR a 220 " (cutoff:3.500A) Processing helix chain 'b' and resid 29 through 48 removed outlier: 3.691A pdb=" N VAL b 34 " --> pdb=" O PHE b 31 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N ILE b 40 " --> pdb=" O ILE b 37 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N SER b 46 " --> pdb=" O GLY b 43 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N TRP b 48 " --> pdb=" O ILE b 45 " (cutoff:3.500A) Processing helix chain 'b' and resid 50 through 160 removed outlier: 4.836A pdb=" N SER b 146 " --> pdb=" O SER b 142 " (cutoff:3.500A) removed outlier: 5.333A pdb=" N SER b 147 " --> pdb=" O GLY b 143 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N VAL b 148 " --> pdb=" O LEU b 144 " (cutoff:3.500A) removed outlier: 4.976A pdb=" N ASP b 149 " --> pdb=" O GLU b 145 " (cutoff:3.500A) removed outlier: 4.733A 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 136 Processing helix chain 'd' and resid 140 through 155 Processing helix chain 'd' and resid 174 through 192 removed outlier: 3.887A pdb=" N GLY d 192 " --> pdb=" O ASP d 188 " (cutoff:3.500A) Processing helix chain 'd' and resid 196 through 215 Processing helix chain 'd' and resid 217 through 224 Processing helix chain 'd' and resid 231 through 241 Processing helix chain 'd' and resid 247 through 258 Processing helix chain 'd' and resid 264 through 286 Processing helix chain 'd' and resid 289 through 305 Processing helix chain 'd' and resid 307 through 313 Processing helix chain 'd' and resid 320 through 330 Processing helix chain 'd' and resid 339 through 350 Processing helix chain 'd' and resid 357 through 372 removed outlier: 4.083A pdb=" N ARG d 372 " --> pdb=" O ALA d 368 " (cutoff:3.500A) Processing helix chain 'd' and resid 387 through 401 Processing helix chain 'd' and resid 413 through 415 No H-bonds generated for 'chain 'd' and resid 413 through 415' Processing helix chain 'd' and resid 432 through 441 Processing sheet with id= A, first strand: chain 'A' and resid 31 through 33 removed outlier: 6.415A pdb=" N GLY A 75 " --> pdb=" O LEU A 67 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ASP A 36 " --> pdb=" O HIS A 43 " (cutoff:3.500A) removed outlier: 6.123A pdb=" N GLU A 45 " --> pdb=" O VAL A 34 " (cutoff:3.500A) removed outlier: 5.582A 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: 6.533A pdb=" N LEU A 169 " --> pdb=" O CYS A 353 " (cutoff:3.500A) removed outlier: 7.320A pdb=" N LEU A 355 " --> pdb=" O LEU A 169 " (cutoff:3.500A) removed outlier: 6.644A 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: 6.576A pdb=" N CYS A 204 " --> pdb=" O THR A 233 " (cutoff:3.500A) removed outlier: 7.705A pdb=" N VAL A 235 " --> pdb=" O CYS A 204 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N TYR A 206 " --> pdb=" O VAL A 235 " (cutoff:3.500A) removed outlier: 7.629A pdb=" N ALA A 237 " --> pdb=" O TYR A 206 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N ALA A 208 " --> pdb=" O ALA A 237 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N SER A 323 " --> pdb=" O VAL A 267 " (cutoff:3.500A) removed outlier: 7.613A pdb=" N ILE A 269 " --> pdb=" O SER A 323 " (cutoff:3.500A) removed outlier: 6.202A pdb=" N THR A 325 " --> pdb=" O ILE A 269 " (cutoff:3.500A) removed outlier: 7.618A pdb=" N PHE A 271 " --> pdb=" O THR A 325 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N LEU A 327 " --> pdb=" O PHE A 271 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 31 through 33 removed outlier: 4.187A pdb=" N LEU B 63 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N GLY B 75 " --> pdb=" O LEU B 67 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ASP B 36 " --> pdb=" O HIS B 43 " (cutoff:3.500A) removed outlier: 6.121A pdb=" N GLU B 45 " --> pdb=" O VAL B 34 " (cutoff:3.500A) removed outlier: 5.625A 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: 6.526A pdb=" N LEU B 169 " --> pdb=" O CYS B 353 " (cutoff:3.500A) removed outlier: 7.118A pdb=" N LEU B 355 " --> pdb=" O LEU B 169 " (cutoff:3.500A) removed outlier: 6.958A 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: 6.608A pdb=" N CYS B 204 " --> pdb=" O THR B 233 " (cutoff:3.500A) removed outlier: 7.822A pdb=" N VAL B 235 " --> pdb=" O CYS B 204 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N TYR B 206 " --> pdb=" O VAL B 235 " (cutoff:3.500A) removed outlier: 7.443A pdb=" N ALA B 237 " --> pdb=" O TYR B 206 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N ALA B 208 " --> pdb=" O ALA B 237 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N SER B 323 " --> pdb=" O VAL B 267 " (cutoff:3.500A) removed outlier: 7.495A pdb=" N ILE B 269 " --> pdb=" O SER B 323 " (cutoff:3.500A) removed outlier: 6.177A pdb=" N THR B 325 " --> pdb=" O ILE B 269 " (cutoff:3.500A) removed outlier: 7.612A pdb=" N PHE B 271 " --> pdb=" O THR B 325 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N LEU B 327 " --> pdb=" O PHE B 271 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'C' and resid 90 through 92 removed outlier: 6.706A pdb=" N HIS C 43 " --> pdb=" O ILE C 35 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N ALA C 37 " --> pdb=" O ILE C 41 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N ILE C 41 " --> pdb=" O ALA C 37 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N VAL C 77 " --> pdb=" O ALA C 66 " (cutoff:3.500A) removed outlier: 5.840A pdb=" N ALA C 66 " --> pdb=" O VAL C 77 " (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: 6.377A pdb=" N LEU C 169 " --> pdb=" O CYS C 353 " (cutoff:3.500A) removed outlier: 7.273A pdb=" N LEU C 355 " --> pdb=" O LEU C 169 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N ILE C 171 " --> pdb=" O LEU C 355 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'C' and resid 232 through 237 removed outlier: 8.588A pdb=" N THR C 233 " --> pdb=" O VAL C 202 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N CYS C 204 " --> pdb=" O THR C 233 " (cutoff:3.500A) removed outlier: 7.740A pdb=" N VAL C 235 " --> pdb=" O CYS C 204 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N TYR C 206 " --> pdb=" O VAL C 235 " (cutoff:3.500A) removed outlier: 7.381A pdb=" N ALA C 237 " --> pdb=" O TYR C 206 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N ALA C 208 " --> pdb=" O ALA C 237 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N HIS C 266 " --> pdb=" O ARG C 203 " (cutoff:3.500A) removed outlier: 7.994A pdb=" N VAL C 205 " --> pdb=" O HIS C 266 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N LEU C 268 " --> pdb=" O VAL C 205 " (cutoff:3.500A) removed outlier: 7.491A pdb=" N VAL C 207 " --> pdb=" O LEU C 268 " (cutoff:3.500A) removed outlier: 6.201A pdb=" N VAL C 270 " --> pdb=" O VAL C 207 " (cutoff:3.500A) removed outlier: 7.249A pdb=" N ILE C 209 " --> pdb=" O VAL C 270 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N ASP C 272 " --> pdb=" O ILE C 209 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N SER C 323 " --> pdb=" O VAL C 267 " (cutoff:3.500A) removed outlier: 7.731A pdb=" N ILE C 269 " --> pdb=" O SER C 323 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N THR C 325 " --> pdb=" O ILE C 269 " (cutoff:3.500A) removed outlier: 7.611A pdb=" N PHE C 271 " --> pdb=" O THR C 325 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N LEU C 327 " --> pdb=" O PHE C 271 " (cutoff:3.500A) No H-bonds generated for sheet with id= L Processing sheet with id= M, first strand: chain 'D' and resid 11 through 16 removed outlier: 6.529A pdb=" N ASP D 21 " --> pdb=" O VAL D 13 " (cutoff:3.500A) removed outlier: 4.681A pdb=" N ILE D 15 " --> pdb=" O VAL D 19 " (cutoff:3.500A) removed outlier: 7.123A pdb=" N VAL D 19 " --> pdb=" O ILE D 15 " (cutoff:3.500A) removed outlier: 6.197A pdb=" N ILE D 65 " --> pdb=" O VAL D 53 " (cutoff:3.500A) removed outlier: 5.714A 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: 7.327A pdb=" N ILE D 156 " --> pdb=" O ILE D 302 " (cutoff:3.500A) removed outlier: 6.188A pdb=" N SER D 304 " --> pdb=" O ILE D 156 " (cutoff:3.500A) removed outlier: 7.884A pdb=" N LEU D 158 " --> pdb=" O SER D 304 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N GLN D 306 " --> pdb=" O LEU D 158 " (cutoff:3.500A) removed outlier: 7.938A pdb=" N GLY D 160 " --> pdb=" O GLN D 306 " (cutoff:3.500A) removed outlier: 6.150A pdb=" N VAL D 308 " --> pdb=" O GLY D 160 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N VAL D 249 " --> pdb=" O THR D 303 " (cutoff:3.500A) removed outlier: 7.740A pdb=" N MET D 305 " --> pdb=" O VAL D 249 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N LEU D 251 " --> pdb=" O MET D 305 " (cutoff:3.500A) removed outlier: 7.688A pdb=" N ALA D 307 " --> pdb=" O LEU D 251 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N ILE D 253 " --> pdb=" O ALA D 307 " (cutoff:3.500A) removed outlier: 8.118A pdb=" N TYR D 309 " --> pdb=" O ILE D 253 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N THR D 184 " --> pdb=" O LEU D 250 " (cutoff:3.500A) removed outlier: 7.932A pdb=" N PHE D 252 " --> pdb=" O THR D 184 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N VAL D 186 " --> pdb=" O PHE D 252 " (cutoff:3.500A) removed outlier: 7.966A pdb=" N ASP D 254 " --> pdb=" O VAL D 186 " (cutoff:3.500A) removed outlier: 6.231A 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: 6.535A pdb=" N ASP E 21 " --> pdb=" O VAL E 13 " (cutoff:3.500A) removed outlier: 4.563A pdb=" N ILE E 15 " --> pdb=" O VAL E 19 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N VAL E 19 " --> pdb=" O ILE E 15 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N ILE E 65 " --> pdb=" O VAL E 53 " (cutoff:3.500A) removed outlier: 5.615A 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: 8.504A pdb=" N ILE E 156 " --> pdb=" O ILE E 302 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N SER E 304 " --> pdb=" O ILE E 156 " (cutoff:3.500A) removed outlier: 7.439A pdb=" N LEU E 158 " --> pdb=" O SER E 304 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N GLN E 306 " --> pdb=" O LEU E 158 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N VAL E 249 " --> pdb=" O THR E 303 " (cutoff:3.500A) removed outlier: 7.897A pdb=" N MET E 305 " --> pdb=" O VAL E 249 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N LEU E 251 " --> pdb=" O MET E 305 " (cutoff:3.500A) removed outlier: 7.912A pdb=" N ALA E 307 " --> pdb=" O LEU E 251 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N ILE E 253 " --> pdb=" O ALA E 307 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N THR E 184 " --> pdb=" O LEU E 250 " (cutoff:3.500A) removed outlier: 7.888A pdb=" N PHE E 252 " --> pdb=" O THR E 184 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N VAL E 186 " --> pdb=" O PHE E 252 " (cutoff:3.500A) removed outlier: 8.050A pdb=" N ASP E 254 " --> pdb=" O VAL E 186 " (cutoff:3.500A) removed outlier: 6.485A 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: 6.559A pdb=" N ASP F 21 " --> pdb=" O VAL F 13 " (cutoff:3.500A) removed outlier: 4.692A pdb=" N ILE F 15 " --> pdb=" O VAL F 19 " (cutoff:3.500A) removed outlier: 7.056A pdb=" N VAL F 19 " --> pdb=" O ILE F 15 " (cutoff:3.500A) removed outlier: 5.985A pdb=" N ILE F 65 " --> pdb=" O VAL F 53 " (cutoff:3.500A) removed outlier: 5.649A pdb=" N VAL F 53 " --> pdb=" O ILE F 65 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'F' and resid 87 through 89 Processing sheet with id= U, first strand: chain 'F' and resid 329 through 332 removed outlier: 7.463A pdb=" N ILE F 156 " --> pdb=" O ILE F 302 " (cutoff:3.500A) removed outlier: 6.224A pdb=" N SER F 304 " --> pdb=" O ILE F 156 " (cutoff:3.500A) removed outlier: 7.948A pdb=" N LEU F 158 " --> pdb=" O SER F 304 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N GLN F 306 " --> pdb=" O LEU F 158 " (cutoff:3.500A) removed outlier: 7.995A pdb=" N GLY F 160 " --> pdb=" O GLN F 306 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N VAL F 308 " --> pdb=" O GLY F 160 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N VAL F 249 " --> pdb=" O THR F 303 " (cutoff:3.500A) removed outlier: 7.819A pdb=" N MET F 305 " --> pdb=" O VAL F 249 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N LEU F 251 " --> pdb=" O MET F 305 " (cutoff:3.500A) removed outlier: 7.671A pdb=" N ALA F 307 " --> pdb=" O LEU F 251 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N ILE F 253 " --> pdb=" O ALA F 307 " (cutoff:3.500A) removed outlier: 8.235A pdb=" N TYR F 309 " --> pdb=" O ILE F 253 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N THR F 184 " --> pdb=" O LEU F 250 " (cutoff:3.500A) removed outlier: 7.990A pdb=" N PHE F 252 " --> pdb=" O THR F 184 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N VAL F 186 " --> pdb=" O PHE F 252 " (cutoff:3.500A) removed outlier: 7.935A pdb=" N ASP F 254 " --> pdb=" O VAL F 186 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N ALA F 188 " --> pdb=" O ASP F 254 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'G' and resid 113 through 119 removed outlier: 3.695A pdb=" N ALA G 77 " --> pdb=" O ASP G 113 " (cutoff:3.500A) removed outlier: 5.044A pdb=" N THR G 188 " --> pdb=" O VAL G 82 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N ILE G 185 " --> pdb=" O ARG G 202 " (cutoff:3.500A) removed outlier: 5.323A pdb=" N ARG G 202 " --> pdb=" O ILE G 185 " (cutoff:3.500A) removed outlier: 7.236A pdb=" N PHE G 187 " --> pdb=" O ALA G 200 " (cutoff:3.500A) removed outlier: 5.232A pdb=" N ALA G 200 " --> pdb=" O PHE G 187 " (cutoff:3.500A) removed outlier: 6.045A pdb=" N GLU G 189 " --> pdb=" O ALA G 198 " (cutoff:3.500A) removed outlier: 5.524A pdb=" N ALA G 198 " --> pdb=" O GLU G 189 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'H' and resid 41 through 44 removed outlier: 6.115A pdb=" N ASN H 5 " --> pdb=" O VAL H 77 " (cutoff:3.500A) removed outlier: 7.368A pdb=" N ILE H 79 " --> pdb=" O ASN H 5 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N GLU H 7 " --> pdb=" O ILE H 79 " (cutoff:3.500A) removed outlier: 7.498A pdb=" N VAL H 81 " --> pdb=" O GLU H 7 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N VAL H 9 " --> pdb=" O VAL H 81 " (cutoff:3.500A) removed outlier: 5.989A pdb=" N ALA H 10 " --> pdb=" O GLU H 14 " (cutoff:3.500A) removed outlier: 4.379A 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: 4.125A pdb=" N ARG H 26 " --> pdb=" O MET H 50 " (cutoff:3.500A) removed outlier: 5.906A pdb=" N MET H 50 " --> pdb=" O ARG H 26 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ASN H 83 " --> pdb=" O ASP H 66 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'a' and resid 20 through 22 Processing sheet with id= Z, first strand: chain 'a' and resid 112 through 114 Processing sheet with id= AA, first strand: chain 'd' and resid 405 through 409 removed outlier: 6.187A pdb=" N VAL d 375 " --> pdb=" O SER d 406 " (cutoff:3.500A) removed outlier: 7.619A pdb=" N GLN d 408 " --> pdb=" O VAL d 375 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N ALA d 377 " --> pdb=" O GLN d 408 " (cutoff:3.500A) 2076 hydrogen bonds defined for protein. 5229 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 28.32 Time building geometry restraints manager: 53.69 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: 37339 1.03 - 1.23: 94 1.23 - 1.42: 15258 1.42 - 1.62: 22358 1.62 - 1.81: 194 Bond restraints: 75243 Sorted by residual: 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=" CG PRO F 344 " pdb=" CD PRO F 344 " ideal model delta sigma weight residual 1.512 1.476 0.036 2.70e-02 1.37e+03 1.73e+00 bond pdb=" CA VAL B 374 " pdb=" CB VAL B 374 " ideal model delta sigma weight residual 1.550 1.538 0.012 1.03e-02 9.43e+03 1.47e+00 bond pdb=" CG MET M 75 " pdb=" SD MET M 75 " ideal model delta sigma weight residual 1.803 1.774 0.029 2.50e-02 1.60e+03 1.38e+00 bond pdb=" C4 ADP E 600 " pdb=" C5 ADP E 600 " ideal model delta sigma weight residual 1.490 1.467 0.023 2.00e-02 2.50e+03 1.33e+00 ... (remaining 75238 not shown) Histogram of bond angle deviations from ideal: 99.26 - 107.42: 2510 107.42 - 115.57: 95489 115.57 - 123.73: 32804 123.73 - 131.89: 5488 131.89 - 140.04: 43 Bond angle restraints: 136334 Sorted by residual: angle pdb=" C ASP E 254 " pdb=" N ASN E 255 " pdb=" CA ASN E 255 " ideal model delta sigma weight residual 121.70 127.38 -5.68 1.80e+00 3.09e-01 9.95e+00 angle pdb=" C ASP A 272 " pdb=" N ASP A 273 " pdb=" CA ASP A 273 " ideal model delta sigma weight residual 121.70 127.36 -5.66 1.80e+00 3.09e-01 9.89e+00 angle pdb=" C ASP D 254 " pdb=" N ASN D 255 " pdb=" CA ASN D 255 " ideal model delta sigma weight residual 121.70 127.22 -5.52 1.80e+00 3.09e-01 9.42e+00 angle pdb=" C ASP F 254 " pdb=" N ASN F 255 " pdb=" CA ASN F 255 " ideal model delta sigma weight residual 121.70 127.21 -5.51 1.80e+00 3.09e-01 9.35e+00 angle pdb=" N ILE A 35 " pdb=" CA ILE A 35 " pdb=" C ILE A 35 " ideal model delta sigma weight residual 112.96 110.03 2.93 1.00e+00 1.00e+00 8.59e+00 ... (remaining 136329 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.72: 33436 28.72 - 57.44: 1578 57.44 - 86.15: 148 86.15 - 114.87: 12 114.87 - 143.59: 2 Dihedral angle restraints: 35176 sinusoidal: 19501 harmonic: 15675 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 83.59 -143.59 1 2.00e+01 2.50e-03 4.33e+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 66.25 -126.25 1 2.00e+01 2.50e-03 3.82e+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 -60.00 -171.79 111.80 1 2.00e+01 2.50e-03 3.29e+01 ... (remaining 35173 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.060: 5230 0.060 - 0.120: 683 0.120 - 0.181: 43 0.181 - 0.241: 2 0.241 - 0.301: 10 Chirality restraints: 5968 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 2.27e+00 chirality pdb=" C2' ATP C 600 " pdb=" C1' ATP C 600 " pdb=" C3' ATP C 600 " pdb=" O2' ATP C 600 " both_signs ideal model delta sigma weight residual False -2.68 -2.97 0.29 2.00e-01 2.50e+01 2.07e+00 chirality pdb=" C2' ATP A 600 " pdb=" C1' ATP A 600 " pdb=" C3' ATP A 600 " pdb=" O2' ATP A 600 " both_signs ideal model delta sigma weight residual False -2.68 -2.97 0.29 2.00e-01 2.50e+01 2.03e+00 ... (remaining 5965 not shown) Planarity restraints: 11425 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN S 46 " -0.041 5.00e-02 4.00e+02 6.08e-02 5.92e+00 pdb=" N PRO S 47 " 0.105 5.00e-02 4.00e+02 pdb=" CA PRO S 47 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO S 47 " -0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA SER C 469 " -0.008 2.00e-02 2.50e+03 1.60e-02 2.55e+00 pdb=" C SER C 469 " 0.028 2.00e-02 2.50e+03 pdb=" O SER C 469 " -0.010 2.00e-02 2.50e+03 pdb=" N GLU C 470 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 245 " 0.016 2.00e-02 2.50e+03 8.52e-03 2.18e+00 pdb=" CG PHE B 245 " -0.024 2.00e-02 2.50e+03 pdb=" CD1 PHE B 245 " 0.001 2.00e-02 2.50e+03 pdb=" CD2 PHE B 245 " -0.000 2.00e-02 2.50e+03 pdb=" CE1 PHE B 245 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE B 245 " 0.002 2.00e-02 2.50e+03 pdb=" CZ PHE B 245 " 0.004 2.00e-02 2.50e+03 pdb=" HD1 PHE B 245 " -0.002 2.00e-02 2.50e+03 pdb=" HD2 PHE B 245 " -0.001 2.00e-02 2.50e+03 pdb=" HE1 PHE B 245 " 0.002 2.00e-02 2.50e+03 pdb=" HE2 PHE B 245 " 0.001 2.00e-02 2.50e+03 pdb=" HZ PHE B 245 " -0.000 2.00e-02 2.50e+03 ... (remaining 11422 not shown) Histogram of nonbonded interaction distances: 1.54 - 2.15: 2977 2.15 - 2.76: 146720 2.76 - 3.37: 227115 3.37 - 3.99: 295994 3.99 - 4.60: 463315 Nonbonded interactions: 1136121 Sorted by model distance: nonbonded pdb="HH12 ARG R 52 " pdb=" O ILE S 43 " model vdw 1.535 1.850 nonbonded pdb=" OE1 GLU a 177 " pdb=" H GLU a 177 " model vdw 1.558 1.850 nonbonded pdb=" OD2 ASP G 167 " pdb=" H GLY G 179 " model vdw 1.561 1.850 nonbonded pdb="HH12 ARG G 39 " pdb=" O PRO G 145 " model vdw 1.564 1.850 nonbonded pdb="HH12 ARG F 26 " pdb=" OD2 ASP d 358 " model vdw 1.588 1.850 ... (remaining 1136116 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and ((resid 6 and (name N or name CA or name C or name O or name CB o \ r name CG1 or name CG2 or name CD1 or name HA or name HB or name HG12 or name HG \ 13 or name HG21 or name HG22 or name HG23 or name HD11 or name HD12 or name HD13 \ )) or resid 7 through 173 or resid 175 through 406 or (resid 414 and (name N or \ name CA or name C or name O or name CB or name CG or name OD1 or name OD2 or nam \ e HA or name HB2 or name HB3)) or resid 415 through 521 or resid 600 through 601 \ )) selection = (chain 'B' and ((resid 6 and (name N or name CA or name C or name O or name CB o \ r name CG1 or name CG2 or name CD1 or name HA or name HB or name HG12 or name HG \ 13 or name HG21 or name HG22 or name HG23 or name HD11 or name HD12 or name HD13 \ )) or resid 7 through 173 or resid 175 through 521 or resid 600 through 601)) selection = (chain 'C' and (resid 6 through 22 or (resid 29 and (name N or name CA or name C \ or name O or name CB or name CG or name CD or name OE1 or name OE2 or name HA o \ r name HB2 or name HB3 or name HG2 or name HG3)) or resid 30 through 173 or resi \ d 175 through 406 or (resid 414 and (name N or name CA or name C or name O or na \ me CB or name CG or name OD1 or name OD2 or name HA or name HB2 or name HB3)) or \ resid 415 through 521 or resid 600 through 601)) } ncs_group { reference = (chain 'D' and (resid 8 through 452 or resid 455 through 471)) selection = (chain 'E' and (resid 8 through 166 or (resid 167 and (name N or name CA or name \ C or name O or name CB or name OG1 or name CG2 or name H or name HA or name HB \ or name HG21 or name HG22 or name HG23)) or resid 168 through 452 or resid 455 t \ hrough 471)) selection = (chain 'F' and ((resid 8 and (name N or name CA or name C or name O or name CB o \ r name OG1 or name CG2 or name HA or name HB or name HG1 or name HG21 or name HG \ 22 or name HG23)) or resid 9 through 452 or resid 455 through 471)) } ncs_group { reference = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' } 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: 5.440 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.880 Extract box with map and model: 25.540 Check model and map are aligned: 0.820 Set scattering table: 0.520 Process input model: 199.820 Find NCS groups from input model: 2.650 Set up NCS constraints: 0.370 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:13.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 249.190 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8618 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 0.044 37884 Z= 0.254 Angle : 0.515 7.463 51382 Z= 0.273 Chirality : 0.042 0.301 5968 Planarity : 0.003 0.061 6721 Dihedral : 14.885 143.591 13873 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.36 % Favored : 97.58 % Rotamer: Outliers : 0.00 % Allowed : 0.10 % Favored : 99.90 % 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: 1.64 (0.12), residues: 4882 helix: 1.71 (0.10), residues: 2637 sheet: -0.16 (0.21), residues: 530 loop : 0.70 (0.16), residues: 1715 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP a 218 HIS 0.004 0.001 HIS F 97 PHE 0.024 0.001 PHE B 245 TYR 0.012 0.001 TYR C 18 ARG 0.005 0.000 ARG F 26 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9764 Ramachandran restraints generated. 4882 Oldfield, 0 Emsley, 4882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9764 Ramachandran restraints generated. 4882 Oldfield, 0 Emsley, 4882 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 369 residues out of total 3843 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 369 time to evaluate : 4.501 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 418 LYS cc_start: 0.7252 (mptt) cc_final: 0.7049 (mptt) REVERT: P 86 GLN cc_start: 0.7132 (pp30) cc_final: 0.6522 (pp30) REVERT: a 25 MET cc_start: 0.8000 (mtm) cc_final: 0.7729 (mtm) outliers start: 0 outliers final: 2 residues processed: 369 average time/residue: 2.9985 time to fit residues: 1324.9328 Evaluate side-chains 268 residues out of total 3843 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 266 time to evaluate : 4.516 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 21 MET Chi-restraints excluded: chain b residue 117 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 483 random chunks: chunk 407 optimal weight: 3.9990 chunk 366 optimal weight: 2.9990 chunk 203 optimal weight: 2.9990 chunk 125 optimal weight: 2.9990 chunk 246 optimal weight: 1.9990 chunk 195 optimal weight: 0.9980 chunk 378 optimal weight: 1.9990 chunk 146 optimal weight: 1.9990 chunk 230 optimal weight: 2.9990 chunk 281 optimal weight: 1.9990 chunk 438 optimal weight: 4.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 399 GLN ** C 512 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 245 GLN G 288 GLN N 71 ASN T 86 GLN d 127 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8641 moved from start: 0.0476 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 37884 Z= 0.313 Angle : 0.520 7.685 51382 Z= 0.274 Chirality : 0.040 0.167 5968 Planarity : 0.004 0.056 6721 Dihedral : 7.458 125.134 5415 Min Nonbonded Distance : 1.647 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.38 % Favored : 97.56 % Rotamer: Outliers : 0.34 % Allowed : 5.28 % Favored : 94.39 % 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: 1.51 (0.12), residues: 4882 helix: 1.60 (0.10), residues: 2638 sheet: -0.18 (0.21), residues: 532 loop : 0.64 (0.16), residues: 1712 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP a 218 HIS 0.005 0.001 HIS F 97 PHE 0.017 0.001 PHE A 245 TYR 0.027 0.001 TYR a 145 ARG 0.006 0.000 ARG E 26 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9764 Ramachandran restraints generated. 4882 Oldfield, 0 Emsley, 4882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9764 Ramachandran restraints generated. 4882 Oldfield, 0 Emsley, 4882 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: 13 poor density : 280 time to evaluate : 4.546 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 48 GLU cc_start: 0.7602 (OUTLIER) cc_final: 0.6946 (mp0) REVERT: P 50 GLN cc_start: 0.8035 (tm-30) cc_final: 0.7802 (tp-100) REVERT: P 86 GLN cc_start: 0.7136 (pp30) cc_final: 0.6535 (pp30) outliers start: 13 outliers final: 4 residues processed: 286 average time/residue: 2.9739 time to fit residues: 1024.5835 Evaluate side-chains 270 residues out of total 3843 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 265 time to evaluate : 4.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 383 GLN Chi-restraints excluded: chain G residue 177 ILE Chi-restraints excluded: chain L residue 48 GLU Chi-restraints excluded: chain L residue 86 GLN Chi-restraints excluded: chain Q residue 72 LEU 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: 1.9990 chunk 365 optimal weight: 2.9990 chunk 298 optimal weight: 0.6980 chunk 120 optimal weight: 1.9990 chunk 439 optimal weight: 3.9990 chunk 474 optimal weight: 3.9990 chunk 391 optimal weight: 1.9990 chunk 435 optimal weight: 4.9990 chunk 149 optimal weight: 2.9990 chunk 352 optimal weight: 1.9990 overall best weight: 1.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 121 GLN ** C 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 399 GLN F 245 GLN G 288 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8642 moved from start: 0.0556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 37884 Z= 0.304 Angle : 0.517 8.015 51382 Z= 0.272 Chirality : 0.040 0.187 5968 Planarity : 0.004 0.057 6721 Dihedral : 7.334 120.287 5409 Min Nonbonded Distance : 1.710 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.52 % Favored : 97.42 % Rotamer: Outliers : 0.31 % Allowed : 6.47 % Favored : 93.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.90 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.49 (0.12), residues: 4882 helix: 1.60 (0.10), residues: 2635 sheet: -0.17 (0.21), residues: 530 loop : 0.62 (0.16), residues: 1717 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP a 218 HIS 0.005 0.001 HIS F 97 PHE 0.014 0.001 PHE O 69 TYR 0.024 0.001 TYR a 145 ARG 0.008 0.000 ARG E 26 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9764 Ramachandran restraints generated. 4882 Oldfield, 0 Emsley, 4882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9764 Ramachandran restraints generated. 4882 Oldfield, 0 Emsley, 4882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 179 is missing expected H atoms. Skipping. Residue THR 179 is missing expected H atoms. Skipping. Residue THR 179 is missing expected H atoms. Skipping. Residue THR 167 is missing expected H atoms. Skipping. Residue THR 167 is missing expected H atoms. Skipping. Evaluate side-chains 292 residues out of total 3843 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 280 time to evaluate : 4.461 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 298 ARG cc_start: 0.7917 (OUTLIER) cc_final: 0.7619 (ptt-90) REVERT: P 50 GLN cc_start: 0.8037 (tm-30) cc_final: 0.7822 (tp-100) REVERT: P 86 GLN cc_start: 0.7140 (pp30) cc_final: 0.6542 (pp30) REVERT: a 122 GLU cc_start: 0.7731 (OUTLIER) cc_final: 0.7254 (mt-10) REVERT: a 245 MET cc_start: 0.8966 (mtm) cc_final: 0.8719 (mtm) outliers start: 12 outliers final: 6 residues processed: 288 average time/residue: 2.9499 time to fit residues: 1024.7315 Evaluate side-chains 271 residues out of total 3843 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 263 time to evaluate : 4.508 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 383 GLN Chi-restraints excluded: chain E residue 298 ARG Chi-restraints excluded: chain G residue 177 ILE Chi-restraints excluded: chain L residue 86 GLN Chi-restraints excluded: chain Q residue 72 LEU Chi-restraints excluded: chain a residue 122 GLU Chi-restraints excluded: chain b residue 73 LYS Chi-restraints excluded: chain d residue 201 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 483 random chunks: chunk 434 optimal weight: 4.9990 chunk 330 optimal weight: 4.9990 chunk 228 optimal weight: 2.9990 chunk 48 optimal weight: 1.9990 chunk 209 optimal weight: 1.9990 chunk 295 optimal weight: 3.9990 chunk 440 optimal weight: 2.9990 chunk 466 optimal weight: 2.9990 chunk 230 optimal weight: 0.0970 chunk 417 optimal weight: 1.9990 chunk 125 optimal weight: 2.9990 overall best weight: 1.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 399 GLN F 245 GLN ** O 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 75 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8646 moved from start: 0.0647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 37884 Z= 0.317 Angle : 0.523 8.038 51382 Z= 0.275 Chirality : 0.040 0.169 5968 Planarity : 0.004 0.075 6721 Dihedral : 7.320 118.331 5409 Min Nonbonded Distance : 1.702 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.54 % Favored : 97.42 % Rotamer: Outliers : 0.49 % Allowed : 7.25 % Favored : 92.25 % 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: 1.48 (0.12), residues: 4882 helix: 1.58 (0.10), residues: 2634 sheet: -0.16 (0.21), residues: 540 loop : 0.61 (0.16), residues: 1708 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP a 218 HIS 0.005 0.001 HIS F 97 PHE 0.015 0.001 PHE O 69 TYR 0.022 0.001 TYR a 145 ARG 0.010 0.000 ARG E 26 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9764 Ramachandran restraints generated. 4882 Oldfield, 0 Emsley, 4882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9764 Ramachandran restraints generated. 4882 Oldfield, 0 Emsley, 4882 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 291 residues out of total 3843 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 272 time to evaluate : 4.441 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 298 ARG cc_start: 0.7891 (OUTLIER) cc_final: 0.7599 (ptt-90) REVERT: F 245 GLN cc_start: 0.8276 (OUTLIER) cc_final: 0.8046 (mt0) REVERT: P 86 GLN cc_start: 0.7146 (pp30) cc_final: 0.6548 (pp30) REVERT: a 78 GLU cc_start: 0.8149 (mt-10) cc_final: 0.7910 (mt-10) REVERT: a 122 GLU cc_start: 0.7739 (OUTLIER) cc_final: 0.7256 (mt-10) REVERT: a 245 MET cc_start: 0.8983 (mtm) cc_final: 0.8745 (mtm) outliers start: 19 outliers final: 6 residues processed: 281 average time/residue: 3.0041 time to fit residues: 1026.3813 Evaluate side-chains 269 residues out of total 3843 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 260 time to evaluate : 4.435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 51 MET Chi-restraints excluded: chain E residue 298 ARG Chi-restraints excluded: chain F residue 245 GLN Chi-restraints excluded: chain G residue 177 ILE Chi-restraints excluded: chain L residue 86 GLN Chi-restraints excluded: chain Q residue 72 LEU Chi-restraints excluded: chain a residue 122 GLU Chi-restraints excluded: chain b residue 73 LYS Chi-restraints excluded: chain d residue 201 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 483 random chunks: chunk 388 optimal weight: 3.9990 chunk 265 optimal weight: 2.9990 chunk 6 optimal weight: 2.9990 chunk 347 optimal weight: 0.9990 chunk 192 optimal weight: 0.5980 chunk 398 optimal weight: 2.9990 chunk 322 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 238 optimal weight: 3.9990 chunk 419 optimal weight: 4.9990 chunk 117 optimal weight: 1.9990 overall best weight: 1.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 399 GLN L 46 GLN ** O 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 75 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8649 moved from start: 0.0689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 37884 Z= 0.331 Angle : 0.527 8.122 51382 Z= 0.278 Chirality : 0.041 0.170 5968 Planarity : 0.004 0.078 6721 Dihedral : 7.335 117.671 5409 Min Nonbonded Distance : 1.688 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.60 % Favored : 97.36 % Rotamer: Outliers : 0.52 % Allowed : 7.85 % Favored : 91.63 % 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: 1.46 (0.12), residues: 4882 helix: 1.56 (0.10), residues: 2634 sheet: -0.16 (0.21), residues: 540 loop : 0.61 (0.16), residues: 1708 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP a 218 HIS 0.005 0.001 HIS F 97 PHE 0.015 0.001 PHE O 69 TYR 0.021 0.001 TYR a 145 ARG 0.009 0.000 ARG E 26 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9764 Ramachandran restraints generated. 4882 Oldfield, 0 Emsley, 4882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9764 Ramachandran restraints generated. 4882 Oldfield, 0 Emsley, 4882 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: 20 poor density : 274 time to evaluate : 4.460 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 476 LYS cc_start: 0.8282 (OUTLIER) cc_final: 0.7880 (tmtt) REVERT: E 298 ARG cc_start: 0.7882 (OUTLIER) cc_final: 0.7594 (ptt-90) REVERT: F 433 LYS cc_start: 0.8223 (OUTLIER) cc_final: 0.7971 (tppp) REVERT: P 86 GLN cc_start: 0.7151 (pp30) cc_final: 0.6553 (pp30) REVERT: a 122 GLU cc_start: 0.7737 (OUTLIER) cc_final: 0.7241 (mt-10) REVERT: b 72 ARG cc_start: 0.7482 (tmm-80) cc_final: 0.7234 (tmm-80) outliers start: 20 outliers final: 9 residues processed: 286 average time/residue: 3.0579 time to fit residues: 1062.4615 Evaluate side-chains 273 residues out of total 3843 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 260 time to evaluate : 4.726 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 476 LYS Chi-restraints excluded: chain C residue 51 MET Chi-restraints excluded: chain D residue 383 GLN Chi-restraints excluded: chain E residue 298 ARG Chi-restraints excluded: chain E residue 469 GLU Chi-restraints excluded: chain F residue 433 LYS Chi-restraints excluded: chain G residue 177 ILE Chi-restraints excluded: chain L residue 86 GLN Chi-restraints excluded: chain Q residue 72 LEU Chi-restraints excluded: chain a residue 122 GLU Chi-restraints excluded: chain b residue 73 LYS Chi-restraints excluded: chain d residue 155 GLU Chi-restraints excluded: chain d residue 201 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 483 random chunks: chunk 157 optimal weight: 2.9990 chunk 420 optimal weight: 1.9990 chunk 92 optimal weight: 0.4980 chunk 274 optimal weight: 3.9990 chunk 115 optimal weight: 0.6980 chunk 467 optimal weight: 2.9990 chunk 387 optimal weight: 0.7980 chunk 216 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 154 optimal weight: 0.9980 chunk 245 optimal weight: 2.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 399 GLN F 245 GLN L 46 GLN O 50 GLN ** P 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 75 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8630 moved from start: 0.0688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 37884 Z= 0.206 Angle : 0.494 7.790 51382 Z= 0.258 Chirality : 0.039 0.158 5968 Planarity : 0.004 0.083 6721 Dihedral : 7.140 113.672 5409 Min Nonbonded Distance : 1.731 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.40 % Favored : 97.56 % Rotamer: Outliers : 0.42 % Allowed : 8.32 % Favored : 91.27 % 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: 1.63 (0.12), residues: 4882 helix: 1.70 (0.10), residues: 2631 sheet: -0.13 (0.21), residues: 540 loop : 0.71 (0.16), residues: 1711 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP a 218 HIS 0.004 0.001 HIS F 97 PHE 0.013 0.001 PHE O 69 TYR 0.021 0.001 TYR a 145 ARG 0.012 0.000 ARG E 26 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9764 Ramachandran restraints generated. 4882 Oldfield, 0 Emsley, 4882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9764 Ramachandran restraints generated. 4882 Oldfield, 0 Emsley, 4882 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: 16 poor density : 280 time to evaluate : 4.501 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: O 65 GLU cc_start: 0.7736 (mm-30) cc_final: 0.7356 (mt-10) REVERT: P 86 GLN cc_start: 0.7130 (pp30) cc_final: 0.6533 (pp30) REVERT: a 78 GLU cc_start: 0.8130 (mt-10) cc_final: 0.7858 (mt-10) REVERT: a 122 GLU cc_start: 0.7713 (OUTLIER) cc_final: 0.7237 (mt-10) REVERT: b 76 GLU cc_start: 0.8716 (pp20) cc_final: 0.8495 (pp20) outliers start: 16 outliers final: 9 residues processed: 289 average time/residue: 2.9430 time to fit residues: 1026.3494 Evaluate side-chains 271 residues out of total 3843 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 261 time to evaluate : 4.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 51 MET Chi-restraints excluded: chain D residue 383 GLN Chi-restraints excluded: chain E residue 469 GLU Chi-restraints excluded: chain G residue 177 ILE Chi-restraints excluded: chain L residue 46 GLN Chi-restraints excluded: chain L residue 86 GLN Chi-restraints excluded: chain Q residue 72 LEU Chi-restraints excluded: chain a residue 122 GLU Chi-restraints excluded: chain d residue 155 GLU Chi-restraints excluded: chain d residue 201 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 483 random chunks: chunk 450 optimal weight: 4.9990 chunk 52 optimal weight: 2.9990 chunk 266 optimal weight: 2.9990 chunk 341 optimal weight: 3.9990 chunk 264 optimal weight: 1.9990 chunk 393 optimal weight: 1.9990 chunk 260 optimal weight: 0.9990 chunk 465 optimal weight: 4.9990 chunk 291 optimal weight: 0.6980 chunk 283 optimal weight: 2.9990 chunk 214 optimal weight: 3.9990 overall best weight: 1.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 399 GLN L 46 GLN a 75 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8643 moved from start: 0.0711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 37884 Z= 0.308 Angle : 0.519 8.050 51382 Z= 0.272 Chirality : 0.040 0.167 5968 Planarity : 0.004 0.086 6721 Dihedral : 7.221 113.722 5409 Min Nonbonded Distance : 1.699 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.58 % Favored : 97.38 % Rotamer: Outliers : 0.47 % Allowed : 8.60 % Favored : 90.93 % 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: 1.55 (0.12), residues: 4882 helix: 1.64 (0.10), residues: 2633 sheet: -0.14 (0.21), residues: 540 loop : 0.65 (0.16), residues: 1709 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP a 218 HIS 0.005 0.001 HIS F 97 PHE 0.017 0.001 PHE E 422 TYR 0.020 0.001 TYR a 145 ARG 0.011 0.000 ARG E 26 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9764 Ramachandran restraints generated. 4882 Oldfield, 0 Emsley, 4882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9764 Ramachandran restraints generated. 4882 Oldfield, 0 Emsley, 4882 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 289 residues out of total 3843 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 271 time to evaluate : 4.636 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 298 ARG cc_start: 0.7899 (OUTLIER) cc_final: 0.7624 (ptt-90) REVERT: F 433 LYS cc_start: 0.8213 (OUTLIER) cc_final: 0.7962 (tppp) REVERT: L 46 GLN cc_start: 0.8175 (tm130) cc_final: 0.7785 (tm-30) REVERT: L 75 MET cc_start: 0.8462 (tmm) cc_final: 0.8239 (tmt) REVERT: P 86 GLN cc_start: 0.7146 (pp30) cc_final: 0.6547 (pp30) REVERT: a 78 GLU cc_start: 0.8116 (mt-10) cc_final: 0.7838 (mt-10) REVERT: a 122 GLU cc_start: 0.7724 (OUTLIER) cc_final: 0.7249 (mt-10) REVERT: b 72 ARG cc_start: 0.7457 (tmm-80) cc_final: 0.7220 (tmm-80) REVERT: b 76 GLU cc_start: 0.8746 (pp20) cc_final: 0.8527 (pp20) outliers start: 18 outliers final: 12 residues processed: 282 average time/residue: 2.9392 time to fit residues: 999.2998 Evaluate side-chains 275 residues out of total 3843 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 260 time to evaluate : 4.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 PHE Chi-restraints excluded: chain B residue 414 ASP Chi-restraints excluded: chain C residue 51 MET Chi-restraints excluded: chain D residue 383 GLN Chi-restraints excluded: chain E residue 298 ARG Chi-restraints excluded: chain E residue 469 GLU Chi-restraints excluded: chain F residue 148 THR Chi-restraints excluded: chain F residue 433 LYS Chi-restraints excluded: chain G residue 177 ILE Chi-restraints excluded: chain L residue 61 VAL Chi-restraints excluded: chain L residue 86 GLN Chi-restraints excluded: chain Q residue 72 LEU Chi-restraints excluded: chain a residue 122 GLU Chi-restraints excluded: chain d residue 155 GLU Chi-restraints excluded: chain d residue 201 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 483 random chunks: chunk 288 optimal weight: 2.9990 chunk 185 optimal weight: 1.9990 chunk 278 optimal weight: 0.6980 chunk 140 optimal weight: 3.9990 chunk 91 optimal weight: 1.9990 chunk 90 optimal weight: 3.9990 chunk 295 optimal weight: 3.9990 chunk 317 optimal weight: 2.9990 chunk 230 optimal weight: 2.9990 chunk 43 optimal weight: 1.9990 chunk 365 optimal weight: 2.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 399 GLN ** O 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 75 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8649 moved from start: 0.0764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 37884 Z= 0.334 Angle : 0.535 8.172 51382 Z= 0.281 Chirality : 0.041 0.172 5968 Planarity : 0.004 0.092 6721 Dihedral : 7.298 114.445 5409 Min Nonbonded Distance : 1.687 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.54 % Favored : 97.42 % Rotamer: Outliers : 0.62 % Allowed : 8.79 % Favored : 90.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.90 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.49 (0.12), residues: 4882 helix: 1.59 (0.10), residues: 2633 sheet: -0.16 (0.21), residues: 540 loop : 0.62 (0.16), residues: 1709 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP a 218 HIS 0.005 0.001 HIS F 97 PHE 0.017 0.001 PHE E 422 TYR 0.020 0.001 TYR a 145 ARG 0.013 0.000 ARG E 26 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9764 Ramachandran restraints generated. 4882 Oldfield, 0 Emsley, 4882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9764 Ramachandran restraints generated. 4882 Oldfield, 0 Emsley, 4882 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: 24 poor density : 269 time to evaluate : 4.495 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 476 LYS cc_start: 0.8245 (OUTLIER) cc_final: 0.7822 (tmtt) REVERT: E 298 ARG cc_start: 0.7906 (OUTLIER) cc_final: 0.7680 (ptt-90) REVERT: F 433 LYS cc_start: 0.8230 (OUTLIER) cc_final: 0.7976 (tppp) REVERT: L 46 GLN cc_start: 0.8211 (tm130) cc_final: 0.7743 (tm-30) REVERT: O 65 GLU cc_start: 0.7735 (mm-30) cc_final: 0.7416 (mt-10) REVERT: P 86 GLN cc_start: 0.7152 (pp30) cc_final: 0.6554 (pp30) REVERT: T 21 MET cc_start: 0.8339 (mmm) cc_final: 0.8030 (mmp) REVERT: a 122 GLU cc_start: 0.7725 (OUTLIER) cc_final: 0.7248 (mt-10) REVERT: b 72 ARG cc_start: 0.7536 (tmm-80) cc_final: 0.7281 (tmm-80) outliers start: 24 outliers final: 14 residues processed: 284 average time/residue: 2.9864 time to fit residues: 1023.7268 Evaluate side-chains 279 residues out of total 3843 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 261 time to evaluate : 4.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 414 ASP Chi-restraints excluded: chain B residue 476 LYS Chi-restraints excluded: chain C residue 51 MET Chi-restraints excluded: chain D residue 383 GLN Chi-restraints excluded: chain E residue 71 ASP Chi-restraints excluded: chain E residue 228 MET Chi-restraints excluded: chain E residue 298 ARG Chi-restraints excluded: chain E residue 469 GLU Chi-restraints excluded: chain F residue 148 THR Chi-restraints excluded: chain F residue 433 LYS Chi-restraints excluded: chain G residue 177 ILE Chi-restraints excluded: chain L residue 61 VAL Chi-restraints excluded: chain L residue 86 GLN Chi-restraints excluded: chain P residue 55 THR Chi-restraints excluded: chain Q residue 72 LEU Chi-restraints excluded: chain a residue 122 GLU Chi-restraints excluded: chain d residue 155 GLU Chi-restraints excluded: chain d residue 201 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 483 random chunks: chunk 423 optimal weight: 0.5980 chunk 445 optimal weight: 4.9990 chunk 406 optimal weight: 3.9990 chunk 433 optimal weight: 3.9990 chunk 261 optimal weight: 0.9990 chunk 188 optimal weight: 0.7980 chunk 340 optimal weight: 3.9990 chunk 133 optimal weight: 1.9990 chunk 392 optimal weight: 1.9990 chunk 410 optimal weight: 0.9990 chunk 432 optimal weight: 1.9990 overall best weight: 1.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 399 GLN ** O 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8631 moved from start: 0.0748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 37884 Z= 0.215 Angle : 0.503 7.860 51382 Z= 0.261 Chirality : 0.039 0.190 5968 Planarity : 0.004 0.099 6721 Dihedral : 7.132 111.765 5409 Min Nonbonded Distance : 1.736 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.36 % Favored : 97.60 % Rotamer: Outliers : 0.39 % Allowed : 9.07 % Favored : 90.54 % 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: 1.62 (0.12), residues: 4882 helix: 1.69 (0.10), residues: 2633 sheet: -0.14 (0.21), residues: 540 loop : 0.71 (0.16), residues: 1709 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP a 218 HIS 0.004 0.001 HIS H 38 PHE 0.016 0.001 PHE E 422 TYR 0.021 0.001 TYR a 145 ARG 0.015 0.000 ARG E 26 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9764 Ramachandran restraints generated. 4882 Oldfield, 0 Emsley, 4882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9764 Ramachandran restraints generated. 4882 Oldfield, 0 Emsley, 4882 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 289 residues out of total 3843 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 274 time to evaluate : 4.569 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 46 GLN cc_start: 0.8170 (tm130) cc_final: 0.7678 (tm-30) REVERT: O 65 GLU cc_start: 0.7719 (mm-30) cc_final: 0.7410 (mt-10) REVERT: P 86 GLN cc_start: 0.7135 (pp30) cc_final: 0.6539 (pp30) REVERT: T 21 MET cc_start: 0.8326 (mmm) cc_final: 0.7993 (mmp) REVERT: a 78 GLU cc_start: 0.8183 (mt-10) cc_final: 0.7877 (mt-10) REVERT: a 122 GLU cc_start: 0.7708 (OUTLIER) cc_final: 0.7231 (mt-10) outliers start: 15 outliers final: 11 residues processed: 284 average time/residue: 2.9464 time to fit residues: 1023.1124 Evaluate side-chains 275 residues out of total 3843 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 263 time to evaluate : 4.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 51 MET Chi-restraints excluded: chain D residue 383 GLN Chi-restraints excluded: chain E residue 228 MET Chi-restraints excluded: chain E residue 469 GLU Chi-restraints excluded: chain F residue 148 THR Chi-restraints excluded: chain L residue 61 VAL Chi-restraints excluded: chain L residue 86 GLN Chi-restraints excluded: chain P residue 55 THR Chi-restraints excluded: chain Q residue 72 LEU Chi-restraints excluded: chain a residue 122 GLU Chi-restraints excluded: chain d residue 155 GLU Chi-restraints excluded: chain d residue 201 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 483 random chunks: chunk 284 optimal weight: 0.7980 chunk 458 optimal weight: 7.9990 chunk 279 optimal weight: 0.5980 chunk 217 optimal weight: 3.9990 chunk 318 optimal weight: 2.9990 chunk 481 optimal weight: 2.9990 chunk 442 optimal weight: 0.9990 chunk 383 optimal weight: 0.8980 chunk 39 optimal weight: 3.9990 chunk 295 optimal weight: 2.9990 chunk 234 optimal weight: 0.4980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 399 GLN ** O 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8620 moved from start: 0.0798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 37884 Z= 0.177 Angle : 0.496 9.231 51382 Z= 0.257 Chirality : 0.039 0.203 5968 Planarity : 0.004 0.101 6721 Dihedral : 6.982 108.470 5409 Min Nonbonded Distance : 1.778 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.30 % Favored : 97.66 % Rotamer: Outliers : 0.42 % Allowed : 9.15 % Favored : 90.43 % 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: 1.73 (0.13), residues: 4882 helix: 1.79 (0.10), residues: 2630 sheet: -0.11 (0.21), residues: 530 loop : 0.75 (0.16), residues: 1722 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP a 218 HIS 0.003 0.001 HIS F 97 PHE 0.020 0.001 PHE E 422 TYR 0.021 0.001 TYR a 145 ARG 0.015 0.000 ARG E 26 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9764 Ramachandran restraints generated. 4882 Oldfield, 0 Emsley, 4882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9764 Ramachandran restraints generated. 4882 Oldfield, 0 Emsley, 4882 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: 16 poor density : 277 time to evaluate : 4.425 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 46 GLN cc_start: 0.8118 (OUTLIER) cc_final: 0.7817 (tm-30) REVERT: O 65 GLU cc_start: 0.7670 (mm-30) cc_final: 0.7363 (mt-10) REVERT: P 86 GLN cc_start: 0.7130 (pp30) cc_final: 0.6532 (pp30) REVERT: T 21 MET cc_start: 0.8339 (mmm) cc_final: 0.8002 (mmp) REVERT: a 122 GLU cc_start: 0.7690 (OUTLIER) cc_final: 0.7210 (mt-10) outliers start: 16 outliers final: 11 residues processed: 288 average time/residue: 2.9030 time to fit residues: 1009.2043 Evaluate side-chains 280 residues out of total 3843 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 267 time to evaluate : 4.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 414 ASP Chi-restraints excluded: chain E residue 71 ASP Chi-restraints excluded: chain E residue 228 MET Chi-restraints excluded: chain E residue 469 GLU Chi-restraints excluded: chain F residue 148 THR Chi-restraints excluded: chain L residue 46 GLN Chi-restraints excluded: chain L residue 61 VAL Chi-restraints excluded: chain L residue 86 GLN Chi-restraints excluded: chain P residue 55 THR Chi-restraints excluded: chain Q residue 72 LEU Chi-restraints excluded: chain a residue 122 GLU Chi-restraints excluded: chain d residue 155 GLU Chi-restraints excluded: chain d residue 201 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 483 random chunks: chunk 304 optimal weight: 4.9990 chunk 408 optimal weight: 0.8980 chunk 117 optimal weight: 1.9990 chunk 353 optimal weight: 2.9990 chunk 56 optimal weight: 2.9990 chunk 106 optimal weight: 0.7980 chunk 383 optimal weight: 0.7980 chunk 160 optimal weight: 0.2980 chunk 394 optimal weight: 2.9990 chunk 48 optimal weight: 0.9980 chunk 70 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 399 GLN ** O 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 86 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.073962 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2909 r_free = 0.2909 target = 0.056594 restraints weight = 257560.470| |-----------------------------------------------------------------------------| r_work (start): 0.2894 rms_B_bonded: 1.60 r_work: 0.2809 rms_B_bonded: 1.76 restraints_weight: 0.5000 r_work: 0.2708 rms_B_bonded: 3.06 restraints_weight: 0.2500 r_work (final): 0.2708 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2711 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2711 r_free = 0.2711 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 = 0.2711 r_free = 0.2711 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2711 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8830 moved from start: 0.0839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 37884 Z= 0.176 Angle : 0.489 7.421 51382 Z= 0.253 Chirality : 0.039 0.209 5968 Planarity : 0.004 0.100 6721 Dihedral : 6.914 106.560 5409 Min Nonbonded Distance : 1.780 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.36 % Favored : 97.60 % Rotamer: Outliers : 0.36 % Allowed : 9.28 % Favored : 90.36 % 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: 1.79 (0.13), residues: 4882 helix: 1.84 (0.10), residues: 2629 sheet: -0.09 (0.21), residues: 530 loop : 0.78 (0.16), residues: 1723 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP a 218 HIS 0.003 0.001 HIS H 38 PHE 0.015 0.001 PHE E 422 TYR 0.021 0.001 TYR a 145 ARG 0.015 0.000 ARG E 26 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 18446.72 seconds wall clock time: 318 minutes 39.37 seconds (19119.37 seconds total)