Starting phenix.real_space_refine (version: dev) on Wed Dec 14 23:38:26 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7njp_12402/12_2022/7njp_12402_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7njp_12402/12_2022/7njp_12402.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.84 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7njp_12402/12_2022/7njp_12402.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7njp_12402/12_2022/7njp_12402.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7njp_12402/12_2022/7njp_12402_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7njp_12402/12_2022/7njp_12402_trim_updated.pdb" } resolution = 2.84 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "C ASP 273": "OD1" <-> "OD2" Residue "D TYR 111": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D ASP 384": "OD1" <-> "OD2" Residue "D ASP 398": "OD1" <-> "OD2" Residue "D ASP 463": "OD1" <-> "OD2" Residue "E ASP 384": "OD1" <-> "OD2" Residue "F GLU 192": "OE1" <-> "OE2" Residue "F ASP 363": "OD1" <-> "OD2" Residue "L PHE 74": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "N ASP 32": "OD1" <-> "OD2" Residue "N PHE 69": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "R PHE 58": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "T PHE 58": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "d PHE 16": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "d PHE 187": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/chem_data/mon_lib" Total number of atoms: 74554 Number of models: 1 Model: "" Number of chains: 31 Chain: "A" Number of atoms: 7688 Number of conformers: 1 Conformer: "" Number of residues, atoms: 509, 7688 Classifications: {'peptide': 509} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 19, 'TRANS': 487} Chain breaks: 1 Chain: "B" Number of atoms: 7715 Number of conformers: 1 Conformer: "" Number of residues, atoms: 510, 7715 Classifications: {'peptide': 510} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 19, 'TRANS': 488} Chain breaks: 1 Chain: "C" Number of atoms: 8009 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 526, 7967 Classifications: {'peptide': 526} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 21, 'TRANS': 502} Chain breaks: 2 Conformer: "B" Number of residues, atoms: 526, 7967 Classifications: {'peptide': 526} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 21, 'TRANS': 502} Chain breaks: 2 bond proxies already assigned to first conformer: 7982 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: 1175 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 1175 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 4, 'TRANS': 78} Chain: "M" Number of atoms: 1187 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 1187 Classifications: {'peptide': 84} Link IDs: {'PTRANS': 4, 'TRANS': 79} Chain: "N" Number of atoms: 1175 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 1175 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 4, 'TRANS': 78} Chain: "O" Number of atoms: 1156 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 1156 Classifications: {'peptide': 82} Link IDs: {'PTRANS': 4, 'TRANS': 77} Chain: "P" Number of atoms: 1175 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 1175 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 4, 'TRANS': 78} Chain: "Q" Number of atoms: 1175 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 1175 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 4, 'TRANS': 78} Chain: "R" Number of atoms: 1187 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 1187 Classifications: {'peptide': 84} Link IDs: {'PTRANS': 4, 'TRANS': 79} Chain: "S" Number of atoms: 1175 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 1175 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 4, 'TRANS': 78} Chain: "T" Number of atoms: 1175 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 1175 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 4, 'TRANS': 78} 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: 2 residue: pdb=" N APHE C 354 " occ=0.80 ... (38 atoms not shown) pdb=" HZ BPHE C 354 " occ=0.20 residue: pdb=" N AGLN D 453 " occ=0.50 ... (32 atoms not shown) pdb="HE22BGLN D 453 " occ=0.50 Time building chain proxies: 31.55, per 1000 atoms: 0.42 Number of scatterers: 74554 At special positions: 0 Unit cell: (141.93, 126.16, 250.66, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) S 107 16.00 P 16 15.00 Mg 5 11.99 O 7172 8.00 N 6393 7.00 C 23556 6.00 H 37305 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: 52.53 Conformation dependent library (CDL) restraints added in 6.1 seconds 9768 Ramachandran restraints generated. 4884 Oldfield, 0 Emsley, 4884 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8876 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 179 helices and 27 sheets defined 55.5% alpha, 9.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.18 Creating SS restraints... Processing helix chain 'A' and resid 10 through 21 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 139 through 141 No H-bonds generated for 'chain 'A' and resid 139 through 141' Processing helix chain 'A' and resid 154 through 159 Processing helix chain 'A' and resid 178 through 195 removed outlier: 4.247A pdb=" N ARG A 190 " --> pdb=" O ILE A 186 " (cutoff:3.500A) removed outlier: 5.133A pdb=" N GLU A 191 " --> pdb=" O LEU A 187 " (cutoff:3.500A) removed outlier: 4.819A pdb=" N ALA A 192 " --> pdb=" O ASN A 188 " (cutoff:3.500A) Processing helix chain 'A' and resid 213 through 225 Processing helix chain 'A' and resid 243 through 263 Proline residue: A 250 - end of helix removed outlier: 3.696A pdb=" N TRP A 260 " --> pdb=" O ILE A 256 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ASN A 263 " --> pdb=" O HIS A 259 " (cutoff:3.500A) Processing helix chain 'A' and resid 274 through 287 Processing helix chain 'A' and resid 294 through 296 No H-bonds generated for 'chain 'A' and resid 294 through 296' Processing helix chain 'A' and resid 301 through 309 Processing helix chain 'A' and resid 317 through 319 No H-bonds generated for 'chain 'A' and resid 317 through 319' Processing helix chain 'A' and resid 340 through 348 Processing helix chain 'A' and resid 357 through 361 Processing helix chain 'A' and resid 378 through 381 Processing helix chain 'A' and resid 384 through 390 Processing helix chain 'A' and resid 393 through 406 removed outlier: 4.982A pdb=" N ALA A 405 " --> pdb=" O ARG A 401 " (cutoff:3.500A) removed outlier: 5.461A pdb=" N PHE A 406 " --> pdb=" O GLU A 402 " (cutoff:3.500A) Processing helix chain 'A' and resid 410 through 412 No H-bonds generated for 'chain 'A' and resid 410 through 412' Processing helix chain 'A' and resid 415 through 431 Processing helix chain 'A' and resid 441 through 452 Processing helix chain 'A' and resid 461 through 478 removed outlier: 4.682A pdb=" N GLN A 465 " --> pdb=" O GLU A 462 " (cutoff:3.500A) Processing helix chain 'A' and resid 481 through 489 Processing helix chain 'A' and resid 494 through 510 removed outlier: 3.659A pdb=" N GLY A 510 " --> pdb=" O GLU A 506 " (cutoff:3.500A) Processing helix chain 'B' and resid 8 through 20 Processing helix chain 'B' and resid 82 through 84 No H-bonds generated for 'chain 'B' and resid 82 through 84' Processing helix chain 'B' and resid 104 through 106 No H-bonds generated for 'chain 'B' and resid 104 through 106' Processing helix chain 'B' and resid 154 through 159 Processing helix chain 'B' and resid 178 through 194 removed outlier: 3.796A pdb=" N GLN B 189 " --> pdb=" O THR B 185 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N ARG B 190 " --> pdb=" O ILE B 186 " (cutoff:3.500A) removed outlier: 5.249A pdb=" N GLU B 191 " --> pdb=" O LEU B 187 " (cutoff:3.500A) removed outlier: 4.821A pdb=" N ALA B 192 " --> pdb=" O ASN B 188 " (cutoff:3.500A) Processing helix chain 'B' and resid 213 through 225 Processing helix chain 'B' and resid 229 through 231 No H-bonds generated for 'chain 'B' and resid 229 through 231' Processing helix chain 'B' and resid 243 through 263 Proline residue: B 250 - end of helix removed outlier: 3.718A pdb=" N TRP B 260 " --> pdb=" O ILE B 256 " (cutoff:3.500A) removed outlier: 3.553A 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: 3.602A pdb=" N LEU B 308 " --> pdb=" O LEU B 304 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N ARG B 311 " --> pdb=" O ARG B 307 " (cutoff:3.500A) Processing helix chain 'B' and resid 340 through 348 Processing helix chain 'B' and resid 357 through 362 Processing helix chain 'B' and resid 384 through 405 removed outlier: 4.985A pdb=" N SER B 392 " --> pdb=" O GLU B 388 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N LEU B 393 " --> pdb=" O VAL B 389 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N LEU B 395 " --> pdb=" O GLY B 391 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N GLU B 402 " --> pdb=" O SER B 398 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ALA B 405 " --> pdb=" O ARG B 401 " (cutoff:3.500A) Processing helix chain 'B' and resid 415 through 431 Processing helix chain 'B' and resid 441 through 452 Processing helix chain 'B' and resid 461 through 477 removed outlier: 4.815A pdb=" N GLN B 465 " --> pdb=" O GLU B 462 " (cutoff:3.500A) Processing helix chain 'B' and resid 481 through 489 Processing helix chain 'B' and resid 494 through 509 Processing helix chain 'C' and resid 9 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 154 through 159 Processing helix chain 'C' and resid 178 through 195 removed outlier: 3.763A pdb=" N GLN C 189 " --> pdb=" O THR C 185 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N ARG C 190 " --> pdb=" O ILE C 186 " (cutoff:3.500A) removed outlier: 5.380A pdb=" N GLU C 191 " --> pdb=" O LEU C 187 " (cutoff:3.500A) removed outlier: 4.967A 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 243 through 263 Proline residue: C 250 - end of helix removed outlier: 3.622A pdb=" N TRP C 260 " --> pdb=" O ILE C 256 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ASN C 263 " --> pdb=" O HIS C 259 " (cutoff:3.500A) Processing helix chain 'C' and resid 274 through 288 Processing helix chain 'C' and resid 294 through 296 No H-bonds generated for 'chain 'C' and resid 294 through 296' Processing helix chain 'C' and resid 301 through 311 removed outlier: 4.182A pdb=" N ARG C 311 " --> pdb=" O ARG C 307 " (cutoff:3.500A) Processing helix chain 'C' and resid 317 through 319 No H-bonds generated for 'chain 'C' and resid 317 through 319' Processing helix chain 'C' and resid 333 through 335 No H-bonds generated for 'chain 'C' and resid 333 through 335' Processing helix chain 'C' and resid 340 through 348 Processing helix chain 'C' and resid 357 through 361 Processing helix chain 'C' and resid 378 through 381 Processing helix chain 'C' and resid 384 through 389 Processing helix chain 'C' and resid 393 through 406 Processing helix chain 'C' and resid 415 through 431 Processing helix chain 'C' and resid 441 through 452 Processing helix chain 'C' and resid 461 through 478 removed outlier: 4.951A pdb=" N GLN C 465 " --> pdb=" O GLU C 462 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N SER C 478 " --> pdb=" O VAL C 475 " (cutoff:3.500A) Processing helix chain 'C' and resid 481 through 489 Processing helix chain 'C' and resid 494 through 509 removed outlier: 3.615A pdb=" N LYS C 509 " --> pdb=" O ASN C 505 " (cutoff:3.500A) Processing helix chain 'D' and resid 43 through 45 No H-bonds generated for 'chain 'D' and resid 43 through 45' Processing helix chain 'D' and resid 92 through 94 No H-bonds generated for 'chain 'D' and resid 92 through 94' Processing helix chain 'D' and resid 127 through 129 No H-bonds generated for 'chain 'D' and resid 127 through 129' Processing helix chain 'D' and resid 142 through 147 Processing helix chain 'D' and resid 166 through 176 Processing helix chain 'D' and resid 194 through 206 Processing helix chain 'D' and resid 210 through 212 No H-bonds generated for 'chain 'D' and resid 210 through 212' Processing helix chain 'D' and resid 224 through 243 removed outlier: 4.936A pdb=" N ALA D 231 " --> pdb=" O ARG D 227 " (cutoff:3.500A) removed outlier: 5.031A pdb=" N LEU D 232 " --> pdb=" O MET D 228 " (cutoff:3.500A) Processing helix chain 'D' and resid 256 through 265 Processing helix chain 'D' and resid 276 through 278 No H-bonds generated for 'chain 'D' and resid 276 through 278' Processing helix chain 'D' and resid 283 through 293 Processing helix chain 'D' and resid 311 through 313 No H-bonds generated for 'chain 'D' and resid 311 through 313' Processing helix chain 'D' and resid 318 through 326 removed outlier: 4.276A pdb=" N ALA D 325 " --> pdb=" O ALA D 321 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N HIS D 326 " --> pdb=" O THR D 322 " (cutoff:3.500A) Processing helix chain 'D' and resid 335 through 339 Processing helix chain 'D' and resid 358 through 361 No H-bonds generated for 'chain 'D' and resid 358 through 361' Processing helix chain 'D' and resid 363 through 389 removed outlier: 4.681A pdb=" N ASP D 384 " --> pdb=" O LYS D 380 " (cutoff:3.500A) removed outlier: 4.796A pdb=" N ILE D 385 " --> pdb=" O ASP D 381 " (cutoff:3.500A) Processing helix chain 'D' and resid 396 through 412 Processing helix chain 'D' and resid 420 through 423 No H-bonds generated for 'chain 'D' and resid 420 through 423' Processing helix chain 'D' and resid 432 through 443 Processing helix chain 'D' and resid 452 through 455 Processing helix chain 'D' and resid 461 through 470 Processing helix chain 'E' and resid 26 through 28 No H-bonds generated for 'chain 'E' and resid 26 through 28' Processing helix chain 'E' and resid 43 through 45 No H-bonds generated for 'chain 'E' and resid 43 through 45' Processing helix chain 'E' and resid 92 through 94 No H-bonds generated for 'chain 'E' and resid 92 through 94' Processing helix chain 'E' and resid 127 through 129 No H-bonds generated for 'chain 'E' and resid 127 through 129' Processing helix chain 'E' and resid 142 through 146 Processing helix chain 'E' and resid 166 through 179 Processing helix chain 'E' and resid 194 through 207 Processing helix chain 'E' and resid 209 through 212 Processing helix chain 'E' and resid 224 through 243 removed outlier: 5.153A pdb=" N ALA E 231 " --> pdb=" O ARG E 227 " (cutoff:3.500A) removed outlier: 4.774A 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 292 Processing helix chain 'E' and resid 311 through 313 No H-bonds generated for 'chain 'E' and resid 311 through 313' Processing helix chain 'E' and resid 318 through 325 removed outlier: 3.628A pdb=" N ALA E 325 " --> pdb=" O ALA E 321 " (cutoff:3.500A) Processing helix chain 'E' and resid 335 through 339 Processing helix chain 'E' and resid 358 through 361 No H-bonds generated for 'chain 'E' and resid 358 through 361' Processing helix chain 'E' and resid 363 through 389 removed outlier: 4.460A pdb=" N ASP E 384 " --> pdb=" O LYS E 380 " (cutoff:3.500A) removed outlier: 4.702A pdb=" N ILE E 385 " --> pdb=" O ASP E 381 " (cutoff:3.500A) 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 469 Processing helix chain 'F' and resid 92 through 94 No H-bonds generated for 'chain 'F' and resid 92 through 94' Processing helix chain 'F' and resid 127 through 129 No H-bonds generated for 'chain 'F' and resid 127 through 129' Processing helix chain 'F' and resid 142 through 147 Processing helix chain 'F' and resid 166 through 177 Processing helix chain 'F' and resid 194 through 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: 4.971A pdb=" N ALA F 231 " --> pdb=" O ARG F 227 " (cutoff:3.500A) removed outlier: 4.633A pdb=" N LEU F 232 " --> pdb=" O MET F 228 " (cutoff:3.500A) Processing helix chain 'F' and resid 256 through 269 Processing helix chain 'F' and resid 276 through 278 No H-bonds generated for 'chain 'F' and resid 276 through 278' Processing helix chain 'F' and resid 283 through 293 Processing helix chain 'F' and resid 311 through 313 No H-bonds generated for 'chain 'F' and resid 311 through 313' Processing helix chain 'F' and resid 318 through 326 removed outlier: 4.476A pdb=" N ALA F 325 " --> pdb=" O ALA F 321 " (cutoff:3.500A) removed outlier: 4.524A pdb=" N HIS F 326 " --> pdb=" O THR F 322 " (cutoff:3.500A) Processing helix chain 'F' and resid 335 through 340 Processing helix chain 'F' and resid 358 through 361 No H-bonds generated for 'chain 'F' and resid 358 through 361' Processing helix chain 'F' and resid 363 through 389 removed outlier: 4.337A pdb=" N ASP F 384 " --> pdb=" O LYS F 380 " (cutoff:3.500A) removed outlier: 5.031A pdb=" N ILE F 385 " --> pdb=" O ASP F 381 " (cutoff:3.500A) removed outlier: 3.835A 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 418 through 423 removed outlier: 3.939A pdb=" N GLN F 421 " --> pdb=" O ALA F 418 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N THR F 423 " --> pdb=" O GLU F 420 " (cutoff:3.500A) Processing helix chain 'F' and resid 432 through 444 Processing helix chain 'F' and resid 452 through 455 Processing helix chain 'F' and resid 461 through 470 Processing helix chain 'G' and resid 4 through 60 Proline residue: G 45 - end of helix Processing helix chain 'G' and resid 66 through 68 No H-bonds generated for 'chain 'G' and resid 66 through 68' Processing helix chain 'G' and resid 92 through 109 Processing helix chain 'G' and resid 121 through 130 Processing helix chain 'G' and resid 147 through 163 Processing helix chain 'G' and resid 173 through 175 No H-bonds generated for 'chain 'G' and resid 173 through 175' Processing helix chain 'G' and resid 228 through 303 Proline residue: G 237 - end of helix Processing helix chain 'H' and resid 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: 3.623A pdb=" N GLN L 50 " --> pdb=" O PRO L 47 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N GLY L 51 " --> pdb=" O GLU L 48 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N PHE L 54 " --> pdb=" O GLY L 51 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N THR L 55 " --> pdb=" O ARG L 52 " (cutoff:3.500A) Proline residue: L 56 - end of helix removed outlier: 3.646A pdb=" N ALA L 66 " --> pdb=" O LEU L 63 " (cutoff:3.500A) removed outlier: 3.727A 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 79 removed outlier: 4.391A pdb=" N GLY M 51 " --> pdb=" O GLU M 48 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N PHE M 54 " --> pdb=" O GLY M 51 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N THR M 55 " --> pdb=" O ARG M 52 " (cutoff:3.500A) Proline residue: M 56 - end of helix removed outlier: 3.763A pdb=" N GLY M 62 " --> pdb=" O ILE M 59 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ALA M 67 " --> pdb=" O VAL M 64 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N VAL M 79 " --> pdb=" O ALA M 76 " (cutoff:3.500A) Processing helix chain 'N' and resid 5 through 45 Processing helix chain 'N' and resid 49 through 80 removed outlier: 4.081A pdb=" N PHE N 54 " --> pdb=" O GLY N 51 " (cutoff:3.500A) removed outlier: 4.860A pdb=" N THR N 55 " --> pdb=" O ARG N 52 " (cutoff:3.500A) Proline residue: N 56 - end of helix removed outlier: 3.535A pdb=" N VAL N 61 " --> pdb=" O PHE N 58 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N PHE N 80 " --> pdb=" O LEU N 77 " (cutoff:3.500A) Processing helix chain 'O' and resid 5 through 45 Processing helix chain 'O' and resid 47 through 80 removed outlier: 3.669A pdb=" N GLY O 51 " --> pdb=" O GLU O 48 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LEU O 53 " --> pdb=" O GLN O 50 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N PHE O 54 " --> pdb=" O GLY O 51 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N THR O 55 " --> pdb=" O ARG O 52 " (cutoff:3.500A) Proline residue: O 56 - end of helix removed outlier: 3.961A pdb=" N ALA O 66 " --> pdb=" O LEU O 63 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N PHE O 80 " --> pdb=" O LEU O 77 " (cutoff:3.500A) Processing helix chain 'P' and resid 5 through 45 Processing helix chain 'P' and resid 47 through 80 removed outlier: 3.735A pdb=" N GLN P 50 " --> pdb=" O PRO P 47 " (cutoff:3.500A) removed outlier: 4.607A pdb=" N GLY P 51 " --> pdb=" O GLU P 48 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N THR P 55 " --> pdb=" O ARG P 52 " (cutoff:3.500A) Proline residue: P 56 - end of helix removed outlier: 3.554A pdb=" N GLU P 65 " --> pdb=" O GLY P 62 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N PHE P 80 " --> pdb=" O LEU P 77 " (cutoff:3.500A) Processing helix chain 'Q' and resid 5 through 45 Processing helix chain 'Q' and resid 47 through 80 removed outlier: 3.631A pdb=" N GLN Q 50 " --> pdb=" O PRO Q 47 " (cutoff:3.500A) removed outlier: 4.861A pdb=" N GLY Q 51 " --> pdb=" O GLU Q 48 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N THR Q 55 " --> pdb=" O ARG Q 52 " (cutoff:3.500A) Proline residue: Q 56 - end of helix removed outlier: 3.623A pdb=" N GLU Q 65 " --> pdb=" O GLY Q 62 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N VAL Q 79 " --> pdb=" O ALA Q 76 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N PHE Q 80 " --> pdb=" O LEU Q 77 " (cutoff:3.500A) Processing helix chain 'R' and resid 5 through 45 Processing helix chain 'R' and resid 47 through 80 removed outlier: 3.604A pdb=" N GLN R 50 " --> pdb=" O PRO R 47 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLY R 51 " --> pdb=" O GLU R 48 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N PHE R 54 " --> pdb=" O GLY R 51 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N THR R 55 " --> pdb=" O ARG R 52 " (cutoff:3.500A) Proline residue: R 56 - end of helix removed outlier: 4.314A pdb=" N GLY R 62 " --> pdb=" O ILE R 59 " (cutoff:3.500A) removed outlier: 4.044A 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 80 removed outlier: 3.859A pdb=" N GLN S 50 " --> pdb=" O PRO S 47 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N GLY S 51 " --> pdb=" O GLU S 48 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N PHE S 54 " --> pdb=" O GLY S 51 " (cutoff:3.500A) Proline residue: S 56 - end of helix removed outlier: 3.746A pdb=" N ILE S 70 " --> pdb=" O ALA S 67 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N PHE S 80 " --> pdb=" O LEU S 77 " (cutoff:3.500A) Processing helix chain 'T' and resid 5 through 45 Processing helix chain 'T' and resid 47 through 80 removed outlier: 4.258A pdb=" N GLY T 51 " --> pdb=" O GLU T 48 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N PHE T 54 " --> pdb=" O GLY T 51 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N THR T 55 " --> pdb=" O ARG T 52 " (cutoff:3.500A) Proline residue: T 56 - end of helix removed outlier: 3.506A pdb=" N VAL T 61 " --> pdb=" O PHE T 58 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N ALA T 66 " --> pdb=" O LEU T 63 " (cutoff:3.500A) Processing helix chain 'a' and resid 29 through 51 Processing helix chain 'a' and resid 61 through 80 Processing helix chain 'a' and resid 87 through 108 Proline residue: a 91 - end of helix removed outlier: 3.722A pdb=" N VAL a 94 " --> pdb=" O PRO a 91 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N THR a 95 " --> pdb=" O LEU a 92 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N PHE a 99 " --> pdb=" O ILE a 96 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ILE a 100 " --> pdb=" O PHE a 97 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N ILE a 102 " --> pdb=" O PHE a 99 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N LEU a 106 " --> pdb=" O SER a 103 " (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 164 removed outlier: 6.618A pdb=" N ILE a 155 " --> pdb=" O TRP a 151 " (cutoff:3.500A) removed outlier: 9.467A pdb=" N VAL a 156 " --> pdb=" O ARG a 152 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLY a 157 " --> pdb=" O ARG a 153 " (cutoff:3.500A) Proline residue: a 159 - end of helix Processing helix chain 'a' and resid 168 through 205 Proline residue: a 172 - end of helix Proline residue: a 182 - end of helix removed outlier: 3.945A pdb=" N LEU a 187 " --> pdb=" O SER a 184 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N ARG a 188 " --> pdb=" O LEU a 185 " (cutoff:3.500A) removed outlier: 4.966A pdb=" N ALA a 195 " --> pdb=" O ASN a 192 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N VAL a 200 " --> pdb=" O GLY a 197 " (cutoff:3.500A) Processing helix chain 'a' and resid 208 through 243 removed outlier: 6.026A pdb=" N PHE a 213 " --> pdb=" O TYR a 209 " (cutoff:3.500A) Proline residue: a 214 - end of helix removed outlier: 3.657A pdb=" N PHE a 224 " --> pdb=" O THR a 220 " (cutoff:3.500A) Processing helix chain 'b' and resid 29 through 45 removed outlier: 3.865A pdb=" N VAL b 34 " --> pdb=" O PHE b 31 " (cutoff:3.500A) Processing helix chain 'b' and resid 50 through 160 removed outlier: 4.528A pdb=" N SER b 146 " --> pdb=" O SER b 142 " (cutoff:3.500A) removed outlier: 4.609A pdb=" N SER b 147 " --> pdb=" O GLY b 143 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N VAL b 148 " --> pdb=" O LEU b 144 " (cutoff:3.500A) removed outlier: 5.583A pdb=" N ASP b 149 " --> pdb=" O GLU b 145 " (cutoff:3.500A) removed outlier: 5.927A pdb=" N GLY b 150 " --> pdb=" O SER b 146 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N LEU b 151 " --> pdb=" O SER b 147 " (cutoff:3.500A) Processing helix chain 'd' and resid 2 through 138 removed outlier: 4.135A pdb=" N VAL d 23 " --> pdb=" O VAL d 19 " (cutoff:3.500A) Proline residue: d 24 - end of helix removed outlier: 3.677A pdb=" N GLU d 70 " --> pdb=" O LYS d 66 " (cutoff:3.500A) Processing helix chain 'd' and resid 140 through 156 removed outlier: 3.516A pdb=" N GLN d 156 " --> pdb=" O SER d 152 " (cutoff:3.500A) Processing helix chain 'd' and resid 174 through 191 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 304 Processing helix chain 'd' and resid 307 through 314 Processing helix chain 'd' and resid 320 through 330 Processing helix chain 'd' and resid 339 through 350 Processing helix chain 'd' and resid 357 through 372 removed outlier: 4.123A 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 432 through 441 Processing sheet with id= A, first strand: chain 'A' and resid 31 through 33 removed outlier: 6.370A pdb=" N GLY A 75 " --> pdb=" O LEU A 67 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ASP A 36 " --> pdb=" O HIS A 43 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N GLU A 45 " --> pdb=" O VAL A 34 " (cutoff:3.500A) removed outlier: 5.563A pdb=" N VAL A 34 " --> pdb=" O GLU A 45 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 99 through 102 Processing sheet with id= C, first strand: chain 'A' and resid 351 through 355 Processing sheet with id= D, first strand: chain 'A' and resid 232 through 237 removed outlier: 6.671A pdb=" N CYS A 204 " --> pdb=" O THR A 233 " (cutoff:3.500A) removed outlier: 7.870A pdb=" N VAL A 235 " --> pdb=" O CYS A 204 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N TYR A 206 " --> pdb=" O VAL A 235 " (cutoff:3.500A) removed outlier: 7.495A pdb=" N ALA A 237 " --> pdb=" O TYR A 206 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N ALA A 208 " --> pdb=" O ALA A 237 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N SER A 323 " --> pdb=" O VAL A 267 " (cutoff:3.500A) removed outlier: 7.718A pdb=" N ILE A 269 " --> pdb=" O SER A 323 " (cutoff:3.500A) removed outlier: 6.110A pdb=" N THR A 325 " --> pdb=" O ILE A 269 " (cutoff:3.500A) removed outlier: 7.627A pdb=" N PHE A 271 " --> pdb=" O THR A 325 " (cutoff:3.500A) removed outlier: 6.804A 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: 3.947A pdb=" N LEU B 63 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N GLY B 75 " --> pdb=" O LEU B 67 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ASP B 36 " --> pdb=" O HIS B 43 " (cutoff:3.500A) removed outlier: 6.141A pdb=" N GLU B 45 " --> pdb=" O VAL B 34 " (cutoff:3.500A) removed outlier: 5.570A 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: 6.720A pdb=" N LEU B 169 " --> pdb=" O CYS B 353 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N LEU B 355 " --> pdb=" O LEU B 169 " (cutoff:3.500A) removed outlier: 6.313A 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: 8.700A pdb=" N THR B 233 " --> pdb=" O VAL B 202 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N CYS B 204 " --> pdb=" O THR B 233 " (cutoff:3.500A) removed outlier: 7.996A pdb=" N VAL B 235 " --> pdb=" O CYS B 204 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N TYR B 206 " --> pdb=" O VAL B 235 " (cutoff:3.500A) removed outlier: 7.444A pdb=" N ALA B 237 " --> pdb=" O TYR B 206 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N ALA B 208 " --> pdb=" O ALA B 237 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N HIS B 266 " --> pdb=" O ARG B 203 " (cutoff:3.500A) removed outlier: 8.016A pdb=" N VAL B 205 " --> pdb=" O HIS B 266 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N LEU B 268 " --> pdb=" O VAL B 205 " (cutoff:3.500A) removed outlier: 7.534A pdb=" N VAL B 207 " --> pdb=" O LEU B 268 " (cutoff:3.500A) removed outlier: 6.209A pdb=" N VAL B 270 " --> pdb=" O VAL B 207 " (cutoff:3.500A) removed outlier: 7.010A pdb=" N ILE B 209 " --> pdb=" O VAL B 270 " (cutoff:3.500A) removed outlier: 6.040A pdb=" N ASP B 272 " --> pdb=" O ILE B 209 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N SER B 323 " --> pdb=" O VAL B 267 " (cutoff:3.500A) removed outlier: 7.781A pdb=" N ILE B 269 " --> pdb=" O SER B 323 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N THR B 325 " --> pdb=" O ILE B 269 " (cutoff:3.500A) removed outlier: 7.566A pdb=" N PHE B 271 " --> pdb=" O THR B 325 " (cutoff:3.500A) No H-bonds generated for sheet with id= H Processing sheet with id= I, first strand: chain 'C' and resid 31 through 33 removed outlier: 6.569A pdb=" N GLY C 75 " --> pdb=" O LEU C 67 " (cutoff:3.500A) removed outlier: 6.099A pdb=" N GLU C 45 " --> pdb=" O VAL C 34 " (cutoff:3.500A) removed outlier: 5.543A pdb=" N VAL C 34 " --> pdb=" O GLU C 45 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'C' and resid 99 through 102 Processing sheet with id= K, first strand: chain 'C' and resid 352 through 355 removed outlier: 6.487A pdb=" N LEU C 169 " --> pdb=" O CYS C 353 " (cutoff:3.500A) removed outlier: 7.166A pdb=" N LEU C 355 " --> pdb=" O LEU C 169 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N ILE C 171 " --> pdb=" O LEU C 355 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'C' and resid 232 through 237 removed outlier: 6.470A pdb=" N CYS C 204 " --> pdb=" O THR C 233 " (cutoff:3.500A) removed outlier: 7.709A pdb=" N VAL C 235 " --> pdb=" O CYS C 204 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N TYR C 206 " --> pdb=" O VAL C 235 " (cutoff:3.500A) removed outlier: 7.504A pdb=" N ALA C 237 " --> pdb=" O TYR C 206 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N ALA C 208 " --> pdb=" O ALA C 237 " (cutoff:3.500A) removed outlier: 6.149A pdb=" N SER C 323 " --> pdb=" O VAL C 267 " (cutoff:3.500A) removed outlier: 7.552A pdb=" N ILE C 269 " --> pdb=" O SER C 323 " (cutoff:3.500A) removed outlier: 6.085A pdb=" N THR C 325 " --> pdb=" O ILE C 269 " (cutoff:3.500A) removed outlier: 7.560A pdb=" N PHE C 271 " --> pdb=" O THR C 325 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N LEU C 327 " --> pdb=" O PHE C 271 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'D' and resid 11 through 16 removed outlier: 6.575A pdb=" N ASP D 21 " --> pdb=" O VAL D 13 " (cutoff:3.500A) removed outlier: 4.613A pdb=" N ILE D 15 " --> pdb=" O VAL D 19 " (cutoff:3.500A) removed outlier: 7.067A pdb=" N VAL D 19 " --> pdb=" O ILE D 15 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N ILE D 65 " --> pdb=" O VAL D 53 " (cutoff:3.500A) removed outlier: 5.641A 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: 7.318A pdb=" N ILE D 156 " --> pdb=" O ILE D 302 " (cutoff:3.500A) removed outlier: 6.136A pdb=" N SER D 304 " --> pdb=" O ILE D 156 " (cutoff:3.500A) removed outlier: 7.803A pdb=" N LEU D 158 " --> pdb=" O SER D 304 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N GLN D 306 " --> pdb=" O LEU D 158 " (cutoff:3.500A) removed outlier: 7.819A pdb=" N GLY D 160 " --> pdb=" O GLN D 306 " (cutoff:3.500A) removed outlier: 5.949A pdb=" N VAL D 308 " --> pdb=" O GLY D 160 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N VAL D 249 " --> pdb=" O THR D 303 " (cutoff:3.500A) removed outlier: 7.813A pdb=" N MET D 305 " --> pdb=" O VAL D 249 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N LEU D 251 " --> pdb=" O MET D 305 " (cutoff:3.500A) removed outlier: 7.753A pdb=" N ALA D 307 " --> pdb=" O LEU D 251 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N ILE D 253 " --> pdb=" O ALA D 307 " (cutoff:3.500A) removed outlier: 8.255A pdb=" N TYR D 309 " --> pdb=" O ILE D 253 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N THR D 184 " --> pdb=" O LEU D 250 " (cutoff:3.500A) removed outlier: 8.160A pdb=" N PHE D 252 " --> pdb=" O THR D 184 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N VAL D 186 " --> pdb=" O PHE D 252 " (cutoff:3.500A) removed outlier: 8.016A pdb=" N ASP D 254 " --> pdb=" O VAL D 186 " (cutoff:3.500A) removed outlier: 6.255A 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: 6.522A pdb=" N ASP E 21 " --> pdb=" O VAL E 13 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N ILE E 15 " --> pdb=" O VAL E 19 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N VAL E 19 " --> pdb=" O ILE E 15 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N ILE E 65 " --> pdb=" O VAL E 53 " (cutoff:3.500A) removed outlier: 5.847A 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 333 removed outlier: 8.170A pdb=" N ILE E 156 " --> pdb=" O ILE E 302 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N SER E 304 " --> pdb=" O ILE E 156 " (cutoff:3.500A) removed outlier: 7.475A pdb=" N LEU E 158 " --> pdb=" O SER E 304 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N GLN E 306 " --> pdb=" O LEU E 158 " (cutoff:3.500A) removed outlier: 8.538A pdb=" N GLY E 160 " --> pdb=" O GLN E 306 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N VAL E 249 " --> pdb=" O THR E 303 " (cutoff:3.500A) removed outlier: 8.055A pdb=" N MET E 305 " --> pdb=" O VAL E 249 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N LEU E 251 " --> pdb=" O MET E 305 " (cutoff:3.500A) removed outlier: 7.555A pdb=" N ALA E 307 " --> pdb=" O LEU E 251 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N ILE E 253 " --> pdb=" O ALA E 307 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'F' and resid 11 through 16 removed outlier: 6.578A pdb=" N ASP F 21 " --> pdb=" O VAL F 13 " (cutoff:3.500A) removed outlier: 4.713A pdb=" N ILE F 15 " --> pdb=" O VAL F 19 " (cutoff:3.500A) removed outlier: 7.096A pdb=" N VAL F 19 " --> pdb=" O ILE F 15 " (cutoff:3.500A) removed outlier: 6.169A pdb=" N ILE F 65 " --> pdb=" O VAL F 53 " (cutoff:3.500A) removed outlier: 5.609A 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: 7.481A pdb=" N ILE F 156 " --> pdb=" O ILE F 302 " (cutoff:3.500A) removed outlier: 6.160A pdb=" N SER F 304 " --> pdb=" O ILE F 156 " (cutoff:3.500A) removed outlier: 7.848A pdb=" N LEU F 158 " --> pdb=" O SER F 304 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N GLN F 306 " --> pdb=" O LEU F 158 " (cutoff:3.500A) removed outlier: 8.028A pdb=" N GLY F 160 " --> pdb=" O GLN F 306 " (cutoff:3.500A) removed outlier: 6.242A pdb=" N VAL F 308 " --> pdb=" O GLY F 160 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N THR F 184 " --> pdb=" O LEU F 250 " (cutoff:3.500A) removed outlier: 7.986A pdb=" N PHE F 252 " --> pdb=" O THR F 184 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N VAL F 186 " --> pdb=" O PHE F 252 " (cutoff:3.500A) removed outlier: 7.979A pdb=" N ASP F 254 " --> pdb=" O VAL F 186 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N ALA F 188 " --> pdb=" O ASP F 254 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'G' and resid 197 through 204 removed outlier: 6.530A pdb=" N LEU G 183 " --> pdb=" O ALA G 203 " (cutoff:3.500A) removed outlier: 8.515A pdb=" N HIS G 184 " --> pdb=" O ARG G 76 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N GLY G 78 " --> pdb=" O HIS G 184 " (cutoff:3.500A) removed outlier: 7.412A pdb=" N VAL G 186 " --> pdb=" O GLY G 78 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N LEU G 80 " --> pdb=" O VAL G 186 " (cutoff:3.500A) removed outlier: 8.502A pdb=" N THR G 188 " --> pdb=" O LEU G 80 " (cutoff:3.500A) removed outlier: 9.129A pdb=" N VAL G 82 " --> pdb=" O THR G 188 " (cutoff:3.500A) removed outlier: 6.128A pdb=" N ASP G 113 " --> pdb=" O ALA G 77 " (cutoff:3.500A) removed outlier: 7.297A pdb=" N VAL G 79 " --> pdb=" O ASP G 113 " (cutoff:3.500A) removed outlier: 5.959A pdb=" N VAL G 115 " --> pdb=" O VAL G 79 " (cutoff:3.500A) removed outlier: 7.145A pdb=" N VAL G 81 " --> pdb=" O VAL G 115 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N TYR G 117 " --> pdb=" O VAL G 81 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N GLU G 136 " --> pdb=" O VAL G 118 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'H' and resid 41 through 44 removed outlier: 6.065A pdb=" N ASN H 5 " --> pdb=" O VAL H 77 " (cutoff:3.500A) removed outlier: 7.754A pdb=" N ILE H 79 " --> pdb=" O ASN H 5 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N GLU H 7 " --> pdb=" O ILE H 79 " (cutoff:3.500A) removed outlier: 7.092A pdb=" N VAL H 81 " --> pdb=" O GLU H 7 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N VAL H 9 " --> pdb=" O VAL H 81 " (cutoff:3.500A) removed outlier: 5.672A pdb=" N ALA H 10 " --> pdb=" O GLU H 14 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N GLU H 14 " --> pdb=" O ALA H 10 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'H' and resid 31 through 34 removed outlier: 3.987A pdb=" N ARG H 26 " --> pdb=" O MET H 50 " (cutoff:3.500A) removed outlier: 5.533A pdb=" N MET H 50 " --> pdb=" O ARG H 26 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'a' and resid 20 through 22 Processing sheet with id= Z, first strand: chain 'a' and resid 112 through 114 Processing sheet with id= AA, first strand: chain 'd' and resid 406 through 411 2133 hydrogen bonds defined for protein. 5307 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 27.82 Time building geometry restraints manager: 55.20 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: 37285 1.03 - 1.23: 22 1.23 - 1.42: 15324 1.42 - 1.61: 22327 1.61 - 1.81: 194 Bond restraints: 75152 Sorted by residual: bond pdb=" CG1 ILE R 30 " pdb=" CD1 ILE R 30 " ideal model delta sigma weight residual 1.513 1.442 0.071 3.90e-02 6.57e+02 3.30e+00 bond pdb=" C4 ADP D 600 " pdb=" C5 ADP D 600 " ideal model delta sigma weight residual 1.490 1.464 0.026 2.00e-02 2.50e+03 1.67e+00 bond pdb=" CG PRO F 344 " pdb=" CD PRO F 344 " ideal model delta sigma weight residual 1.512 1.481 0.031 2.70e-02 1.37e+03 1.36e+00 bond pdb=" CG1 ILE S 30 " pdb=" CD1 ILE S 30 " ideal model delta sigma weight residual 1.513 1.468 0.045 3.90e-02 6.57e+02 1.34e+00 bond pdb=" C4 ADP E 600 " pdb=" C5 ADP E 600 " ideal model delta sigma weight residual 1.490 1.468 0.022 2.00e-02 2.50e+03 1.25e+00 ... (remaining 75147 not shown) Histogram of bond angle deviations from ideal: 98.56 - 106.84: 1199 106.84 - 115.12: 96115 115.12 - 123.40: 32840 123.40 - 131.69: 5967 131.69 - 139.97: 43 Bond angle restraints: 136164 Sorted by residual: angle pdb=" N GLU b 102 " pdb=" CA GLU b 102 " pdb=" CB GLU b 102 " ideal model delta sigma weight residual 110.28 115.21 -4.93 1.55e+00 4.16e-01 1.01e+01 angle pdb=" N ILE C 337 " pdb=" CA ILE C 337 " pdb=" C ILE C 337 " ideal model delta sigma weight residual 112.80 109.64 3.16 1.15e+00 7.56e-01 7.56e+00 angle pdb=" C ASP b 101 " pdb=" N GLU b 102 " pdb=" CA GLU b 102 " ideal model delta sigma weight residual 120.31 116.17 4.14 1.52e+00 4.33e-01 7.43e+00 angle pdb=" C3' ATP F 600 " pdb=" C4' ATP F 600 " pdb=" O4' ATP F 600 " ideal model delta sigma weight residual 105.22 101.80 3.42 1.30e+00 5.94e-01 6.96e+00 angle pdb=" N GLY E 218 " pdb=" CA GLY E 218 " pdb=" C GLY E 218 " ideal model delta sigma weight residual 113.18 107.00 6.18 2.37e+00 1.78e-01 6.80e+00 ... (remaining 136159 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.10: 29001 34.10 - 68.19: 415 68.19 - 102.29: 57 102.29 - 136.39: 1 136.39 - 170.48: 1 Dihedral angle restraints: 29475 sinusoidal: 13794 harmonic: 15681 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 -60.00 110.48 -170.48 1 2.00e+01 2.50e-03 4.77e+01 dihedral pdb=" C5' ADP E 600 " pdb=" O5' ADP E 600 " pdb=" PA ADP E 600 " pdb=" O2A ADP E 600 " ideal model delta sinusoidal sigma weight residual 300.00 167.56 132.44 1 2.00e+01 2.50e-03 4.02e+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 -155.58 95.57 1 2.00e+01 2.50e-03 2.63e+01 ... (remaining 29472 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.060: 5222 0.060 - 0.119: 672 0.119 - 0.179: 55 0.179 - 0.239: 2 0.239 - 0.299: 10 Chirality restraints: 5961 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 2.23e+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 2.04e+00 chirality pdb=" C2' ATP F 600 " pdb=" C1' ATP F 600 " pdb=" C3' ATP F 600 " pdb=" O2' ATP F 600 " both_signs ideal model delta sigma weight residual False -2.68 -2.97 0.29 2.00e-01 2.50e+01 2.03e+00 ... (remaining 5958 not shown) Planarity restraints: 11419 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP B 484 " 0.012 2.00e-02 2.50e+03 2.40e-02 5.76e+00 pdb=" C ASP B 484 " -0.042 2.00e-02 2.50e+03 pdb=" O ASP B 484 " 0.015 2.00e-02 2.50e+03 pdb=" N GLY B 485 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG E 26 " 0.208 9.50e-02 1.11e+02 6.94e-02 5.28e+00 pdb=" NE ARG E 26 " -0.013 2.00e-02 2.50e+03 pdb=" CZ ARG E 26 " 0.003 2.00e-02 2.50e+03 pdb=" NH1 ARG E 26 " -0.001 2.00e-02 2.50e+03 pdb=" NH2 ARG E 26 " 0.003 2.00e-02 2.50e+03 pdb="HH11 ARG E 26 " -0.002 2.00e-02 2.50e+03 pdb="HH12 ARG E 26 " 0.001 2.00e-02 2.50e+03 pdb="HH21 ARG E 26 " 0.001 2.00e-02 2.50e+03 pdb="HH22 ARG E 26 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY T 22 " 0.009 2.00e-02 2.50e+03 1.86e-02 3.45e+00 pdb=" C GLY T 22 " -0.032 2.00e-02 2.50e+03 pdb=" O GLY T 22 " 0.012 2.00e-02 2.50e+03 pdb=" N GLY T 23 " 0.011 2.00e-02 2.50e+03 ... (remaining 11416 not shown) Histogram of nonbonded interaction distances: 1.54 - 2.15: 3195 2.15 - 2.77: 147941 2.77 - 3.38: 225742 3.38 - 3.99: 291542 3.99 - 4.60: 459154 Nonbonded interactions: 1127574 Sorted by model distance: nonbonded pdb="HH21 ARG H 55 " pdb=" O ASP H 59 " model vdw 1.543 1.850 nonbonded pdb=" O GLY B 485 " pdb=" HG1 THR B 489 " model vdw 1.554 1.850 nonbonded pdb=" O PRO a 207 " pdb=" H GLN a 211 " model vdw 1.563 1.850 nonbonded pdb=" OG SER d 176 " pdb=" H SER d 262 " model vdw 1.584 1.850 nonbonded pdb=" O PHE a 190 " pdb=" H PHE a 194 " model vdw 1.587 1.850 ... (remaining 1127569 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 7 through 173 or resid 175 through 353 or resid 356 throug \ h 406 or (resid 414 and (name N or name CA or name C or name O or name CB or nam \ e CG or name OD1 or name OD2 or name HA or name HB2 or name HB3)) or resid 415 t \ hrough 521 or resid 600 through 601)) selection = (chain 'B' and ((resid 7 and (name N or name CA or name C or name O or name CB o \ r name OG or name HA or name HB2 or name HB3 or name HG )) or resid 8 through 22 \ or (resid 29 and (name N or name CA or name C or name O or name CB or name CG o \ r name CD or name OE1 or name OE2 or name HA or name HB2 or name HB3 or name HG2 \ or name HG3)) or resid 30 through 173 or resid 175 through 353 or resid 356 thr \ ough 521 or resid 600 through 601)) selection = (chain 'C' and ((resid 7 and (name N or name CA or name C or name O or name CB o \ r name OG or name HA or name HB2 or name HB3 or name HG )) or resid 8 through 17 \ 3 or resid 175 through 353 or resid 356 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 na \ me HA or name HB2 or name HB3)) or resid 415 through 521 or resid 600 through 60 \ 1)) } 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' and ((resid 4 and (name N or name CA or name C or name O or name CB o \ r name CG or name OD1 or name OD2 or name HA or name HB2 or name HB3)) or resid \ 5 through 85)) selection = (chain 'M' and ((resid 4 and (name N or name CA or name C or name O or name CB o \ r name CG or name OD1 or name OD2 or name HA or name HB2 or name HB3)) or resid \ 5 through 85)) selection = (chain 'N' and ((resid 4 and (name N or name CA or name C or name O or name CB o \ r name CG or name OD1 or name OD2 or name HA or name HB2 or name HB3)) or resid \ 5 through 85)) selection = chain 'O' selection = (chain 'P' and ((resid 4 and (name N or name CA or name C or name O or name CB o \ r name CG or name OD1 or name OD2 or name HA or name HB2 or name HB3)) or resid \ 5 through 85)) selection = (chain 'Q' and ((resid 4 and (name N or name CA or name C or name O or name CB o \ r name CG or name OD1 or name OD2 or name HA or name HB2 or name HB3)) or resid \ 5 through 85)) selection = (chain 'R' and ((resid 4 and (name N or name CA or name C or name O or name CB o \ r name CG or name OD1 or name OD2 or name HA or name HB2 or name HB3)) or resid \ 5 through 85)) selection = (chain 'S' and ((resid 4 and (name N or name CA or name C or name O or name CB o \ r name CG or name OD1 or name OD2 or name HA or name HB2 or name HB3)) or resid \ 5 through 85)) selection = (chain 'T' and ((resid 4 and (name N or name CA or name C or name O or name CB o \ r name CG or name OD1 or name OD2 or name HA or name HB2 or name HB3)) or resid \ 5 through 85)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians P 16 5.49 5 Mg 5 5.21 5 S 107 5.16 5 C 23556 2.51 5 N 6393 2.21 5 O 7172 1.98 5 H 37305 0.53 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.20 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 14.840 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: 0.910 Extract box with map and model: 31.100 Check model and map are aligned: 0.860 Convert atoms to be neutral: 0.510 Process input model: 199.800 Find NCS groups from input model: 3.550 Set up NCS constraints: 0.330 Set refine NCS operators: 0.000 Set scattering table: 0.020 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:13.490 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 265.420 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8604 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.071 37847 Z= 0.205 Angle : 0.494 6.743 51337 Z= 0.263 Chirality : 0.041 0.299 5961 Planarity : 0.003 0.092 6715 Dihedral : 14.363 170.482 13723 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.26 % Favored : 97.70 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.92 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.92 (0.13), residues: 4884 helix: 2.15 (0.10), residues: 2664 sheet: 0.09 (0.22), residues: 526 loop : 0.36 (0.16), residues: 1694 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9768 Ramachandran restraints generated. 4884 Oldfield, 0 Emsley, 4884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9768 Ramachandran restraints generated. 4884 Oldfield, 0 Emsley, 4884 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 360 residues out of total 3833 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 360 time to evaluate : 4.708 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 360 average time/residue: 2.3059 time to fit residues: 1047.4840 Evaluate side-chains 224 residues out of total 3833 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 224 time to evaluate : 4.528 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 5.3836 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 483 random chunks: chunk 407 optimal weight: 10.0000 chunk 366 optimal weight: 5.9990 chunk 203 optimal weight: 2.9990 chunk 125 optimal weight: 2.9990 chunk 246 optimal weight: 2.9990 chunk 195 optimal weight: 1.9990 chunk 378 optimal weight: 4.9990 chunk 146 optimal weight: 1.9990 chunk 230 optimal weight: 1.9990 chunk 281 optimal weight: 1.9990 chunk 438 optimal weight: 10.0000 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 420 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 399 GLN ** S 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 178 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8639 moved from start: 0.0675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.076 37847 Z= 0.354 Angle : 0.537 8.489 51337 Z= 0.285 Chirality : 0.041 0.148 5961 Planarity : 0.004 0.038 6715 Dihedral : 5.153 145.740 5284 Min Nonbonded Distance : 1.608 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.65 % Favored : 97.31 % Rotamer Outliers : 0.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.92 % 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: 4884 helix: 1.80 (0.10), residues: 2632 sheet: 0.07 (0.22), residues: 528 loop : 0.26 (0.16), residues: 1724 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9768 Ramachandran restraints generated. 4884 Oldfield, 0 Emsley, 4884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9768 Ramachandran restraints generated. 4884 Oldfield, 0 Emsley, 4884 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 272 residues out of total 3833 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 246 time to evaluate : 5.032 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 26 outliers final: 13 residues processed: 262 average time/residue: 2.1502 time to fit residues: 722.0482 Evaluate side-chains 237 residues out of total 3833 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 224 time to evaluate : 4.586 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 8 residues processed: 6 average time/residue: 1.2562 time to fit residues: 16.4422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 483 random chunks: chunk 243 optimal weight: 5.9990 chunk 136 optimal weight: 1.9990 chunk 365 optimal weight: 2.9990 chunk 298 optimal weight: 3.9990 chunk 120 optimal weight: 1.9990 chunk 439 optimal weight: 5.9990 chunk 474 optimal weight: 4.9990 chunk 391 optimal weight: 1.9990 chunk 435 optimal weight: 0.9980 chunk 149 optimal weight: 2.9990 chunk 352 optimal weight: 0.0050 overall best weight: 1.4000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 420 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 399 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8628 moved from start: 0.0708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.064 37847 Z= 0.241 Angle : 0.509 8.720 51337 Z= 0.265 Chirality : 0.040 0.148 5961 Planarity : 0.004 0.047 6715 Dihedral : 4.918 125.710 5284 Min Nonbonded Distance : 1.698 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.46 % Favored : 97.50 % Rotamer Outliers : 0.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.92 % 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: 1.53 (0.12), residues: 4884 helix: 1.73 (0.10), residues: 2663 sheet: 0.06 (0.22), residues: 528 loop : 0.34 (0.16), residues: 1693 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9768 Ramachandran restraints generated. 4884 Oldfield, 0 Emsley, 4884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9768 Ramachandran restraints generated. 4884 Oldfield, 0 Emsley, 4884 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 259 residues out of total 3833 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 240 time to evaluate : 4.656 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 19 outliers final: 7 residues processed: 254 average time/residue: 2.0826 time to fit residues: 684.2258 Evaluate side-chains 232 residues out of total 3833 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 225 time to evaluate : 4.509 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 5 residues processed: 2 average time/residue: 1.2264 time to fit residues: 8.9442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 483 random chunks: chunk 434 optimal weight: 5.9990 chunk 330 optimal weight: 9.9990 chunk 228 optimal weight: 2.9990 chunk 48 optimal weight: 0.3980 chunk 209 optimal weight: 0.0980 chunk 295 optimal weight: 0.6980 chunk 440 optimal weight: 6.9990 chunk 466 optimal weight: 3.9990 chunk 230 optimal weight: 1.9990 chunk 417 optimal weight: 6.9990 chunk 125 optimal weight: 1.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 420 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 399 GLN R 71 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8620 moved from start: 0.0768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.064 37847 Z= 0.200 Angle : 0.494 8.678 51337 Z= 0.256 Chirality : 0.039 0.175 5961 Planarity : 0.003 0.038 6715 Dihedral : 4.704 111.972 5284 Min Nonbonded Distance : 1.740 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.46 % Favored : 97.50 % Rotamer Outliers : 0.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.92 % 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 (0.13), residues: 4884 helix: 1.79 (0.10), residues: 2675 sheet: 0.07 (0.22), residues: 528 loop : 0.40 (0.16), residues: 1681 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9768 Ramachandran restraints generated. 4884 Oldfield, 0 Emsley, 4884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9768 Ramachandran restraints generated. 4884 Oldfield, 0 Emsley, 4884 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 266 residues out of total 3833 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 242 time to evaluate : 4.669 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 24 outliers final: 8 residues processed: 261 average time/residue: 2.1462 time to fit residues: 722.1455 Evaluate side-chains 233 residues out of total 3833 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 225 time to evaluate : 4.568 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 5 residues processed: 3 average time/residue: 1.2578 time to fit residues: 11.7771 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 483 random chunks: chunk 388 optimal weight: 5.9990 chunk 265 optimal weight: 2.9990 chunk 6 optimal weight: 2.9990 chunk 347 optimal weight: 9.9990 chunk 192 optimal weight: 2.9990 chunk 398 optimal weight: 5.9990 chunk 322 optimal weight: 8.9990 chunk 0 optimal weight: 8.9990 chunk 238 optimal weight: 3.9990 chunk 419 optimal weight: 2.9990 chunk 117 optimal weight: 0.5980 overall best weight: 2.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 420 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 399 GLN T 71 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8651 moved from start: 0.0933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.080 37847 Z= 0.407 Angle : 0.546 9.041 51337 Z= 0.286 Chirality : 0.042 0.159 5961 Planarity : 0.004 0.038 6715 Dihedral : 4.872 107.463 5284 Min Nonbonded Distance : 1.649 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.81 % Favored : 97.15 % Rotamer Outliers : 0.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.92 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.42 (0.12), residues: 4884 helix: 1.64 (0.10), residues: 2662 sheet: 0.08 (0.22), residues: 528 loop : 0.24 (0.16), residues: 1694 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9768 Ramachandran restraints generated. 4884 Oldfield, 0 Emsley, 4884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9768 Ramachandran restraints generated. 4884 Oldfield, 0 Emsley, 4884 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 252 residues out of total 3833 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 223 time to evaluate : 4.573 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 29 outliers final: 18 residues processed: 244 average time/residue: 2.1065 time to fit residues: 663.0780 Evaluate side-chains 235 residues out of total 3833 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 217 time to evaluate : 4.456 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 14 residues processed: 6 average time/residue: 1.3742 time to fit residues: 17.0818 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 483 random chunks: chunk 157 optimal weight: 1.9990 chunk 420 optimal weight: 1.9990 chunk 92 optimal weight: 0.3980 chunk 274 optimal weight: 0.9990 chunk 115 optimal weight: 0.9990 chunk 467 optimal weight: 3.9990 chunk 387 optimal weight: 5.9990 chunk 216 optimal weight: 2.9990 chunk 38 optimal weight: 3.9990 chunk 154 optimal weight: 1.9990 chunk 245 optimal weight: 0.6980 overall best weight: 1.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 420 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 399 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8625 moved from start: 0.0891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.060 37847 Z= 0.197 Angle : 0.500 8.828 51337 Z= 0.257 Chirality : 0.039 0.164 5961 Planarity : 0.003 0.034 6715 Dihedral : 4.707 104.312 5284 Min Nonbonded Distance : 1.731 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.38 % Favored : 97.58 % Rotamer Outliers : 0.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.92 % 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: 1.60 (0.13), residues: 4884 helix: 1.78 (0.10), residues: 2661 sheet: 0.07 (0.22), residues: 528 loop : 0.39 (0.16), residues: 1695 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9768 Ramachandran restraints generated. 4884 Oldfield, 0 Emsley, 4884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9768 Ramachandran restraints generated. 4884 Oldfield, 0 Emsley, 4884 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 257 residues out of total 3833 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 236 time to evaluate : 4.676 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 21 outliers final: 14 residues processed: 250 average time/residue: 2.2025 time to fit residues: 715.1768 Evaluate side-chains 234 residues out of total 3833 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 220 time to evaluate : 4.559 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 11 residues processed: 4 average time/residue: 1.3603 time to fit residues: 13.3526 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 483 random chunks: chunk 450 optimal weight: 4.9990 chunk 52 optimal weight: 4.9990 chunk 266 optimal weight: 0.9980 chunk 341 optimal weight: 6.9990 chunk 264 optimal weight: 1.9990 chunk 393 optimal weight: 2.9990 chunk 260 optimal weight: 2.9990 chunk 465 optimal weight: 5.9990 chunk 291 optimal weight: 2.9990 chunk 283 optimal weight: 2.9990 chunk 214 optimal weight: 3.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 420 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 399 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8652 moved from start: 0.1019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.079 37847 Z= 0.382 Angle : 0.544 8.957 51337 Z= 0.284 Chirality : 0.041 0.181 5961 Planarity : 0.004 0.037 6715 Dihedral : 4.849 100.269 5284 Min Nonbonded Distance : 1.644 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.95 % Favored : 97.01 % Rotamer Outliers : 0.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.92 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.42 (0.12), residues: 4884 helix: 1.64 (0.10), residues: 2659 sheet: 0.07 (0.22), residues: 528 loop : 0.25 (0.16), residues: 1697 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9768 Ramachandran restraints generated. 4884 Oldfield, 0 Emsley, 4884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9768 Ramachandran restraints generated. 4884 Oldfield, 0 Emsley, 4884 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 251 residues out of total 3833 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 223 time to evaluate : 4.651 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 28 outliers final: 15 residues processed: 246 average time/residue: 2.1481 time to fit residues: 681.9070 Evaluate side-chains 230 residues out of total 3833 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 215 time to evaluate : 4.538 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 12 residues processed: 4 average time/residue: 1.3763 time to fit residues: 13.2564 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 483 random chunks: chunk 288 optimal weight: 1.9990 chunk 185 optimal weight: 2.9990 chunk 278 optimal weight: 0.4980 chunk 140 optimal weight: 0.4980 chunk 91 optimal weight: 3.9990 chunk 90 optimal weight: 3.9990 chunk 295 optimal weight: 0.5980 chunk 317 optimal weight: 2.9990 chunk 230 optimal weight: 0.9990 chunk 43 optimal weight: 1.9990 chunk 365 optimal weight: 0.8980 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 420 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 399 GLN T 71 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8619 moved from start: 0.0965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.043 37847 Z= 0.164 Angle : 0.500 8.690 51337 Z= 0.255 Chirality : 0.039 0.186 5961 Planarity : 0.003 0.035 6715 Dihedral : 4.647 96.587 5284 Min Nonbonded Distance : 1.760 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.30 % Favored : 97.66 % Rotamer Outliers : 0.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.92 % 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 (0.13), residues: 4884 helix: 1.82 (0.10), residues: 2656 sheet: 0.05 (0.22), residues: 528 loop : 0.41 (0.16), residues: 1700 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9768 Ramachandran restraints generated. 4884 Oldfield, 0 Emsley, 4884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9768 Ramachandran restraints generated. 4884 Oldfield, 0 Emsley, 4884 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 257 residues out of total 3833 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 233 time to evaluate : 4.628 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 24 outliers final: 14 residues processed: 251 average time/residue: 2.1748 time to fit residues: 711.3386 Evaluate side-chains 235 residues out of total 3833 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 221 time to evaluate : 4.610 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 12 residues processed: 3 average time/residue: 1.6394 time to fit residues: 12.2295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 483 random chunks: chunk 423 optimal weight: 0.8980 chunk 445 optimal weight: 5.9990 chunk 406 optimal weight: 6.9990 chunk 433 optimal weight: 6.9990 chunk 261 optimal weight: 0.0770 chunk 188 optimal weight: 0.0040 chunk 340 optimal weight: 4.9990 chunk 133 optimal weight: 3.9990 chunk 392 optimal weight: 4.9990 chunk 410 optimal weight: 0.8980 chunk 432 optimal weight: 0.6980 overall best weight: 0.5150 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 420 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 399 GLN T 71 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8609 moved from start: 0.1014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.049 37847 Z= 0.156 Angle : 0.495 10.818 51337 Z= 0.251 Chirality : 0.039 0.201 5961 Planarity : 0.003 0.075 6715 Dihedral : 4.489 86.627 5284 Min Nonbonded Distance : 1.804 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.40 % Favored : 97.56 % Rotamer Outliers : 0.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.92 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.77 (0.13), residues: 4884 helix: 1.92 (0.10), residues: 2658 sheet: 0.08 (0.22), residues: 528 loop : 0.47 (0.17), residues: 1698 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9768 Ramachandran restraints generated. 4884 Oldfield, 0 Emsley, 4884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9768 Ramachandran restraints generated. 4884 Oldfield, 0 Emsley, 4884 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 247 residues out of total 3833 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 233 time to evaluate : 4.564 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 14 outliers final: 11 residues processed: 244 average time/residue: 2.2453 time to fit residues: 709.6083 Evaluate side-chains 233 residues out of total 3833 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 222 time to evaluate : 4.620 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 10 residues processed: 1 average time/residue: 2.3761 time to fit residues: 8.4958 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 483 random chunks: chunk 284 optimal weight: 2.9990 chunk 458 optimal weight: 5.9990 chunk 279 optimal weight: 0.0970 chunk 217 optimal weight: 2.9990 chunk 318 optimal weight: 1.9990 chunk 481 optimal weight: 2.9990 chunk 442 optimal weight: 0.4980 chunk 383 optimal weight: 0.5980 chunk 39 optimal weight: 4.9990 chunk 295 optimal weight: 0.9990 chunk 234 optimal weight: 0.0970 overall best weight: 0.4578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 420 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 399 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8600 moved from start: 0.1132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.044 37847 Z= 0.149 Angle : 0.493 11.306 51337 Z= 0.248 Chirality : 0.039 0.147 5961 Planarity : 0.003 0.075 6715 Dihedral : 4.376 76.698 5284 Min Nonbonded Distance : 1.817 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.13 % Favored : 97.83 % Rotamer Outliers : 0.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.92 % 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: 1.87 (0.13), residues: 4884 helix: 2.01 (0.10), residues: 2658 sheet: 0.12 (0.22), residues: 528 loop : 0.52 (0.17), residues: 1698 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9768 Ramachandran restraints generated. 4884 Oldfield, 0 Emsley, 4884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9768 Ramachandran restraints generated. 4884 Oldfield, 0 Emsley, 4884 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 253 residues out of total 3833 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 239 time to evaluate : 4.745 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 14 outliers final: 11 residues processed: 250 average time/residue: 2.1386 time to fit residues: 694.6580 Evaluate side-chains 238 residues out of total 3833 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 227 time to evaluate : 4.556 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 10 residues processed: 1 average time/residue: 2.2367 time to fit residues: 8.2884 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 483 random chunks: chunk 304 optimal weight: 3.9990 chunk 408 optimal weight: 3.9990 chunk 117 optimal weight: 0.9990 chunk 353 optimal weight: 1.9990 chunk 56 optimal weight: 2.9990 chunk 106 optimal weight: 2.9990 chunk 383 optimal weight: 0.6980 chunk 160 optimal weight: 0.1980 chunk 394 optimal weight: 4.9990 chunk 48 optimal weight: 2.9990 chunk 70 optimal weight: 2.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 420 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 399 GLN G 159 ASN T 71 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.081229 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.057470 restraints weight = 327129.849| |-----------------------------------------------------------------------------| r_work (start): 0.2959 rms_B_bonded: 1.89 r_work: 0.2873 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.2766 rms_B_bonded: 3.48 restraints_weight: 0.2500 r_work (final): 0.2766 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3527 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3527 r_free = 0.3527 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3527 r_free = 0.3527 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3527 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8805 moved from start: 0.1102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.050 37847 Z= 0.246 Angle : 0.519 12.250 51337 Z= 0.264 Chirality : 0.039 0.145 5961 Planarity : 0.003 0.071 6715 Dihedral : 4.473 70.677 5284 Min Nonbonded Distance : 1.700 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.56 % Favored : 97.40 % Rotamer Outliers : 0.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.92 % 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: 4884 helix: 1.95 (0.10), residues: 2657 sheet: 0.12 (0.22), residues: 528 loop : 0.45 (0.16), residues: 1699 =============================================================================== Job complete usr+sys time: 14833.61 seconds wall clock time: 257 minutes 5.72 seconds (15425.72 seconds total)