Starting phenix.real_space_refine on Mon Mar 25 00:16:42 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nkh_12439/03_2024/7nkh_12439_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nkh_12439/03_2024/7nkh_12439.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.78 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nkh_12439/03_2024/7nkh_12439.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nkh_12439/03_2024/7nkh_12439.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nkh_12439/03_2024/7nkh_12439_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nkh_12439/03_2024/7nkh_12439_trim_updated.pdb" } resolution = 2.78 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians P 16 5.49 5 Mg 5 5.21 5 S 71 5.16 5 C 14224 2.51 5 N 3941 2.21 5 O 4455 1.98 5 H 22565 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 29": "OE1" <-> "OE2" Residue "B PHE 406": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ASP 273": "OD1" <-> "OD2" Residue "D GLU 397": "OE1" <-> "OE2" Residue "E PHE 159": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E ASP 384": "OD1" <-> "OD2" Residue "F GLU 332": "OE1" <-> "OE2" Residue "F ASP 398": "OD1" <-> "OD2" Residue "G GLU 7": "OE1" <-> "OE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 45277 Number of models: 1 Model: "" Number of chains: 18 Chain: "A" Number of atoms: 7470 Number of conformers: 1 Conformer: "" Number of residues, atoms: 493, 7470 Classifications: {'peptide': 493} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 19, 'TRANS': 471} Chain: "B" Number of atoms: 7377 Number of conformers: 1 Conformer: "" Number of residues, atoms: 486, 7377 Classifications: {'peptide': 486} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 19, 'TRANS': 464} Chain breaks: 1 Chain: "C" Number of atoms: 7476 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 492, 7455 Classifications: {'peptide': 492} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 19, 'TRANS': 470} Conformer: "B" Number of residues, atoms: 492, 7455 Classifications: {'peptide': 492} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 19, 'TRANS': 470} bond proxies already assigned to first conformer: 7491 Chain: "D" Number of atoms: 7143 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 467, 7125 Classifications: {'peptide': 467} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 22, 'TRANS': 442} Conformer: "B" Number of residues, atoms: 467, 7125 Classifications: {'peptide': 467} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 22, 'TRANS': 442} bond proxies already assigned to first conformer: 7171 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: 7147 Number of conformers: 1 Conformer: "" Number of residues, atoms: 468, 7147 Classifications: {'peptide': 468} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 22, 'TRANS': 443} Chain: "G" Number of atoms: 1378 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 1378 Classifications: {'peptide': 89} Link IDs: {'TRANS': 88} Chain breaks: 2 Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "F" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N AGLN D 453 " occ=0.50 ... (32 atoms not shown) pdb="HE22BGLN D 453 " occ=0.50 Time building chain proxies: 25.16, per 1000 atoms: 0.56 Number of scatterers: 45277 At special positions: 0 Unit cell: (122.84, 126.16, 112.05, 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 71 16.00 P 16 15.00 Mg 5 11.99 O 4455 8.00 N 3941 7.00 C 14224 6.00 H 22565 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: 38.79 Conformation dependent library (CDL) restraints added in 6.7 seconds 5886 Ramachandran restraints generated. 2943 Oldfield, 0 Emsley, 2943 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5366 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 125 helices and 21 sheets defined 42.8% alpha, 13.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 7.75 Creating SS restraints... 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: 4.264A pdb=" N ARG A 190 " --> pdb=" O ILE A 186 " (cutoff:3.500A) removed outlier: 5.060A pdb=" N GLU A 191 " --> pdb=" O LEU A 187 " (cutoff:3.500A) removed outlier: 4.771A pdb=" N ALA A 192 " --> pdb=" O ASN A 188 " (cutoff:3.500A) Processing helix chain 'A' and resid 213 through 225 Processing helix chain 'A' and resid 243 through 263 Proline residue: A 250 - end of helix removed outlier: 3.671A pdb=" N TRP A 260 " --> pdb=" O ILE A 256 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ASN A 263 " --> pdb=" O HIS A 259 " (cutoff:3.500A) Processing helix chain 'A' and resid 274 through 287 Processing helix chain 'A' and resid 294 through 296 No H-bonds generated for 'chain 'A' and resid 294 through 296' Processing helix chain 'A' and resid 301 through 311 removed outlier: 4.106A pdb=" N ARG A 311 " --> pdb=" O ARG A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 317 through 319 No H-bonds generated for 'chain 'A' and resid 317 through 319' Processing helix chain 'A' and resid 340 through 348 Processing helix chain 'A' and resid 357 through 361 Processing helix chain 'A' and resid 378 through 381 Processing helix chain 'A' and resid 384 through 390 Processing helix chain 'A' and resid 393 through 406 removed outlier: 5.139A pdb=" N ALA A 405 " --> pdb=" O ARG A 401 " (cutoff:3.500A) removed outlier: 5.834A pdb=" N PHE A 406 " --> pdb=" O GLU A 402 " (cutoff:3.500A) Processing helix chain 'A' and resid 415 through 430 Processing helix chain 'A' and resid 441 through 452 Processing helix chain 'A' and resid 461 through 478 removed outlier: 4.792A pdb=" N GLN A 465 " --> pdb=" O GLU A 462 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N SER A 478 " --> pdb=" O VAL A 475 " (cutoff:3.500A) Processing helix chain 'A' and resid 481 through 489 Processing helix chain 'A' and resid 494 through 510 Processing helix chain 'B' and resid 82 through 84 No H-bonds generated for 'chain 'B' and resid 82 through 84' Processing helix chain 'B' and resid 104 through 106 No H-bonds generated for 'chain 'B' and resid 104 through 106' Processing helix chain 'B' and resid 154 through 159 Processing helix chain 'B' and resid 178 through 195 removed outlier: 3.745A pdb=" N GLN B 189 " --> pdb=" O THR B 185 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N ARG B 190 " --> pdb=" O ILE B 186 " (cutoff:3.500A) removed outlier: 5.293A pdb=" N GLU B 191 " --> pdb=" O LEU B 187 " (cutoff:3.500A) removed outlier: 4.911A pdb=" N ALA B 192 " --> pdb=" O ASN B 188 " (cutoff:3.500A) Processing helix chain 'B' and resid 213 through 225 Processing helix chain 'B' and resid 228 through 231 Processing helix chain 'B' and resid 243 through 263 Proline residue: B 250 - end of helix removed outlier: 3.689A pdb=" N TRP B 260 " --> pdb=" O ILE B 256 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ASN B 263 " --> pdb=" O HIS B 259 " (cutoff:3.500A) Processing helix chain 'B' and resid 274 through 287 Processing helix chain 'B' and resid 294 through 296 No H-bonds generated for 'chain 'B' and resid 294 through 296' Processing helix chain 'B' and resid 301 through 311 removed outlier: 4.180A pdb=" N ARG B 311 " --> pdb=" O ARG B 307 " (cutoff:3.500A) Processing helix chain 'B' and resid 317 through 319 No H-bonds generated for 'chain 'B' and resid 317 through 319' Processing helix chain 'B' and resid 340 through 348 Processing helix chain 'B' and resid 357 through 362 Processing helix chain 'B' and resid 384 through 405 removed outlier: 5.460A pdb=" N SER B 392 " --> pdb=" O GLU B 388 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N LEU B 393 " --> pdb=" O VAL B 389 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N LEU B 395 " --> pdb=" O GLY B 391 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N GLU B 402 " --> pdb=" O SER B 398 " (cutoff:3.500A) Processing helix chain 'B' and resid 415 through 431 Processing helix chain 'B' and resid 441 through 452 Processing helix chain 'B' and resid 461 through 477 removed outlier: 5.158A pdb=" N GLN B 465 " --> pdb=" O GLU B 462 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N VAL B 475 " --> pdb=" O LEU B 472 " (cutoff:3.500A) Processing helix chain 'B' and resid 480 through 489 Processing helix chain 'B' and resid 494 through 510 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: 3.754A pdb=" N GLN C 189 " --> pdb=" O THR C 185 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N ARG C 190 " --> pdb=" O ILE C 186 " (cutoff:3.500A) removed outlier: 5.258A pdb=" N GLU C 191 " --> pdb=" O LEU C 187 " (cutoff:3.500A) removed outlier: 4.960A pdb=" N ALA C 192 " --> pdb=" O ASN C 188 " (cutoff:3.500A) Processing helix chain 'C' and resid 213 through 225 Processing helix chain 'C' and resid 229 through 231 No H-bonds generated for 'chain 'C' and resid 229 through 231' Processing helix chain 'C' and resid 243 through 263 Proline residue: C 250 - end of helix removed outlier: 3.664A pdb=" N TRP C 260 " --> pdb=" O ILE C 256 " (cutoff:3.500A) removed outlier: 3.580A 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: 4.196A 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 477 removed outlier: 5.106A pdb=" N GLN C 465 " --> pdb=" O GLU C 462 " (cutoff:3.500A) Processing helix chain 'C' and resid 481 through 489 Processing helix chain 'C' and resid 494 through 510 removed outlier: 3.650A pdb=" N GLY C 510 " --> pdb=" O GLU C 506 " (cutoff:3.500A) Processing helix chain 'D' and resid 92 through 94 No H-bonds generated for 'chain 'D' and resid 92 through 94' Processing helix chain 'D' and resid 142 through 147 Processing helix chain 'D' and resid 166 through 177 Processing helix chain 'D' and resid 194 through 206 Processing helix chain 'D' and resid 210 through 212 No H-bonds generated for 'chain 'D' and resid 210 through 212' Processing helix chain 'D' and resid 224 through 243 removed outlier: 4.701A pdb=" N ALA D 231 " --> pdb=" O ARG D 227 " (cutoff:3.500A) removed outlier: 4.486A 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 268 through 270 No H-bonds generated for 'chain 'D' and resid 268 through 270' 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: 4.263A pdb=" N ALA D 325 " --> pdb=" O ALA D 321 " (cutoff:3.500A) removed outlier: 4.568A 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: 4.606A pdb=" N ASP D 384 " --> pdb=" O LYS D 380 " (cutoff:3.500A) removed outlier: 4.772A pdb=" N ILE D 385 " --> pdb=" O ASP D 381 " (cutoff:3.500A) Processing helix chain 'D' and resid 391 through 393 No H-bonds generated for 'chain 'D' and resid 391 through 393' Processing helix chain 'D' and resid 396 through 412 Processing helix chain 'D' and resid 417 through 423 removed outlier: 4.548A pdb=" N GLN D 421 " --> pdb=" O ALA D 418 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N THR D 423 " --> pdb=" O GLU D 420 " (cutoff:3.500A) Processing helix chain 'D' and resid 432 through 443 Processing helix chain 'D' and resid 452 through 455 Processing helix chain 'D' and resid 461 through 471 Processing helix chain 'E' and resid 92 through 94 No H-bonds generated for 'chain 'E' and resid 92 through 94' Processing helix chain 'E' and resid 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 210 through 212 No H-bonds generated for 'chain 'E' and resid 210 through 212' Processing helix chain 'E' and resid 224 through 244 removed outlier: 5.045A pdb=" N ALA E 231 " --> pdb=" O ARG E 227 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N LEU E 232 " --> pdb=" O MET E 228 " (cutoff:3.500A) Processing helix chain 'E' and resid 256 through 270 Processing helix chain 'E' and resid 276 through 278 No H-bonds generated for 'chain 'E' and resid 276 through 278' Processing helix chain 'E' and resid 283 through 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 326 removed outlier: 3.601A pdb=" N ALA E 325 " --> pdb=" O ALA E 321 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N HIS E 326 " --> pdb=" O THR E 322 " (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: 4.359A pdb=" N ASP E 384 " --> pdb=" O LYS E 380 " (cutoff:3.500A) removed outlier: 4.686A pdb=" N ILE E 385 " --> pdb=" O ASP E 381 " (cutoff:3.500A) Processing helix chain 'E' and resid 391 through 393 No H-bonds generated for 'chain 'E' and resid 391 through 393' Processing helix chain 'E' and resid 396 through 411 Processing helix chain 'E' and resid 417 through 420 Processing helix chain 'E' and resid 432 through 444 Processing helix chain 'E' and resid 452 through 455 Processing helix chain 'E' and resid 461 through 470 Processing helix chain 'F' and resid 92 through 94 No H-bonds generated for 'chain 'F' and resid 92 through 94' Processing helix chain 'F' and resid 127 through 129 No H-bonds generated for 'chain 'F' and resid 127 through 129' Processing helix chain 'F' and resid 142 through 147 Processing helix chain 'F' and resid 166 through 177 Processing helix chain 'F' and resid 194 through 206 Processing helix chain 'F' and resid 210 through 212 No H-bonds generated for 'chain 'F' and resid 210 through 212' Processing helix chain 'F' and resid 224 through 243 removed outlier: 4.803A pdb=" N ALA F 231 " --> pdb=" O ARG F 227 " (cutoff:3.500A) removed outlier: 4.605A 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 294 removed outlier: 3.536A pdb=" N ILE F 294 " --> pdb=" O LEU F 290 " (cutoff:3.500A) Processing helix chain 'F' and resid 311 through 313 No H-bonds generated for 'chain 'F' and resid 311 through 313' Processing helix chain 'F' and resid 318 through 326 removed outlier: 4.520A pdb=" N ALA F 325 " --> pdb=" O ALA F 321 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N HIS F 326 " --> pdb=" O THR F 322 " (cutoff:3.500A) Processing helix chain 'F' and resid 335 through 339 Processing helix chain 'F' and resid 358 through 361 No H-bonds generated for 'chain 'F' and resid 358 through 361' Processing helix chain 'F' and resid 363 through 389 removed outlier: 4.332A pdb=" N ASP F 384 " --> pdb=" O LYS F 380 " (cutoff:3.500A) removed outlier: 4.939A pdb=" N ILE F 385 " --> pdb=" O ASP F 381 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N ILE F 388 " --> pdb=" O ASP F 384 " (cutoff:3.500A) Processing helix chain 'F' and resid 396 through 412 Processing helix chain 'F' and resid 417 through 423 removed outlier: 4.086A pdb=" N GLN F 421 " --> pdb=" O ALA F 418 " (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 34 Processing helix chain 'G' and resid 259 through 303 Processing sheet with id= A, first strand: chain 'A' and resid 31 through 33 removed outlier: 6.508A pdb=" N GLY A 75 " --> pdb=" O LEU A 67 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ASP A 36 " --> pdb=" O HIS A 43 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N GLU A 45 " --> pdb=" O VAL A 34 " (cutoff:3.500A) removed outlier: 5.574A 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: 6.641A pdb=" N CYS A 204 " --> pdb=" O THR A 233 " (cutoff:3.500A) removed outlier: 7.831A pdb=" N VAL A 235 " --> pdb=" O CYS A 204 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N TYR A 206 " --> pdb=" O VAL A 235 " (cutoff:3.500A) removed outlier: 7.443A pdb=" N ALA A 237 " --> pdb=" O TYR A 206 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N ALA A 208 " --> pdb=" O ALA A 237 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N SER A 323 " --> pdb=" O VAL A 267 " (cutoff:3.500A) removed outlier: 7.681A pdb=" N ILE A 269 " --> pdb=" O SER A 323 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N THR A 325 " --> pdb=" O ILE A 269 " (cutoff:3.500A) removed outlier: 7.616A pdb=" N PHE A 271 " --> pdb=" O THR A 325 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N LEU A 327 " --> pdb=" O PHE A 271 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 31 through 33 removed outlier: 4.162A pdb=" N LEU B 63 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N GLY B 75 " --> pdb=" O LEU B 67 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ASP B 36 " --> pdb=" O HIS B 43 " (cutoff:3.500A) removed outlier: 6.055A pdb=" N GLU B 45 " --> pdb=" O VAL B 34 " (cutoff:3.500A) removed outlier: 5.607A 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: 7.029A pdb=" N LEU B 355 " --> pdb=" O LEU B 169 " (cutoff:3.500A) removed outlier: 6.338A 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: 8.662A pdb=" N THR B 233 " --> pdb=" O VAL B 202 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N CYS B 204 " --> pdb=" O THR B 233 " (cutoff:3.500A) removed outlier: 7.982A pdb=" N VAL B 235 " --> pdb=" O CYS B 204 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N TYR B 206 " --> pdb=" O VAL B 235 " (cutoff:3.500A) removed outlier: 7.515A pdb=" N ALA B 237 " --> pdb=" O TYR B 206 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N ALA B 208 " --> pdb=" O ALA B 237 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N HIS B 266 " --> pdb=" O ARG B 203 " (cutoff:3.500A) removed outlier: 8.017A pdb=" N VAL B 205 " --> pdb=" O HIS B 266 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N LEU B 268 " --> pdb=" O VAL B 205 " (cutoff:3.500A) removed outlier: 7.516A pdb=" N VAL B 207 " --> pdb=" O LEU B 268 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N VAL B 270 " --> pdb=" O VAL B 207 " (cutoff:3.500A) removed outlier: 7.082A pdb=" N ILE B 209 " --> pdb=" O VAL B 270 " (cutoff:3.500A) removed outlier: 6.153A pdb=" N ASP B 272 " --> pdb=" O ILE B 209 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N SER B 323 " --> pdb=" O VAL B 267 " (cutoff:3.500A) removed outlier: 7.746A pdb=" N ILE B 269 " --> pdb=" O SER B 323 " (cutoff:3.500A) removed outlier: 6.135A pdb=" N THR B 325 " --> pdb=" O ILE B 269 " (cutoff:3.500A) removed outlier: 7.514A pdb=" N PHE B 271 " --> pdb=" O THR B 325 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N LEU B 327 " --> pdb=" O PHE B 271 " (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: 6.491A pdb=" N GLY C 75 " --> pdb=" O LEU C 67 " (cutoff:3.500A) removed outlier: 6.137A pdb=" N GLU C 45 " --> pdb=" O VAL C 34 " (cutoff:3.500A) removed outlier: 5.500A 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: 6.746A pdb=" N LEU C 169 " --> pdb=" O CYS C 353 " (cutoff:3.500A) removed outlier: 7.126A pdb=" N LEU C 355 " --> pdb=" O LEU C 169 " (cutoff:3.500A) removed outlier: 6.733A 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: 6.547A pdb=" N CYS C 204 " --> pdb=" O THR C 233 " (cutoff:3.500A) removed outlier: 7.778A pdb=" N VAL C 235 " --> pdb=" O CYS C 204 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N TYR C 206 " --> pdb=" O VAL C 235 " (cutoff:3.500A) removed outlier: 7.474A pdb=" N ALA C 237 " --> pdb=" O TYR C 206 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N ALA C 208 " --> pdb=" O ALA C 237 " (cutoff:3.500A) removed outlier: 6.242A pdb=" N SER C 323 " --> pdb=" O VAL C 267 " (cutoff:3.500A) removed outlier: 7.664A pdb=" N ILE C 269 " --> pdb=" O SER C 323 " (cutoff:3.500A) removed outlier: 6.138A pdb=" N THR C 325 " --> pdb=" O ILE C 269 " (cutoff:3.500A) removed outlier: 7.635A pdb=" N PHE C 271 " --> pdb=" O THR C 325 " (cutoff:3.500A) removed outlier: 6.608A 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: 6.555A pdb=" N ASP D 21 " --> pdb=" O VAL D 13 " (cutoff:3.500A) removed outlier: 4.627A pdb=" N ILE D 15 " --> pdb=" O VAL D 19 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N VAL D 19 " --> pdb=" O ILE D 15 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N ILE D 65 " --> pdb=" O VAL D 53 " (cutoff:3.500A) removed outlier: 5.749A 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: 7.443A 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: 7.798A pdb=" N LEU D 158 " --> pdb=" O SER D 304 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N GLN D 306 " --> pdb=" O LEU D 158 " (cutoff:3.500A) removed outlier: 7.939A pdb=" N GLY D 160 " --> pdb=" O GLN D 306 " (cutoff:3.500A) removed outlier: 5.958A pdb=" N VAL D 308 " --> pdb=" O GLY D 160 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N VAL D 249 " --> pdb=" O THR D 303 " (cutoff:3.500A) removed outlier: 7.768A pdb=" N MET D 305 " --> pdb=" O VAL D 249 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N LEU D 251 " --> pdb=" O MET D 305 " (cutoff:3.500A) removed outlier: 7.770A pdb=" N ALA D 307 " --> pdb=" O LEU D 251 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N ILE D 253 " --> pdb=" O ALA D 307 " (cutoff:3.500A) removed outlier: 8.217A pdb=" N TYR D 309 " --> pdb=" O ILE D 253 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N THR D 184 " --> pdb=" O LEU D 250 " (cutoff:3.500A) removed outlier: 8.169A pdb=" N PHE D 252 " --> pdb=" O THR D 184 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N VAL D 186 " --> pdb=" O PHE D 252 " (cutoff:3.500A) removed outlier: 8.023A pdb=" N ASP D 254 " --> pdb=" O VAL D 186 " (cutoff:3.500A) removed outlier: 6.262A 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: 6.542A pdb=" N ASP E 21 " --> pdb=" O VAL E 13 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N ILE E 15 " --> pdb=" O VAL E 19 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N VAL E 19 " --> pdb=" O ILE E 15 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N ILE E 65 " --> pdb=" O VAL E 53 " (cutoff:3.500A) removed outlier: 5.784A pdb=" N VAL E 53 " --> pdb=" O ILE E 65 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'E' and resid 87 through 89 Processing sheet with id= R, first strand: chain 'E' and resid 329 through 332 removed outlier: 8.315A pdb=" N ILE E 156 " --> pdb=" O ILE E 302 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N SER E 304 " --> pdb=" O ILE E 156 " (cutoff:3.500A) removed outlier: 7.431A pdb=" N LEU E 158 " --> pdb=" O SER E 304 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N GLN E 306 " --> pdb=" O LEU E 158 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N VAL E 249 " --> pdb=" O THR E 303 " (cutoff:3.500A) removed outlier: 8.061A pdb=" N MET E 305 " --> pdb=" O VAL E 249 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N LEU E 251 " --> pdb=" O MET E 305 " (cutoff:3.500A) removed outlier: 7.616A pdb=" N ALA E 307 " --> pdb=" O LEU E 251 " (cutoff:3.500A) removed outlier: 6.891A 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: 6.612A pdb=" N ASP F 21 " --> pdb=" O VAL F 13 " (cutoff:3.500A) removed outlier: 4.756A pdb=" N ILE F 15 " --> pdb=" O VAL F 19 " (cutoff:3.500A) removed outlier: 7.138A pdb=" N VAL F 19 " --> pdb=" O ILE F 15 " (cutoff:3.500A) removed outlier: 6.190A pdb=" N ILE F 65 " --> pdb=" O VAL F 53 " (cutoff:3.500A) removed outlier: 5.602A 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: 7.485A pdb=" N ILE F 156 " --> pdb=" O ILE F 302 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N SER F 304 " --> pdb=" O ILE F 156 " (cutoff:3.500A) removed outlier: 8.051A pdb=" N LEU F 158 " --> pdb=" O SER F 304 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N GLN F 306 " --> pdb=" O LEU F 158 " (cutoff:3.500A) removed outlier: 8.191A pdb=" N GLY F 160 " --> pdb=" O GLN F 306 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N VAL F 308 " --> pdb=" O GLY F 160 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N VAL F 249 " --> pdb=" O THR F 303 " (cutoff:3.500A) removed outlier: 7.705A pdb=" N MET F 305 " --> pdb=" O VAL F 249 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N LEU F 251 " --> pdb=" O MET F 305 " (cutoff:3.500A) removed outlier: 7.707A pdb=" N ALA F 307 " --> pdb=" O LEU F 251 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N ILE F 253 " --> pdb=" O ALA F 307 " (cutoff:3.500A) removed outlier: 8.266A pdb=" N TYR F 309 " --> pdb=" O ILE F 253 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N THR F 184 " --> pdb=" O LEU F 250 " (cutoff:3.500A) removed outlier: 8.026A pdb=" N PHE F 252 " --> pdb=" O THR F 184 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N VAL F 186 " --> pdb=" O PHE F 252 " (cutoff:3.500A) removed outlier: 7.977A pdb=" N ASP F 254 " --> pdb=" O VAL F 186 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N ALA F 188 " --> pdb=" O ASP F 254 " (cutoff:3.500A) 924 hydrogen bonds defined for protein. 2532 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: 18.75 Time building geometry restraints manager: 40.00 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.83 - 1.03: 22546 1.03 - 1.22: 19 1.22 - 1.42: 9311 1.42 - 1.61: 13634 1.61 - 1.81: 125 Bond restraints: 45635 Sorted by residual: bond pdb=" C4 ADP D 600 " pdb=" C5 ADP D 600 " ideal model delta sigma weight residual 1.490 1.467 0.023 2.00e-02 2.50e+03 1.34e+00 bond pdb=" C4 ADP E 600 " pdb=" C5 ADP E 600 " ideal model delta sigma weight residual 1.490 1.467 0.023 2.00e-02 2.50e+03 1.27e+00 bond pdb=" CB GLN A 420 " pdb=" CG GLN A 420 " ideal model delta sigma weight residual 1.520 1.488 0.032 3.00e-02 1.11e+03 1.11e+00 bond pdb=" CG PRO F 344 " pdb=" CD PRO F 344 " ideal model delta sigma weight residual 1.512 1.484 0.028 2.70e-02 1.37e+03 1.11e+00 bond pdb=" C ALA B 390 " pdb=" O ALA B 390 " ideal model delta sigma weight residual 1.236 1.248 -0.012 1.34e-02 5.57e+03 8.40e-01 ... (remaining 45630 not shown) Histogram of bond angle deviations from ideal: 99.70 - 107.76: 3729 107.76 - 115.81: 56092 115.81 - 123.87: 19720 123.87 - 131.93: 3105 131.93 - 139.99: 31 Bond angle restraints: 82677 Sorted by residual: angle pdb=" C ASP E 254 " pdb=" N ASN E 255 " pdb=" CA ASN E 255 " ideal model delta sigma weight residual 121.70 127.43 -5.73 1.80e+00 3.09e-01 1.01e+01 angle pdb=" C ASP F 254 " pdb=" N ASN F 255 " pdb=" CA ASN F 255 " ideal model delta sigma weight residual 121.70 127.10 -5.40 1.80e+00 3.09e-01 8.98e+00 angle pdb=" N GLY E 218 " pdb=" CA GLY E 218 " pdb=" C GLY E 218 " ideal model delta sigma weight residual 113.18 106.35 6.83 2.37e+00 1.78e-01 8.31e+00 angle pdb=" C ASP D 254 " pdb=" N ASN D 255 " pdb=" CA ASN D 255 " ideal model delta sigma weight residual 121.70 126.86 -5.16 1.80e+00 3.09e-01 8.21e+00 angle pdb=" C ASP C 272 " pdb=" N ASP C 273 " pdb=" CA ASP C 273 " ideal model delta sigma weight residual 121.70 126.72 -5.02 1.80e+00 3.09e-01 7.79e+00 ... (remaining 82672 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.52: 20751 35.52 - 71.05: 564 71.05 - 106.57: 50 106.57 - 142.10: 0 142.10 - 177.62: 2 Dihedral angle restraints: 21367 sinusoidal: 11974 harmonic: 9393 Sorted by residual: dihedral pdb=" C5' ADP D 600 " pdb=" O5' ADP D 600 " pdb=" PA ADP D 600 " pdb=" O2A ADP D 600 " ideal model delta sinusoidal sigma weight residual -60.00 117.62 -177.62 1 2.00e+01 2.50e-03 4.80e+01 dihedral pdb=" C5' ADP E 600 " pdb=" O5' ADP E 600 " pdb=" PA ADP E 600 " pdb=" O2A ADP E 600 " ideal model delta sinusoidal sigma weight residual 300.00 144.50 155.50 1 2.00e+01 2.50e-03 4.58e+01 dihedral pdb=" O2A ADP E 600 " pdb=" O3A ADP E 600 " pdb=" PA ADP E 600 " pdb=" PB ADP E 600 " ideal model delta sinusoidal sigma weight residual -60.00 -156.26 96.26 1 2.00e+01 2.50e-03 2.66e+01 ... (remaining 21364 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.060: 3166 0.060 - 0.121: 381 0.121 - 0.181: 32 0.181 - 0.241: 2 0.241 - 0.301: 10 Chirality restraints: 3591 Sorted by residual: chirality pdb=" C2' ATP B 600 " pdb=" C1' ATP B 600 " pdb=" C3' ATP B 600 " pdb=" O2' ATP B 600 " both_signs ideal model delta sigma weight residual False -2.68 -2.98 0.30 2.00e-01 2.50e+01 2.27e+00 chirality pdb=" C2' ATP C 600 " pdb=" C1' ATP C 600 " pdb=" C3' ATP C 600 " pdb=" O2' ATP C 600 " both_signs ideal model delta sigma weight residual False -2.68 -2.97 0.29 2.00e-01 2.50e+01 2.13e+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 2.10e+00 ... (remaining 3588 not shown) Planarity restraints: 6921 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG E 374 " 0.158 9.50e-02 1.11e+02 5.27e-02 3.13e+00 pdb=" NE ARG E 374 " -0.010 2.00e-02 2.50e+03 pdb=" CZ ARG E 374 " 0.005 2.00e-02 2.50e+03 pdb=" NH1 ARG E 374 " 0.000 2.00e-02 2.50e+03 pdb=" NH2 ARG E 374 " 0.000 2.00e-02 2.50e+03 pdb="HH11 ARG E 374 " -0.005 2.00e-02 2.50e+03 pdb="HH12 ARG E 374 " 0.002 2.00e-02 2.50e+03 pdb="HH21 ARG E 374 " -0.000 2.00e-02 2.50e+03 pdb="HH22 ARG E 374 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY F 17 " -0.026 5.00e-02 4.00e+02 4.01e-02 2.57e+00 pdb=" N PRO F 18 " 0.069 5.00e-02 4.00e+02 pdb=" CA PRO F 18 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO F 18 " -0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLY B 485 " 0.007 2.00e-02 2.50e+03 1.39e-02 1.93e+00 pdb=" C GLY B 485 " -0.024 2.00e-02 2.50e+03 pdb=" O GLY B 485 " 0.009 2.00e-02 2.50e+03 pdb=" N ILE B 486 " 0.008 2.00e-02 2.50e+03 ... (remaining 6918 not shown) Histogram of nonbonded interaction distances: 1.57 - 2.18: 2224 2.18 - 2.78: 93646 2.78 - 3.39: 134548 3.39 - 3.99: 181116 3.99 - 4.60: 281070 Nonbonded interactions: 692604 Sorted by model distance: nonbonded pdb=" H VAL D 277 " pdb=" OE2 GLU G 292 " model vdw 1.572 1.850 nonbonded pdb=" H GLY D 165 " pdb=" O1B ADP D 600 " model vdw 1.580 1.850 nonbonded pdb=" O ALA C 192 " pdb=" HG1 THR C 195 " model vdw 1.603 1.850 nonbonded pdb=" O PRO B 161 " pdb=" HG SER B 375 " model vdw 1.604 1.850 nonbonded pdb=" OE2 GLU F 52 " pdb=" HE2 HIS F 121 " model vdw 1.605 1.850 ... (remaining 692599 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 30 and (name N or name CA or name C or name O or name CB \ or name CG or name CD or name OE1 or name OE2 or name HA or name HB2 or name HB3 \ or name HG2 or name HG3)) or resid 31 through 173 or resid 175 through 406 or ( \ resid 414 and (name N or name CA or name C or name O or name CB or name CG or na \ me OD1 or name OD2 or name HA or name HB2 or name HB3)) or resid 415 through 521 \ or resid 600 through 601)) selection = (chain 'B' and ((resid 30 and (name N or name CA or name C or name O or name CB \ or name CG or name CD or name OE1 or name OE2 or name HA or name HB2 or name HB3 \ or name HG2 or name HG3)) or resid 31 through 173 or resid 175 through 521 or r \ esid 600 through 601)) selection = (chain 'C' and (resid 30 through 173 or resid 175 through 406 or (resid 414 and \ (name N or name CA or name C or name O or name CB or name CG or name OD1 or name \ OD2 or name HA or name HB2 or name HB3)) or resid 415 through 521 or resid 600 \ through 601)) } ncs_group { reference = (chain 'D' and (resid 8 through 452 or resid 455 through 471)) selection = (chain 'E' and (resid 8 through 166 or (resid 167 and (name N or name CA or name \ C or name O or name CB or name OG1 or name CG2 or name H or name HA or name HB \ or name HG21 or name HG22 or name HG23)) or resid 168 through 452 or resid 455 t \ hrough 471)) selection = (chain 'F' and ((resid 8 and (name N or name CA or name C or name O or name CB o \ r name OG1 or name CG2 or name HA or name HB or name HG1 or name HG21 or name HG \ 22 or name HG23)) or resid 9 through 452 or resid 455 through 471)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 24.090 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: 0.730 Extract box with map and model: 38.900 Check model and map are aligned: 0.680 Set scattering table: 0.440 Process input model: 156.780 Find NCS groups from input model: 2.460 Set up NCS constraints: 0.180 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:10.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 235.180 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8684 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 23070 Z= 0.162 Angle : 0.502 6.832 31280 Z= 0.260 Chirality : 0.043 0.301 3591 Planarity : 0.003 0.068 4098 Dihedral : 15.097 177.620 8644 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 3.97 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.11 % Favored : 97.82 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % Cis-general : 0.21 % 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: 1.32 (0.16), residues: 2943 helix: 1.59 (0.15), residues: 1205 sheet: -0.03 (0.24), residues: 432 loop : 0.70 (0.19), residues: 1306 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 247 HIS 0.002 0.001 HIS D 121 PHE 0.011 0.001 PHE F 257 TYR 0.006 0.001 TYR E 366 ARG 0.007 0.000 ARG E 378 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5886 Ramachandran restraints generated. 2943 Oldfield, 0 Emsley, 2943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5886 Ramachandran restraints generated. 2943 Oldfield, 0 Emsley, 2943 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 165 residues out of total 2393 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 165 time to evaluate : 3.840 Fit side-chains REVERT: B 418 LYS cc_start: 0.6441 (mptt) cc_final: 0.6126 (mptt) REVERT: D 173 MET cc_start: 0.9020 (mmt) cc_final: 0.8720 (mmt) outliers start: 0 outliers final: 0 residues processed: 165 average time/residue: 3.2779 time to fit residues: 615.0776 Evaluate side-chains 108 residues out of total 2393 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 108 time to evaluate : 3.980 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 292 random chunks: chunk 246 optimal weight: 0.8980 chunk 221 optimal weight: 3.9990 chunk 122 optimal weight: 1.9990 chunk 75 optimal weight: 0.9980 chunk 149 optimal weight: 2.9990 chunk 118 optimal weight: 1.9990 chunk 228 optimal weight: 0.9980 chunk 88 optimal weight: 1.9990 chunk 139 optimal weight: 2.9990 chunk 170 optimal weight: 1.9990 chunk 265 optimal weight: 0.9980 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 277 GLN E 171 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8714 moved from start: 0.0432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 23070 Z= 0.270 Angle : 0.492 6.767 31280 Z= 0.254 Chirality : 0.041 0.141 3591 Planarity : 0.003 0.059 4098 Dihedral : 8.482 156.289 3328 Min Nonbonded Distance : 1.682 Molprobity Statistics. All-atom Clashscore : 3.86 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.25 % Favored : 97.69 % Rotamer: Outliers : 0.21 % Allowed : 4.30 % Favored : 95.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.27 (0.16), residues: 2943 helix: 1.58 (0.15), residues: 1207 sheet: -0.08 (0.24), residues: 426 loop : 0.65 (0.19), residues: 1310 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 247 HIS 0.003 0.001 HIS D 121 PHE 0.012 0.001 PHE E 439 TYR 0.010 0.001 TYR C 251 ARG 0.006 0.000 ARG E 374 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5886 Ramachandran restraints generated. 2943 Oldfield, 0 Emsley, 2943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5886 Ramachandran restraints generated. 2943 Oldfield, 0 Emsley, 2943 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 113 residues out of total 2393 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 108 time to evaluate : 3.634 Fit side-chains REVERT: C 273 ASP cc_start: 0.7975 (OUTLIER) cc_final: 0.7415 (m-30) REVERT: D 173 MET cc_start: 0.9024 (mmt) cc_final: 0.8707 (mmt) outliers start: 5 outliers final: 1 residues processed: 111 average time/residue: 3.0611 time to fit residues: 392.9237 Evaluate side-chains 109 residues out of total 2393 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 107 time to evaluate : 3.635 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 279 ASP Chi-restraints excluded: chain C residue 273 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 292 random chunks: chunk 147 optimal weight: 0.6980 chunk 82 optimal weight: 0.6980 chunk 220 optimal weight: 1.9990 chunk 180 optimal weight: 0.8980 chunk 73 optimal weight: 0.9980 chunk 265 optimal weight: 0.9990 chunk 286 optimal weight: 2.9990 chunk 236 optimal weight: 4.9990 chunk 263 optimal weight: 1.9990 chunk 90 optimal weight: 2.9990 chunk 213 optimal weight: 0.7980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 171 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8702 moved from start: 0.0460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 23070 Z= 0.196 Angle : 0.469 6.913 31280 Z= 0.241 Chirality : 0.040 0.142 3591 Planarity : 0.003 0.040 4098 Dihedral : 8.153 136.169 3328 Min Nonbonded Distance : 1.719 Molprobity Statistics. All-atom Clashscore : 3.64 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.04 % Favored : 97.89 % Rotamer: Outliers : 0.33 % Allowed : 4.67 % Favored : 94.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % Cis-general : 0.21 % 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: 1.39 (0.16), residues: 2943 helix: 1.67 (0.15), residues: 1207 sheet: -0.06 (0.24), residues: 426 loop : 0.73 (0.19), residues: 1310 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 193 HIS 0.003 0.001 HIS D 121 PHE 0.012 0.001 PHE F 257 TYR 0.008 0.001 TYR C 251 ARG 0.002 0.000 ARG E 374 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5886 Ramachandran restraints generated. 2943 Oldfield, 0 Emsley, 2943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5886 Ramachandran restraints generated. 2943 Oldfield, 0 Emsley, 2943 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 120 residues out of total 2393 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 112 time to evaluate : 3.657 Fit side-chains REVERT: D 173 MET cc_start: 0.9001 (mmt) cc_final: 0.8693 (mmt) outliers start: 8 outliers final: 2 residues processed: 116 average time/residue: 2.8597 time to fit residues: 387.1126 Evaluate side-chains 110 residues out of total 2393 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 108 time to evaluate : 3.694 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 279 ASP Chi-restraints excluded: chain F residue 148 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 292 random chunks: chunk 262 optimal weight: 1.9990 chunk 199 optimal weight: 0.9980 chunk 137 optimal weight: 1.9990 chunk 29 optimal weight: 2.9990 chunk 126 optimal weight: 1.9990 chunk 178 optimal weight: 1.9990 chunk 266 optimal weight: 1.9990 chunk 282 optimal weight: 1.9990 chunk 139 optimal weight: 2.9990 chunk 252 optimal weight: 0.9980 chunk 76 optimal weight: 1.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 171 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8730 moved from start: 0.0633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.092 23070 Z= 0.353 Angle : 0.513 6.791 31280 Z= 0.267 Chirality : 0.042 0.144 3591 Planarity : 0.003 0.042 4098 Dihedral : 8.207 123.389 3328 Min Nonbonded Distance : 1.693 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.48 % Favored : 97.45 % Rotamer: Outliers : 0.42 % Allowed : 5.47 % Favored : 94.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % Cis-general : 0.21 % 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: 1.22 (0.16), residues: 2943 helix: 1.52 (0.15), residues: 1204 sheet: -0.00 (0.24), residues: 424 loop : 0.60 (0.18), residues: 1315 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP E 201 HIS 0.005 0.001 HIS D 121 PHE 0.012 0.001 PHE B 467 TYR 0.013 0.001 TYR C 251 ARG 0.003 0.000 ARG F 195 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5886 Ramachandran restraints generated. 2943 Oldfield, 0 Emsley, 2943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5886 Ramachandran restraints generated. 2943 Oldfield, 0 Emsley, 2943 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 120 residues out of total 2393 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 110 time to evaluate : 3.679 Fit side-chains revert: symmetry clash REVERT: C 36 ASP cc_start: 0.8077 (p0) cc_final: 0.7849 (p0) REVERT: C 273 ASP cc_start: 0.8036 (OUTLIER) cc_final: 0.7470 (m-30) REVERT: D 173 MET cc_start: 0.8979 (mmt) cc_final: 0.8629 (mmt) outliers start: 10 outliers final: 6 residues processed: 116 average time/residue: 2.8878 time to fit residues: 389.8200 Evaluate side-chains 114 residues out of total 2393 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 107 time to evaluate : 3.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 273 ASP Chi-restraints excluded: chain B residue 279 ASP Chi-restraints excluded: chain C residue 273 ASP Chi-restraints excluded: chain F residue 71 ASP Chi-restraints excluded: chain F residue 148 THR Chi-restraints excluded: chain F residue 248 ASP Chi-restraints excluded: chain F residue 410 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 292 random chunks: chunk 235 optimal weight: 2.9990 chunk 160 optimal weight: 1.9990 chunk 4 optimal weight: 1.9990 chunk 210 optimal weight: 2.9990 chunk 116 optimal weight: 0.9990 chunk 240 optimal weight: 1.9990 chunk 195 optimal weight: 2.9990 chunk 0 optimal weight: 1.9990 chunk 144 optimal weight: 1.9990 chunk 253 optimal weight: 0.8980 chunk 71 optimal weight: 1.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 171 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8731 moved from start: 0.0697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.075 23070 Z= 0.337 Angle : 0.512 6.988 31280 Z= 0.266 Chirality : 0.042 0.143 3591 Planarity : 0.003 0.045 4098 Dihedral : 8.160 116.814 3328 Min Nonbonded Distance : 1.701 Molprobity Statistics. All-atom Clashscore : 3.73 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.38 % Favored : 97.55 % Rotamer: Outliers : 0.46 % Allowed : 5.92 % Favored : 93.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % Cis-general : 0.21 % 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: 1.17 (0.16), residues: 2943 helix: 1.47 (0.15), residues: 1204 sheet: -0.02 (0.25), residues: 424 loop : 0.57 (0.18), residues: 1315 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP E 201 HIS 0.004 0.001 HIS D 121 PHE 0.012 0.001 PHE E 439 TYR 0.012 0.001 TYR C 251 ARG 0.003 0.000 ARG F 195 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5886 Ramachandran restraints generated. 2943 Oldfield, 0 Emsley, 2943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5886 Ramachandran restraints generated. 2943 Oldfield, 0 Emsley, 2943 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 119 residues out of total 2393 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 108 time to evaluate : 3.669 Fit side-chains revert: symmetry clash REVERT: C 273 ASP cc_start: 0.8004 (OUTLIER) cc_final: 0.7450 (m-30) REVERT: D 173 MET cc_start: 0.8964 (mmt) cc_final: 0.8626 (mmt) outliers start: 11 outliers final: 6 residues processed: 113 average time/residue: 2.9159 time to fit residues: 382.3486 Evaluate side-chains 109 residues out of total 2393 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 102 time to evaluate : 3.604 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 273 ASP Chi-restraints excluded: chain B residue 279 ASP Chi-restraints excluded: chain C residue 273 ASP Chi-restraints excluded: chain F residue 71 ASP Chi-restraints excluded: chain F residue 148 THR Chi-restraints excluded: chain F residue 248 ASP Chi-restraints excluded: chain F residue 410 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 292 random chunks: chunk 94 optimal weight: 0.0980 chunk 254 optimal weight: 0.9980 chunk 55 optimal weight: 0.9980 chunk 165 optimal weight: 0.9990 chunk 69 optimal weight: 1.9990 chunk 282 optimal weight: 0.1980 chunk 234 optimal weight: 0.9990 chunk 130 optimal weight: 0.9980 chunk 23 optimal weight: 1.9990 chunk 93 optimal weight: 0.5980 chunk 148 optimal weight: 0.8980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 171 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8703 moved from start: 0.0581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 23070 Z= 0.155 Angle : 0.466 6.847 31280 Z= 0.239 Chirality : 0.040 0.144 3591 Planarity : 0.003 0.042 4098 Dihedral : 7.862 110.740 3328 Min Nonbonded Distance : 1.780 Molprobity Statistics. All-atom Clashscore : 3.95 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.04 % Favored : 97.89 % Rotamer: Outliers : 0.33 % Allowed : 6.09 % Favored : 93.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % Cis-general : 0.21 % 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 (0.16), residues: 2943 helix: 1.71 (0.15), residues: 1205 sheet: -0.04 (0.24), residues: 426 loop : 0.75 (0.19), residues: 1312 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP E 201 HIS 0.002 0.001 HIS C 43 PHE 0.013 0.001 PHE F 257 TYR 0.007 0.001 TYR C 251 ARG 0.002 0.000 ARG E 407 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5886 Ramachandran restraints generated. 2943 Oldfield, 0 Emsley, 2943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5886 Ramachandran restraints generated. 2943 Oldfield, 0 Emsley, 2943 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 121 residues out of total 2393 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 113 time to evaluate : 3.689 Fit side-chains revert: symmetry clash REVERT: D 173 MET cc_start: 0.8935 (mmt) cc_final: 0.8660 (mmt) REVERT: E 208 ASN cc_start: 0.8074 (OUTLIER) cc_final: 0.7763 (m110) outliers start: 8 outliers final: 4 residues processed: 116 average time/residue: 2.9561 time to fit residues: 400.1081 Evaluate side-chains 111 residues out of total 2393 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 106 time to evaluate : 3.822 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 273 ASP Chi-restraints excluded: chain B residue 279 ASP Chi-restraints excluded: chain E residue 208 ASN Chi-restraints excluded: chain F residue 148 THR Chi-restraints excluded: chain F residue 410 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 292 random chunks: chunk 272 optimal weight: 1.9990 chunk 31 optimal weight: 0.9990 chunk 160 optimal weight: 1.9990 chunk 206 optimal weight: 1.9990 chunk 159 optimal weight: 0.6980 chunk 237 optimal weight: 2.9990 chunk 157 optimal weight: 2.9990 chunk 281 optimal weight: 1.9990 chunk 176 optimal weight: 0.5980 chunk 171 optimal weight: 0.9990 chunk 129 optimal weight: 1.9990 overall best weight: 1.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 171 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8715 moved from start: 0.0627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 23070 Z= 0.246 Angle : 0.480 6.759 31280 Z= 0.247 Chirality : 0.040 0.141 3591 Planarity : 0.003 0.042 4098 Dihedral : 7.794 107.288 3328 Min Nonbonded Distance : 1.741 Molprobity Statistics. All-atom Clashscore : 3.86 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.18 % Favored : 97.75 % Rotamer: Outliers : 0.46 % Allowed : 6.17 % Favored : 93.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.40 (0.16), residues: 2943 helix: 1.69 (0.15), residues: 1203 sheet: 0.00 (0.24), residues: 426 loop : 0.70 (0.19), residues: 1314 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 247 HIS 0.003 0.001 HIS D 121 PHE 0.012 0.001 PHE F 257 TYR 0.010 0.001 TYR C 251 ARG 0.004 0.000 ARG E 335 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5886 Ramachandran restraints generated. 2943 Oldfield, 0 Emsley, 2943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5886 Ramachandran restraints generated. 2943 Oldfield, 0 Emsley, 2943 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 119 residues out of total 2393 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 108 time to evaluate : 3.706 Fit side-chains revert: symmetry clash REVERT: C 36 ASP cc_start: 0.8007 (p0) cc_final: 0.7688 (p0) REVERT: C 273 ASP cc_start: 0.7840 (OUTLIER) cc_final: 0.7319 (m-30) REVERT: D 173 MET cc_start: 0.8936 (mmt) cc_final: 0.8619 (mmt) outliers start: 11 outliers final: 5 residues processed: 113 average time/residue: 2.9030 time to fit residues: 381.2615 Evaluate side-chains 114 residues out of total 2393 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 108 time to evaluate : 3.679 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 273 ASP Chi-restraints excluded: chain B residue 279 ASP Chi-restraints excluded: chain C residue 273 ASP Chi-restraints excluded: chain E residue 208 ASN Chi-restraints excluded: chain F residue 148 THR Chi-restraints excluded: chain F residue 410 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 292 random chunks: chunk 174 optimal weight: 1.9990 chunk 112 optimal weight: 1.9990 chunk 168 optimal weight: 1.9990 chunk 84 optimal weight: 2.9990 chunk 55 optimal weight: 0.6980 chunk 54 optimal weight: 1.9990 chunk 178 optimal weight: 1.9990 chunk 191 optimal weight: 0.9990 chunk 139 optimal weight: 0.9990 chunk 26 optimal weight: 1.9990 chunk 221 optimal weight: 2.9990 overall best weight: 1.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 171 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8725 moved from start: 0.0696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.075 23070 Z= 0.300 Angle : 0.500 6.894 31280 Z= 0.259 Chirality : 0.041 0.142 3591 Planarity : 0.003 0.051 4098 Dihedral : 7.825 107.764 3328 Min Nonbonded Distance : 1.711 Molprobity Statistics. All-atom Clashscore : 3.77 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.25 % Favored : 97.69 % Rotamer: Outliers : 0.42 % Allowed : 6.34 % Favored : 93.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % Cis-general : 0.21 % 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: 1.31 (0.16), residues: 2943 helix: 1.61 (0.15), residues: 1203 sheet: 0.03 (0.25), residues: 424 loop : 0.64 (0.18), residues: 1316 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 247 HIS 0.004 0.001 HIS D 121 PHE 0.012 0.001 PHE F 257 TYR 0.012 0.001 TYR C 251 ARG 0.008 0.000 ARG E 335 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5886 Ramachandran restraints generated. 2943 Oldfield, 0 Emsley, 2943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5886 Ramachandran restraints generated. 2943 Oldfield, 0 Emsley, 2943 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 119 residues out of total 2393 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 109 time to evaluate : 3.720 Fit side-chains revert: symmetry clash REVERT: C 36 ASP cc_start: 0.8113 (p0) cc_final: 0.7798 (p0) REVERT: C 273 ASP cc_start: 0.7903 (OUTLIER) cc_final: 0.7355 (m-30) REVERT: D 173 MET cc_start: 0.8933 (mmt) cc_final: 0.8616 (mmt) outliers start: 10 outliers final: 5 residues processed: 114 average time/residue: 2.9261 time to fit residues: 389.0321 Evaluate side-chains 112 residues out of total 2393 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 106 time to evaluate : 3.705 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 273 ASP Chi-restraints excluded: chain B residue 279 ASP Chi-restraints excluded: chain C residue 273 ASP Chi-restraints excluded: chain F residue 148 THR Chi-restraints excluded: chain F residue 248 ASP Chi-restraints excluded: chain F residue 410 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 292 random chunks: chunk 256 optimal weight: 1.9990 chunk 269 optimal weight: 0.9980 chunk 245 optimal weight: 0.6980 chunk 262 optimal weight: 0.7980 chunk 157 optimal weight: 2.9990 chunk 114 optimal weight: 0.8980 chunk 205 optimal weight: 2.9990 chunk 80 optimal weight: 0.9980 chunk 236 optimal weight: 1.9990 chunk 248 optimal weight: 0.0670 chunk 261 optimal weight: 0.9980 overall best weight: 0.6918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 171 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8704 moved from start: 0.0627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 23070 Z= 0.178 Angle : 0.466 6.937 31280 Z= 0.239 Chirality : 0.040 0.143 3591 Planarity : 0.003 0.039 4098 Dihedral : 7.555 102.401 3328 Min Nonbonded Distance : 1.761 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.01 % Favored : 97.92 % Rotamer: Outliers : 0.33 % Allowed : 6.47 % Favored : 93.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.49 (0.16), residues: 2943 helix: 1.76 (0.15), residues: 1206 sheet: -0.01 (0.25), residues: 417 loop : 0.78 (0.19), residues: 1320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP E 201 HIS 0.002 0.001 HIS C 259 PHE 0.012 0.001 PHE F 257 TYR 0.009 0.001 TYR E 366 ARG 0.007 0.000 ARG E 335 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5886 Ramachandran restraints generated. 2943 Oldfield, 0 Emsley, 2943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5886 Ramachandran restraints generated. 2943 Oldfield, 0 Emsley, 2943 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 118 residues out of total 2393 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 110 time to evaluate : 3.935 Fit side-chains revert: symmetry clash REVERT: D 173 MET cc_start: 0.8913 (mmt) cc_final: 0.8632 (mmt) outliers start: 8 outliers final: 5 residues processed: 115 average time/residue: 2.9073 time to fit residues: 389.7533 Evaluate side-chains 114 residues out of total 2393 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 109 time to evaluate : 2.916 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 273 ASP Chi-restraints excluded: chain B residue 279 ASP Chi-restraints excluded: chain F residue 148 THR Chi-restraints excluded: chain F residue 248 ASP Chi-restraints excluded: chain F residue 410 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 292 random chunks: chunk 172 optimal weight: 1.9990 chunk 277 optimal weight: 1.9990 chunk 169 optimal weight: 0.5980 chunk 131 optimal weight: 2.9990 chunk 192 optimal weight: 1.9990 chunk 290 optimal weight: 1.9990 chunk 267 optimal weight: 2.9990 chunk 231 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 chunk 178 optimal weight: 2.9990 chunk 142 optimal weight: 2.9990 overall best weight: 1.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 171 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8732 moved from start: 0.0753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.093 23070 Z= 0.375 Angle : 0.520 7.016 31280 Z= 0.270 Chirality : 0.042 0.144 3591 Planarity : 0.003 0.044 4098 Dihedral : 7.797 105.051 3328 Min Nonbonded Distance : 1.684 Molprobity Statistics. All-atom Clashscore : 3.90 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.42 % Favored : 97.52 % Rotamer: Outliers : 0.33 % Allowed : 6.55 % Favored : 93.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % Cis-general : 0.21 % 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: 1.28 (0.16), residues: 2943 helix: 1.57 (0.15), residues: 1203 sheet: 0.01 (0.25), residues: 419 loop : 0.64 (0.18), residues: 1321 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 247 HIS 0.005 0.001 HIS D 121 PHE 0.012 0.001 PHE E 439 TYR 0.014 0.001 TYR C 251 ARG 0.006 0.000 ARG E 335 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5886 Ramachandran restraints generated. 2943 Oldfield, 0 Emsley, 2943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5886 Ramachandran restraints generated. 2943 Oldfield, 0 Emsley, 2943 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 115 residues out of total 2393 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 107 time to evaluate : 3.462 Fit side-chains revert: symmetry clash REVERT: C 36 ASP cc_start: 0.8067 (p0) cc_final: 0.7830 (p0) REVERT: D 173 MET cc_start: 0.8936 (mmt) cc_final: 0.8629 (mmt) outliers start: 8 outliers final: 5 residues processed: 111 average time/residue: 3.0033 time to fit residues: 388.7632 Evaluate side-chains 111 residues out of total 2393 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 106 time to evaluate : 3.517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 273 ASP Chi-restraints excluded: chain B residue 279 ASP Chi-restraints excluded: chain F residue 148 THR Chi-restraints excluded: chain F residue 248 ASP Chi-restraints excluded: chain F residue 410 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 292 random chunks: chunk 184 optimal weight: 2.9990 chunk 246 optimal weight: 0.6980 chunk 70 optimal weight: 0.0980 chunk 213 optimal weight: 0.6980 chunk 34 optimal weight: 2.9990 chunk 64 optimal weight: 1.9990 chunk 232 optimal weight: 3.9990 chunk 97 optimal weight: 1.9990 chunk 238 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 42 optimal weight: 1.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 171 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.075236 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2815 r_free = 0.2815 target = 0.062978 restraints weight = 152105.769| |-----------------------------------------------------------------------------| r_work (start): 0.2814 rms_B_bonded: 1.89 r_work: 0.2723 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.2618 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.2618 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2623 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2623 r_free = 0.2623 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2623 r_free = 0.2623 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2623 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8905 moved from start: 0.0703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 23070 Z= 0.252 Angle : 0.490 7.936 31280 Z= 0.253 Chirality : 0.041 0.141 3591 Planarity : 0.003 0.044 4098 Dihedral : 7.696 104.118 3328 Min Nonbonded Distance : 1.729 Molprobity Statistics. All-atom Clashscore : 4.01 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.08 % Favored : 97.86 % Rotamer: Outliers : 0.38 % Allowed : 6.51 % Favored : 93.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % Cis-general : 0.21 % 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: 1.35 (0.16), residues: 2943 helix: 1.63 (0.15), residues: 1203 sheet: -0.01 (0.25), residues: 415 loop : 0.69 (0.18), residues: 1325 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP E 201 HIS 0.003 0.001 HIS C 259 PHE 0.012 0.001 PHE F 257 TYR 0.010 0.001 TYR C 251 ARG 0.006 0.000 ARG E 335 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10501.62 seconds wall clock time: 189 minutes 5.82 seconds (11345.82 seconds total)