Starting phenix.real_space_refine on Tue Mar 19 13:09:10 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hh8_34755/03_2024/8hh8_34755_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hh8_34755/03_2024/8hh8_34755.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hh8_34755/03_2024/8hh8_34755.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hh8_34755/03_2024/8hh8_34755.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hh8_34755/03_2024/8hh8_34755_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hh8_34755/03_2024/8hh8_34755_updated.pdb" } resolution = 2.8 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: 6 Type Number sf(0) Gaussians P 16 5.49 5 Mg 5 5.21 5 S 77 5.16 5 C 15277 2.51 5 N 4214 2.21 5 O 4661 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 299": "OE1" <-> "OE2" Residue "A GLU 492": "OE1" <-> "OE2" Residue "B GLU 68": "OE1" <-> "OE2" Residue "D PHE 125": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 125": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 133": "OE1" <-> "OE2" Residue "F PHE 250": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 182": "OE1" <-> "OE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 24250 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 3661 Number of conformers: 1 Conformer: "" Number of residues, atoms: 478, 3661 Classifications: {'peptide': 478} Link IDs: {'PTRANS': 23, 'TRANS': 454} Chain: "B" Number of atoms: 3661 Number of conformers: 1 Conformer: "" Number of residues, atoms: 478, 3661 Classifications: {'peptide': 478} Link IDs: {'PTRANS': 23, 'TRANS': 454} Chain: "C" Number of atoms: 3661 Number of conformers: 1 Conformer: "" Number of residues, atoms: 478, 3661 Classifications: {'peptide': 478} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 454} Chain: "D" Number of atoms: 3630 Number of conformers: 1 Conformer: "" Number of residues, atoms: 471, 3630 Classifications: {'peptide': 471} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 447} Chain: "E" Number of atoms: 3623 Number of conformers: 1 Conformer: "" Number of residues, atoms: 470, 3623 Classifications: {'peptide': 470} Link IDs: {'PTRANS': 23, 'TRANS': 446} Chain: "F" Number of atoms: 3630 Number of conformers: 1 Conformer: "" Number of residues, atoms: 471, 3630 Classifications: {'peptide': 471} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 447} Chain: "G" Number of atoms: 2218 Number of conformers: 1 Conformer: "" Number of residues, atoms: 283, 2218 Classifications: {'peptide': 283} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 272} 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: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, 'ADP': 1, 'PO4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "E" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 5 Unusual residues: {'PO4': 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} Time building chain proxies: 11.80, per 1000 atoms: 0.49 Number of scatterers: 24250 At special positions: 0 Unit cell: (127.6, 122.32, 154.88, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 77 16.00 P 16 15.00 Mg 5 11.99 O 4661 8.00 N 4214 7.00 C 15277 6.00 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: 9.45 Conformation dependent library (CDL) restraints added in 4.7 seconds 6230 Ramachandran restraints generated. 3115 Oldfield, 0 Emsley, 3115 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5712 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 122 helices and 23 sheets defined 41.9% alpha, 13.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.85 Creating SS restraints... Processing helix chain 'A' and resid 101 through 103 No H-bonds generated for 'chain 'A' and resid 101 through 103' Processing helix chain 'A' and resid 151 through 156 Processing helix chain 'A' and resid 175 through 187 removed outlier: 3.605A pdb=" N GLN A 186 " --> pdb=" O THR A 182 " (cutoff:3.500A) removed outlier: 4.612A pdb=" N LYS A 187 " --> pdb=" O ILE A 183 " (cutoff:3.500A) Processing helix chain 'A' and resid 202 through 215 Processing helix chain 'A' and resid 217 through 219 No H-bonds generated for 'chain 'A' and resid 217 through 219' Processing helix chain 'A' and resid 232 through 251 Proline residue: A 239 - end of helix removed outlier: 3.645A pdb=" N TYR A 248 " --> pdb=" O ALA A 244 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N PHE A 249 " --> pdb=" O MET A 245 " (cutoff:3.500A) Processing helix chain 'A' and resid 263 through 276 Processing helix chain 'A' and resid 283 through 285 No H-bonds generated for 'chain 'A' and resid 283 through 285' Processing helix chain 'A' and resid 288 through 300 removed outlier: 4.506A pdb=" N PHE A 291 " --> pdb=" O GLY A 288 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N GLU A 299 " --> pdb=" O ARG A 296 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ARG A 300 " --> pdb=" O LEU A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 306 through 308 No H-bonds generated for 'chain 'A' and resid 306 through 308' Processing helix chain 'A' and resid 329 through 337 Processing helix chain 'A' and resid 346 through 350 Processing helix chain 'A' and resid 373 through 390 removed outlier: 3.803A pdb=" N VAL A 378 " --> pdb=" O ALA A 374 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N GLY A 380 " --> pdb=" O LYS A 376 " (cutoff:3.500A) removed outlier: 5.438A pdb=" N THR A 381 " --> pdb=" O LYS A 377 " (cutoff:3.500A) Processing helix chain 'A' and resid 394 through 396 No H-bonds generated for 'chain 'A' and resid 394 through 396' Processing helix chain 'A' and resid 406 through 420 Processing helix chain 'A' and resid 430 through 441 removed outlier: 3.623A pdb=" N LEU A 435 " --> pdb=" O GLU A 431 " (cutoff:3.500A) Processing helix chain 'A' and resid 450 through 467 removed outlier: 4.727A pdb=" N ARG A 454 " --> pdb=" O GLU A 451 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N ASP A 465 " --> pdb=" O LEU A 462 " (cutoff:3.500A) Processing helix chain 'A' and resid 469 through 478 Processing helix chain 'A' and resid 484 through 497 removed outlier: 3.572A pdb=" N THR A 497 " --> pdb=" O ALA A 493 " (cutoff:3.500A) Processing helix chain 'B' and resid 101 through 103 No H-bonds generated for 'chain 'B' and resid 101 through 103' Processing helix chain 'B' and resid 136 through 138 No H-bonds generated for 'chain 'B' and resid 136 through 138' Processing helix chain 'B' and resid 151 through 156 Processing helix chain 'B' and resid 175 through 187 removed outlier: 3.602A pdb=" N GLN B 186 " --> pdb=" O THR B 182 " (cutoff:3.500A) removed outlier: 4.759A pdb=" N LYS B 187 " --> pdb=" O ILE B 183 " (cutoff:3.500A) Processing helix chain 'B' and resid 202 through 215 Processing helix chain 'B' and resid 217 through 219 No H-bonds generated for 'chain 'B' and resid 217 through 219' Processing helix chain 'B' and resid 232 through 251 Proline residue: B 239 - end of helix removed outlier: 3.668A pdb=" N TYR B 248 " --> pdb=" O ALA B 244 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N PHE B 249 " --> pdb=" O MET B 245 " (cutoff:3.500A) Processing helix chain 'B' and resid 263 through 276 Processing helix chain 'B' and resid 283 through 285 No H-bonds generated for 'chain 'B' and resid 283 through 285' Processing helix chain 'B' and resid 288 through 300 removed outlier: 4.312A pdb=" N PHE B 291 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N LEU B 293 " --> pdb=" O ILE B 290 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N ARG B 296 " --> pdb=" O LEU B 293 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N GLU B 299 " --> pdb=" O ARG B 296 " (cutoff:3.500A) Processing helix chain 'B' and resid 329 through 335 Processing helix chain 'B' and resid 346 through 351 removed outlier: 3.673A pdb=" N SER B 351 " --> pdb=" O ASP B 347 " (cutoff:3.500A) Processing helix chain 'B' and resid 373 through 398 removed outlier: 3.979A pdb=" N GLY B 380 " --> pdb=" O LYS B 376 " (cutoff:3.500A) removed outlier: 5.560A pdb=" N THR B 381 " --> pdb=" O LYS B 377 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N LEU B 382 " --> pdb=" O VAL B 378 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N LEU B 392 " --> pdb=" O ALA B 388 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N ALA B 394 " --> pdb=" O ARG B 390 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N PHE B 395 " --> pdb=" O GLU B 391 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N PHE B 398 " --> pdb=" O ALA B 394 " (cutoff:3.500A) Processing helix chain 'B' and resid 404 through 420 removed outlier: 3.543A pdb=" N ARG B 415 " --> pdb=" O ALA B 411 " (cutoff:3.500A) Processing helix chain 'B' and resid 430 through 441 Processing helix chain 'B' and resid 450 through 467 removed outlier: 4.865A pdb=" N ARG B 454 " --> pdb=" O GLU B 451 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N TYR B 461 " --> pdb=" O LYS B 458 " (cutoff:3.500A) Processing helix chain 'B' and resid 469 through 478 Processing helix chain 'B' and resid 484 through 497 Processing helix chain 'C' and resid 101 through 103 No H-bonds generated for 'chain 'C' and resid 101 through 103' Processing helix chain 'C' and resid 151 through 156 Processing helix chain 'C' and resid 175 through 186 removed outlier: 3.586A pdb=" N GLN C 186 " --> pdb=" O THR C 182 " (cutoff:3.500A) Processing helix chain 'C' and resid 202 through 215 Processing helix chain 'C' and resid 217 through 220 Processing helix chain 'C' and resid 232 through 252 Proline residue: C 239 - end of helix removed outlier: 3.768A pdb=" N PHE C 249 " --> pdb=" O MET C 245 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N LYS C 252 " --> pdb=" O TYR C 248 " (cutoff:3.500A) Processing helix chain 'C' and resid 263 through 276 Processing helix chain 'C' and resid 283 through 285 No H-bonds generated for 'chain 'C' and resid 283 through 285' Processing helix chain 'C' and resid 288 through 300 removed outlier: 4.561A pdb=" N PHE C 291 " --> pdb=" O GLY C 288 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LEU C 293 " --> pdb=" O ILE C 290 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N GLU C 299 " --> pdb=" O ARG C 296 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ARG C 300 " --> pdb=" O LEU C 297 " (cutoff:3.500A) Processing helix chain 'C' and resid 306 through 308 No H-bonds generated for 'chain 'C' and resid 306 through 308' Processing helix chain 'C' and resid 329 through 335 Processing helix chain 'C' and resid 346 through 350 Processing helix chain 'C' and resid 373 through 395 removed outlier: 3.702A pdb=" N GLY C 380 " --> pdb=" O LYS C 376 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N THR C 381 " --> pdb=" O LYS C 377 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLU C 393 " --> pdb=" O TYR C 389 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N PHE C 395 " --> pdb=" O GLU C 391 " (cutoff:3.500A) Processing helix chain 'C' and resid 404 through 420 Processing helix chain 'C' and resid 430 through 441 Processing helix chain 'C' and resid 450 through 466 removed outlier: 5.131A pdb=" N ARG C 454 " --> pdb=" O GLU C 451 " (cutoff:3.500A) Processing helix chain 'C' and resid 469 through 478 Processing helix chain 'C' and resid 484 through 497 removed outlier: 3.509A pdb=" N THR C 497 " --> pdb=" O ALA C 493 " (cutoff:3.500A) Processing helix chain 'D' and resid 89 through 91 No H-bonds generated for 'chain 'D' and resid 89 through 91' Processing helix chain 'D' and resid 140 through 145 Processing helix chain 'D' and resid 164 through 175 Processing helix chain 'D' and resid 192 through 205 Processing helix chain 'D' and resid 207 through 210 Processing helix chain 'D' and resid 222 through 241 removed outlier: 4.970A pdb=" N ALA D 229 " --> pdb=" O ARG D 225 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N LEU D 230 " --> pdb=" O MET D 226 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N TYR D 238 " --> pdb=" O THR D 234 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N PHE D 239 " --> pdb=" O MET D 235 " (cutoff:3.500A) Processing helix chain 'D' and resid 254 through 263 Processing helix chain 'D' and resid 265 through 268 No H-bonds generated for 'chain 'D' and resid 265 through 268' Processing helix chain 'D' and resid 281 through 291 removed outlier: 4.341A pdb=" N ARG D 291 " --> pdb=" O GLN D 287 " (cutoff:3.500A) Processing helix chain 'D' and resid 309 through 311 No H-bonds generated for 'chain 'D' and resid 309 through 311' Processing helix chain 'D' and resid 316 through 324 removed outlier: 4.693A pdb=" N SER D 323 " --> pdb=" O ALA D 319 " (cutoff:3.500A) removed outlier: 4.805A pdb=" N HIS D 324 " --> pdb=" O THR D 320 " (cutoff:3.500A) Processing helix chain 'D' and resid 333 through 338 Processing helix chain 'D' and resid 356 through 359 No H-bonds generated for 'chain 'D' and resid 356 through 359' Processing helix chain 'D' and resid 361 through 387 removed outlier: 4.179A pdb=" N ASP D 382 " --> pdb=" O LYS D 378 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N ILE D 383 " --> pdb=" O GLU D 379 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N ILE D 386 " --> pdb=" O ASP D 382 " (cutoff:3.500A) Processing helix chain 'D' and resid 396 through 409 removed outlier: 3.831A pdb=" N ARG D 405 " --> pdb=" O HIS D 401 " (cutoff:3.500A) Processing helix chain 'D' and resid 416 through 421 removed outlier: 3.912A pdb=" N GLN D 419 " --> pdb=" O VAL D 416 " (cutoff:3.500A) Processing helix chain 'D' and resid 430 through 442 Processing helix chain 'D' and resid 450 through 453 Processing helix chain 'D' and resid 459 through 468 removed outlier: 3.843A pdb=" N VAL D 463 " --> pdb=" O ILE D 459 " (cutoff:3.500A) Processing helix chain 'E' and resid 89 through 91 No H-bonds generated for 'chain 'E' and resid 89 through 91' Processing helix chain 'E' and resid 125 through 127 No H-bonds generated for 'chain 'E' and resid 125 through 127' Processing helix chain 'E' and resid 140 through 145 Processing helix chain 'E' and resid 164 through 179 Processing helix chain 'E' and resid 192 through 205 Processing helix chain 'E' and resid 207 through 210 Processing helix chain 'E' and resid 222 through 242 removed outlier: 5.142A pdb=" N ALA E 229 " --> pdb=" O ARG E 225 " (cutoff:3.500A) removed outlier: 4.889A pdb=" N LEU E 230 " --> pdb=" O MET E 226 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N PHE E 239 " --> pdb=" O MET E 235 " (cutoff:3.500A) Processing helix chain 'E' and resid 254 through 268 Processing helix chain 'E' and resid 281 through 291 removed outlier: 4.374A pdb=" N ARG E 291 " --> pdb=" O GLN E 287 " (cutoff:3.500A) Processing helix chain 'E' and resid 309 through 311 No H-bonds generated for 'chain 'E' and resid 309 through 311' Processing helix chain 'E' and resid 316 through 324 removed outlier: 3.530A pdb=" N SER E 323 " --> pdb=" O ALA E 319 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N HIS E 324 " --> pdb=" O THR E 320 " (cutoff:3.500A) Processing helix chain 'E' and resid 333 through 338 Processing helix chain 'E' and resid 356 through 359 No H-bonds generated for 'chain 'E' and resid 356 through 359' Processing helix chain 'E' and resid 361 through 387 removed outlier: 3.598A pdb=" N LEU E 380 " --> pdb=" O ARG E 376 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N GLN E 381 " --> pdb=" O TYR E 377 " (cutoff:3.500A) removed outlier: 5.270A pdb=" N ASP E 382 " --> pdb=" O LYS E 378 " (cutoff:3.500A) removed outlier: 5.344A pdb=" N ILE E 383 " --> pdb=" O GLU E 379 " (cutoff:3.500A) Processing helix chain 'E' and resid 389 through 391 No H-bonds generated for 'chain 'E' and resid 389 through 391' Processing helix chain 'E' and resid 394 through 409 removed outlier: 3.523A pdb=" N ARG E 405 " --> pdb=" O HIS E 401 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N PHE E 408 " --> pdb=" O ARG E 404 " (cutoff:3.500A) Processing helix chain 'E' and resid 418 through 421 No H-bonds generated for 'chain 'E' and resid 418 through 421' Processing helix chain 'E' and resid 430 through 441 Processing helix chain 'E' and resid 450 through 453 Processing helix chain 'E' and resid 459 through 469 removed outlier: 4.073A pdb=" N VAL E 463 " --> pdb=" O ILE E 459 " (cutoff:3.500A) Processing helix chain 'F' and resid 89 through 91 No H-bonds generated for 'chain 'F' and resid 89 through 91' Processing helix chain 'F' and resid 125 through 127 No H-bonds generated for 'chain 'F' and resid 125 through 127' Processing helix chain 'F' and resid 140 through 145 Processing helix chain 'F' and resid 164 through 178 removed outlier: 4.683A pdb=" N GLN F 177 " --> pdb=" O HIS F 173 " (cutoff:3.500A) removed outlier: 5.805A pdb=" N GLU F 178 " --> pdb=" O ASN F 174 " (cutoff:3.500A) Processing helix chain 'F' and resid 192 through 205 Processing helix chain 'F' and resid 207 through 210 Processing helix chain 'F' and resid 222 through 241 removed outlier: 5.199A pdb=" N ALA F 229 " --> pdb=" O ARG F 225 " (cutoff:3.500A) removed outlier: 4.690A pdb=" N LEU F 230 " --> pdb=" O MET F 226 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N TYR F 238 " --> pdb=" O THR F 234 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N PHE F 239 " --> pdb=" O MET F 235 " (cutoff:3.500A) Processing helix chain 'F' and resid 255 through 268 removed outlier: 3.849A pdb=" N ALA F 266 " --> pdb=" O SER F 262 " (cutoff:3.500A) removed outlier: 4.657A pdb=" N LEU F 267 " --> pdb=" O GLU F 263 " (cutoff:3.500A) Processing helix chain 'F' and resid 281 through 291 removed outlier: 4.116A pdb=" N ARG F 291 " --> pdb=" O GLN F 287 " (cutoff:3.500A) Processing helix chain 'F' and resid 309 through 311 No H-bonds generated for 'chain 'F' and resid 309 through 311' Processing helix chain 'F' and resid 316 through 324 removed outlier: 3.639A pdb=" N PHE F 322 " --> pdb=" O PRO F 318 " (cutoff:3.500A) removed outlier: 4.675A pdb=" N SER F 323 " --> pdb=" O ALA F 319 " (cutoff:3.500A) removed outlier: 4.653A pdb=" N HIS F 324 " --> pdb=" O THR F 320 " (cutoff:3.500A) Processing helix chain 'F' and resid 333 through 337 Processing helix chain 'F' and resid 356 through 359 No H-bonds generated for 'chain 'F' and resid 356 through 359' Processing helix chain 'F' and resid 361 through 379 Processing helix chain 'F' and resid 381 through 387 Processing helix chain 'F' and resid 389 through 391 No H-bonds generated for 'chain 'F' and resid 389 through 391' Processing helix chain 'F' and resid 394 through 409 removed outlier: 3.710A pdb=" N ARG F 405 " --> pdb=" O HIS F 401 " (cutoff:3.500A) Processing helix chain 'F' and resid 416 through 418 No H-bonds generated for 'chain 'F' and resid 416 through 418' Processing helix chain 'F' and resid 430 through 442 Processing helix chain 'F' and resid 450 through 453 Processing helix chain 'F' and resid 459 through 464 Processing helix chain 'G' and resid 4 through 41 removed outlier: 3.711A pdb=" N SER G 30 " --> pdb=" O MET G 26 " (cutoff:3.500A) Processing helix chain 'G' and resid 43 through 58 removed outlier: 4.597A pdb=" N LEU G 58 " --> pdb=" O ALA G 54 " (cutoff:3.500A) Processing helix chain 'G' and resid 91 through 106 removed outlier: 3.972A pdb=" N VAL G 95 " --> pdb=" O TYR G 91 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LEU G 98 " --> pdb=" O ASN G 94 " (cutoff:3.500A) Processing helix chain 'G' and resid 120 through 128 Processing helix chain 'G' and resid 150 through 161 removed outlier: 3.550A pdb=" N PHE G 160 " --> pdb=" O THR G 156 " (cutoff:3.500A) Processing helix chain 'G' and resid 211 through 226 removed outlier: 3.835A pdb=" N VAL G 215 " --> pdb=" O GLU G 211 " (cutoff:3.500A) Proline residue: G 218 - end of helix removed outlier: 4.085A pdb=" N GLU G 222 " --> pdb=" O PRO G 218 " (cutoff:3.500A) removed outlier: 5.050A pdb=" N SER G 223 " --> pdb=" O GLN G 219 " (cutoff:3.500A) removed outlier: 5.403A pdb=" N LEU G 224 " --> pdb=" O TYR G 220 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N ILE G 225 " --> pdb=" O ALA G 221 " (cutoff:3.500A) Processing helix chain 'G' and resid 229 through 282 Processing sheet with id= A, first strand: chain 'A' and resid 28 through 30 removed outlier: 6.411A pdb=" N GLY A 72 " --> pdb=" O LEU A 64 " (cutoff:3.500A) removed outlier: 4.964A pdb=" N LEU A 66 " --> pdb=" O ASN A 70 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N ASN A 70 " --> pdb=" O LEU A 66 " (cutoff:3.500A) removed outlier: 6.073A pdb=" N HIS A 42 " --> pdb=" O VAL A 31 " (cutoff:3.500A) removed outlier: 5.726A pdb=" N VAL A 31 " --> pdb=" O HIS A 42 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 96 through 99 removed outlier: 4.050A pdb=" N GLU A 125 " --> pdb=" O VAL A 99 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 107 through 109 removed outlier: 8.760A pdb=" N VAL A 108 " --> pdb=" O THR A 221 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N VAL A 223 " --> pdb=" O VAL A 108 " (cutoff:3.500A) removed outlier: 8.832A pdb=" N ILE A 222 " --> pdb=" O MET A 191 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N SER A 193 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 8.139A pdb=" N VAL A 224 " --> pdb=" O SER A 193 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N TYR A 195 " --> pdb=" O VAL A 224 " (cutoff:3.500A) removed outlier: 7.947A pdb=" N ALA A 226 " --> pdb=" O TYR A 195 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N ALA A 197 " --> pdb=" O ALA A 226 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N HIS A 255 " --> pdb=" O ILE A 192 " (cutoff:3.500A) removed outlier: 8.100A pdb=" N ILE A 194 " --> pdb=" O HIS A 255 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N LEU A 257 " --> pdb=" O ILE A 194 " (cutoff:3.500A) removed outlier: 7.639A pdb=" N VAL A 196 " --> pdb=" O LEU A 257 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N VAL A 259 " --> pdb=" O VAL A 196 " (cutoff:3.500A) removed outlier: 7.318A pdb=" N ILE A 198 " --> pdb=" O VAL A 259 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N SER A 312 " --> pdb=" O VAL A 256 " (cutoff:3.500A) removed outlier: 7.973A pdb=" N VAL A 258 " --> pdb=" O SER A 312 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N THR A 314 " --> pdb=" O VAL A 258 " (cutoff:3.500A) removed outlier: 7.910A pdb=" N TYR A 260 " --> pdb=" O THR A 314 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N LEU A 316 " --> pdb=" O TYR A 260 " (cutoff:3.500A) No H-bonds generated for sheet with id= C Processing sheet with id= D, first strand: chain 'A' and resid 341 through 344 removed outlier: 6.889A pdb=" N LEU A 166 " --> pdb=" O ILE A 342 " (cutoff:3.500A) removed outlier: 7.976A pdb=" N LEU A 344 " --> pdb=" O LEU A 166 " (cutoff:3.500A) removed outlier: 7.056A pdb=" N ILE A 168 " --> pdb=" O LEU A 344 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 28 through 30 removed outlier: 4.563A pdb=" N MET B 60 " --> pdb=" O LEU B 76 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N GLY B 72 " --> pdb=" O LEU B 64 " (cutoff:3.500A) removed outlier: 5.854A pdb=" N HIS B 42 " --> pdb=" O VAL B 31 " (cutoff:3.500A) removed outlier: 5.516A pdb=" N VAL B 31 " --> pdb=" O HIS B 42 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 96 through 99 removed outlier: 4.198A pdb=" N GLU B 125 " --> pdb=" O VAL B 99 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 341 through 344 removed outlier: 6.527A pdb=" N LEU B 166 " --> pdb=" O ILE B 342 " (cutoff:3.500A) removed outlier: 7.510A pdb=" N LEU B 344 " --> pdb=" O LEU B 166 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N ILE B 168 " --> pdb=" O LEU B 344 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 221 through 226 removed outlier: 6.652A pdb=" N SER B 193 " --> pdb=" O ILE B 222 " (cutoff:3.500A) removed outlier: 7.969A pdb=" N VAL B 224 " --> pdb=" O SER B 193 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N TYR B 195 " --> pdb=" O VAL B 224 " (cutoff:3.500A) removed outlier: 7.796A pdb=" N ALA B 226 " --> pdb=" O TYR B 195 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N ALA B 197 " --> pdb=" O ALA B 226 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N SER B 312 " --> pdb=" O VAL B 256 " (cutoff:3.500A) removed outlier: 8.015A pdb=" N VAL B 258 " --> pdb=" O SER B 312 " (cutoff:3.500A) removed outlier: 6.156A pdb=" N THR B 314 " --> pdb=" O VAL B 258 " (cutoff:3.500A) removed outlier: 7.535A pdb=" N TYR B 260 " --> pdb=" O THR B 314 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N LEU B 316 " --> pdb=" O TYR B 260 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'C' and resid 28 through 30 removed outlier: 6.392A pdb=" N GLY C 72 " --> pdb=" O LEU C 64 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLN C 33 " --> pdb=" O ARG C 40 " (cutoff:3.500A) removed outlier: 5.985A pdb=" N HIS C 42 " --> pdb=" O VAL C 31 " (cutoff:3.500A) removed outlier: 5.541A pdb=" N VAL C 31 " --> pdb=" O HIS C 42 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'C' and resid 96 through 99 removed outlier: 3.875A pdb=" N GLU C 125 " --> pdb=" O VAL C 99 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'C' and resid 341 through 344 removed outlier: 6.880A pdb=" N LEU C 166 " --> pdb=" O ILE C 342 " (cutoff:3.500A) removed outlier: 7.862A pdb=" N LEU C 344 " --> pdb=" O LEU C 166 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N ILE C 168 " --> pdb=" O LEU C 344 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'C' and resid 221 through 226 removed outlier: 6.809A pdb=" N SER C 193 " --> pdb=" O ILE C 222 " (cutoff:3.500A) removed outlier: 8.140A pdb=" N VAL C 224 " --> pdb=" O SER C 193 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N TYR C 195 " --> pdb=" O VAL C 224 " (cutoff:3.500A) removed outlier: 7.899A pdb=" N ALA C 226 " --> pdb=" O TYR C 195 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N ALA C 197 " --> pdb=" O ALA C 226 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N SER C 312 " --> pdb=" O VAL C 256 " (cutoff:3.500A) removed outlier: 8.098A pdb=" N VAL C 258 " --> pdb=" O SER C 312 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N THR C 314 " --> pdb=" O VAL C 258 " (cutoff:3.500A) removed outlier: 7.646A pdb=" N TYR C 260 " --> pdb=" O THR C 314 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N LEU C 316 " --> pdb=" O TYR C 260 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'D' and resid 5 through 10 removed outlier: 6.714A pdb=" N ASP D 15 " --> pdb=" O ILE D 7 " (cutoff:3.500A) removed outlier: 4.804A pdb=" N VAL D 9 " --> pdb=" O VAL D 13 " (cutoff:3.500A) removed outlier: 7.164A pdb=" N VAL D 13 " --> pdb=" O VAL D 9 " (cutoff:3.500A) removed outlier: 6.102A pdb=" N ILE D 62 " --> pdb=" O VAL D 50 " (cutoff:3.500A) removed outlier: 5.708A pdb=" N VAL D 50 " --> pdb=" O ILE D 62 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'D' and resid 84 through 86 Processing sheet with id= O, first strand: chain 'D' and resid 327 through 330 removed outlier: 8.025A pdb=" N ILE D 154 " --> pdb=" O ILE D 300 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N SER D 302 " --> pdb=" O ILE D 154 " (cutoff:3.500A) removed outlier: 7.813A pdb=" N LEU D 156 " --> pdb=" O SER D 302 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N GLN D 304 " --> pdb=" O LEU D 156 " (cutoff:3.500A) removed outlier: 8.089A pdb=" N GLY D 158 " --> pdb=" O GLN D 304 " (cutoff:3.500A) removed outlier: 6.226A pdb=" N ILE D 306 " --> pdb=" O GLY D 158 " (cutoff:3.500A) removed outlier: 7.067A pdb=" N ILE D 182 " --> pdb=" O LEU D 248 " (cutoff:3.500A) removed outlier: 7.948A pdb=" N PHE D 250 " --> pdb=" O ILE D 182 " (cutoff:3.500A) removed outlier: 6.198A pdb=" N VAL D 184 " --> pdb=" O PHE D 250 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'E' and resid 3 through 5 Processing sheet with id= Q, first strand: chain 'E' and resid 6 through 10 removed outlier: 6.699A pdb=" N ASP E 15 " --> pdb=" O ILE E 7 " (cutoff:3.500A) removed outlier: 4.680A pdb=" N VAL E 9 " --> pdb=" O VAL E 13 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N VAL E 13 " --> pdb=" O VAL E 9 " (cutoff:3.500A) removed outlier: 6.118A pdb=" N ILE E 62 " --> pdb=" O VAL E 50 " (cutoff:3.500A) removed outlier: 5.734A pdb=" N VAL E 50 " --> pdb=" O ILE E 62 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'E' and resid 84 through 86 Processing sheet with id= S, first strand: chain 'E' and resid 327 through 330 removed outlier: 3.531A pdb=" N ALA E 327 " --> pdb=" O LYS E 153 " (cutoff:3.500A) removed outlier: 8.321A pdb=" N ILE E 154 " --> pdb=" O ILE E 300 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N SER E 302 " --> pdb=" O ILE E 154 " (cutoff:3.500A) removed outlier: 7.502A pdb=" N LEU E 156 " --> pdb=" O SER E 302 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N GLN E 304 " --> pdb=" O LEU E 156 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'F' and resid 75 through 77 removed outlier: 6.527A pdb=" N ASP F 15 " --> pdb=" O ILE F 7 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N VAL F 9 " --> pdb=" O VAL F 13 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N VAL F 13 " --> pdb=" O VAL F 9 " (cutoff:3.500A) removed outlier: 6.108A pdb=" N ILE F 62 " --> pdb=" O VAL F 50 " (cutoff:3.500A) removed outlier: 5.687A pdb=" N VAL F 50 " --> pdb=" O ILE F 62 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'F' and resid 84 through 86 Processing sheet with id= V, first strand: chain 'F' and resid 327 through 330 removed outlier: 7.878A pdb=" N ILE F 154 " --> pdb=" O ILE F 300 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N SER F 302 " --> pdb=" O ILE F 154 " (cutoff:3.500A) removed outlier: 7.701A pdb=" N LEU F 156 " --> pdb=" O SER F 302 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N GLN F 304 " --> pdb=" O LEU F 156 " (cutoff:3.500A) removed outlier: 8.045A pdb=" N GLY F 158 " --> pdb=" O GLN F 304 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N ILE F 306 " --> pdb=" O GLY F 158 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N ILE F 182 " --> pdb=" O LEU F 248 " (cutoff:3.500A) removed outlier: 8.116A pdb=" N PHE F 250 " --> pdb=" O ILE F 182 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N VAL F 184 " --> pdb=" O PHE F 250 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'G' and resid 181 through 189 removed outlier: 6.370A pdb=" N LEU G 168 " --> pdb=" O LEU G 188 " (cutoff:3.500A) removed outlier: 5.274A pdb=" N ASN G 173 " --> pdb=" O ILE G 81 " (cutoff:3.500A) removed outlier: 7.654A pdb=" N VAL G 117 " --> pdb=" O ILE G 134 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N ASP G 136 " --> pdb=" O VAL G 117 " (cutoff:3.500A) 945 hydrogen bonds defined for protein. 2574 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: 7.70 Time building geometry restraints manager: 10.18 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 8226 1.34 - 1.46: 4591 1.46 - 1.58: 11666 1.58 - 1.70: 18 1.70 - 1.82: 154 Bond restraints: 24655 Sorted by residual: bond pdb=" N THR C 406 " pdb=" CA THR C 406 " ideal model delta sigma weight residual 1.459 1.498 -0.039 1.21e-02 6.83e+03 1.05e+01 bond pdb=" O3 PO4 D 603 " pdb=" P PO4 D 603 " ideal model delta sigma weight residual 1.569 1.509 0.060 2.00e-02 2.50e+03 9.02e+00 bond pdb=" O3 PO4 E 501 " pdb=" P PO4 E 501 " ideal model delta sigma weight residual 1.569 1.510 0.059 2.00e-02 2.50e+03 8.80e+00 bond pdb=" O4 PO4 E 501 " pdb=" P PO4 E 501 " ideal model delta sigma weight residual 1.568 1.510 0.058 2.00e-02 2.50e+03 8.51e+00 bond pdb=" O4 PO4 D 603 " pdb=" P PO4 D 603 " ideal model delta sigma weight residual 1.568 1.510 0.058 2.00e-02 2.50e+03 8.45e+00 ... (remaining 24650 not shown) Histogram of bond angle deviations from ideal: 99.80 - 107.81: 944 107.81 - 115.81: 15452 115.81 - 123.82: 16560 123.82 - 131.83: 463 131.83 - 139.84: 14 Bond angle restraints: 33433 Sorted by residual: angle pdb=" C LYS C 409 " pdb=" CA LYS C 409 " pdb=" CB LYS C 409 " ideal model delta sigma weight residual 110.79 103.92 6.87 1.66e+00 3.63e-01 1.71e+01 angle pdb=" N LYS C 409 " pdb=" CA LYS C 409 " pdb=" C LYS C 409 " ideal model delta sigma weight residual 111.28 107.40 3.88 1.09e+00 8.42e-01 1.27e+01 angle pdb=" N GLN C 407 " pdb=" CA GLN C 407 " pdb=" C GLN C 407 " ideal model delta sigma weight residual 111.28 107.45 3.83 1.09e+00 8.42e-01 1.23e+01 angle pdb=" C LEU D 455 " pdb=" N VAL D 456 " pdb=" CA VAL D 456 " ideal model delta sigma weight residual 123.08 119.89 3.19 1.01e+00 9.80e-01 9.97e+00 angle pdb=" C ILE G 225 " pdb=" N TYR G 226 " pdb=" CA TYR G 226 " ideal model delta sigma weight residual 122.79 117.44 5.35 1.70e+00 3.46e-01 9.90e+00 ... (remaining 33428 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.31: 14195 22.31 - 44.63: 689 44.63 - 66.94: 129 66.94 - 89.26: 44 89.26 - 111.57: 2 Dihedral angle restraints: 15059 sinusoidal: 6134 harmonic: 8925 Sorted by residual: dihedral pdb=" O1B ADP D 602 " pdb=" O3A ADP D 602 " pdb=" PB ADP D 602 " pdb=" PA ADP D 602 " ideal model delta sinusoidal sigma weight residual -60.00 -171.57 111.57 1 2.00e+01 2.50e-03 3.28e+01 dihedral pdb=" CA GLU G 222 " pdb=" C GLU G 222 " pdb=" N SER G 223 " pdb=" CA SER G 223 " ideal model delta harmonic sigma weight residual 180.00 159.72 20.28 0 5.00e+00 4.00e-02 1.65e+01 dihedral pdb=" C LYS C 409 " pdb=" N LYS C 409 " pdb=" CA LYS C 409 " pdb=" CB LYS C 409 " ideal model delta harmonic sigma weight residual -122.60 -112.97 -9.63 0 2.50e+00 1.60e-01 1.48e+01 ... (remaining 15056 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 3248 0.059 - 0.117: 552 0.117 - 0.176: 49 0.176 - 0.234: 2 0.234 - 0.293: 1 Chirality restraints: 3852 Sorted by residual: chirality pdb=" CA LYS C 409 " pdb=" N LYS C 409 " pdb=" C LYS C 409 " pdb=" CB LYS C 409 " both_signs ideal model delta sigma weight residual False 2.51 2.80 -0.29 2.00e-01 2.50e+01 2.15e+00 chirality pdb=" CG LEU G 194 " pdb=" CB LEU G 194 " pdb=" CD1 LEU G 194 " pdb=" CD2 LEU G 194 " both_signs ideal model delta sigma weight residual False -2.59 -2.37 -0.22 2.00e-01 2.50e+01 1.20e+00 chirality pdb=" CA TYR G 226 " pdb=" N TYR G 226 " pdb=" C TYR G 226 " pdb=" CB TYR G 226 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 9.99e-01 ... (remaining 3849 not shown) Planarity restraints: 4362 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN C 109 " -0.039 5.00e-02 4.00e+02 5.83e-02 5.44e+00 pdb=" N PRO C 110 " 0.101 5.00e-02 4.00e+02 pdb=" CA PRO C 110 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO C 110 " -0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU D 220 " 0.032 5.00e-02 4.00e+02 4.77e-02 3.64e+00 pdb=" N PRO D 221 " -0.082 5.00e-02 4.00e+02 pdb=" CA PRO D 221 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO D 221 " 0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU F 220 " -0.029 5.00e-02 4.00e+02 4.41e-02 3.11e+00 pdb=" N PRO F 221 " 0.076 5.00e-02 4.00e+02 pdb=" CA PRO F 221 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO F 221 " -0.024 5.00e-02 4.00e+02 ... (remaining 4359 not shown) Histogram of nonbonded interaction distances: 1.98 - 2.57: 115 2.57 - 3.15: 19482 3.15 - 3.73: 36490 3.73 - 4.32: 52966 4.32 - 4.90: 89221 Nonbonded interactions: 198274 Sorted by model distance: nonbonded pdb="MG MG F 601 " pdb=" O3G ATP F 602 " model vdw 1.983 2.170 nonbonded pdb=" OG1 THR F 165 " pdb="MG MG F 601 " model vdw 2.010 2.170 nonbonded pdb=" O1G ATP C 600 " pdb="MG MG C 601 " model vdw 2.016 2.170 nonbonded pdb=" OG1 THR C 176 " pdb="MG MG C 601 " model vdw 2.020 2.170 nonbonded pdb=" OG1 THR B 176 " pdb="MG MG B 601 " model vdw 2.058 2.170 ... (remaining 198269 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' selection = chain 'B' selection = chain 'C' } ncs_group { reference = (chain 'D' and resid 1 through 470) selection = (chain 'E' and resid 1 through 470) selection = (chain 'F' and resid 1 through 470) } 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=1.00 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: 3.520 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 11.090 Check model and map are aligned: 0.350 Set scattering table: 0.210 Process input model: 60.830 Find NCS groups from input model: 1.660 Set up NCS constraints: 0.130 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:12.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 90.790 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8727 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 0.060 24655 Z= 0.197 Angle : 0.556 9.254 33433 Z= 0.319 Chirality : 0.044 0.293 3852 Planarity : 0.004 0.058 4362 Dihedral : 14.033 111.572 9347 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 3.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 0.08 % Allowed : 0.39 % Favored : 99.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % 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: 1.14 (0.15), residues: 3115 helix: 1.63 (0.15), residues: 1260 sheet: 0.96 (0.23), residues: 536 loop : -0.12 (0.17), residues: 1319 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS E 363 PHE 0.014 0.001 PHE A 463 TYR 0.025 0.001 TYR G 226 ARG 0.003 0.000 ARG A 164 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6230 Ramachandran restraints generated. 3115 Oldfield, 0 Emsley, 3115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6230 Ramachandran restraints generated. 3115 Oldfield, 0 Emsley, 3115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 2568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 138 time to evaluate : 2.756 Fit side-chains revert: symmetry clash REVERT: B 465 ASP cc_start: 0.8126 (m-30) cc_final: 0.7835 (m-30) REVERT: E 1 MET cc_start: 0.5116 (ptm) cc_final: 0.4567 (ptm) outliers start: 2 outliers final: 0 residues processed: 140 average time/residue: 1.5000 time to fit residues: 240.5278 Evaluate side-chains 98 residues out of total 2568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 98 time to evaluate : 2.728 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 261 optimal weight: 5.9990 chunk 234 optimal weight: 10.0000 chunk 130 optimal weight: 6.9990 chunk 80 optimal weight: 9.9990 chunk 158 optimal weight: 2.9990 chunk 125 optimal weight: 4.9990 chunk 242 optimal weight: 0.8980 chunk 94 optimal weight: 10.0000 chunk 147 optimal weight: 10.0000 chunk 180 optimal weight: 10.0000 chunk 281 optimal weight: 0.2980 overall best weight: 3.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 46 ASN A 266 GLN ** A 483 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 189 GLN G 174 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8855 moved from start: 0.1480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 24655 Z= 0.330 Angle : 0.556 9.426 33433 Z= 0.289 Chirality : 0.046 0.262 3852 Planarity : 0.005 0.045 4362 Dihedral : 7.576 83.697 3546 Min Nonbonded Distance : 1.870 Molprobity Statistics. All-atom Clashscore : 3.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 0.78 % Allowed : 5.69 % Favored : 93.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % 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: 0.98 (0.15), residues: 3115 helix: 1.53 (0.15), residues: 1242 sheet: 0.84 (0.22), residues: 551 loop : -0.20 (0.17), residues: 1322 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS F 363 PHE 0.015 0.002 PHE F 257 TYR 0.020 0.001 TYR A 329 ARG 0.004 0.000 ARG F 193 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6230 Ramachandran restraints generated. 3115 Oldfield, 0 Emsley, 3115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6230 Ramachandran restraints generated. 3115 Oldfield, 0 Emsley, 3115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 2568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 98 time to evaluate : 2.654 Fit side-chains REVERT: B 465 ASP cc_start: 0.8367 (m-30) cc_final: 0.8044 (m-30) REVERT: E 1 MET cc_start: 0.5254 (ptm) cc_final: 0.4713 (ptm) REVERT: G 67 MET cc_start: 0.6883 (ptt) cc_final: 0.6651 (mmp) outliers start: 20 outliers final: 7 residues processed: 110 average time/residue: 1.4128 time to fit residues: 180.6919 Evaluate side-chains 99 residues out of total 2568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 92 time to evaluate : 2.788 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 384 LEU Chi-restraints excluded: chain C residue 392 LEU Chi-restraints excluded: chain D residue 10 MET Chi-restraints excluded: chain D residue 301 THR Chi-restraints excluded: chain D residue 456 VAL Chi-restraints excluded: chain D residue 467 LYS Chi-restraints excluded: chain G residue 111 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 156 optimal weight: 7.9990 chunk 87 optimal weight: 1.9990 chunk 234 optimal weight: 6.9990 chunk 191 optimal weight: 4.9990 chunk 77 optimal weight: 0.8980 chunk 282 optimal weight: 6.9990 chunk 304 optimal weight: 8.9990 chunk 251 optimal weight: 4.9990 chunk 279 optimal weight: 7.9990 chunk 96 optimal weight: 5.9990 chunk 226 optimal weight: 0.6980 overall best weight: 2.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 483 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8865 moved from start: 0.1864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 24655 Z= 0.287 Angle : 0.515 9.270 33433 Z= 0.266 Chirality : 0.045 0.251 3852 Planarity : 0.004 0.040 4362 Dihedral : 7.334 88.585 3546 Min Nonbonded Distance : 1.883 Molprobity Statistics. All-atom Clashscore : 3.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 1.17 % Allowed : 7.24 % Favored : 91.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % 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: 0.91 (0.15), residues: 3115 helix: 1.50 (0.15), residues: 1246 sheet: 0.82 (0.22), residues: 559 loop : -0.30 (0.17), residues: 1310 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS F 363 PHE 0.014 0.001 PHE D 125 TYR 0.016 0.001 TYR A 329 ARG 0.002 0.000 ARG F 193 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6230 Ramachandran restraints generated. 3115 Oldfield, 0 Emsley, 3115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6230 Ramachandran restraints generated. 3115 Oldfield, 0 Emsley, 3115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 2568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 92 time to evaluate : 2.917 Fit side-chains REVERT: E 1 MET cc_start: 0.5173 (ptm) cc_final: 0.4675 (ptm) REVERT: G 48 LYS cc_start: 0.5389 (OUTLIER) cc_final: 0.4798 (tmtt) outliers start: 30 outliers final: 8 residues processed: 113 average time/residue: 1.3968 time to fit residues: 184.0675 Evaluate side-chains 102 residues out of total 2568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 93 time to evaluate : 2.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 353 VAL Chi-restraints excluded: chain C residue 384 LEU Chi-restraints excluded: chain D residue 10 MET Chi-restraints excluded: chain D residue 383 ILE Chi-restraints excluded: chain D residue 456 VAL Chi-restraints excluded: chain G residue 48 LYS Chi-restraints excluded: chain G residue 68 LEU Chi-restraints excluded: chain G residue 191 LEU Chi-restraints excluded: chain G residue 224 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 278 optimal weight: 7.9990 chunk 212 optimal weight: 6.9990 chunk 146 optimal weight: 7.9990 chunk 31 optimal weight: 4.9990 chunk 134 optimal weight: 6.9990 chunk 189 optimal weight: 5.9990 chunk 283 optimal weight: 5.9990 chunk 299 optimal weight: 0.8980 chunk 147 optimal weight: 3.9990 chunk 268 optimal weight: 0.4980 chunk 80 optimal weight: 8.9990 overall best weight: 3.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 470 HIS ** A 483 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 143 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8883 moved from start: 0.2075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 24655 Z= 0.344 Angle : 0.539 9.287 33433 Z= 0.278 Chirality : 0.045 0.210 3852 Planarity : 0.004 0.041 4362 Dihedral : 7.284 94.916 3546 Min Nonbonded Distance : 1.853 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 1.48 % Allowed : 8.26 % Favored : 90.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % 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: 0.82 (0.15), residues: 3115 helix: 1.41 (0.15), residues: 1245 sheet: 0.81 (0.22), residues: 552 loop : -0.35 (0.17), residues: 1318 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS F 363 PHE 0.015 0.002 PHE F 257 TYR 0.015 0.001 TYR A 329 ARG 0.003 0.000 ARG F 193 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6230 Ramachandran restraints generated. 3115 Oldfield, 0 Emsley, 3115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6230 Ramachandran restraints generated. 3115 Oldfield, 0 Emsley, 3115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 2568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 93 time to evaluate : 2.848 Fit side-chains REVERT: E 1 MET cc_start: 0.5238 (ptm) cc_final: 0.4732 (ptm) REVERT: G 48 LYS cc_start: 0.5397 (OUTLIER) cc_final: 0.4789 (tmtt) REVERT: G 131 MET cc_start: 0.8052 (OUTLIER) cc_final: 0.7367 (mmm) outliers start: 38 outliers final: 19 residues processed: 121 average time/residue: 1.2537 time to fit residues: 178.6828 Evaluate side-chains 113 residues out of total 2568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 92 time to evaluate : 2.653 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 VAL Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 353 VAL Chi-restraints excluded: chain A residue 500 VAL Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 381 THR Chi-restraints excluded: chain C residue 347 ASP Chi-restraints excluded: chain C residue 384 LEU Chi-restraints excluded: chain C residue 500 VAL Chi-restraints excluded: chain D residue 10 MET Chi-restraints excluded: chain D residue 132 VAL Chi-restraints excluded: chain D residue 301 THR Chi-restraints excluded: chain D residue 383 ILE Chi-restraints excluded: chain D residue 394 ASP Chi-restraints excluded: chain D residue 456 VAL Chi-restraints excluded: chain D residue 467 LYS Chi-restraints excluded: chain E residue 433 THR Chi-restraints excluded: chain G residue 48 LYS Chi-restraints excluded: chain G residue 111 ASP Chi-restraints excluded: chain G residue 131 MET Chi-restraints excluded: chain G residue 191 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 249 optimal weight: 4.9990 chunk 170 optimal weight: 7.9990 chunk 4 optimal weight: 4.9990 chunk 223 optimal weight: 9.9990 chunk 123 optimal weight: 3.9990 chunk 255 optimal weight: 5.9990 chunk 207 optimal weight: 7.9990 chunk 0 optimal weight: 8.9990 chunk 153 optimal weight: 0.0770 chunk 268 optimal weight: 0.0270 chunk 75 optimal weight: 10.0000 overall best weight: 2.8202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 483 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8877 moved from start: 0.2162 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 24655 Z= 0.298 Angle : 0.519 9.243 33433 Z= 0.267 Chirality : 0.044 0.184 3852 Planarity : 0.004 0.041 4362 Dihedral : 7.152 95.115 3546 Min Nonbonded Distance : 1.870 Molprobity Statistics. All-atom Clashscore : 4.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 1.71 % Allowed : 9.11 % Favored : 89.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % 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: 0.85 (0.15), residues: 3115 helix: 1.43 (0.15), residues: 1247 sheet: 0.83 (0.22), residues: 552 loop : -0.33 (0.17), residues: 1316 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.001 HIS E 363 PHE 0.014 0.001 PHE D 125 TYR 0.014 0.001 TYR G 226 ARG 0.003 0.000 ARG F 193 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6230 Ramachandran restraints generated. 3115 Oldfield, 0 Emsley, 3115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6230 Ramachandran restraints generated. 3115 Oldfield, 0 Emsley, 3115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 2568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 98 time to evaluate : 3.024 Fit side-chains REVERT: D 469 MET cc_start: 0.7548 (ptm) cc_final: 0.7263 (ptp) REVERT: E 1 MET cc_start: 0.5162 (ptm) cc_final: 0.4717 (ptm) REVERT: F 387 LEU cc_start: 0.8987 (OUTLIER) cc_final: 0.8708 (pp) REVERT: G 48 LYS cc_start: 0.5455 (OUTLIER) cc_final: 0.4872 (tmtt) REVERT: G 192 THR cc_start: 0.8364 (OUTLIER) cc_final: 0.8134 (t) outliers start: 44 outliers final: 23 residues processed: 133 average time/residue: 1.1928 time to fit residues: 188.7206 Evaluate side-chains 119 residues out of total 2568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 93 time to evaluate : 2.723 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 353 VAL Chi-restraints excluded: chain A residue 500 VAL Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 188 ASP Chi-restraints excluded: chain B residue 250 MET Chi-restraints excluded: chain B residue 262 ASP Chi-restraints excluded: chain B residue 500 VAL Chi-restraints excluded: chain C residue 347 ASP Chi-restraints excluded: chain C residue 384 LEU Chi-restraints excluded: chain C residue 500 VAL Chi-restraints excluded: chain D residue 10 MET Chi-restraints excluded: chain D residue 132 VAL Chi-restraints excluded: chain D residue 301 THR Chi-restraints excluded: chain D residue 383 ILE Chi-restraints excluded: chain D residue 392 LEU Chi-restraints excluded: chain D residue 456 VAL Chi-restraints excluded: chain D residue 467 LYS Chi-restraints excluded: chain E residue 359 VAL Chi-restraints excluded: chain E residue 433 THR Chi-restraints excluded: chain E residue 462 VAL Chi-restraints excluded: chain F residue 387 LEU Chi-restraints excluded: chain G residue 48 LYS Chi-restraints excluded: chain G residue 111 ASP Chi-restraints excluded: chain G residue 191 LEU Chi-restraints excluded: chain G residue 192 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 100 optimal weight: 6.9990 chunk 269 optimal weight: 0.9990 chunk 59 optimal weight: 0.9980 chunk 175 optimal weight: 0.7980 chunk 73 optimal weight: 5.9990 chunk 299 optimal weight: 7.9990 chunk 248 optimal weight: 0.0070 chunk 138 optimal weight: 7.9990 chunk 24 optimal weight: 5.9990 chunk 99 optimal weight: 0.8980 chunk 157 optimal weight: 4.9990 overall best weight: 0.7400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 483 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 474 HIS D 200 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8818 moved from start: 0.2198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 24655 Z= 0.123 Angle : 0.447 9.101 33433 Z= 0.228 Chirality : 0.041 0.172 3852 Planarity : 0.003 0.038 4362 Dihedral : 6.638 87.756 3546 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 1.13 % Allowed : 9.93 % Favored : 88.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % 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: 1.23 (0.15), residues: 3115 helix: 1.85 (0.15), residues: 1227 sheet: 0.92 (0.22), residues: 559 loop : -0.16 (0.17), residues: 1329 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.000 HIS E 363 PHE 0.012 0.001 PHE D 125 TYR 0.008 0.001 TYR E 238 ARG 0.002 0.000 ARG G 240 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6230 Ramachandran restraints generated. 3115 Oldfield, 0 Emsley, 3115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6230 Ramachandran restraints generated. 3115 Oldfield, 0 Emsley, 3115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 2568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 98 time to evaluate : 2.604 Fit side-chains REVERT: D 392 LEU cc_start: 0.9067 (OUTLIER) cc_final: 0.8844 (tp) REVERT: D 469 MET cc_start: 0.7516 (ptm) cc_final: 0.7239 (ptp) REVERT: E 1 MET cc_start: 0.5115 (ptm) cc_final: 0.4573 (ptm) REVERT: F 387 LEU cc_start: 0.8909 (OUTLIER) cc_final: 0.8647 (pp) REVERT: G 192 THR cc_start: 0.8200 (OUTLIER) cc_final: 0.7962 (t) outliers start: 29 outliers final: 14 residues processed: 120 average time/residue: 1.1964 time to fit residues: 170.0206 Evaluate side-chains 112 residues out of total 2568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 95 time to evaluate : 2.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 VAL Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 262 ASP Chi-restraints excluded: chain A residue 500 VAL Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 500 VAL Chi-restraints excluded: chain C residue 384 LEU Chi-restraints excluded: chain D residue 132 VAL Chi-restraints excluded: chain D residue 301 THR Chi-restraints excluded: chain D residue 383 ILE Chi-restraints excluded: chain D residue 392 LEU Chi-restraints excluded: chain D residue 456 VAL Chi-restraints excluded: chain E residue 359 VAL Chi-restraints excluded: chain E residue 462 VAL Chi-restraints excluded: chain F residue 387 LEU Chi-restraints excluded: chain G residue 191 LEU Chi-restraints excluded: chain G residue 192 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 289 optimal weight: 0.0570 chunk 33 optimal weight: 0.7980 chunk 170 optimal weight: 9.9990 chunk 219 optimal weight: 7.9990 chunk 169 optimal weight: 1.9990 chunk 252 optimal weight: 0.6980 chunk 167 optimal weight: 5.9990 chunk 298 optimal weight: 1.9990 chunk 186 optimal weight: 0.7980 chunk 182 optimal weight: 1.9990 chunk 137 optimal weight: 5.9990 overall best weight: 0.8700 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 483 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 65 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8815 moved from start: 0.2253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 24655 Z= 0.132 Angle : 0.447 10.164 33433 Z= 0.227 Chirality : 0.041 0.144 3852 Planarity : 0.003 0.038 4362 Dihedral : 6.471 88.934 3546 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 1.13 % Allowed : 10.20 % Favored : 88.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % 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: 1.33 (0.15), residues: 3115 helix: 1.93 (0.15), residues: 1235 sheet: 1.00 (0.22), residues: 559 loop : -0.12 (0.17), residues: 1321 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS E 363 PHE 0.012 0.001 PHE D 125 TYR 0.011 0.001 TYR C 251 ARG 0.002 0.000 ARG A 164 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6230 Ramachandran restraints generated. 3115 Oldfield, 0 Emsley, 3115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6230 Ramachandran restraints generated. 3115 Oldfield, 0 Emsley, 3115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 2568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 100 time to evaluate : 2.983 Fit side-chains REVERT: D 392 LEU cc_start: 0.9058 (OUTLIER) cc_final: 0.8849 (tp) REVERT: D 469 MET cc_start: 0.7501 (ptm) cc_final: 0.7246 (ptp) REVERT: E 1 MET cc_start: 0.5110 (ptm) cc_final: 0.4577 (ptm) REVERT: F 387 LEU cc_start: 0.8908 (OUTLIER) cc_final: 0.8652 (pp) REVERT: G 130 ASN cc_start: 0.8029 (m110) cc_final: 0.7812 (m-40) REVERT: G 192 THR cc_start: 0.8269 (OUTLIER) cc_final: 0.8031 (t) outliers start: 29 outliers final: 17 residues processed: 121 average time/residue: 1.2633 time to fit residues: 180.6762 Evaluate side-chains 118 residues out of total 2568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 98 time to evaluate : 2.718 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 VAL Chi-restraints excluded: chain A residue 48 MET Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 262 ASP Chi-restraints excluded: chain A residue 500 VAL Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 262 ASP Chi-restraints excluded: chain B residue 500 VAL Chi-restraints excluded: chain C residue 384 LEU Chi-restraints excluded: chain D residue 132 VAL Chi-restraints excluded: chain D residue 301 THR Chi-restraints excluded: chain D residue 383 ILE Chi-restraints excluded: chain D residue 392 LEU Chi-restraints excluded: chain D residue 456 VAL Chi-restraints excluded: chain E residue 359 VAL Chi-restraints excluded: chain E residue 462 VAL Chi-restraints excluded: chain F residue 387 LEU Chi-restraints excluded: chain G residue 191 LEU Chi-restraints excluded: chain G residue 192 THR Chi-restraints excluded: chain G residue 245 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 184 optimal weight: 6.9990 chunk 119 optimal weight: 3.9990 chunk 178 optimal weight: 6.9990 chunk 90 optimal weight: 0.9980 chunk 58 optimal weight: 6.9990 chunk 57 optimal weight: 2.9990 chunk 189 optimal weight: 7.9990 chunk 203 optimal weight: 6.9990 chunk 147 optimal weight: 9.9990 chunk 27 optimal weight: 5.9990 chunk 234 optimal weight: 5.9990 overall best weight: 3.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 483 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8891 moved from start: 0.2342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 24655 Z= 0.406 Angle : 0.560 9.875 33433 Z= 0.288 Chirality : 0.046 0.190 3852 Planarity : 0.004 0.039 4362 Dihedral : 7.050 88.540 3546 Min Nonbonded Distance : 1.838 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 1.17 % Allowed : 10.40 % Favored : 88.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % 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: 0.95 (0.15), residues: 3115 helix: 1.51 (0.15), residues: 1245 sheet: 0.91 (0.22), residues: 552 loop : -0.29 (0.17), residues: 1318 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.001 HIS F 363 PHE 0.015 0.002 PHE F 215 TYR 0.018 0.001 TYR G 226 ARG 0.004 0.000 ARG F 193 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6230 Ramachandran restraints generated. 3115 Oldfield, 0 Emsley, 3115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6230 Ramachandran restraints generated. 3115 Oldfield, 0 Emsley, 3115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 2568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 95 time to evaluate : 2.942 Fit side-chains REVERT: D 469 MET cc_start: 0.7534 (ptm) cc_final: 0.7267 (ptp) REVERT: E 1 MET cc_start: 0.5163 (ptm) cc_final: 0.4688 (ptm) REVERT: F 387 LEU cc_start: 0.9007 (OUTLIER) cc_final: 0.8724 (pp) REVERT: G 46 MET cc_start: 0.8172 (tpt) cc_final: 0.7924 (tpp) outliers start: 30 outliers final: 22 residues processed: 117 average time/residue: 1.3043 time to fit residues: 179.0076 Evaluate side-chains 117 residues out of total 2568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 94 time to evaluate : 2.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 VAL Chi-restraints excluded: chain A residue 48 MET Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 188 ASP Chi-restraints excluded: chain B residue 404 LYS Chi-restraints excluded: chain B residue 500 VAL Chi-restraints excluded: chain C residue 384 LEU Chi-restraints excluded: chain C residue 487 LEU Chi-restraints excluded: chain D residue 132 VAL Chi-restraints excluded: chain D residue 301 THR Chi-restraints excluded: chain D residue 383 ILE Chi-restraints excluded: chain D residue 456 VAL Chi-restraints excluded: chain E residue 359 VAL Chi-restraints excluded: chain E residue 433 THR Chi-restraints excluded: chain E residue 462 VAL Chi-restraints excluded: chain F residue 168 ILE Chi-restraints excluded: chain F residue 387 LEU Chi-restraints excluded: chain G residue 111 ASP Chi-restraints excluded: chain G residue 149 ILE Chi-restraints excluded: chain G residue 191 LEU Chi-restraints excluded: chain G residue 245 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 271 optimal weight: 2.9990 chunk 286 optimal weight: 4.9990 chunk 261 optimal weight: 0.9990 chunk 278 optimal weight: 6.9990 chunk 167 optimal weight: 4.9990 chunk 121 optimal weight: 0.7980 chunk 218 optimal weight: 1.9990 chunk 85 optimal weight: 2.9990 chunk 251 optimal weight: 0.8980 chunk 263 optimal weight: 3.9990 chunk 277 optimal weight: 4.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 483 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 65 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8851 moved from start: 0.2324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 24655 Z= 0.186 Angle : 0.475 9.207 33433 Z= 0.243 Chirality : 0.042 0.144 3852 Planarity : 0.004 0.037 4362 Dihedral : 6.752 87.631 3546 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 4.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 0.97 % Allowed : 10.67 % Favored : 88.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % 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: 1.14 (0.15), residues: 3115 helix: 1.72 (0.15), residues: 1234 sheet: 0.93 (0.23), residues: 558 loop : -0.18 (0.17), residues: 1323 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS E 363 PHE 0.013 0.001 PHE D 125 TYR 0.010 0.001 TYR G 226 ARG 0.001 0.000 ARG C 89 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6230 Ramachandran restraints generated. 3115 Oldfield, 0 Emsley, 3115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6230 Ramachandran restraints generated. 3115 Oldfield, 0 Emsley, 3115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 2568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 96 time to evaluate : 3.146 Fit side-chains REVERT: D 469 MET cc_start: 0.7535 (ptm) cc_final: 0.7272 (ptp) REVERT: E 1 MET cc_start: 0.5164 (ptm) cc_final: 0.4701 (ptm) REVERT: F 387 LEU cc_start: 0.8975 (OUTLIER) cc_final: 0.8712 (pp) REVERT: G 46 MET cc_start: 0.8150 (tpt) cc_final: 0.7906 (tpp) outliers start: 25 outliers final: 17 residues processed: 115 average time/residue: 1.3553 time to fit residues: 184.1734 Evaluate side-chains 115 residues out of total 2568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 97 time to evaluate : 2.570 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 VAL Chi-restraints excluded: chain A residue 48 MET Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 188 ASP Chi-restraints excluded: chain B residue 250 MET Chi-restraints excluded: chain B residue 500 VAL Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain C residue 384 LEU Chi-restraints excluded: chain D residue 132 VAL Chi-restraints excluded: chain D residue 301 THR Chi-restraints excluded: chain D residue 383 ILE Chi-restraints excluded: chain D residue 456 VAL Chi-restraints excluded: chain E residue 359 VAL Chi-restraints excluded: chain E residue 462 VAL Chi-restraints excluded: chain F residue 387 LEU Chi-restraints excluded: chain G residue 191 LEU Chi-restraints excluded: chain G residue 245 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 182 optimal weight: 1.9990 chunk 294 optimal weight: 4.9990 chunk 179 optimal weight: 0.8980 chunk 139 optimal weight: 8.9990 chunk 204 optimal weight: 2.9990 chunk 308 optimal weight: 2.9990 chunk 284 optimal weight: 8.9990 chunk 245 optimal weight: 0.8980 chunk 25 optimal weight: 0.3980 chunk 189 optimal weight: 6.9990 chunk 150 optimal weight: 3.9990 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 483 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8842 moved from start: 0.2338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 24655 Z= 0.178 Angle : 0.467 9.109 33433 Z= 0.238 Chirality : 0.042 0.145 3852 Planarity : 0.003 0.038 4362 Dihedral : 6.614 87.509 3546 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 0.82 % Allowed : 10.98 % Favored : 88.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.24 (0.15), residues: 3115 helix: 1.83 (0.15), residues: 1230 sheet: 0.98 (0.23), residues: 558 loop : -0.16 (0.17), residues: 1327 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS E 363 PHE 0.013 0.001 PHE D 125 TYR 0.012 0.001 TYR G 226 ARG 0.001 0.000 ARG F 193 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6230 Ramachandran restraints generated. 3115 Oldfield, 0 Emsley, 3115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6230 Ramachandran restraints generated. 3115 Oldfield, 0 Emsley, 3115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 2568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 97 time to evaluate : 2.920 Fit side-chains REVERT: D 469 MET cc_start: 0.7569 (ptm) cc_final: 0.7323 (ptp) REVERT: E 1 MET cc_start: 0.5165 (ptm) cc_final: 0.4654 (ptm) REVERT: F 387 LEU cc_start: 0.8962 (OUTLIER) cc_final: 0.8703 (pp) REVERT: G 192 THR cc_start: 0.8314 (OUTLIER) cc_final: 0.8106 (t) outliers start: 21 outliers final: 17 residues processed: 113 average time/residue: 1.2367 time to fit residues: 165.1338 Evaluate side-chains 117 residues out of total 2568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 98 time to evaluate : 2.695 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 VAL Chi-restraints excluded: chain A residue 48 MET Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 262 ASP Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 188 ASP Chi-restraints excluded: chain B residue 500 VAL Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain C residue 384 LEU Chi-restraints excluded: chain D residue 132 VAL Chi-restraints excluded: chain D residue 301 THR Chi-restraints excluded: chain D residue 383 ILE Chi-restraints excluded: chain D residue 456 VAL Chi-restraints excluded: chain E residue 359 VAL Chi-restraints excluded: chain E residue 462 VAL Chi-restraints excluded: chain F residue 387 LEU Chi-restraints excluded: chain G residue 191 LEU Chi-restraints excluded: chain G residue 192 THR Chi-restraints excluded: chain G residue 245 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 195 optimal weight: 6.9990 chunk 261 optimal weight: 6.9990 chunk 75 optimal weight: 10.0000 chunk 226 optimal weight: 10.0000 chunk 36 optimal weight: 8.9990 chunk 68 optimal weight: 4.9990 chunk 246 optimal weight: 0.0470 chunk 103 optimal weight: 0.0770 chunk 252 optimal weight: 0.9990 chunk 31 optimal weight: 7.9990 chunk 45 optimal weight: 0.0470 overall best weight: 1.2338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 24 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.072519 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2825 r_free = 0.2825 target = 0.054376 restraints weight = 53876.047| |-----------------------------------------------------------------------------| r_work (start): 0.2807 rms_B_bonded: 2.35 r_work: 0.2689 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2564 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.2564 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9070 moved from start: 0.2366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 24655 Z= 0.155 Angle : 0.457 9.265 33433 Z= 0.232 Chirality : 0.042 0.146 3852 Planarity : 0.003 0.038 4362 Dihedral : 6.494 89.022 3546 Min Nonbonded Distance : 1.931 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 0.82 % Allowed : 10.94 % Favored : 88.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % 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 (0.15), residues: 3115 helix: 1.87 (0.15), residues: 1233 sheet: 1.01 (0.23), residues: 558 loop : -0.10 (0.17), residues: 1324 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS E 363 PHE 0.013 0.001 PHE D 125 TYR 0.010 0.001 TYR G 226 ARG 0.002 0.000 ARG A 354 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5374.74 seconds wall clock time: 99 minutes 25.39 seconds (5965.39 seconds total)