Starting phenix.real_space_refine on Tue Mar 19 12:22:36 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xkp_33259/03_2024/7xkp_33259_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xkp_33259/03_2024/7xkp_33259.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xkp_33259/03_2024/7xkp_33259.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xkp_33259/03_2024/7xkp_33259.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xkp_33259/03_2024/7xkp_33259_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xkp_33259/03_2024/7xkp_33259_updated.pdb" } resolution = 3.0 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 2 5.49 5 Mg 1 5.21 5 S 77 5.16 5 C 15232 2.51 5 N 4193 2.21 5 O 4600 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 343": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 463": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 261": "OD1" <-> "OD2" Residue "B PHE 456": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 349": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 239": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 125": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 427": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 190": "OE1" <-> "OE2" Residue "F TYR 238": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 165": "CD1" <-> "CD2" "CE1" <-> "CE2" 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: 24105 Number of models: 1 Model: "" Number of chains: 8 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: 3623 Number of conformers: 1 Conformer: "" Number of residues, atoms: 470, 3623 Classifications: {'peptide': 470} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 446} 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': 2, 'PTRANS': 8, 'TRANS': 272} Chain: "F" 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} Time building chain proxies: 12.32, per 1000 atoms: 0.51 Number of scatterers: 24105 At special positions: 0 Unit cell: (128.48, 126.72, 157.52, 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 2 15.00 Mg 1 11.99 O 4600 8.00 N 4193 7.00 C 15232 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: 9.31 Conformation dependent library (CDL) restraints added in 5.3 seconds 6228 Ramachandran restraints generated. 3114 Oldfield, 0 Emsley, 3114 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5710 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 121 helices and 22 sheets defined 41.9% alpha, 13.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.55 Creating SS restraints... Processing helix chain 'A' and resid 79 through 81 No H-bonds generated for 'chain 'A' and resid 79 through 81' 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 136 through 138 No H-bonds generated for 'chain 'A' and resid 136 through 138' Processing helix chain 'A' and resid 151 through 156 Processing helix chain 'A' and resid 175 through 186 removed outlier: 3.886A pdb=" N GLN A 186 " --> pdb=" O THR A 182 " (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 252 Proline residue: A 239 - end of helix removed outlier: 3.599A pdb=" N TYR A 248 " --> pdb=" O ALA A 244 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N PHE A 249 " --> pdb=" O MET A 245 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N LYS A 252 " --> pdb=" O TYR A 248 " (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 290 through 300 removed outlier: 4.332A pdb=" N ARG A 300 " --> pdb=" O ARG A 296 " (cutoff:3.500A) 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 391 removed outlier: 3.772A pdb=" N VAL A 378 " --> pdb=" O ALA A 374 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N GLY A 380 " --> pdb=" O LYS A 376 " (cutoff:3.500A) removed outlier: 5.977A pdb=" N THR A 381 " --> pdb=" O LYS A 377 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LEU A 382 " --> pdb=" O VAL A 378 " (cutoff:3.500A) Processing helix chain 'A' and resid 393 through 395 No H-bonds generated for 'chain 'A' and resid 393 through 395' Processing helix chain 'A' and resid 405 through 420 Processing helix chain 'A' and resid 430 through 441 Processing helix chain 'A' and resid 453 through 467 Processing helix chain 'A' and resid 469 through 478 Processing helix chain 'A' and resid 484 through 497 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 151 through 156 Processing helix chain 'B' and resid 175 through 186 removed outlier: 3.732A pdb=" N GLN B 186 " --> pdb=" O THR B 182 " (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 252 Proline residue: B 239 - end of helix removed outlier: 3.608A pdb=" N TYR B 248 " --> pdb=" O ALA B 244 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N PHE B 249 " --> pdb=" O MET B 245 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N LYS B 252 " --> pdb=" O TYR B 248 " (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: 4.381A pdb=" N PHE B 291 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LEU B 293 " --> pdb=" O ILE B 290 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N ARG B 296 " --> pdb=" O LEU B 293 " (cutoff:3.500A) removed outlier: 4.236A 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 347 through 351 removed outlier: 3.514A pdb=" N PHE B 350 " --> pdb=" O ASP B 347 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N SER B 351 " --> pdb=" O LEU B 348 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 347 through 351' Processing helix chain 'B' and resid 373 through 392 removed outlier: 4.134A pdb=" N GLY B 380 " --> pdb=" O LYS B 376 " (cutoff:3.500A) removed outlier: 5.362A pdb=" N THR B 381 " --> pdb=" O LYS B 377 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N LEU B 382 " --> pdb=" O VAL B 378 " (cutoff:3.500A) Processing helix chain 'B' and resid 403 through 420 removed outlier: 4.716A pdb=" N ALA B 408 " --> pdb=" O LYS B 404 " (cutoff:3.500A) removed outlier: 4.994A pdb=" N LYS B 409 " --> pdb=" O ALA B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 430 through 439 Processing helix chain 'B' and resid 450 through 467 removed outlier: 5.143A pdb=" N ARG B 454 " --> pdb=" O GLU B 451 " (cutoff:3.500A) Processing helix chain 'B' and resid 469 through 477 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 136 through 138 No H-bonds generated for 'chain 'C' and resid 136 through 138' Processing helix chain 'C' and resid 151 through 156 Processing helix chain 'C' and resid 175 through 187 removed outlier: 4.263A pdb=" N LYS C 187 " --> pdb=" O ILE C 183 " (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: 3.645A pdb=" N TYR C 248 " --> pdb=" O ALA C 244 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N PHE C 249 " --> pdb=" O MET C 245 " (cutoff:3.500A) removed outlier: 3.628A 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 290 through 300 removed outlier: 3.740A pdb=" N HIS C 294 " --> pdb=" O ILE C 290 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N ARG C 300 " --> pdb=" O ARG C 296 " (cutoff:3.500A) 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 379 Processing helix chain 'C' and resid 382 through 399 removed outlier: 4.416A pdb=" N PHE C 395 " --> pdb=" O GLU C 391 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N GLN C 397 " --> pdb=" O GLU C 393 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N PHE C 398 " --> pdb=" O ALA C 394 " (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: 4.362A pdb=" N ARG C 454 " --> pdb=" O VAL C 450 " (cutoff:3.500A) removed outlier: 4.896A pdb=" N ARG C 455 " --> pdb=" O GLU C 451 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLN C 466 " --> pdb=" O LEU C 462 " (cutoff:3.500A) Processing helix chain 'C' and resid 469 through 478 Processing helix chain 'C' and resid 484 through 497 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 125 through 127 No H-bonds generated for 'chain 'D' and resid 125 through 127' Processing helix chain 'D' and resid 140 through 145 Processing helix chain 'D' and resid 164 through 178 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: 3.670A pdb=" N ARG D 227 " --> pdb=" O GLY D 223 " (cutoff:3.500A) removed outlier: 5.194A pdb=" N ALA D 229 " --> pdb=" O ARG D 225 " (cutoff:3.500A) removed outlier: 4.766A pdb=" N LEU D 230 " --> pdb=" O MET D 226 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N PHE D 239 " --> pdb=" O MET D 235 " (cutoff:3.500A) Processing helix chain 'D' and resid 255 through 268 removed outlier: 3.658A pdb=" N GLY D 261 " --> pdb=" O PHE D 257 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N ALA D 266 " --> pdb=" O SER D 262 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N LEU D 267 " --> pdb=" O GLU D 263 " (cutoff:3.500A) Processing helix chain 'D' and resid 281 through 291 removed outlier: 4.499A 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: 3.753A pdb=" N SER D 323 " --> pdb=" O ALA D 319 " (cutoff:3.500A) removed outlier: 4.362A 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 384 Processing helix chain 'D' and resid 394 through 409 removed outlier: 3.583A pdb=" N ARG D 405 " --> pdb=" O HIS D 401 " (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 469 removed outlier: 3.972A 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 140 through 145 Processing helix chain 'E' and resid 164 through 179 Processing helix chain 'E' and resid 192 through 204 Processing helix chain 'E' and resid 208 through 210 No H-bonds generated for 'chain 'E' and resid 208 through 210' Processing helix chain 'E' and resid 222 through 241 removed outlier: 5.204A pdb=" N ALA E 229 " --> pdb=" O ARG E 225 " (cutoff:3.500A) removed outlier: 4.650A pdb=" N LEU E 230 " --> pdb=" O MET E 226 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N TYR E 238 " --> pdb=" O THR E 234 " (cutoff:3.500A) removed outlier: 4.149A 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: 4.349A 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 322 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 386 removed outlier: 4.420A pdb=" N ASP E 382 " --> pdb=" O LYS E 378 " (cutoff:3.500A) removed outlier: 4.119A 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: 3.568A pdb=" N ARG E 404 " --> pdb=" O VAL E 400 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ARG E 405 " --> pdb=" O HIS E 401 " (cutoff:3.500A) Processing helix chain 'E' and resid 416 through 421 removed outlier: 3.669A pdb=" N GLN E 419 " --> pdb=" O VAL E 416 " (cutoff:3.500A) 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: 3.589A 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 179 removed outlier: 4.735A pdb=" N GLN F 177 " --> pdb=" O HIS F 173 " (cutoff:3.500A) removed outlier: 5.198A 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 225 No H-bonds generated for 'chain 'F' and resid 222 through 225' Processing helix chain 'F' and resid 228 through 241 removed outlier: 3.800A pdb=" N MET F 235 " --> pdb=" O THR F 231 " (cutoff:3.500A) Processing helix chain 'F' and resid 254 through 268 removed outlier: 3.978A pdb=" N ALA F 266 " --> pdb=" O GLU F 263 " (cutoff:3.500A) Processing helix chain 'F' and resid 281 through 291 removed outlier: 3.556A pdb=" N LEU F 288 " --> pdb=" O GLU F 284 " (cutoff:3.500A) removed outlier: 4.255A 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: 3.599A pdb=" N THR F 321 " --> pdb=" O ALA F 317 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N PHE F 322 " --> pdb=" O PRO F 318 " (cutoff:3.500A) removed outlier: 4.737A pdb=" N SER F 323 " --> pdb=" O ALA F 319 " (cutoff:3.500A) removed outlier: 4.661A pdb=" N HIS F 324 " --> pdb=" O THR F 320 " (cutoff:3.500A) Processing helix chain 'F' and resid 333 through 338 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 386 removed outlier: 3.524A pdb=" N GLN F 381 " --> pdb=" O TYR F 377 " (cutoff:3.500A) removed outlier: 4.897A pdb=" N ASP F 382 " --> pdb=" O LYS F 378 " (cutoff:3.500A) removed outlier: 5.014A pdb=" N ILE F 383 " --> pdb=" O GLU F 379 " (cutoff:3.500A) 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: 3.631A pdb=" N LEU F 398 " --> pdb=" O ASP F 394 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ARG F 405 " --> pdb=" O HIS F 401 " (cutoff:3.500A) Processing helix chain 'F' and resid 418 through 421 No H-bonds generated for 'chain 'F' and resid 418 through 421' Processing helix chain 'F' and resid 430 through 441 Processing helix chain 'F' and resid 450 through 453 Processing helix chain 'F' and resid 459 through 469 removed outlier: 3.649A pdb=" N VAL F 463 " --> pdb=" O ILE F 459 " (cutoff:3.500A) Processing helix chain 'G' and resid 3 through 41 removed outlier: 3.541A pdb=" N ARG G 34 " --> pdb=" O SER G 30 " (cutoff:3.500A) Processing helix chain 'G' and resid 43 through 57 Processing helix chain 'G' and resid 66 through 68 No H-bonds generated for 'chain 'G' and resid 66 through 68' Processing helix chain 'G' and resid 91 through 106 removed outlier: 3.971A pdb=" N VAL G 95 " --> pdb=" O TYR G 91 " (cutoff:3.500A) Processing helix chain 'G' and resid 120 through 128 Processing helix chain 'G' and resid 146 through 161 removed outlier: 4.754A pdb=" N GLU G 151 " --> pdb=" O ALA G 147 " (cutoff:3.500A) removed outlier: 5.230A pdb=" N ILE G 152 " --> pdb=" O ASP G 148 " (cutoff:3.500A) Processing helix chain 'G' and resid 209 through 283 Proline residue: G 218 - end of helix removed outlier: 3.746A pdb=" N SER G 261 " --> pdb=" O THR G 257 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 87 through 89 removed outlier: 6.597A pdb=" N ARG A 40 " --> pdb=" O ILE A 32 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N VAL A 34 " --> pdb=" O ILE A 38 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N ILE A 38 " --> pdb=" O VAL A 34 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N VAL A 74 " --> pdb=" O ALA A 63 " (cutoff:3.500A) removed outlier: 5.536A pdb=" N ALA A 63 " --> pdb=" O VAL A 74 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N GLU A 51 " --> pdb=" O ALA A 63 " (cutoff:3.500A) removed outlier: 4.779A pdb=" N ARG A 93 " --> pdb=" O LEU A 52 " (cutoff:3.500A) removed outlier: 8.140A pdb=" N GLU A 54 " --> pdb=" O THR A 91 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N THR A 91 " --> pdb=" O GLU A 54 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 96 through 99 removed outlier: 4.395A 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: 8.916A pdb=" N VAL A 108 " --> pdb=" O THR A 221 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N VAL A 223 " --> pdb=" O VAL A 108 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N SER A 193 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 8.103A pdb=" N VAL A 224 " --> pdb=" O SER A 193 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N TYR A 195 " --> pdb=" O VAL A 224 " (cutoff:3.500A) removed outlier: 7.864A pdb=" N ALA A 226 " --> pdb=" O TYR A 195 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N ALA A 197 " --> pdb=" O ALA A 226 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N SER A 312 " --> pdb=" O VAL A 256 " (cutoff:3.500A) removed outlier: 7.910A pdb=" N VAL A 258 " --> pdb=" O SER A 312 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N THR A 314 " --> pdb=" O VAL A 258 " (cutoff:3.500A) removed outlier: 7.714A pdb=" N TYR A 260 " --> pdb=" O THR A 314 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N LEU A 316 " --> pdb=" O TYR A 260 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 341 through 344 removed outlier: 6.583A pdb=" N LEU A 166 " --> pdb=" O ILE A 342 " (cutoff:3.500A) removed outlier: 7.747A pdb=" N LEU A 344 " --> pdb=" O LEU A 166 " (cutoff:3.500A) removed outlier: 7.011A 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: 6.586A pdb=" N GLY B 72 " --> pdb=" O LEU B 64 " (cutoff:3.500A) removed outlier: 5.086A pdb=" N LEU B 66 " --> pdb=" O ASN B 70 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N ASN B 70 " --> pdb=" O LEU B 66 " (cutoff:3.500A) removed outlier: 5.804A pdb=" N HIS B 42 " --> pdb=" O VAL B 31 " (cutoff:3.500A) removed outlier: 5.491A 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: 3.915A 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: 6.599A pdb=" N LEU B 166 " --> pdb=" O ILE B 342 " (cutoff:3.500A) removed outlier: 7.682A pdb=" N LEU B 344 " --> pdb=" O LEU B 166 " (cutoff:3.500A) removed outlier: 7.175A pdb=" N ILE B 168 " --> pdb=" O LEU B 344 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 312 through 315 removed outlier: 6.330A pdb=" N ILE B 192 " --> pdb=" O LEU B 257 " (cutoff:3.500A) removed outlier: 8.006A pdb=" N VAL B 259 " --> pdb=" O ILE B 192 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N ILE B 194 " --> pdb=" O VAL B 259 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'C' and resid 28 through 30 removed outlier: 6.456A pdb=" N GLY C 72 " --> pdb=" O LEU C 64 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'C' and resid 96 through 99 removed outlier: 4.292A 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: 6.698A pdb=" N LEU C 166 " --> pdb=" O ILE C 342 " (cutoff:3.500A) removed outlier: 7.859A pdb=" N LEU C 344 " --> pdb=" O LEU C 166 " (cutoff:3.500A) removed outlier: 6.974A 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: 8.839A pdb=" N ILE C 222 " --> pdb=" O MET C 191 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N SER C 193 " --> pdb=" O ILE C 222 " (cutoff:3.500A) removed outlier: 8.117A pdb=" N VAL C 224 " --> pdb=" O SER C 193 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N TYR C 195 " --> pdb=" O VAL C 224 " (cutoff:3.500A) removed outlier: 7.848A pdb=" N ALA C 226 " --> pdb=" O TYR C 195 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N ALA C 197 " --> pdb=" O ALA C 226 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N HIS C 255 " --> pdb=" O ILE C 192 " (cutoff:3.500A) removed outlier: 8.095A pdb=" N ILE C 194 " --> pdb=" O HIS C 255 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N LEU C 257 " --> pdb=" O ILE C 194 " (cutoff:3.500A) removed outlier: 7.656A pdb=" N VAL C 196 " --> pdb=" O LEU C 257 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N VAL C 259 " --> pdb=" O VAL C 196 " (cutoff:3.500A) removed outlier: 7.378A pdb=" N ILE C 198 " --> pdb=" O VAL C 259 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N SER C 312 " --> pdb=" O VAL C 256 " (cutoff:3.500A) removed outlier: 7.854A pdb=" N VAL C 258 " --> pdb=" O SER C 312 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N THR C 314 " --> pdb=" O VAL C 258 " (cutoff:3.500A) removed outlier: 7.792A pdb=" N TYR C 260 " --> pdb=" O THR C 314 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N LEU C 316 " --> pdb=" O TYR C 260 " (cutoff:3.500A) No H-bonds generated for sheet with id= L Processing sheet with id= M, first strand: chain 'D' and resid 5 through 10 removed outlier: 6.720A pdb=" N ASP D 15 " --> pdb=" O ILE D 7 " (cutoff:3.500A) removed outlier: 4.791A pdb=" N VAL D 9 " --> pdb=" O VAL D 13 " (cutoff:3.500A) removed outlier: 7.167A pdb=" N VAL D 13 " --> pdb=" O VAL D 9 " (cutoff:3.500A) removed outlier: 6.209A pdb=" N ILE D 62 " --> pdb=" O VAL D 50 " (cutoff:3.500A) removed outlier: 5.667A 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: 8.433A pdb=" N ILE D 154 " --> pdb=" O ILE D 300 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N SER D 302 " --> pdb=" O ILE D 154 " (cutoff:3.500A) removed outlier: 7.299A pdb=" N LEU D 156 " --> pdb=" O SER D 302 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N GLN D 304 " --> pdb=" O LEU D 156 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'E' and resid 75 through 77 removed outlier: 6.600A pdb=" N ASP E 15 " --> pdb=" O ILE E 7 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N VAL E 9 " --> pdb=" O VAL E 13 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N VAL E 13 " --> pdb=" O VAL E 9 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N ILE E 62 " --> pdb=" O VAL E 50 " (cutoff:3.500A) removed outlier: 5.928A pdb=" N VAL E 50 " --> pdb=" O ILE E 62 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'E' and resid 84 through 86 Processing sheet with id= R, first strand: chain 'E' and resid 327 through 330 removed outlier: 8.583A pdb=" N ILE E 154 " --> pdb=" O ILE E 300 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N SER E 302 " --> pdb=" O ILE E 154 " (cutoff:3.500A) removed outlier: 7.367A pdb=" N LEU E 156 " --> pdb=" O SER E 302 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N GLN E 304 " --> pdb=" O LEU E 156 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'F' and resid 75 through 77 removed outlier: 6.446A pdb=" N ASP F 15 " --> pdb=" O ILE F 7 " (cutoff:3.500A) removed outlier: 4.667A pdb=" N VAL F 9 " --> pdb=" O VAL F 13 " (cutoff:3.500A) removed outlier: 7.066A pdb=" N VAL F 13 " --> pdb=" O VAL F 9 " (cutoff:3.500A) removed outlier: 6.054A pdb=" N ILE F 62 " --> pdb=" O VAL F 50 " (cutoff:3.500A) removed outlier: 5.698A pdb=" N VAL F 50 " --> pdb=" O ILE F 62 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'F' and resid 84 through 86 Processing sheet with id= U, first strand: chain 'F' and resid 327 through 330 removed outlier: 7.940A pdb=" N ILE F 154 " --> pdb=" O ILE F 300 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N SER F 302 " --> pdb=" O ILE F 154 " (cutoff:3.500A) removed outlier: 7.944A pdb=" N LEU F 156 " --> pdb=" O SER F 302 " (cutoff:3.500A) removed outlier: 7.072A pdb=" N GLN F 304 " --> pdb=" O LEU F 156 " (cutoff:3.500A) removed outlier: 8.147A pdb=" N GLY F 158 " --> pdb=" O GLN F 304 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N ILE F 306 " --> pdb=" O GLY F 158 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N ILE F 182 " --> pdb=" O LEU F 248 " (cutoff:3.500A) removed outlier: 8.006A pdb=" N PHE F 250 " --> pdb=" O ILE F 182 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N VAL F 184 " --> pdb=" O PHE F 250 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'G' and resid 181 through 189 removed outlier: 6.690A pdb=" N LEU G 168 " --> pdb=" O LEU G 188 " (cutoff:3.500A) removed outlier: 5.341A pdb=" N ASN G 173 " --> pdb=" O ILE G 81 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N LEU G 135 " --> pdb=" O VAL G 117 " (cutoff:3.500A) 970 hydrogen bonds defined for protein. 2760 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: 6.81 Time building geometry restraints manager: 10.21 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: 8203 1.34 - 1.46: 3528 1.46 - 1.57: 12620 1.57 - 1.69: 3 1.69 - 1.81: 154 Bond restraints: 24508 Sorted by residual: bond pdb=" CA ASP C 289 " pdb=" CB ASP C 289 " ideal model delta sigma weight residual 1.532 1.546 -0.015 1.33e-02 5.65e+03 1.22e+00 bond pdb=" CD GLU D 464 " pdb=" OE1 GLU D 464 " ideal model delta sigma weight residual 1.249 1.229 0.020 1.90e-02 2.77e+03 1.14e+00 bond pdb=" CB ASP C 289 " pdb=" CG ASP C 289 " ideal model delta sigma weight residual 1.516 1.542 -0.026 2.50e-02 1.60e+03 1.05e+00 bond pdb=" C4 ADP F 602 " pdb=" C5 ADP F 602 " ideal model delta sigma weight residual 1.490 1.470 0.020 2.00e-02 2.50e+03 1.03e+00 bond pdb=" C ARG G 256 " pdb=" O ARG G 256 " ideal model delta sigma weight residual 1.237 1.249 -0.012 1.19e-02 7.06e+03 1.02e+00 ... (remaining 24503 not shown) Histogram of bond angle deviations from ideal: 97.18 - 104.94: 496 104.94 - 112.70: 13178 112.70 - 120.45: 10106 120.45 - 128.21: 9329 128.21 - 135.97: 94 Bond angle restraints: 33203 Sorted by residual: angle pdb=" CA GLY B 340 " pdb=" C GLY B 340 " pdb=" N GLN B 341 " ideal model delta sigma weight residual 114.23 117.49 -3.26 8.80e-01 1.29e+00 1.37e+01 angle pdb=" C GLY C 288 " pdb=" N ASP C 289 " pdb=" CA ASP C 289 " ideal model delta sigma weight residual 124.82 130.29 -5.47 1.78e+00 3.16e-01 9.44e+00 angle pdb=" N GLU E 379 " pdb=" CA GLU E 379 " pdb=" CB GLU E 379 " ideal model delta sigma weight residual 110.16 114.58 -4.42 1.48e+00 4.57e-01 8.91e+00 angle pdb=" C VAL F 214 " pdb=" N PHE F 215 " pdb=" CA PHE F 215 " ideal model delta sigma weight residual 122.42 117.89 4.53 1.55e+00 4.16e-01 8.54e+00 angle pdb=" N GLU E 337 " pdb=" CA GLU E 337 " pdb=" CB GLU E 337 " ideal model delta sigma weight residual 110.16 114.39 -4.23 1.48e+00 4.57e-01 8.17e+00 ... (remaining 33198 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.88: 14520 29.88 - 59.76: 350 59.76 - 89.63: 46 89.63 - 119.51: 2 119.51 - 149.39: 1 Dihedral angle restraints: 14919 sinusoidal: 5997 harmonic: 8922 Sorted by residual: dihedral pdb=" CA ALA G 108 " pdb=" C ALA G 108 " pdb=" N SER G 109 " pdb=" CA SER G 109 " ideal model delta harmonic sigma weight residual 180.00 145.71 34.29 0 5.00e+00 4.00e-02 4.70e+01 dihedral pdb=" C5' ADP F 602 " pdb=" O5' ADP F 602 " pdb=" PA ADP F 602 " pdb=" O2A ADP F 602 " ideal model delta sinusoidal sigma weight residual -60.00 89.39 -149.39 1 2.00e+01 2.50e-03 4.47e+01 dihedral pdb=" O2A ADP F 602 " pdb=" O3A ADP F 602 " pdb=" PA ADP F 602 " pdb=" PB ADP F 602 " ideal model delta sinusoidal sigma weight residual -60.00 50.84 -110.84 1 2.00e+01 2.50e-03 3.25e+01 ... (remaining 14916 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 2604 0.037 - 0.074: 853 0.074 - 0.111: 289 0.111 - 0.148: 86 0.148 - 0.185: 2 Chirality restraints: 3834 Sorted by residual: chirality pdb=" CB VAL D 463 " pdb=" CA VAL D 463 " pdb=" CG1 VAL D 463 " pdb=" CG2 VAL D 463 " both_signs ideal model delta sigma weight residual False -2.63 -2.44 -0.18 2.00e-01 2.50e+01 8.56e-01 chirality pdb=" CA GLU D 464 " pdb=" N GLU D 464 " pdb=" C GLU D 464 " pdb=" CB GLU D 464 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.97e-01 chirality pdb=" CA GLU A 459 " pdb=" N GLU A 459 " pdb=" C GLU A 459 " pdb=" CB GLU A 459 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.63e-01 ... (remaining 3831 not shown) Planarity restraints: 4357 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C HIS G 65 " 0.031 5.00e-02 4.00e+02 4.68e-02 3.51e+00 pdb=" N PRO G 66 " -0.081 5.00e-02 4.00e+02 pdb=" CA PRO G 66 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO G 66 " 0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR D 341 " -0.030 5.00e-02 4.00e+02 4.58e-02 3.36e+00 pdb=" N PRO D 342 " 0.079 5.00e-02 4.00e+02 pdb=" CA PRO D 342 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO D 342 " -0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU D 220 " 0.028 5.00e-02 4.00e+02 4.22e-02 2.85e+00 pdb=" N PRO D 221 " -0.073 5.00e-02 4.00e+02 pdb=" CA PRO D 221 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO D 221 " 0.023 5.00e-02 4.00e+02 ... (remaining 4354 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 210 2.65 - 3.21: 22589 3.21 - 3.78: 36102 3.78 - 4.34: 51218 4.34 - 4.90: 85746 Nonbonded interactions: 195865 Sorted by model distance: nonbonded pdb="MG MG F 601 " pdb=" O1B ADP F 602 " model vdw 2.089 2.170 nonbonded pdb=" OG1 THR F 165 " pdb="MG MG F 601 " model vdw 2.214 2.170 nonbonded pdb=" O LEU B 402 " pdb=" OG1 THR B 406 " model vdw 2.240 2.440 nonbonded pdb=" OE1 GLN G 50 " pdb=" OH TYR G 220 " model vdw 2.251 2.440 nonbonded pdb=" NH2 ARG A 106 " pdb=" O GLY A 119 " model vdw 2.265 2.520 ... (remaining 195860 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' selection = chain 'E' 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: 4.040 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: 0.050 Extract box with map and model: 12.380 Check model and map are aligned: 0.330 Set scattering table: 0.190 Process input model: 60.940 Find NCS groups from input model: 1.210 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.010 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 91.250 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8779 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 0.038 24508 Z= 0.164 Angle : 0.479 8.472 33203 Z= 0.259 Chirality : 0.043 0.185 3834 Planarity : 0.004 0.047 4357 Dihedral : 13.187 149.390 9209 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 3.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 0.00 % Allowed : 0.23 % Favored : 99.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.63 (0.15), residues: 3114 helix: 2.17 (0.15), residues: 1254 sheet: 0.89 (0.23), residues: 524 loop : 0.18 (0.17), residues: 1336 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS D 363 PHE 0.017 0.001 PHE B 494 TYR 0.006 0.001 TYR E 341 ARG 0.004 0.000 ARG C 354 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6228 Ramachandran restraints generated. 3114 Oldfield, 0 Emsley, 3114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6228 Ramachandran restraints generated. 3114 Oldfield, 0 Emsley, 3114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 2567 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 112 time to evaluate : 3.043 Fit side-chains revert: symmetry clash REVERT: G 131 MET cc_start: 0.6235 (mmp) cc_final: 0.5952 (mtp) outliers start: 0 outliers final: 0 residues processed: 112 average time/residue: 1.5519 time to fit residues: 199.0853 Evaluate side-chains 87 residues out of total 2567 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 87 time to evaluate : 2.730 ------------------------------------------------------------------------------- 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: 1.9990 chunk 234 optimal weight: 10.0000 chunk 130 optimal weight: 20.0000 chunk 80 optimal weight: 5.9990 chunk 158 optimal weight: 8.9990 chunk 125 optimal weight: 0.9980 chunk 242 optimal weight: 7.9990 chunk 94 optimal weight: 9.9990 chunk 147 optimal weight: 7.9990 chunk 180 optimal weight: 0.9980 chunk 281 optimal weight: 10.0000 overall best weight: 3.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 266 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8836 moved from start: 0.0810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 24508 Z= 0.344 Angle : 0.536 7.451 33203 Z= 0.278 Chirality : 0.046 0.204 3834 Planarity : 0.004 0.046 4357 Dihedral : 5.472 143.740 3409 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 4.19 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.79 % Favored : 97.17 % Rotamer: Outliers : 0.51 % Allowed : 5.38 % Favored : 94.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: 1.43 (0.15), residues: 3114 helix: 2.03 (0.15), residues: 1239 sheet: 0.74 (0.22), residues: 560 loop : 0.07 (0.17), residues: 1315 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS D 363 PHE 0.015 0.001 PHE B 494 TYR 0.013 0.001 TYR B 438 ARG 0.004 0.000 ARG D 402 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6228 Ramachandran restraints generated. 3114 Oldfield, 0 Emsley, 3114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6228 Ramachandran restraints generated. 3114 Oldfield, 0 Emsley, 3114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 2567 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 89 time to evaluate : 2.643 Fit side-chains revert: symmetry clash REVERT: F 202 MET cc_start: 0.8867 (OUTLIER) cc_final: 0.8185 (mtt) REVERT: G 131 MET cc_start: 0.6302 (mmp) cc_final: 0.6081 (mtp) outliers start: 13 outliers final: 3 residues processed: 93 average time/residue: 1.5647 time to fit residues: 167.6104 Evaluate side-chains 87 residues out of total 2567 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 83 time to evaluate : 2.643 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 366 VAL Chi-restraints excluded: chain D residue 105 LEU Chi-restraints excluded: chain F residue 202 MET Chi-restraints excluded: chain G residue 165 PHE 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: 8.9990 chunk 234 optimal weight: 5.9990 chunk 191 optimal weight: 8.9990 chunk 77 optimal weight: 4.9990 chunk 282 optimal weight: 0.3980 chunk 304 optimal weight: 9.9990 chunk 251 optimal weight: 3.9990 chunk 279 optimal weight: 10.0000 chunk 96 optimal weight: 5.9990 chunk 226 optimal weight: 1.9990 overall best weight: 3.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 474 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8845 moved from start: 0.1015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 24508 Z= 0.332 Angle : 0.522 8.147 33203 Z= 0.271 Chirality : 0.045 0.156 3834 Planarity : 0.004 0.044 4357 Dihedral : 5.400 124.575 3409 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.67 % Favored : 97.30 % Rotamer: Outliers : 0.82 % Allowed : 7.36 % Favored : 91.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: 1.30 (0.15), residues: 3114 helix: 1.92 (0.15), residues: 1233 sheet: 0.72 (0.22), residues: 532 loop : -0.01 (0.17), residues: 1349 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS D 363 PHE 0.015 0.001 PHE B 494 TYR 0.012 0.001 TYR E 341 ARG 0.003 0.000 ARG D 402 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6228 Ramachandran restraints generated. 3114 Oldfield, 0 Emsley, 3114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6228 Ramachandran restraints generated. 3114 Oldfield, 0 Emsley, 3114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 2567 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 87 time to evaluate : 2.474 Fit side-chains revert: symmetry clash REVERT: B 250 MET cc_start: 0.9335 (OUTLIER) cc_final: 0.9125 (ttt) REVERT: D 389 MET cc_start: 0.7290 (mpt) cc_final: 0.6986 (mpt) REVERT: F 202 MET cc_start: 0.8872 (OUTLIER) cc_final: 0.8321 (mtt) REVERT: F 340 ILE cc_start: 0.9099 (OUTLIER) cc_final: 0.8759 (mt) outliers start: 21 outliers final: 5 residues processed: 99 average time/residue: 1.5725 time to fit residues: 179.6109 Evaluate side-chains 93 residues out of total 2567 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 85 time to evaluate : 3.051 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain B residue 250 MET Chi-restraints excluded: chain C residue 366 VAL Chi-restraints excluded: chain D residue 105 LEU Chi-restraints excluded: chain F residue 188 VAL Chi-restraints excluded: chain F residue 202 MET Chi-restraints excluded: chain F residue 340 ILE Chi-restraints excluded: chain G residue 165 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 278 optimal weight: 5.9990 chunk 212 optimal weight: 4.9990 chunk 146 optimal weight: 7.9990 chunk 31 optimal weight: 1.9990 chunk 134 optimal weight: 10.0000 chunk 189 optimal weight: 7.9990 chunk 283 optimal weight: 10.0000 chunk 299 optimal weight: 10.0000 chunk 147 optimal weight: 1.9990 chunk 268 optimal weight: 8.9990 chunk 80 optimal weight: 8.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 345 GLN C 185 ASN F 22 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8871 moved from start: 0.1309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 24508 Z= 0.432 Angle : 0.572 7.507 33203 Z= 0.298 Chirality : 0.047 0.183 3834 Planarity : 0.004 0.043 4357 Dihedral : 5.539 152.783 3409 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.18 % Favored : 96.79 % Rotamer: Outliers : 1.56 % Allowed : 8.65 % Favored : 89.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: 1.07 (0.15), residues: 3114 helix: 1.71 (0.15), residues: 1233 sheet: 0.66 (0.22), residues: 529 loop : -0.14 (0.17), residues: 1352 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.001 HIS D 363 PHE 0.017 0.002 PHE B 494 TYR 0.015 0.001 TYR E 341 ARG 0.004 0.000 ARG D 402 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6228 Ramachandran restraints generated. 3114 Oldfield, 0 Emsley, 3114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6228 Ramachandran restraints generated. 3114 Oldfield, 0 Emsley, 3114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 2567 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 87 time to evaluate : 2.767 Fit side-chains revert: symmetry clash REVERT: B 176 THR cc_start: 0.9015 (OUTLIER) cc_final: 0.8795 (m) REVERT: C 138 ASP cc_start: 0.8532 (OUTLIER) cc_final: 0.8331 (m-30) REVERT: D 338 MET cc_start: 0.8147 (mmp) cc_final: 0.7929 (mmp) REVERT: F 202 MET cc_start: 0.8879 (OUTLIER) cc_final: 0.8233 (mtt) REVERT: G 79 LEU cc_start: 0.8963 (OUTLIER) cc_final: 0.8644 (tp) outliers start: 40 outliers final: 17 residues processed: 118 average time/residue: 1.3977 time to fit residues: 191.4943 Evaluate side-chains 106 residues out of total 2567 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 85 time to evaluate : 2.792 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain B residue 176 THR Chi-restraints excluded: chain B residue 314 THR Chi-restraints excluded: chain C residue 138 ASP Chi-restraints excluded: chain C residue 314 THR Chi-restraints excluded: chain C residue 366 VAL Chi-restraints excluded: chain D residue 464 GLU Chi-restraints excluded: chain E residue 77 ILE Chi-restraints excluded: chain E residue 218 MET Chi-restraints excluded: chain E residue 258 THR Chi-restraints excluded: chain E residue 301 THR Chi-restraints excluded: chain F residue 47 THR Chi-restraints excluded: chain F residue 141 VAL Chi-restraints excluded: chain F residue 188 VAL Chi-restraints excluded: chain F residue 202 MET Chi-restraints excluded: chain F residue 301 THR Chi-restraints excluded: chain F residue 344 VAL Chi-restraints excluded: chain G residue 79 LEU Chi-restraints excluded: chain G residue 165 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 249 optimal weight: 3.9990 chunk 170 optimal weight: 7.9990 chunk 4 optimal weight: 4.9990 chunk 223 optimal weight: 5.9990 chunk 123 optimal weight: 2.9990 chunk 255 optimal weight: 0.9990 chunk 207 optimal weight: 10.0000 chunk 0 optimal weight: 7.9990 chunk 153 optimal weight: 2.9990 chunk 268 optimal weight: 3.9990 chunk 75 optimal weight: 9.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8853 moved from start: 0.1282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 24508 Z= 0.293 Angle : 0.511 8.962 33203 Z= 0.265 Chirality : 0.045 0.155 3834 Planarity : 0.004 0.042 4357 Dihedral : 5.422 161.247 3409 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.70 % Favored : 97.27 % Rotamer: Outliers : 1.17 % Allowed : 9.70 % Favored : 89.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: 1.18 (0.15), residues: 3114 helix: 1.85 (0.15), residues: 1232 sheet: 0.64 (0.22), residues: 532 loop : -0.09 (0.17), residues: 1350 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS D 363 PHE 0.014 0.001 PHE B 494 TYR 0.012 0.001 TYR E 341 ARG 0.003 0.000 ARG D 402 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6228 Ramachandran restraints generated. 3114 Oldfield, 0 Emsley, 3114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6228 Ramachandran restraints generated. 3114 Oldfield, 0 Emsley, 3114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 2567 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 90 time to evaluate : 2.670 Fit side-chains revert: symmetry clash REVERT: A 459 GLU cc_start: 0.8835 (OUTLIER) cc_final: 0.8404 (mp0) REVERT: C 467 ASN cc_start: 0.7752 (OUTLIER) cc_final: 0.7312 (p0) REVERT: F 202 MET cc_start: 0.8869 (OUTLIER) cc_final: 0.8257 (mtt) outliers start: 30 outliers final: 16 residues processed: 112 average time/residue: 1.4730 time to fit residues: 190.7355 Evaluate side-chains 104 residues out of total 2567 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 85 time to evaluate : 2.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain A residue 459 GLU Chi-restraints excluded: chain C residue 314 THR Chi-restraints excluded: chain C residue 366 VAL Chi-restraints excluded: chain C residue 386 LEU Chi-restraints excluded: chain C residue 467 ASN Chi-restraints excluded: chain D residue 59 VAL Chi-restraints excluded: chain D residue 105 LEU Chi-restraints excluded: chain D residue 464 GLU Chi-restraints excluded: chain E residue 218 MET Chi-restraints excluded: chain E residue 301 THR Chi-restraints excluded: chain F residue 141 VAL Chi-restraints excluded: chain F residue 188 VAL Chi-restraints excluded: chain F residue 202 MET Chi-restraints excluded: chain F residue 228 VAL Chi-restraints excluded: chain F residue 301 THR Chi-restraints excluded: chain F residue 344 VAL Chi-restraints excluded: chain G residue 165 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 100 optimal weight: 9.9990 chunk 269 optimal weight: 0.7980 chunk 59 optimal weight: 3.9990 chunk 175 optimal weight: 8.9990 chunk 73 optimal weight: 6.9990 chunk 299 optimal weight: 10.0000 chunk 248 optimal weight: 5.9990 chunk 138 optimal weight: 9.9990 chunk 24 optimal weight: 5.9990 chunk 99 optimal weight: 0.9990 chunk 157 optimal weight: 4.9990 overall best weight: 3.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8858 moved from start: 0.1353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 24508 Z= 0.322 Angle : 0.525 9.771 33203 Z= 0.271 Chirality : 0.045 0.161 3834 Planarity : 0.004 0.044 4357 Dihedral : 5.353 163.041 3409 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.99 % Favored : 96.98 % Rotamer: Outliers : 1.32 % Allowed : 10.52 % Favored : 88.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: 1.13 (0.15), residues: 3114 helix: 1.82 (0.15), residues: 1232 sheet: 0.60 (0.22), residues: 552 loop : -0.13 (0.17), residues: 1330 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS D 363 PHE 0.015 0.001 PHE B 494 TYR 0.012 0.001 TYR E 341 ARG 0.003 0.000 ARG D 402 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6228 Ramachandran restraints generated. 3114 Oldfield, 0 Emsley, 3114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6228 Ramachandran restraints generated. 3114 Oldfield, 0 Emsley, 3114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 2567 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 87 time to evaluate : 2.786 Fit side-chains revert: symmetry clash REVERT: A 459 GLU cc_start: 0.8820 (OUTLIER) cc_final: 0.8550 (mp0) REVERT: C 467 ASN cc_start: 0.7785 (OUTLIER) cc_final: 0.7336 (p0) REVERT: D 338 MET cc_start: 0.8082 (mmp) cc_final: 0.7877 (mmp) REVERT: F 202 MET cc_start: 0.8860 (OUTLIER) cc_final: 0.8245 (mtt) REVERT: G 79 LEU cc_start: 0.8916 (OUTLIER) cc_final: 0.8604 (tp) outliers start: 34 outliers final: 20 residues processed: 116 average time/residue: 1.3722 time to fit residues: 185.5403 Evaluate side-chains 108 residues out of total 2567 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 84 time to evaluate : 2.641 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain A residue 459 GLU Chi-restraints excluded: chain B residue 314 THR Chi-restraints excluded: chain B residue 478 THR Chi-restraints excluded: chain C residue 314 THR Chi-restraints excluded: chain C residue 366 VAL Chi-restraints excluded: chain C residue 386 LEU Chi-restraints excluded: chain C residue 467 ASN Chi-restraints excluded: chain D residue 59 VAL Chi-restraints excluded: chain D residue 105 LEU Chi-restraints excluded: chain D residue 464 GLU Chi-restraints excluded: chain E residue 77 ILE Chi-restraints excluded: chain E residue 218 MET Chi-restraints excluded: chain E residue 301 THR Chi-restraints excluded: chain F residue 141 VAL Chi-restraints excluded: chain F residue 188 VAL Chi-restraints excluded: chain F residue 202 MET Chi-restraints excluded: chain F residue 228 VAL Chi-restraints excluded: chain F residue 301 THR Chi-restraints excluded: chain F residue 344 VAL Chi-restraints excluded: chain G residue 79 LEU Chi-restraints excluded: chain G residue 165 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 289 optimal weight: 7.9990 chunk 33 optimal weight: 0.0010 chunk 170 optimal weight: 8.9990 chunk 219 optimal weight: 6.9990 chunk 169 optimal weight: 2.9990 chunk 252 optimal weight: 1.9990 chunk 167 optimal weight: 8.9990 chunk 298 optimal weight: 4.9990 chunk 186 optimal weight: 10.0000 chunk 182 optimal weight: 8.9990 chunk 137 optimal weight: 1.9990 overall best weight: 2.3994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8843 moved from start: 0.1330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 24508 Z= 0.239 Angle : 0.494 10.575 33203 Z= 0.253 Chirality : 0.044 0.159 3834 Planarity : 0.004 0.045 4357 Dihedral : 5.115 159.924 3409 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.63 % Favored : 97.33 % Rotamer: Outliers : 1.40 % Allowed : 10.67 % Favored : 87.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: 1.26 (0.15), residues: 3114 helix: 1.93 (0.15), residues: 1234 sheet: 0.67 (0.22), residues: 550 loop : -0.07 (0.17), residues: 1330 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS D 363 PHE 0.014 0.001 PHE B 494 TYR 0.010 0.001 TYR E 341 ARG 0.002 0.000 ARG D 402 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6228 Ramachandran restraints generated. 3114 Oldfield, 0 Emsley, 3114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6228 Ramachandran restraints generated. 3114 Oldfield, 0 Emsley, 3114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 2567 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 86 time to evaluate : 2.820 Fit side-chains revert: symmetry clash REVERT: A 459 GLU cc_start: 0.8840 (OUTLIER) cc_final: 0.8586 (mp0) REVERT: C 467 ASN cc_start: 0.7867 (OUTLIER) cc_final: 0.7419 (p0) REVERT: D 338 MET cc_start: 0.8133 (mmp) cc_final: 0.7908 (mmp) REVERT: F 202 MET cc_start: 0.8861 (OUTLIER) cc_final: 0.8240 (mtt) outliers start: 36 outliers final: 25 residues processed: 117 average time/residue: 1.3747 time to fit residues: 188.1114 Evaluate side-chains 112 residues out of total 2567 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 84 time to evaluate : 2.890 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 94 ILE Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain A residue 459 GLU Chi-restraints excluded: chain B residue 314 THR Chi-restraints excluded: chain B residue 332 THR Chi-restraints excluded: chain B residue 478 THR Chi-restraints excluded: chain C residue 314 THR Chi-restraints excluded: chain C residue 366 VAL Chi-restraints excluded: chain C residue 386 LEU Chi-restraints excluded: chain C residue 467 ASN Chi-restraints excluded: chain D residue 59 VAL Chi-restraints excluded: chain D residue 105 LEU Chi-restraints excluded: chain D residue 464 GLU Chi-restraints excluded: chain E residue 77 ILE Chi-restraints excluded: chain E residue 141 VAL Chi-restraints excluded: chain E residue 218 MET Chi-restraints excluded: chain E residue 228 VAL Chi-restraints excluded: chain E residue 301 THR Chi-restraints excluded: chain F residue 47 THR Chi-restraints excluded: chain F residue 141 VAL Chi-restraints excluded: chain F residue 188 VAL Chi-restraints excluded: chain F residue 202 MET Chi-restraints excluded: chain F residue 228 VAL Chi-restraints excluded: chain F residue 301 THR Chi-restraints excluded: chain F residue 344 VAL Chi-restraints excluded: chain G residue 165 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 184 optimal weight: 9.9990 chunk 119 optimal weight: 0.2980 chunk 178 optimal weight: 2.9990 chunk 90 optimal weight: 0.5980 chunk 58 optimal weight: 3.9990 chunk 57 optimal weight: 7.9990 chunk 189 optimal weight: 7.9990 chunk 203 optimal weight: 2.9990 chunk 147 optimal weight: 6.9990 chunk 27 optimal weight: 9.9990 chunk 234 optimal weight: 7.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8837 moved from start: 0.1336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 24508 Z= 0.224 Angle : 0.488 11.967 33203 Z= 0.249 Chirality : 0.043 0.163 3834 Planarity : 0.004 0.043 4357 Dihedral : 5.019 158.285 3409 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.76 % Favored : 97.21 % Rotamer: Outliers : 1.32 % Allowed : 10.79 % Favored : 87.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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 (0.15), residues: 3114 helix: 1.97 (0.15), residues: 1234 sheet: 0.71 (0.22), residues: 550 loop : -0.03 (0.17), residues: 1330 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS D 363 PHE 0.013 0.001 PHE E 125 TYR 0.009 0.001 TYR E 341 ARG 0.002 0.000 ARG D 402 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6228 Ramachandran restraints generated. 3114 Oldfield, 0 Emsley, 3114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6228 Ramachandran restraints generated. 3114 Oldfield, 0 Emsley, 3114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 2567 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 84 time to evaluate : 2.863 Fit side-chains REVERT: A 459 GLU cc_start: 0.8838 (OUTLIER) cc_final: 0.8588 (mp0) REVERT: C 467 ASN cc_start: 0.7880 (OUTLIER) cc_final: 0.7462 (p0) REVERT: D 338 MET cc_start: 0.8151 (mmp) cc_final: 0.7947 (mmp) REVERT: E 301 THR cc_start: 0.9090 (OUTLIER) cc_final: 0.8883 (m) REVERT: E 469 MET cc_start: 0.8010 (ptp) cc_final: 0.7493 (ppp) REVERT: F 202 MET cc_start: 0.8860 (OUTLIER) cc_final: 0.8323 (mtt) outliers start: 34 outliers final: 21 residues processed: 114 average time/residue: 1.4626 time to fit residues: 194.0234 Evaluate side-chains 108 residues out of total 2567 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 83 time to evaluate : 2.624 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain A residue 459 GLU Chi-restraints excluded: chain B residue 314 THR Chi-restraints excluded: chain B residue 332 THR Chi-restraints excluded: chain B residue 478 THR Chi-restraints excluded: chain C residue 314 THR Chi-restraints excluded: chain C residue 366 VAL Chi-restraints excluded: chain C residue 386 LEU Chi-restraints excluded: chain C residue 467 ASN Chi-restraints excluded: chain D residue 105 LEU Chi-restraints excluded: chain E residue 77 ILE Chi-restraints excluded: chain E residue 141 VAL Chi-restraints excluded: chain E residue 218 MET Chi-restraints excluded: chain E residue 228 VAL Chi-restraints excluded: chain E residue 301 THR Chi-restraints excluded: chain F residue 47 THR Chi-restraints excluded: chain F residue 141 VAL Chi-restraints excluded: chain F residue 188 VAL Chi-restraints excluded: chain F residue 202 MET Chi-restraints excluded: chain F residue 228 VAL Chi-restraints excluded: chain F residue 301 THR Chi-restraints excluded: chain F residue 344 VAL Chi-restraints excluded: chain G residue 165 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 271 optimal weight: 6.9990 chunk 286 optimal weight: 8.9990 chunk 261 optimal weight: 2.9990 chunk 278 optimal weight: 5.9990 chunk 167 optimal weight: 9.9990 chunk 121 optimal weight: 8.9990 chunk 218 optimal weight: 0.0170 chunk 85 optimal weight: 10.0000 chunk 251 optimal weight: 3.9990 chunk 263 optimal weight: 0.2980 chunk 277 optimal weight: 1.9990 overall best weight: 1.8624 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8829 moved from start: 0.1345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 24508 Z= 0.200 Angle : 0.485 12.266 33203 Z= 0.247 Chirality : 0.043 0.172 3834 Planarity : 0.003 0.043 4357 Dihedral : 4.941 157.245 3409 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.54 % Favored : 97.43 % Rotamer: Outliers : 1.29 % Allowed : 10.95 % Favored : 87.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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 (0.15), residues: 3114 helix: 2.04 (0.15), residues: 1233 sheet: 0.78 (0.22), residues: 556 loop : -0.01 (0.17), residues: 1325 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS D 363 PHE 0.013 0.001 PHE E 125 TYR 0.008 0.001 TYR E 341 ARG 0.002 0.000 ARG D 458 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6228 Ramachandran restraints generated. 3114 Oldfield, 0 Emsley, 3114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6228 Ramachandran restraints generated. 3114 Oldfield, 0 Emsley, 3114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 2567 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 84 time to evaluate : 3.090 Fit side-chains REVERT: A 459 GLU cc_start: 0.8831 (OUTLIER) cc_final: 0.8593 (mp0) REVERT: C 467 ASN cc_start: 0.7868 (OUTLIER) cc_final: 0.7457 (p0) REVERT: D 338 MET cc_start: 0.8166 (mmp) cc_final: 0.7958 (mmp) REVERT: E 469 MET cc_start: 0.8013 (ptp) cc_final: 0.7356 (ppp) REVERT: F 202 MET cc_start: 0.8865 (OUTLIER) cc_final: 0.8306 (mtt) outliers start: 33 outliers final: 21 residues processed: 112 average time/residue: 1.4207 time to fit residues: 185.8698 Evaluate side-chains 108 residues out of total 2567 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 84 time to evaluate : 2.759 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 459 GLU Chi-restraints excluded: chain B residue 314 THR Chi-restraints excluded: chain B residue 332 THR Chi-restraints excluded: chain B residue 478 THR Chi-restraints excluded: chain C residue 314 THR Chi-restraints excluded: chain C residue 366 VAL Chi-restraints excluded: chain C residue 386 LEU Chi-restraints excluded: chain C residue 467 ASN Chi-restraints excluded: chain D residue 105 LEU Chi-restraints excluded: chain E residue 77 ILE Chi-restraints excluded: chain E residue 141 VAL Chi-restraints excluded: chain E residue 218 MET Chi-restraints excluded: chain E residue 228 VAL Chi-restraints excluded: chain F residue 47 THR Chi-restraints excluded: chain F residue 141 VAL Chi-restraints excluded: chain F residue 188 VAL Chi-restraints excluded: chain F residue 202 MET Chi-restraints excluded: chain F residue 228 VAL Chi-restraints excluded: chain F residue 301 THR Chi-restraints excluded: chain F residue 344 VAL Chi-restraints excluded: chain G residue 165 PHE Chi-restraints excluded: chain G residue 244 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 182 optimal weight: 0.7980 chunk 294 optimal weight: 6.9990 chunk 179 optimal weight: 0.0020 chunk 139 optimal weight: 6.9990 chunk 204 optimal weight: 8.9990 chunk 308 optimal weight: 1.9990 chunk 284 optimal weight: 3.9990 chunk 245 optimal weight: 1.9990 chunk 25 optimal weight: 0.6980 chunk 189 optimal weight: 0.0770 chunk 150 optimal weight: 7.9990 overall best weight: 0.7148 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8790 moved from start: 0.1363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 24508 Z= 0.127 Angle : 0.460 13.345 33203 Z= 0.232 Chirality : 0.042 0.210 3834 Planarity : 0.003 0.042 4357 Dihedral : 4.687 152.472 3409 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.47 % Favored : 97.50 % Rotamer: Outliers : 0.93 % Allowed : 11.26 % Favored : 87.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.58 (0.15), residues: 3114 helix: 2.16 (0.15), residues: 1247 sheet: 0.93 (0.22), residues: 548 loop : 0.09 (0.17), residues: 1319 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.000 HIS E 363 PHE 0.013 0.001 PHE E 125 TYR 0.007 0.001 TYR F 238 ARG 0.002 0.000 ARG A 161 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6228 Ramachandran restraints generated. 3114 Oldfield, 0 Emsley, 3114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6228 Ramachandran restraints generated. 3114 Oldfield, 0 Emsley, 3114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 2567 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 87 time to evaluate : 2.552 Fit side-chains REVERT: A 459 GLU cc_start: 0.8847 (OUTLIER) cc_final: 0.8582 (mp0) REVERT: D 389 MET cc_start: 0.6735 (mpt) cc_final: 0.6527 (mpp) REVERT: E 469 MET cc_start: 0.7917 (ptp) cc_final: 0.7467 (ppp) REVERT: F 202 MET cc_start: 0.8867 (OUTLIER) cc_final: 0.8335 (mtt) outliers start: 24 outliers final: 16 residues processed: 105 average time/residue: 1.3726 time to fit residues: 167.2118 Evaluate side-chains 102 residues out of total 2567 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 84 time to evaluate : 2.091 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 459 GLU Chi-restraints excluded: chain B residue 402 LEU Chi-restraints excluded: chain B residue 478 THR Chi-restraints excluded: chain C residue 314 THR Chi-restraints excluded: chain C residue 366 VAL Chi-restraints excluded: chain C residue 499 VAL Chi-restraints excluded: chain D residue 105 LEU Chi-restraints excluded: chain E residue 77 ILE Chi-restraints excluded: chain E residue 218 MET Chi-restraints excluded: chain E residue 228 VAL Chi-restraints excluded: chain F residue 141 VAL Chi-restraints excluded: chain F residue 188 VAL Chi-restraints excluded: chain F residue 202 MET Chi-restraints excluded: chain F residue 301 THR Chi-restraints excluded: chain F residue 344 VAL Chi-restraints excluded: chain G residue 165 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 195 optimal weight: 10.0000 chunk 261 optimal weight: 0.9990 chunk 75 optimal weight: 7.9990 chunk 226 optimal weight: 5.9990 chunk 36 optimal weight: 0.8980 chunk 68 optimal weight: 4.9990 chunk 246 optimal weight: 10.0000 chunk 103 optimal weight: 0.0970 chunk 252 optimal weight: 1.9990 chunk 31 optimal weight: 8.9990 chunk 45 optimal weight: 0.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.062680 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2795 r_free = 0.2795 target = 0.046470 restraints weight = 69957.754| |-----------------------------------------------------------------------------| r_work (start): 0.2783 rms_B_bonded: 2.83 r_work: 0.2654 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.2654 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8856 moved from start: 0.1386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 24508 Z= 0.142 Angle : 0.465 13.476 33203 Z= 0.235 Chirality : 0.042 0.168 3834 Planarity : 0.003 0.042 4357 Dihedral : 4.607 148.536 3409 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.44 % Favored : 97.53 % Rotamer: Outliers : 0.86 % Allowed : 11.41 % Favored : 87.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.63 (0.15), residues: 3114 helix: 2.16 (0.15), residues: 1254 sheet: 0.99 (0.22), residues: 548 loop : 0.12 (0.17), residues: 1312 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.000 HIS E 363 PHE 0.013 0.001 PHE E 125 TYR 0.007 0.001 TYR F 238 ARG 0.001 0.000 ARG D 402 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4859.73 seconds wall clock time: 88 minutes 27.88 seconds (5307.88 seconds total)