Starting phenix.real_space_refine on Mon Feb 19 09:19:16 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hha_34757/02_2024/8hha_34757_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hha_34757/02_2024/8hha_34757.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hha_34757/02_2024/8hha_34757.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hha_34757/02_2024/8hha_34757.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hha_34757/02_2024/8hha_34757_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hha_34757/02_2024/8hha_34757_updated.pdb" } resolution = 3.4 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 15 5.49 5 Mg 5 5.21 5 S 77 5.16 5 C 15277 2.51 5 N 4214 2.21 5 O 4657 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 87": "OE1" <-> "OE2" Residue "A GLU 96": "OE1" <-> "OE2" Residue "A GLU 284": "OE1" <-> "OE2" Residue "A GLU 299": "OE1" <-> "OE2" Residue "A TYR 438": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 459": "OE1" <-> "OE2" Residue "B GLU 68": "OE1" <-> "OE2" Residue "B GLU 272": "OE1" <-> "OE2" Residue "B GLU 320": "OE1" <-> "OE2" Residue "B GLU 457": "OE1" <-> "OE2" Residue "C GLU 122": "OE1" <-> "OE2" Residue "C GLU 165": "OE1" <-> "OE2" Residue "C GLU 202": "OE1" <-> "OE2" Residue "C GLU 299": "OE1" <-> "OE2" Residue "C GLU 320": "OE1" <-> "OE2" Residue "C GLU 391": "OE1" <-> "OE2" Residue "C GLU 451": "OE1" <-> "OE2" Residue "C GLU 473": "OE1" <-> "OE2" Residue "D GLU 39": "OE1" <-> "OE2" Residue "D PHE 125": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 170": "OE1" <-> "OE2" Residue "D GLU 432": "OE1" <-> "OE2" Residue "E PHE 125": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 201": "OE1" <-> "OE2" Residue "E GLU 290": "OE1" <-> "OE2" Residue "E GLU 332": "OE1" <-> "OE2" Residue "E TYR 427": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 453": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 460": "OE1" <-> "OE2" Residue "F PHE 125": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 391": "OE1" <-> "OE2" Residue "F GLU 395": "OE1" <-> "OE2" Residue "F GLU 439": "OE1" <-> "OE2" Residue "G GLU 222": "OE1" <-> "OE2" Residue "G GLU 273": "OE1" <-> "OE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 24245 Number of models: 1 Model: "" Number of chains: 12 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: {'PCIS': 1, 'PTRANS': 22, '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: {'PTRANS': 10, '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: "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: 12.11, per 1000 atoms: 0.50 Number of scatterers: 24245 At special positions: 0 Unit cell: (130.24, 120.56, 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 15 15.00 Mg 5 11.99 O 4657 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: 9.58 Conformation dependent library (CDL) restraints added in 4.2 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: 120 helices and 23 sheets defined 42.4% alpha, 12.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.06 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 151 through 156 Processing helix chain 'A' and resid 175 through 188 removed outlier: 3.685A pdb=" N GLN A 186 " --> pdb=" O THR A 182 " (cutoff:3.500A) removed outlier: 4.660A pdb=" N LYS A 187 " --> pdb=" O ILE A 183 " (cutoff:3.500A) removed outlier: 5.667A pdb=" N ASP A 188 " --> pdb=" O ILE A 184 " (cutoff:3.500A) Processing helix chain 'A' and resid 202 through 215 Processing helix chain 'A' and resid 217 through 220 Processing helix chain 'A' and resid 232 through 252 Proline residue: A 239 - end of helix removed outlier: 3.630A pdb=" N TYR A 248 " --> pdb=" O ALA A 244 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N PHE A 249 " --> pdb=" O MET A 245 " (cutoff:3.500A) removed outlier: 3.743A 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 288 through 300 removed outlier: 4.405A pdb=" N PHE A 291 " --> pdb=" O GLY A 288 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N LEU A 293 " --> pdb=" O ILE A 290 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LEU A 298 " --> pdb=" O SER A 295 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N GLU A 299 " --> pdb=" O ARG A 296 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N ARG A 300 " --> pdb=" O LEU A 297 " (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 395 removed outlier: 4.615A pdb=" N GLY A 380 " --> pdb=" O LYS A 376 " (cutoff:3.500A) removed outlier: 5.435A pdb=" N THR A 381 " --> pdb=" O LYS A 377 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N LEU A 382 " --> pdb=" O VAL A 378 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N GLU A 391 " --> pdb=" O ALA A 387 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N LEU A 392 " --> pdb=" O ALA A 388 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N ALA A 394 " --> pdb=" O ARG A 390 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N PHE A 395 " --> pdb=" O GLU A 391 " (cutoff:3.500A) Processing helix chain 'A' and resid 407 through 420 Processing helix chain 'A' and resid 430 through 441 Processing helix chain 'A' and resid 450 through 467 removed outlier: 3.542A pdb=" N VAL A 453 " --> pdb=" O VAL A 450 " (cutoff:3.500A) removed outlier: 4.773A pdb=" N ARG A 454 " --> pdb=" O GLU A 451 " (cutoff:3.500A) 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 154 No H-bonds generated for 'chain 'B' and resid 151 through 154' Processing helix chain 'B' and resid 175 through 188 removed outlier: 3.645A pdb=" N GLN B 186 " --> pdb=" O THR B 182 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N LYS B 187 " --> pdb=" O ILE B 183 " (cutoff:3.500A) removed outlier: 5.707A pdb=" N ASP B 188 " --> pdb=" O ILE B 184 " (cutoff:3.500A) Processing helix chain 'B' and resid 202 through 215 Processing helix chain 'B' and resid 218 through 220 No H-bonds generated for 'chain 'B' and resid 218 through 220' Processing helix chain 'B' and resid 232 through 251 Proline residue: B 239 - end of helix removed outlier: 3.820A pdb=" N TYR B 248 " --> pdb=" O ALA B 244 " (cutoff:3.500A) removed outlier: 4.336A 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: 4.365A pdb=" N PHE B 291 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LEU B 293 " --> pdb=" O ILE B 290 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N ARG B 296 " --> pdb=" O LEU B 293 " (cutoff:3.500A) removed outlier: 4.215A 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 349 No H-bonds generated for 'chain 'B' and resid 346 through 349' Processing helix chain 'B' and resid 373 through 381 removed outlier: 3.874A pdb=" N GLY B 380 " --> pdb=" O LYS B 376 " (cutoff:3.500A) removed outlier: 5.391A pdb=" N THR B 381 " --> pdb=" O LYS B 377 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 394 Processing helix chain 'B' and resid 403 through 410 Processing helix chain 'B' and resid 413 through 419 Processing helix chain 'B' and resid 430 through 441 Processing helix chain 'B' and resid 450 through 467 removed outlier: 3.709A pdb=" N VAL B 453 " --> pdb=" O VAL B 450 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N ARG B 454 " --> pdb=" O GLU B 451 " (cutoff:3.500A) removed outlier: 3.805A 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 486 through 497 Processing helix chain 'C' and resid 79 through 81 No H-bonds generated for 'chain 'C' and resid 79 through 81' 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: 3.656A pdb=" N GLN C 186 " --> pdb=" O THR C 182 " (cutoff:3.500A) removed outlier: 4.686A 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: 3.696A pdb=" N TYR C 248 " --> pdb=" O ALA C 244 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N PHE C 249 " --> pdb=" O MET C 245 " (cutoff:3.500A) removed outlier: 3.754A 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: 4.132A pdb=" N ARG C 300 " --> pdb=" O ARG C 296 " (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 337 Processing helix chain 'C' and resid 346 through 350 Processing helix chain 'C' and resid 373 through 398 removed outlier: 3.621A pdb=" N VAL C 378 " --> pdb=" O ALA C 374 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N THR C 381 " --> pdb=" O LYS C 377 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N LEU C 384 " --> pdb=" O GLY C 380 " (cutoff:3.500A) removed outlier: 4.645A pdb=" N ALA C 394 " --> pdb=" O ARG C 390 " (cutoff:3.500A) removed outlier: 5.745A pdb=" N PHE C 395 " --> pdb=" O GLU C 391 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N ALA C 396 " --> pdb=" O LEU C 392 " (cutoff:3.500A) removed outlier: 4.815A pdb=" N GLN C 397 " --> pdb=" O GLU C 393 " (cutoff:3.500A) removed outlier: 5.243A pdb=" N PHE C 398 " --> pdb=" O ALA C 394 " (cutoff:3.500A) Processing helix chain 'C' and resid 404 through 420 removed outlier: 3.928A pdb=" N ALA C 408 " --> pdb=" O LYS C 404 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N LYS C 409 " --> pdb=" O ALA C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 430 through 441 removed outlier: 4.101A pdb=" N LEU C 435 " --> pdb=" O GLU C 431 " (cutoff:3.500A) Processing helix chain 'C' and resid 450 through 466 removed outlier: 3.534A pdb=" N VAL C 453 " --> pdb=" O VAL C 450 " (cutoff:3.500A) removed outlier: 5.188A 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 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 179 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 242 removed outlier: 4.578A pdb=" N ALA D 229 " --> pdb=" O ARG D 225 " (cutoff:3.500A) removed outlier: 4.717A pdb=" N LEU D 230 " --> pdb=" O MET D 226 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N TYR D 238 " --> pdb=" O THR D 234 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N PHE D 239 " --> pdb=" O MET D 235 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N ARG D 240 " --> pdb=" O ALA D 236 " (cutoff:3.500A) Processing helix chain 'D' and resid 254 through 268 Processing helix chain 'D' and resid 281 through 291 removed outlier: 4.272A 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: 4.208A pdb=" N SER D 323 " --> pdb=" O ALA D 319 " (cutoff:3.500A) removed outlier: 4.638A pdb=" N HIS D 324 " --> pdb=" O THR D 320 " (cutoff:3.500A) Processing helix chain 'D' and resid 333 through 338 removed outlier: 3.725A pdb=" N MET D 338 " --> pdb=" O LYS D 334 " (cutoff:3.500A) 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 386 removed outlier: 3.584A pdb=" N LEU D 380 " --> pdb=" O ARG D 376 " (cutoff:3.500A) removed outlier: 5.254A pdb=" N ASP D 382 " --> pdb=" O LYS D 378 " (cutoff:3.500A) removed outlier: 5.057A pdb=" N ILE D 383 " --> pdb=" O GLU D 379 " (cutoff:3.500A) Processing helix chain 'D' and resid 389 through 391 No H-bonds generated for 'chain 'D' and resid 389 through 391' Processing helix chain 'D' and resid 394 through 410 removed outlier: 3.515A pdb=" N LEU D 398 " --> pdb=" O ASP D 394 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ARG D 405 " --> pdb=" O HIS D 401 " (cutoff:3.500A) Processing helix chain 'D' and resid 416 through 421 removed outlier: 3.768A pdb=" N GLN D 419 " --> pdb=" O VAL D 416 " (cutoff:3.500A) Processing helix chain 'D' and resid 430 through 442 removed outlier: 3.820A pdb=" N ARG D 435 " --> pdb=" O LYS D 431 " (cutoff:3.500A) Processing helix chain 'D' and resid 450 through 453 Processing helix chain 'D' and resid 459 through 468 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 144 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: 5.346A pdb=" N ALA E 229 " --> pdb=" O ARG E 225 " (cutoff:3.500A) removed outlier: 4.737A pdb=" N LEU E 230 " --> pdb=" O MET E 226 " (cutoff:3.500A) removed outlier: 3.978A 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 279 through 291 removed outlier: 4.443A pdb=" N ALA E 282 " --> pdb=" O PRO E 279 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N GLU E 290 " --> pdb=" O GLN E 287 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ARG E 291 " --> pdb=" O LEU E 288 " (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 323 removed outlier: 3.768A pdb=" N SER E 323 " --> pdb=" O ALA E 319 " (cutoff:3.500A) Processing helix chain 'E' and resid 333 through 336 No H-bonds generated for 'chain 'E' and resid 333 through 336' 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: 4.508A pdb=" N ASP E 382 " --> pdb=" O LYS E 378 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N ILE E 383 " --> pdb=" O GLU E 379 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ALA E 385 " --> pdb=" O GLN E 381 " (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: 3.787A pdb=" N ARG E 405 " --> pdb=" O HIS E 401 " (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 442 Processing helix chain 'E' and resid 450 through 453 Processing helix chain 'E' and resid 459 through 469 removed outlier: 3.957A pdb=" N VAL E 463 " --> pdb=" O ILE E 459 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N GLU E 464 " --> pdb=" O GLU E 460 " (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 140 through 145 Processing helix chain 'F' and resid 164 through 178 removed outlier: 4.575A pdb=" N GLN F 177 " --> pdb=" O HIS F 173 " (cutoff:3.500A) removed outlier: 5.113A 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: 5.222A pdb=" N ALA F 229 " --> pdb=" O ARG F 225 " (cutoff:3.500A) removed outlier: 4.818A pdb=" N LEU F 230 " --> pdb=" O MET F 226 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N TYR F 238 " --> pdb=" O THR F 234 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N PHE F 239 " --> pdb=" O MET F 235 " (cutoff:3.500A) Processing helix chain 'F' and resid 255 through 268 removed outlier: 4.279A pdb=" N ALA F 266 " --> pdb=" O SER F 262 " (cutoff:3.500A) removed outlier: 5.096A pdb=" N LEU F 267 " --> pdb=" O GLU F 263 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LEU F 268 " --> pdb=" O VAL F 264 " (cutoff:3.500A) Processing helix chain 'F' and resid 274 through 276 No H-bonds generated for 'chain 'F' and resid 274 through 276' Processing helix chain 'F' and resid 279 through 291 removed outlier: 4.673A pdb=" N ALA F 282 " --> pdb=" O PRO F 279 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N THR F 283 " --> pdb=" O THR F 280 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N GLU F 284 " --> pdb=" O LEU F 281 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N GLN F 287 " --> pdb=" O GLU F 284 " (cutoff:3.500A) removed outlier: 4.892A pdb=" N GLU F 290 " --> 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: 4.994A pdb=" N SER F 323 " --> pdb=" O ALA F 319 " (cutoff:3.500A) removed outlier: 4.737A pdb=" N HIS F 324 " --> pdb=" O THR F 320 " (cutoff:3.500A) Processing helix chain 'F' and resid 333 through 338 removed outlier: 3.530A pdb=" N MET F 338 " --> pdb=" O LYS F 334 " (cutoff:3.500A) 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 387 removed outlier: 3.726A pdb=" N GLN F 381 " --> pdb=" O TYR F 377 " (cutoff:3.500A) removed outlier: 5.228A pdb=" N ASP F 382 " --> pdb=" O LYS F 378 " (cutoff:3.500A) removed outlier: 5.153A 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: 3.703A pdb=" N ARG F 405 " --> pdb=" O HIS F 401 " (cutoff:3.500A) Processing helix chain 'F' and resid 416 through 419 removed outlier: 3.745A pdb=" N GLN F 419 " --> pdb=" O VAL F 416 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 416 through 419' 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: 3.569A pdb=" N VAL F 463 " --> pdb=" O ILE F 459 " (cutoff:3.500A) Processing helix chain 'G' and resid 4 through 55 removed outlier: 4.098A pdb=" N THR G 9 " --> pdb=" O ARG G 5 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ARG G 10 " --> pdb=" O ASP G 6 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ASN G 38 " --> pdb=" O ARG G 34 " (cutoff:3.500A) removed outlier: 5.090A pdb=" N VAL G 43 " --> pdb=" O ALA G 39 " (cutoff:3.500A) Proline residue: G 44 - end of helix removed outlier: 3.563A pdb=" N VAL G 52 " --> pdb=" O LYS G 48 " (cutoff:3.500A) Processing helix chain 'G' and resid 91 through 106 removed outlier: 3.832A pdb=" N VAL G 95 " --> pdb=" O TYR G 91 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N LYS G 105 " --> pdb=" O GLN G 101 " (cutoff:3.500A) Processing helix chain 'G' and resid 120 through 128 Processing helix chain 'G' and resid 149 through 161 Processing helix chain 'G' and resid 212 through 283 removed outlier: 4.163A pdb=" N LEU G 216 " --> pdb=" O ILE G 212 " (cutoff:3.500A) Proline residue: G 218 - end of helix removed outlier: 3.522A pdb=" N LYS G 245 " --> pdb=" O MET G 241 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N ASN G 246 " --> pdb=" O THR G 242 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N ALA G 268 " --> pdb=" O ARG G 264 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 28 through 30 removed outlier: 6.605A pdb=" N GLY A 72 " --> pdb=" O LEU A 64 " (cutoff:3.500A) removed outlier: 5.046A pdb=" N LEU A 66 " --> pdb=" O ASN A 70 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N ASN A 70 " --> pdb=" O LEU A 66 " (cutoff:3.500A) removed outlier: 5.807A pdb=" N HIS A 42 " --> pdb=" O VAL A 31 " (cutoff:3.500A) removed outlier: 5.786A 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 98 Processing sheet with id= C, first strand: chain 'A' and resid 107 through 109 removed outlier: 8.585A pdb=" N VAL A 108 " --> pdb=" O THR A 221 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N VAL A 223 " --> pdb=" O VAL A 108 " (cutoff:3.500A) removed outlier: 8.699A pdb=" N ILE A 222 " --> pdb=" O MET A 191 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N SER A 193 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 7.899A pdb=" N VAL A 224 " --> pdb=" O SER A 193 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N TYR A 195 " --> pdb=" O VAL A 224 " (cutoff:3.500A) removed outlier: 7.845A pdb=" N ALA A 226 " --> pdb=" O TYR A 195 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N ALA A 197 " --> pdb=" O ALA A 226 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N HIS A 255 " --> pdb=" O ILE A 192 " (cutoff:3.500A) removed outlier: 8.187A pdb=" N ILE A 194 " --> pdb=" O HIS A 255 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N LEU A 257 " --> pdb=" O ILE A 194 " (cutoff:3.500A) removed outlier: 7.669A pdb=" N VAL A 196 " --> pdb=" O LEU A 257 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N VAL A 259 " --> pdb=" O VAL A 196 " (cutoff:3.500A) removed outlier: 7.325A pdb=" N ILE A 198 " --> pdb=" O VAL A 259 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N SER A 312 " --> pdb=" O VAL A 256 " (cutoff:3.500A) removed outlier: 7.954A pdb=" N VAL A 258 " --> pdb=" O SER A 312 " (cutoff:3.500A) removed outlier: 6.150A pdb=" N THR A 314 " --> pdb=" O VAL A 258 " (cutoff:3.500A) removed outlier: 7.692A pdb=" N TYR A 260 " --> pdb=" O THR A 314 " (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 343 removed outlier: 6.592A pdb=" N LEU A 166 " --> pdb=" O ILE A 342 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 87 through 89 removed outlier: 6.491A pdb=" N ARG B 40 " --> pdb=" O ILE B 32 " (cutoff:3.500A) removed outlier: 4.598A pdb=" N VAL B 34 " --> pdb=" O ILE B 38 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N ILE B 38 " --> pdb=" O VAL B 34 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ASN B 65 " --> pdb=" O GLY B 72 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N VAL B 74 " --> pdb=" O ALA B 63 " (cutoff:3.500A) removed outlier: 5.554A pdb=" N ALA B 63 " --> pdb=" O VAL B 74 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 96 through 99 removed outlier: 3.707A 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: 6.531A pdb=" N LEU B 166 " --> pdb=" O ILE B 342 " (cutoff:3.500A) removed outlier: 7.469A pdb=" N LEU B 344 " --> pdb=" O LEU B 166 " (cutoff:3.500A) removed outlier: 6.425A 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: 6.650A pdb=" N SER B 193 " --> pdb=" O ILE B 222 " (cutoff:3.500A) removed outlier: 7.980A pdb=" N VAL B 224 " --> pdb=" O SER B 193 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N TYR B 195 " --> pdb=" O VAL B 224 " (cutoff:3.500A) removed outlier: 7.788A pdb=" N ALA B 226 " --> pdb=" O TYR B 195 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N ALA B 197 " --> pdb=" O ALA B 226 " (cutoff:3.500A) removed outlier: 6.550A 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: 6.041A pdb=" N THR B 314 " --> pdb=" O VAL B 258 " (cutoff:3.500A) removed outlier: 7.416A pdb=" N TYR B 260 " --> pdb=" O THR B 314 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'C' and resid 28 through 30 removed outlier: 6.479A pdb=" N GLY C 72 " --> pdb=" O LEU C 64 " (cutoff:3.500A) removed outlier: 5.749A pdb=" N HIS C 42 " --> pdb=" O VAL C 31 " (cutoff:3.500A) removed outlier: 5.351A 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: 3.864A pdb=" N GLU C 125 " --> pdb=" O VAL C 99 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'C' and resid 340 through 344 Processing sheet with id= L, first strand: chain 'C' and resid 221 through 226 removed outlier: 6.821A pdb=" N SER C 193 " --> pdb=" O ILE C 222 " (cutoff:3.500A) removed outlier: 8.135A pdb=" N VAL C 224 " --> pdb=" O SER C 193 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N TYR C 195 " --> pdb=" O VAL C 224 " (cutoff:3.500A) removed outlier: 7.991A pdb=" N ALA C 226 " --> pdb=" O TYR C 195 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N ALA C 197 " --> pdb=" O ALA C 226 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N SER C 312 " --> pdb=" O VAL C 256 " (cutoff:3.500A) removed outlier: 8.011A pdb=" N VAL C 258 " --> pdb=" O SER C 312 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N THR C 314 " --> pdb=" O VAL C 258 " (cutoff:3.500A) removed outlier: 7.763A pdb=" N TYR C 260 " --> pdb=" O THR C 314 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N LEU C 316 " --> pdb=" O TYR C 260 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'D' and resid 75 through 77 removed outlier: 6.555A pdb=" N ASP D 15 " --> pdb=" O ILE D 7 " (cutoff:3.500A) removed outlier: 4.598A pdb=" N VAL D 9 " --> pdb=" O VAL D 13 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N VAL D 13 " --> pdb=" O VAL D 9 " (cutoff:3.500A) removed outlier: 6.154A pdb=" N ILE D 62 " --> pdb=" O VAL D 50 " (cutoff:3.500A) removed outlier: 5.644A 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 removed outlier: 3.532A pdb=" N ASP D 116 " --> pdb=" O VAL D 85 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'D' and resid 327 through 330 removed outlier: 3.536A pdb=" N ALA D 327 " --> pdb=" O LYS D 153 " (cutoff:3.500A) removed outlier: 8.224A pdb=" N ILE D 154 " --> pdb=" O ILE D 300 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N SER D 302 " --> pdb=" O ILE D 154 " (cutoff:3.500A) removed outlier: 7.784A pdb=" N LEU D 156 " --> pdb=" O SER D 302 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N GLN D 304 " --> pdb=" O LEU D 156 " (cutoff:3.500A) removed outlier: 8.265A pdb=" N GLY D 158 " --> pdb=" O GLN D 304 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N ILE D 306 " --> pdb=" O GLY D 158 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ALA D 305 " --> pdb=" O ILE D 251 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N ILE D 182 " --> pdb=" O LEU D 248 " (cutoff:3.500A) removed outlier: 8.143A pdb=" N PHE D 250 " --> pdb=" O ILE D 182 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N VAL D 184 " --> pdb=" O PHE D 250 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'E' and resid 75 through 77 removed outlier: 6.717A pdb=" N ASP E 15 " --> pdb=" O ILE E 7 " (cutoff:3.500A) removed outlier: 4.725A pdb=" N VAL E 9 " --> pdb=" O VAL E 13 " (cutoff:3.500A) removed outlier: 7.102A pdb=" N VAL E 13 " --> pdb=" O VAL E 9 " (cutoff:3.500A) removed outlier: 5.964A pdb=" N ILE E 62 " --> pdb=" O VAL E 50 " (cutoff:3.500A) removed outlier: 5.629A 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 94 through 96 removed outlier: 4.089A pdb=" N ARG E 94 " --> pdb=" O THR E 211 " (cutoff:3.500A) removed outlier: 7.218A pdb=" N SER E 183 " --> pdb=" O ALA E 212 " (cutoff:3.500A) removed outlier: 8.815A pdb=" N VAL E 214 " --> pdb=" O SER E 183 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N PHE E 185 " --> pdb=" O VAL E 214 " (cutoff:3.500A) removed outlier: 8.266A pdb=" N VAL E 184 " --> pdb=" O ASP E 246 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N LEU E 248 " --> pdb=" O VAL E 184 " (cutoff:3.500A) removed outlier: 7.769A pdb=" N ALA E 186 " --> pdb=" O LEU E 248 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N PHE E 250 " --> pdb=" O ALA E 186 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N SER E 299 " --> pdb=" O VAL E 247 " (cutoff:3.500A) removed outlier: 7.813A pdb=" N LEU E 249 " --> pdb=" O SER E 299 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N THR E 301 " --> pdb=" O LEU E 249 " (cutoff:3.500A) removed outlier: 8.023A pdb=" N ILE E 251 " --> pdb=" O THR E 301 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N ILE E 303 " --> pdb=" O ILE E 251 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N ALA E 327 " --> pdb=" O GLY E 155 " (cutoff:3.500A) removed outlier: 7.985A pdb=" N PHE E 157 " --> pdb=" O ALA E 327 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N THR E 329 " --> pdb=" O PHE E 157 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'F' and resid 3 through 5 Processing sheet with id= T, first strand: chain 'F' and resid 6 through 10 removed outlier: 6.597A pdb=" N ASP F 15 " --> pdb=" O ILE F 7 " (cutoff:3.500A) removed outlier: 4.677A pdb=" N VAL F 9 " --> pdb=" O VAL F 13 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N VAL F 13 " --> pdb=" O VAL F 9 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N ILE F 62 " --> pdb=" O VAL F 50 " (cutoff:3.500A) removed outlier: 5.685A 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 94 through 96 removed outlier: 3.780A pdb=" N ARG F 94 " --> pdb=" O THR F 211 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N SER F 183 " --> pdb=" O ALA F 212 " (cutoff:3.500A) removed outlier: 8.388A pdb=" N VAL F 214 " --> pdb=" O SER F 183 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N PHE F 185 " --> pdb=" O VAL F 214 " (cutoff:3.500A) removed outlier: 7.953A pdb=" N GLY F 216 " --> pdb=" O PHE F 185 " (cutoff:3.500A) removed outlier: 5.938A pdb=" N GLY F 187 " --> pdb=" O GLY F 216 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N ALA F 327 " --> pdb=" O GLY F 155 " (cutoff:3.500A) removed outlier: 7.972A pdb=" N PHE F 157 " --> pdb=" O ALA F 327 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N THR F 329 " --> pdb=" O PHE F 157 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'G' and resid 113 through 118 removed outlier: 5.625A pdb=" N THR G 76 " --> pdb=" O ALA G 114 " (cutoff:3.500A) removed outlier: 7.873A pdb=" N ILE G 116 " --> pdb=" O THR G 76 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N TYR G 78 " --> pdb=" O ILE G 116 " (cutoff:3.500A) removed outlier: 8.327A pdb=" N ILE G 118 " --> pdb=" O TYR G 78 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N VAL G 80 " --> pdb=" O ILE G 118 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N TYR G 169 " --> pdb=" O LEU G 79 " (cutoff:3.500A) removed outlier: 8.671A pdb=" N ILE G 81 " --> pdb=" O TYR G 169 " (cutoff:3.500A) removed outlier: 7.475A pdb=" N TYR G 171 " --> pdb=" O ILE G 81 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ARG G 186 " --> pdb=" O MET G 170 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N TYR G 172 " --> pdb=" O THR G 184 " (cutoff:3.500A) 919 hydrogen bonds defined for protein. 2520 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: 8.14 Time building geometry restraints manager: 10.14 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: 8229 1.34 - 1.46: 4003 1.46 - 1.58: 12242 1.58 - 1.69: 23 1.69 - 1.81: 154 Bond restraints: 24651 Sorted by residual: bond pdb=" O3 PO4 D 602 " pdb=" P PO4 D 602 " ideal model delta sigma weight residual 1.569 1.508 0.061 2.00e-02 2.50e+03 9.45e+00 bond pdb=" O4 PO4 D 602 " pdb=" P PO4 D 602 " ideal model delta sigma weight residual 1.568 1.509 0.059 2.00e-02 2.50e+03 8.81e+00 bond pdb=" O2 PO4 D 602 " pdb=" P PO4 D 602 " ideal model delta sigma weight residual 1.567 1.508 0.059 2.00e-02 2.50e+03 8.75e+00 bond pdb=" O1 PO4 D 602 " pdb=" P PO4 D 602 " ideal model delta sigma weight residual 1.565 1.508 0.057 2.00e-02 2.50e+03 8.19e+00 bond pdb=" O2B ATP F 602 " pdb=" PB ATP F 602 " ideal model delta sigma weight residual 1.529 1.474 0.055 2.20e-02 2.07e+03 6.29e+00 ... (remaining 24646 not shown) Histogram of bond angle deviations from ideal: 99.45 - 107.52: 898 107.52 - 115.59: 15306 115.59 - 123.66: 16715 123.66 - 131.74: 494 131.74 - 139.81: 14 Bond angle restraints: 33427 Sorted by residual: angle pdb=" PB ATP F 602 " pdb=" O3B ATP F 602 " pdb=" PG ATP F 602 " ideal model delta sigma weight residual 139.87 134.09 5.78 1.00e+00 1.00e+00 3.34e+01 angle pdb=" C ALA E 274 " pdb=" CA ALA E 274 " pdb=" CB ALA E 274 " ideal model delta sigma weight residual 116.54 110.51 6.03 1.15e+00 7.56e-01 2.75e+01 angle pdb=" O1G ATP F 602 " pdb=" PG ATP F 602 " pdb=" O3B ATP F 602 " ideal model delta sigma weight residual 110.47 103.17 7.30 1.64e+00 3.70e-01 1.97e+01 angle pdb=" C ASN E 97 " pdb=" N VAL E 98 " pdb=" CA VAL E 98 " ideal model delta sigma weight residual 121.97 129.93 -7.96 1.80e+00 3.09e-01 1.96e+01 angle pdb=" N VAL D 275 " pdb=" CA VAL D 275 " pdb=" C VAL D 275 " ideal model delta sigma weight residual 111.91 108.45 3.46 8.90e-01 1.26e+00 1.51e+01 ... (remaining 33422 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.08: 14134 22.08 - 44.17: 770 44.17 - 66.25: 111 66.25 - 88.33: 41 88.33 - 110.42: 3 Dihedral angle restraints: 15059 sinusoidal: 6134 harmonic: 8925 Sorted by residual: dihedral pdb=" C5' ADP D 603 " pdb=" O5' ADP D 603 " pdb=" PA ADP D 603 " pdb=" O2A ADP D 603 " ideal model delta sinusoidal sigma weight residual -60.00 -170.41 110.42 1 2.00e+01 2.50e-03 3.24e+01 dihedral pdb=" CA ARG A 93 " pdb=" C ARG A 93 " pdb=" N ILE A 94 " pdb=" CA ILE A 94 " ideal model delta harmonic sigma weight residual 180.00 160.49 19.51 0 5.00e+00 4.00e-02 1.52e+01 dihedral pdb=" CA LEU G 213 " pdb=" C LEU G 213 " pdb=" N ASP G 214 " pdb=" CA ASP G 214 " ideal model delta harmonic sigma weight residual -180.00 -160.69 -19.31 0 5.00e+00 4.00e-02 1.49e+01 ... (remaining 15056 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 2444 0.035 - 0.070: 946 0.070 - 0.105: 313 0.105 - 0.139: 143 0.139 - 0.174: 6 Chirality restraints: 3852 Sorted by residual: chirality pdb=" CB VAL F 275 " pdb=" CA VAL F 275 " pdb=" CG1 VAL F 275 " pdb=" CG2 VAL F 275 " both_signs ideal model delta sigma weight residual False -2.63 -2.45 -0.17 2.00e-01 2.50e+01 7.59e-01 chirality pdb=" CA LEU G 217 " pdb=" N LEU G 217 " pdb=" C LEU G 217 " pdb=" CB LEU G 217 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.22e-01 chirality pdb=" CB VAL D 275 " pdb=" CA VAL D 275 " pdb=" CG1 VAL D 275 " pdb=" CG2 VAL D 275 " both_signs ideal model delta sigma weight residual False -2.63 -2.47 -0.15 2.00e-01 2.50e+01 6.00e-01 ... (remaining 3849 not shown) Planarity restraints: 4362 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG G 71 " -0.072 5.00e-02 4.00e+02 1.08e-01 1.88e+01 pdb=" N PRO G 72 " 0.187 5.00e-02 4.00e+02 pdb=" CA PRO G 72 " -0.057 5.00e-02 4.00e+02 pdb=" CD PRO G 72 " -0.058 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LEU B 382 " 0.010 2.00e-02 2.50e+03 2.04e-02 4.16e+00 pdb=" C LEU B 382 " -0.035 2.00e-02 2.50e+03 pdb=" O LEU B 382 " 0.013 2.00e-02 2.50e+03 pdb=" N ARG B 383 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE D 322 " 0.012 2.00e-02 2.50e+03 1.50e-02 3.91e+00 pdb=" CG PHE D 322 " -0.034 2.00e-02 2.50e+03 pdb=" CD1 PHE D 322 " 0.011 2.00e-02 2.50e+03 pdb=" CD2 PHE D 322 " 0.011 2.00e-02 2.50e+03 pdb=" CE1 PHE D 322 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE D 322 " 0.000 2.00e-02 2.50e+03 pdb=" CZ PHE D 322 " 0.000 2.00e-02 2.50e+03 ... (remaining 4359 not shown) Histogram of nonbonded interaction distances: 1.97 - 2.56: 158 2.56 - 3.14: 19687 3.14 - 3.73: 36993 3.73 - 4.31: 51873 4.31 - 4.90: 88238 Nonbonded interactions: 196949 Sorted by model distance: nonbonded pdb="MG MG D 601 " pdb=" O4 PO4 D 602 " model vdw 1.970 2.170 nonbonded pdb="MG MG C 601 " pdb=" O1G ATP C 602 " model vdw 2.021 2.170 nonbonded pdb="MG MG C 601 " pdb=" O2B ATP C 602 " model vdw 2.034 2.170 nonbonded pdb=" O1G ATP A 600 " pdb="MG MG A 601 " model vdw 2.062 2.170 nonbonded pdb=" OG1 THR F 165 " pdb="MG MG F 601 " model vdw 2.067 2.170 ... (remaining 196944 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and resid 24 through 501) selection = (chain 'B' and resid 24 through 501) selection = (chain 'C' and resid 24 through 501) } ncs_group { reference = (chain 'D' and resid 1 through 470) 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: 4.580 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: 0.000 Extract box with map and model: 10.660 Check model and map are aligned: 0.350 Set scattering table: 0.230 Process input model: 62.680 Find NCS groups from input model: 1.810 Set up NCS constraints: 0.140 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:2.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 83.280 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8475 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 0.061 24651 Z= 0.206 Angle : 0.603 9.282 33427 Z= 0.349 Chirality : 0.044 0.174 3852 Planarity : 0.004 0.108 4362 Dihedral : 14.058 110.416 9347 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.05 % Favored : 96.92 % Rotamer: Outliers : 0.00 % Allowed : 0.23 % Favored : 99.77 % 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: 0.84 (0.15), residues: 3115 helix: 1.28 (0.15), residues: 1252 sheet: 0.98 (0.23), residues: 511 loop : -0.23 (0.17), residues: 1352 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.001 HIS B 470 PHE 0.034 0.001 PHE D 322 TYR 0.017 0.001 TYR G 175 ARG 0.007 0.000 ARG D 333 *********************** 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 168 residues out of total 2568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 168 time to evaluate : 2.804 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 389 TYR cc_start: 0.8151 (t80) cc_final: 0.7842 (t80) REVERT: G 113 TYR cc_start: 0.6064 (p90) cc_final: 0.5592 (p90) REVERT: G 189 LEU cc_start: 0.6972 (mm) cc_final: 0.6671 (mm) outliers start: 0 outliers final: 0 residues processed: 168 average time/residue: 0.3327 time to fit residues: 91.8431 Evaluate side-chains 128 residues out of total 2568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 128 time to evaluate : 2.341 ------------------------------------------------------------------------------- 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: 6.9990 chunk 234 optimal weight: 10.0000 chunk 130 optimal weight: 9.9990 chunk 80 optimal weight: 9.9990 chunk 158 optimal weight: 9.9990 chunk 125 optimal weight: 0.8980 chunk 242 optimal weight: 10.0000 chunk 94 optimal weight: 10.0000 chunk 147 optimal weight: 10.0000 chunk 180 optimal weight: 4.9990 chunk 281 optimal weight: 10.0000 overall best weight: 6.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 172 GLN B 345 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8575 moved from start: 0.1176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.095 24651 Z= 0.525 Angle : 0.712 11.068 33427 Z= 0.371 Chirality : 0.051 0.266 3852 Planarity : 0.006 0.071 4362 Dihedral : 8.259 110.040 3546 Min Nonbonded Distance : 1.765 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.59 % Favored : 95.38 % Rotamer: Outliers : 0.62 % Allowed : 6.15 % Favored : 93.22 % 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: 0.10 (0.15), residues: 3115 helix: 0.69 (0.15), residues: 1247 sheet: 0.52 (0.22), residues: 521 loop : -0.62 (0.16), residues: 1347 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.010 0.002 HIS B 425 PHE 0.032 0.002 PHE G 160 TYR 0.020 0.002 TYR G 262 ARG 0.006 0.001 ARG D 333 *********************** 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 146 residues out of total 2568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 130 time to evaluate : 2.898 Fit side-chains revert: symmetry clash REVERT: B 395 PHE cc_start: 0.6553 (t80) cc_final: 0.6276 (t80) REVERT: C 262 ASP cc_start: 0.7237 (OUTLIER) cc_final: 0.6987 (m-30) REVERT: G 113 TYR cc_start: 0.6049 (p90) cc_final: 0.5563 (p90) REVERT: G 131 MET cc_start: 0.6584 (mmm) cc_final: 0.6378 (mmm) outliers start: 16 outliers final: 12 residues processed: 141 average time/residue: 0.3387 time to fit residues: 79.0239 Evaluate side-chains 136 residues out of total 2568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 123 time to evaluate : 3.000 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 382 LEU Chi-restraints excluded: chain B residue 191 MET Chi-restraints excluded: chain C residue 190 ASN Chi-restraints excluded: chain C residue 193 SER Chi-restraints excluded: chain C residue 262 ASP Chi-restraints excluded: chain C residue 306 ASP Chi-restraints excluded: chain C residue 452 ASP Chi-restraints excluded: chain D residue 462 VAL Chi-restraints excluded: chain E residue 183 SER Chi-restraints excluded: chain E residue 350 THR Chi-restraints excluded: chain F residue 301 THR Chi-restraints excluded: chain G residue 65 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 156 optimal weight: 2.9990 chunk 87 optimal weight: 7.9990 chunk 234 optimal weight: 8.9990 chunk 191 optimal weight: 9.9990 chunk 77 optimal weight: 0.9990 chunk 282 optimal weight: 9.9990 chunk 304 optimal weight: 1.9990 chunk 251 optimal weight: 1.9990 chunk 279 optimal weight: 6.9990 chunk 96 optimal weight: 0.9990 chunk 226 optimal weight: 0.0070 overall best weight: 1.2006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 200 GLN B 172 GLN ** D 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8505 moved from start: 0.0975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 24651 Z= 0.153 Angle : 0.509 8.224 33427 Z= 0.265 Chirality : 0.043 0.177 3852 Planarity : 0.004 0.048 4362 Dihedral : 7.772 100.378 3546 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.99 % Favored : 96.98 % Rotamer: Outliers : 0.82 % Allowed : 7.48 % Favored : 91.71 % 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: 0.54 (0.15), residues: 3115 helix: 1.09 (0.15), residues: 1255 sheet: 0.74 (0.22), residues: 517 loop : -0.43 (0.17), residues: 1343 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS B 470 PHE 0.022 0.001 PHE G 160 TYR 0.013 0.001 TYR G 262 ARG 0.005 0.000 ARG G 186 *********************** 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 159 residues out of total 2568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 138 time to evaluate : 2.788 Fit side-chains revert: symmetry clash REVERT: B 395 PHE cc_start: 0.6537 (t80) cc_final: 0.6087 (t80) REVERT: F 469 MET cc_start: 0.6753 (mtp) cc_final: 0.6443 (mtp) REVERT: G 113 TYR cc_start: 0.6081 (p90) cc_final: 0.5607 (p90) REVERT: G 131 MET cc_start: 0.6567 (mmm) cc_final: 0.6362 (mmm) outliers start: 21 outliers final: 16 residues processed: 148 average time/residue: 0.3353 time to fit residues: 83.0471 Evaluate side-chains 145 residues out of total 2568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 129 time to evaluate : 2.778 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain A residue 382 LEU Chi-restraints excluded: chain A residue 386 LEU Chi-restraints excluded: chain B residue 48 MET Chi-restraints excluded: chain B residue 191 MET Chi-restraints excluded: chain C residue 190 ASN Chi-restraints excluded: chain C residue 193 SER Chi-restraints excluded: chain C residue 306 ASP Chi-restraints excluded: chain D residue 61 THR Chi-restraints excluded: chain D residue 462 VAL Chi-restraints excluded: chain E residue 183 SER Chi-restraints excluded: chain G residue 65 HIS Chi-restraints excluded: chain G residue 174 HIS Chi-restraints excluded: chain G residue 241 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 278 optimal weight: 0.7980 chunk 212 optimal weight: 0.9990 chunk 146 optimal weight: 5.9990 chunk 31 optimal weight: 2.9990 chunk 134 optimal weight: 9.9990 chunk 189 optimal weight: 9.9990 chunk 283 optimal weight: 8.9990 chunk 299 optimal weight: 0.0370 chunk 147 optimal weight: 4.9990 chunk 268 optimal weight: 9.9990 chunk 80 optimal weight: 9.9990 overall best weight: 1.9664 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8506 moved from start: 0.1100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 24651 Z= 0.190 Angle : 0.500 8.620 33427 Z= 0.259 Chirality : 0.044 0.273 3852 Planarity : 0.004 0.037 4362 Dihedral : 7.435 91.892 3546 Min Nonbonded Distance : 1.892 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.21 % Favored : 96.76 % Rotamer: Outliers : 1.17 % Allowed : 8.84 % Favored : 89.99 % 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: 0.63 (0.15), residues: 3115 helix: 1.17 (0.15), residues: 1254 sheet: 0.81 (0.23), residues: 512 loop : -0.38 (0.17), residues: 1349 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS B 470 PHE 0.019 0.001 PHE G 160 TYR 0.013 0.001 TYR G 262 ARG 0.003 0.000 ARG D 333 *********************** 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 167 residues out of total 2568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 137 time to evaluate : 2.792 Fit side-chains revert: symmetry clash REVERT: A 62 MET cc_start: 0.7733 (tpt) cc_final: 0.7450 (tpp) REVERT: A 74 VAL cc_start: 0.9477 (OUTLIER) cc_final: 0.9236 (m) REVERT: B 395 PHE cc_start: 0.6548 (t80) cc_final: 0.6054 (t80) REVERT: F 5 ARG cc_start: 0.8109 (ttm-80) cc_final: 0.7821 (mtp-110) REVERT: G 113 TYR cc_start: 0.6051 (p90) cc_final: 0.5574 (p90) outliers start: 30 outliers final: 22 residues processed: 157 average time/residue: 0.3477 time to fit residues: 89.7085 Evaluate side-chains 149 residues out of total 2568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 126 time to evaluate : 3.070 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 295 SER Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain A residue 382 LEU Chi-restraints excluded: chain A residue 386 LEU Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 191 MET Chi-restraints excluded: chain B residue 448 ILE Chi-restraints excluded: chain C residue 190 ASN Chi-restraints excluded: chain C residue 193 SER Chi-restraints excluded: chain C residue 306 ASP Chi-restraints excluded: chain D residue 61 THR Chi-restraints excluded: chain D residue 87 VAL Chi-restraints excluded: chain D residue 301 THR Chi-restraints excluded: chain D residue 462 VAL Chi-restraints excluded: chain E residue 2 THR Chi-restraints excluded: chain E residue 183 SER Chi-restraints excluded: chain E residue 301 THR Chi-restraints excluded: chain G residue 65 HIS Chi-restraints excluded: chain G residue 174 HIS Chi-restraints excluded: chain G residue 241 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 249 optimal weight: 5.9990 chunk 170 optimal weight: 9.9990 chunk 4 optimal weight: 9.9990 chunk 223 optimal weight: 9.9990 chunk 123 optimal weight: 4.9990 chunk 255 optimal weight: 3.9990 chunk 207 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 153 optimal weight: 0.0170 chunk 268 optimal weight: 9.9990 chunk 75 optimal weight: 9.9990 overall best weight: 5.0026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 474 HIS ** D 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8562 moved from start: 0.1396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.078 24651 Z= 0.402 Angle : 0.607 10.534 33427 Z= 0.315 Chirality : 0.047 0.165 3852 Planarity : 0.005 0.039 4362 Dihedral : 7.623 104.731 3546 Min Nonbonded Distance : 1.830 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.49 % Favored : 95.47 % Rotamer: Outliers : 1.64 % Allowed : 10.32 % Favored : 88.05 % 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: 0.26 (0.15), residues: 3115 helix: 0.88 (0.15), residues: 1244 sheet: 0.53 (0.23), residues: 516 loop : -0.56 (0.16), residues: 1355 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.001 HIS B 425 PHE 0.020 0.002 PHE G 160 TYR 0.016 0.002 TYR G 262 ARG 0.004 0.000 ARG G 264 *********************** 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 171 residues out of total 2568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 129 time to evaluate : 3.059 Fit side-chains revert: symmetry clash REVERT: A 74 VAL cc_start: 0.9485 (OUTLIER) cc_final: 0.9269 (m) REVERT: B 191 MET cc_start: 0.8225 (OUTLIER) cc_final: 0.7564 (mtp) REVERT: B 395 PHE cc_start: 0.6510 (t80) cc_final: 0.6049 (t80) REVERT: F 469 MET cc_start: 0.6863 (mtp) cc_final: 0.6619 (mtp) REVERT: G 113 TYR cc_start: 0.6134 (p90) cc_final: 0.5760 (p90) REVERT: G 131 MET cc_start: 0.6609 (mmm) cc_final: 0.6076 (mmm) REVERT: G 189 LEU cc_start: 0.7156 (OUTLIER) cc_final: 0.6831 (mm) outliers start: 42 outliers final: 30 residues processed: 160 average time/residue: 0.3132 time to fit residues: 85.1702 Evaluate side-chains 159 residues out of total 2568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 126 time to evaluate : 2.757 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain A residue 382 LEU Chi-restraints excluded: chain A residue 386 LEU Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain B residue 48 MET Chi-restraints excluded: chain B residue 191 MET Chi-restraints excluded: chain B residue 225 THR Chi-restraints excluded: chain B residue 332 THR Chi-restraints excluded: chain B residue 448 ILE Chi-restraints excluded: chain C residue 190 ASN Chi-restraints excluded: chain C residue 193 SER Chi-restraints excluded: chain C residue 306 ASP Chi-restraints excluded: chain C residue 314 THR Chi-restraints excluded: chain D residue 61 THR Chi-restraints excluded: chain D residue 87 VAL Chi-restraints excluded: chain D residue 228 VAL Chi-restraints excluded: chain D residue 301 THR Chi-restraints excluded: chain D residue 462 VAL Chi-restraints excluded: chain E residue 2 THR Chi-restraints excluded: chain E residue 126 GLU Chi-restraints excluded: chain E residue 183 SER Chi-restraints excluded: chain E residue 301 THR Chi-restraints excluded: chain F residue 112 ASP Chi-restraints excluded: chain F residue 293 THR Chi-restraints excluded: chain F residue 301 THR Chi-restraints excluded: chain G residue 65 HIS Chi-restraints excluded: chain G residue 98 LEU Chi-restraints excluded: chain G residue 174 HIS Chi-restraints excluded: chain G residue 189 LEU Chi-restraints excluded: chain G residue 241 MET 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: 0.6980 chunk 59 optimal weight: 3.9990 chunk 175 optimal weight: 20.0000 chunk 73 optimal weight: 0.8980 chunk 299 optimal weight: 10.0000 chunk 248 optimal weight: 7.9990 chunk 138 optimal weight: 8.9990 chunk 24 optimal weight: 3.9990 chunk 99 optimal weight: 0.9980 chunk 157 optimal weight: 3.9990 overall best weight: 2.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 94 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8520 moved from start: 0.1351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 24651 Z= 0.200 Angle : 0.500 8.534 33427 Z= 0.259 Chirality : 0.044 0.160 3852 Planarity : 0.004 0.067 4362 Dihedral : 7.311 96.952 3546 Min Nonbonded Distance : 1.891 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.11 % Favored : 96.85 % Rotamer: Outliers : 1.40 % Allowed : 11.37 % Favored : 87.23 % 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: 0.49 (0.15), residues: 3115 helix: 1.11 (0.15), residues: 1251 sheet: 0.62 (0.23), residues: 520 loop : -0.47 (0.17), residues: 1344 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS B 470 PHE 0.017 0.001 PHE G 160 TYR 0.013 0.001 TYR G 262 ARG 0.003 0.000 ARG C 383 *********************** 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 169 residues out of total 2568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 133 time to evaluate : 2.955 Fit side-chains revert: symmetry clash REVERT: B 191 MET cc_start: 0.8025 (OUTLIER) cc_final: 0.7361 (mtp) REVERT: B 245 MET cc_start: 0.8339 (ttm) cc_final: 0.7964 (mtt) REVERT: B 395 PHE cc_start: 0.6446 (t80) cc_final: 0.6009 (t80) REVERT: B 438 TYR cc_start: 0.8613 (t80) cc_final: 0.8333 (t80) REVERT: F 5 ARG cc_start: 0.8121 (ttm-80) cc_final: 0.7890 (mtp-110) REVERT: F 469 MET cc_start: 0.6831 (mtp) cc_final: 0.6597 (mtp) REVERT: G 113 TYR cc_start: 0.6128 (p90) cc_final: 0.5815 (p90) REVERT: G 131 MET cc_start: 0.6610 (mmm) cc_final: 0.6098 (mmm) outliers start: 36 outliers final: 28 residues processed: 159 average time/residue: 0.3201 time to fit residues: 85.8306 Evaluate side-chains 157 residues out of total 2568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 128 time to evaluate : 2.878 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 ILE Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain A residue 382 LEU Chi-restraints excluded: chain A residue 386 LEU Chi-restraints excluded: chain B residue 48 MET Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 191 MET Chi-restraints excluded: chain B residue 225 THR Chi-restraints excluded: chain B residue 332 THR Chi-restraints excluded: chain B residue 448 ILE Chi-restraints excluded: chain C residue 190 ASN Chi-restraints excluded: chain C residue 193 SER Chi-restraints excluded: chain D residue 61 THR Chi-restraints excluded: chain D residue 228 VAL Chi-restraints excluded: chain D residue 301 THR Chi-restraints excluded: chain D residue 462 VAL Chi-restraints excluded: chain E residue 2 THR Chi-restraints excluded: chain E residue 126 GLU Chi-restraints excluded: chain E residue 183 SER Chi-restraints excluded: chain E residue 301 THR Chi-restraints excluded: chain F residue 112 ASP Chi-restraints excluded: chain F residue 168 ILE Chi-restraints excluded: chain F residue 301 THR Chi-restraints excluded: chain G residue 65 HIS Chi-restraints excluded: chain G residue 98 LEU Chi-restraints excluded: chain G residue 174 HIS Chi-restraints excluded: chain G residue 241 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 289 optimal weight: 20.0000 chunk 33 optimal weight: 10.0000 chunk 170 optimal weight: 9.9990 chunk 219 optimal weight: 1.9990 chunk 169 optimal weight: 0.9980 chunk 252 optimal weight: 6.9990 chunk 167 optimal weight: 8.9990 chunk 298 optimal weight: 5.9990 chunk 186 optimal weight: 8.9990 chunk 182 optimal weight: 0.9980 chunk 137 optimal weight: 2.9990 overall best weight: 2.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8525 moved from start: 0.1393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 24651 Z= 0.231 Angle : 0.509 8.951 33427 Z= 0.263 Chirality : 0.044 0.160 3852 Planarity : 0.004 0.065 4362 Dihedral : 7.183 95.406 3546 Min Nonbonded Distance : 1.871 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.76 % Favored : 96.21 % Rotamer: Outliers : 1.52 % Allowed : 11.64 % Favored : 86.84 % 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: 0.52 (0.15), residues: 3115 helix: 1.14 (0.15), residues: 1250 sheet: 0.68 (0.23), residues: 516 loop : -0.48 (0.16), residues: 1349 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS B 470 PHE 0.017 0.001 PHE G 160 TYR 0.013 0.001 TYR F 427 ARG 0.002 0.000 ARG E 405 *********************** 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 169 residues out of total 2568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 130 time to evaluate : 2.981 Fit side-chains revert: symmetry clash REVERT: B 245 MET cc_start: 0.8341 (ttm) cc_final: 0.7969 (mtt) REVERT: B 395 PHE cc_start: 0.6462 (t80) cc_final: 0.6029 (t80) REVERT: B 438 TYR cc_start: 0.8609 (t80) cc_final: 0.8330 (t80) REVERT: F 5 ARG cc_start: 0.8126 (ttm-80) cc_final: 0.7900 (mtp-110) REVERT: F 469 MET cc_start: 0.6793 (mtp) cc_final: 0.6572 (mtp) REVERT: G 113 TYR cc_start: 0.6132 (p90) cc_final: 0.5832 (p90) REVERT: G 131 MET cc_start: 0.6617 (mmm) cc_final: 0.6102 (mmm) REVERT: G 189 LEU cc_start: 0.6994 (OUTLIER) cc_final: 0.6671 (mm) outliers start: 39 outliers final: 33 residues processed: 160 average time/residue: 0.3194 time to fit residues: 86.2356 Evaluate side-chains 160 residues out of total 2568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 126 time to evaluate : 2.819 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 ILE Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain A residue 382 LEU Chi-restraints excluded: chain A residue 386 LEU Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 191 MET Chi-restraints excluded: chain B residue 225 THR Chi-restraints excluded: chain B residue 332 THR Chi-restraints excluded: chain B residue 448 ILE Chi-restraints excluded: chain C residue 190 ASN Chi-restraints excluded: chain C residue 193 SER Chi-restraints excluded: chain C residue 306 ASP Chi-restraints excluded: chain C residue 314 THR Chi-restraints excluded: chain D residue 61 THR Chi-restraints excluded: chain D residue 118 ILE Chi-restraints excluded: chain D residue 228 VAL Chi-restraints excluded: chain D residue 301 THR Chi-restraints excluded: chain D residue 462 VAL Chi-restraints excluded: chain E residue 2 THR Chi-restraints excluded: chain E residue 126 GLU Chi-restraints excluded: chain E residue 171 LEU Chi-restraints excluded: chain E residue 183 SER Chi-restraints excluded: chain E residue 301 THR Chi-restraints excluded: chain F residue 112 ASP Chi-restraints excluded: chain F residue 168 ILE Chi-restraints excluded: chain F residue 293 THR Chi-restraints excluded: chain F residue 301 THR Chi-restraints excluded: chain F residue 399 VAL Chi-restraints excluded: chain G residue 65 HIS Chi-restraints excluded: chain G residue 174 HIS Chi-restraints excluded: chain G residue 189 LEU Chi-restraints excluded: chain G residue 241 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 184 optimal weight: 5.9990 chunk 119 optimal weight: 10.0000 chunk 178 optimal weight: 5.9990 chunk 90 optimal weight: 0.8980 chunk 58 optimal weight: 0.0970 chunk 57 optimal weight: 0.9980 chunk 189 optimal weight: 5.9990 chunk 203 optimal weight: 10.0000 chunk 147 optimal weight: 10.0000 chunk 27 optimal weight: 7.9990 chunk 234 optimal weight: 9.9990 overall best weight: 2.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8528 moved from start: 0.1446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 24651 Z= 0.243 Angle : 0.513 8.948 33427 Z= 0.265 Chirality : 0.044 0.161 3852 Planarity : 0.004 0.068 4362 Dihedral : 7.102 95.637 3546 Min Nonbonded Distance : 1.870 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.63 % Favored : 96.34 % Rotamer: Outliers : 1.56 % Allowed : 12.07 % Favored : 86.37 % 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: 0.51 (0.15), residues: 3115 helix: 1.13 (0.15), residues: 1252 sheet: 0.67 (0.23), residues: 516 loop : -0.49 (0.16), residues: 1347 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS B 470 PHE 0.016 0.001 PHE G 160 TYR 0.013 0.001 TYR F 427 ARG 0.002 0.000 ARG E 405 *********************** 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 167 residues out of total 2568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 127 time to evaluate : 2.626 Fit side-chains revert: symmetry clash REVERT: B 191 MET cc_start: 0.8045 (OUTLIER) cc_final: 0.7398 (mtp) REVERT: B 245 MET cc_start: 0.8372 (ttm) cc_final: 0.7998 (mtt) REVERT: B 395 PHE cc_start: 0.6348 (t80) cc_final: 0.5902 (t80) REVERT: F 5 ARG cc_start: 0.8129 (ttm-80) cc_final: 0.7906 (mtp-110) REVERT: F 469 MET cc_start: 0.6737 (mtp) cc_final: 0.6505 (mtp) REVERT: G 113 TYR cc_start: 0.6161 (p90) cc_final: 0.5862 (p90) REVERT: G 131 MET cc_start: 0.6602 (mmm) cc_final: 0.6082 (mmm) REVERT: G 189 LEU cc_start: 0.6871 (OUTLIER) cc_final: 0.6554 (mm) outliers start: 40 outliers final: 34 residues processed: 158 average time/residue: 0.2991 time to fit residues: 80.4387 Evaluate side-chains 162 residues out of total 2568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 126 time to evaluate : 2.931 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 ILE Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain A residue 382 LEU Chi-restraints excluded: chain A residue 386 LEU Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 191 MET Chi-restraints excluded: chain B residue 225 THR Chi-restraints excluded: chain B residue 332 THR Chi-restraints excluded: chain B residue 448 ILE Chi-restraints excluded: chain C residue 190 ASN Chi-restraints excluded: chain C residue 193 SER Chi-restraints excluded: chain C residue 306 ASP Chi-restraints excluded: chain C residue 314 THR Chi-restraints excluded: chain D residue 61 THR Chi-restraints excluded: chain D residue 118 ILE Chi-restraints excluded: chain D residue 228 VAL Chi-restraints excluded: chain D residue 301 THR Chi-restraints excluded: chain D residue 456 VAL Chi-restraints excluded: chain D residue 462 VAL Chi-restraints excluded: chain E residue 2 THR Chi-restraints excluded: chain E residue 126 GLU Chi-restraints excluded: chain E residue 171 LEU Chi-restraints excluded: chain E residue 183 SER Chi-restraints excluded: chain E residue 301 THR Chi-restraints excluded: chain F residue 112 ASP Chi-restraints excluded: chain F residue 168 ILE Chi-restraints excluded: chain F residue 211 THR Chi-restraints excluded: chain F residue 293 THR Chi-restraints excluded: chain F residue 301 THR Chi-restraints excluded: chain F residue 399 VAL Chi-restraints excluded: chain G residue 65 HIS Chi-restraints excluded: chain G residue 174 HIS Chi-restraints excluded: chain G residue 189 LEU Chi-restraints excluded: chain G residue 241 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 271 optimal weight: 7.9990 chunk 286 optimal weight: 0.0020 chunk 261 optimal weight: 2.9990 chunk 278 optimal weight: 3.9990 chunk 167 optimal weight: 7.9990 chunk 121 optimal weight: 10.0000 chunk 218 optimal weight: 6.9990 chunk 85 optimal weight: 10.0000 chunk 251 optimal weight: 4.9990 chunk 263 optimal weight: 3.9990 chunk 277 optimal weight: 0.0670 overall best weight: 2.2132 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8516 moved from start: 0.1467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 24651 Z= 0.201 Angle : 0.495 8.424 33427 Z= 0.255 Chirality : 0.043 0.159 3852 Planarity : 0.004 0.072 4362 Dihedral : 6.968 92.200 3546 Min Nonbonded Distance : 1.884 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.53 % Favored : 96.44 % Rotamer: Outliers : 1.52 % Allowed : 12.38 % Favored : 86.10 % 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: 0.61 (0.15), residues: 3115 helix: 1.20 (0.15), residues: 1253 sheet: 0.76 (0.23), residues: 504 loop : -0.43 (0.16), residues: 1358 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS B 470 PHE 0.016 0.001 PHE G 160 TYR 0.013 0.001 TYR F 427 ARG 0.002 0.000 ARG C 383 *********************** 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 170 residues out of total 2568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 131 time to evaluate : 2.983 Fit side-chains revert: symmetry clash REVERT: B 191 MET cc_start: 0.7989 (OUTLIER) cc_final: 0.7347 (mtp) REVERT: B 245 MET cc_start: 0.8343 (ttm) cc_final: 0.7972 (mtt) REVERT: B 395 PHE cc_start: 0.6303 (t80) cc_final: 0.5855 (t80) REVERT: F 5 ARG cc_start: 0.8095 (ttm-80) cc_final: 0.7877 (mtp-110) REVERT: F 469 MET cc_start: 0.6791 (mtp) cc_final: 0.6563 (mtp) REVERT: G 113 TYR cc_start: 0.6161 (p90) cc_final: 0.5866 (p90) REVERT: G 131 MET cc_start: 0.6629 (mmm) cc_final: 0.6093 (mmm) REVERT: G 189 LEU cc_start: 0.6835 (OUTLIER) cc_final: 0.6532 (mm) outliers start: 39 outliers final: 32 residues processed: 163 average time/residue: 0.3207 time to fit residues: 88.5856 Evaluate side-chains 161 residues out of total 2568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 127 time to evaluate : 2.809 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 ILE Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain A residue 382 LEU Chi-restraints excluded: chain A residue 386 LEU Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 191 MET Chi-restraints excluded: chain B residue 225 THR Chi-restraints excluded: chain B residue 332 THR Chi-restraints excluded: chain B residue 448 ILE Chi-restraints excluded: chain C residue 190 ASN Chi-restraints excluded: chain C residue 193 SER Chi-restraints excluded: chain C residue 306 ASP Chi-restraints excluded: chain D residue 61 THR Chi-restraints excluded: chain D residue 118 ILE Chi-restraints excluded: chain D residue 228 VAL Chi-restraints excluded: chain D residue 301 THR Chi-restraints excluded: chain D residue 456 VAL Chi-restraints excluded: chain D residue 462 VAL Chi-restraints excluded: chain E residue 2 THR Chi-restraints excluded: chain E residue 126 GLU Chi-restraints excluded: chain E residue 171 LEU Chi-restraints excluded: chain E residue 183 SER Chi-restraints excluded: chain E residue 301 THR Chi-restraints excluded: chain F residue 112 ASP Chi-restraints excluded: chain F residue 168 ILE Chi-restraints excluded: chain F residue 211 THR Chi-restraints excluded: chain F residue 293 THR Chi-restraints excluded: chain F residue 301 THR Chi-restraints excluded: chain G residue 174 HIS Chi-restraints excluded: chain G residue 189 LEU Chi-restraints excluded: chain G residue 241 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 182 optimal weight: 3.9990 chunk 294 optimal weight: 10.0000 chunk 179 optimal weight: 1.9990 chunk 139 optimal weight: 0.7980 chunk 204 optimal weight: 8.9990 chunk 308 optimal weight: 9.9990 chunk 284 optimal weight: 10.0000 chunk 245 optimal weight: 3.9990 chunk 25 optimal weight: 5.9990 chunk 189 optimal weight: 5.9990 chunk 150 optimal weight: 0.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 266 GLN ** D 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8518 moved from start: 0.1503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 24651 Z= 0.213 Angle : 0.502 8.503 33427 Z= 0.259 Chirality : 0.043 0.159 3852 Planarity : 0.004 0.075 4362 Dihedral : 6.935 91.537 3546 Min Nonbonded Distance : 1.877 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.60 % Favored : 96.37 % Rotamer: Outliers : 1.48 % Allowed : 12.66 % Favored : 85.86 % 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: 0.60 (0.15), residues: 3115 helix: 1.20 (0.15), residues: 1253 sheet: 0.75 (0.23), residues: 506 loop : -0.44 (0.16), residues: 1356 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS B 470 PHE 0.016 0.001 PHE G 160 TYR 0.013 0.001 TYR F 427 ARG 0.002 0.000 ARG E 405 ********************** 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 165 residues out of total 2568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 127 time to evaluate : 2.405 Fit side-chains revert: symmetry clash REVERT: B 191 MET cc_start: 0.7983 (OUTLIER) cc_final: 0.7341 (mtp) REVERT: B 245 MET cc_start: 0.8354 (ttm) cc_final: 0.7984 (mtt) REVERT: B 395 PHE cc_start: 0.6296 (t80) cc_final: 0.5916 (t80) REVERT: F 5 ARG cc_start: 0.8097 (ttm-80) cc_final: 0.7880 (mtp-110) REVERT: F 469 MET cc_start: 0.6794 (mtp) cc_final: 0.6567 (mtp) REVERT: G 113 TYR cc_start: 0.6157 (p90) cc_final: 0.5862 (p90) REVERT: G 131 MET cc_start: 0.6563 (mmm) cc_final: 0.6046 (mmm) REVERT: G 189 LEU cc_start: 0.6832 (OUTLIER) cc_final: 0.6531 (mm) outliers start: 38 outliers final: 33 residues processed: 158 average time/residue: 0.3114 time to fit residues: 83.0747 Evaluate side-chains 162 residues out of total 2568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 127 time to evaluate : 2.839 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 ILE Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 382 LEU Chi-restraints excluded: chain A residue 386 LEU Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 191 MET Chi-restraints excluded: chain B residue 225 THR Chi-restraints excluded: chain B residue 332 THR Chi-restraints excluded: chain B residue 448 ILE Chi-restraints excluded: chain C residue 190 ASN Chi-restraints excluded: chain C residue 193 SER Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain C residue 306 ASP Chi-restraints excluded: chain D residue 61 THR Chi-restraints excluded: chain D residue 118 ILE Chi-restraints excluded: chain D residue 228 VAL Chi-restraints excluded: chain D residue 301 THR Chi-restraints excluded: chain D residue 456 VAL Chi-restraints excluded: chain D residue 462 VAL Chi-restraints excluded: chain E residue 2 THR Chi-restraints excluded: chain E residue 126 GLU Chi-restraints excluded: chain E residue 171 LEU Chi-restraints excluded: chain E residue 183 SER Chi-restraints excluded: chain E residue 301 THR Chi-restraints excluded: chain F residue 112 ASP Chi-restraints excluded: chain F residue 168 ILE Chi-restraints excluded: chain F residue 211 THR Chi-restraints excluded: chain F residue 293 THR Chi-restraints excluded: chain F residue 301 THR Chi-restraints excluded: chain F residue 399 VAL Chi-restraints excluded: chain G residue 174 HIS Chi-restraints excluded: chain G residue 189 LEU Chi-restraints excluded: chain G residue 241 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 195 optimal weight: 0.0980 chunk 261 optimal weight: 0.9980 chunk 75 optimal weight: 10.0000 chunk 226 optimal weight: 10.0000 chunk 36 optimal weight: 5.9990 chunk 68 optimal weight: 3.9990 chunk 246 optimal weight: 8.9990 chunk 103 optimal weight: 7.9990 chunk 252 optimal weight: 0.8980 chunk 31 optimal weight: 10.0000 chunk 45 optimal weight: 6.9990 overall best weight: 2.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.080980 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2968 r_free = 0.2968 target = 0.065447 restraints weight = 62321.150| |-----------------------------------------------------------------------------| r_work (start): 0.2963 rms_B_bonded: 2.43 r_work: 0.2858 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work (final): 0.2858 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8677 moved from start: 0.1524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 24651 Z= 0.216 Angle : 0.502 8.577 33427 Z= 0.259 Chirality : 0.044 0.159 3852 Planarity : 0.004 0.075 4362 Dihedral : 6.894 91.243 3546 Min Nonbonded Distance : 1.875 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.79 % Favored : 96.18 % Rotamer: Outliers : 1.40 % Allowed : 12.69 % Favored : 85.90 % 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: 0.61 (0.15), residues: 3115 helix: 1.20 (0.15), residues: 1251 sheet: 0.76 (0.23), residues: 507 loop : -0.43 (0.16), residues: 1357 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS B 470 PHE 0.015 0.001 PHE G 160 TYR 0.013 0.001 TYR F 427 ARG 0.002 0.000 ARG E 405 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4016.59 seconds wall clock time: 74 minutes 47.06 seconds (4487.06 seconds total)