Starting phenix.real_space_refine on Tue Feb 20 10:00:08 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vok_21267/02_2024/6vok_21267_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vok_21267/02_2024/6vok_21267.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.85 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vok_21267/02_2024/6vok_21267.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vok_21267/02_2024/6vok_21267.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vok_21267/02_2024/6vok_21267_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vok_21267/02_2024/6vok_21267_updated.pdb" } resolution = 3.85 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: 5 Type Number sf(0) Gaussians P 16 5.49 5 S 103 5.16 5 C 17274 2.51 5 N 4747 2.21 5 O 5372 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 15": "OE1" <-> "OE2" Residue "A GLU 23": "OE1" <-> "OE2" Residue "A GLU 68": "OE1" <-> "OE2" Residue "A ARG 416": "NH1" <-> "NH2" Residue "A GLU 499": "OE1" <-> "OE2" Residue "B ARG 5": "NH1" <-> "NH2" Residue "B ARG 14": "NH1" <-> "NH2" Residue "B GLU 15": "OE1" <-> "OE2" Residue "B GLU 52": "OE1" <-> "OE2" Residue "B GLU 131": "OE1" <-> "OE2" Residue "B GLU 145": "OE1" <-> "OE2" Residue "B GLU 285": "OE1" <-> "OE2" Residue "B GLU 432": "OE1" <-> "OE2" Residue "B GLU 484": "OE1" <-> "OE2" Residue "B GLU 492": "OE1" <-> "OE2" Residue "C GLU 8": "OE1" <-> "OE2" Residue "C GLU 15": "OE1" <-> "OE2" Residue "C ARG 22": "NH1" <-> "NH2" Residue "C GLU 52": "OE1" <-> "OE2" Residue "C GLU 68": "OE1" <-> "OE2" Residue "C ARG 107": "NH1" <-> "NH2" Residue "C ARG 216": "NH1" <-> "NH2" Residue "C ARG 297": "NH1" <-> "NH2" Residue "C GLU 450": "OE1" <-> "OE2" Residue "C ARG 455": "NH1" <-> "NH2" Residue "C GLU 471": "OE1" <-> "OE2" Residue "C GLU 492": "OE1" <-> "OE2" Residue "D ARG 52": "NH1" <-> "NH2" Residue "D GLU 224": "OE1" <-> "OE2" Residue "D GLU 305": "OE1" <-> "OE2" Residue "D GLU 412": "OE1" <-> "OE2" Residue "E ARG 163": "NH1" <-> "NH2" Residue "E GLU 208": "OE1" <-> "OE2" Residue "E GLU 224": "OE1" <-> "OE2" Residue "E GLU 258": "OE1" <-> "OE2" Residue "E GLU 265": "OE1" <-> "OE2" Residue "E GLU 284": "OE1" <-> "OE2" Residue "E GLU 382": "OE1" <-> "OE2" Residue "E GLU 383": "OE1" <-> "OE2" Residue "E GLU 393": "OE1" <-> "OE2" Residue "E GLU 415": "OE1" <-> "OE2" Residue "E GLU 428": "OE1" <-> "OE2" Residue "E TYR 448": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 474": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 493": "OE1" <-> "OE2" Residue "F GLU 64": "OE1" <-> "OE2" Residue "F ARG 87": "NH1" <-> "NH2" Residue "F ARG 127": "NH1" <-> "NH2" Residue "F ARG 164": "NH1" <-> "NH2" Residue "F GLU 184": "OE1" <-> "OE2" Residue "F GLU 284": "OE1" <-> "OE2" Residue "d ARG 77": "NH1" <-> "NH2" Residue "d GLU 187": "OE1" <-> "OE2" Residue "d ARG 208": "NH1" <-> "NH2" Residue "d GLU 243": "OE1" <-> "OE2" Residue "d GLU 249": "OE1" <-> "OE2" Residue "e ARG 12": "NH1" <-> "NH2" Residue "e ARG 68": "NH1" <-> "NH2" Residue "e GLU 100": "OE1" <-> "OE2" Residue "e GLU 107": "OE1" <-> "OE2" Residue "e ARG 110": "NH1" <-> "NH2" Residue "e GLU 127": "OE1" <-> "OE2" Residue "g ARG 48": "NH1" <-> "NH2" Residue "g ARG 73": "NH1" <-> "NH2" Residue "g ARG 83": "NH1" <-> "NH2" Residue "g GLU 87": "OE1" <-> "OE2" Residue "g GLU 103": "OE1" <-> "OE2" Residue "g ARG 127": "NH1" <-> "NH2" Residue "g ARG 144": "NH1" <-> "NH2" Residue "g ARG 170": "NH1" <-> "NH2" Residue "g GLU 190": "OE1" <-> "OE2" Residue "g GLU 251": "OE1" <-> "OE2" Residue "g ARG 256": "NH1" <-> "NH2" Residue "g GLU 267": "OE1" <-> "OE2" Residue "g ARG 306": "NH1" <-> "NH2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 27512 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 3827 Number of conformers: 1 Conformer: "" Number of residues, atoms: 498, 3827 Classifications: {'peptide': 498} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 16, 'TRANS': 479} Chain: "B" Number of atoms: 3851 Number of conformers: 1 Conformer: "" Number of residues, atoms: 501, 3851 Classifications: {'peptide': 501} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 16, 'TRANS': 482} Chain: "C" Number of atoms: 3849 Number of conformers: 1 Conformer: "" Number of residues, atoms: 501, 3849 Classifications: {'peptide': 501} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 16, 'TRANS': 482} Chain: "D" Number of atoms: 3636 Number of conformers: 1 Conformer: "" Number of residues, atoms: 480, 3636 Classifications: {'peptide': 480} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 24, 'TRANS': 453} Chain: "E" Number of atoms: 3619 Number of conformers: 1 Conformer: "" Number of residues, atoms: 478, 3619 Classifications: {'peptide': 478} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 24, 'TRANS': 451} Chain: "F" Number of atoms: 3627 Number of conformers: 1 Conformer: "" Number of residues, atoms: 479, 3627 Classifications: {'peptide': 479} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 24, 'TRANS': 452} Chain: "d" Number of atoms: 1383 Number of conformers: 1 Conformer: "" Number of residues, atoms: 179, 1383 Classifications: {'peptide': 179} Link IDs: {'PTRANS': 4, 'TRANS': 174} Chain: "e" Number of atoms: 1010 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1010 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 4, 'TRANS': 126} Chain: "g" Number of atoms: 2502 Number of conformers: 1 Conformer: "" Number of residues, atoms: 322, 2502 Classifications: {'peptide': 322} Link IDs: {'PTRANS': 12, 'TRANS': 309} Chain: "A" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 61 Unusual residues: {'ATP': 1, 'TTX': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 14.34, per 1000 atoms: 0.52 Number of scatterers: 27512 At special positions: 0 Unit cell: (129.519, 127.413, 161.109, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 103 16.00 P 16 15.00 O 5372 8.00 N 4747 7.00 C 17274 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: 11.08 Conformation dependent library (CDL) restraints added in 5.0 seconds 7102 Ramachandran restraints generated. 3551 Oldfield, 0 Emsley, 3551 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6560 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 120 helices and 29 sheets defined 40.0% alpha, 11.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 6.30 Creating SS restraints... Processing helix chain 'A' and resid 11 through 24 Processing helix chain 'A' and resid 57 through 59 No H-bonds generated for 'chain 'A' and resid 57 through 59' Processing helix chain 'A' and resid 152 through 156 Processing helix chain 'A' and resid 176 through 188 removed outlier: 3.724A pdb=" N ILE A 184 " --> pdb=" O ALA A 180 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N GLN A 188 " --> pdb=" O ILE A 184 " (cutoff:3.500A) Processing helix chain 'A' and resid 205 through 215 Processing helix chain 'A' and resid 218 through 220 No H-bonds generated for 'chain 'A' and resid 218 through 220' Processing helix chain 'A' and resid 233 through 252 Proline residue: A 240 - end of helix Processing helix chain 'A' and resid 264 through 278 Processing helix chain 'A' and resid 284 through 286 No H-bonds generated for 'chain 'A' and resid 284 through 286' Processing helix chain 'A' and resid 291 through 299 Processing helix chain 'A' and resid 330 through 338 Processing helix chain 'A' and resid 347 through 350 No H-bonds generated for 'chain 'A' and resid 347 through 350' Processing helix chain 'A' and resid 368 through 371 Processing helix chain 'A' and resid 374 through 391 removed outlier: 4.240A pdb=" N LYS A 378 " --> pdb=" O LYS A 374 " (cutoff:3.500A) removed outlier: 4.748A pdb=" N VAL A 379 " --> pdb=" O ALA A 375 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 421 Processing helix chain 'A' and resid 431 through 442 Processing helix chain 'A' and resid 453 through 467 Processing helix chain 'A' and resid 471 through 479 Processing helix chain 'A' and resid 484 through 503 removed outlier: 3.816A pdb=" N LEU A 503 " --> pdb=" O GLU A 499 " (cutoff:3.500A) Processing helix chain 'B' and resid 12 through 18 Processing helix chain 'B' and resid 152 through 157 Processing helix chain 'B' and resid 176 through 187 removed outlier: 4.164A pdb=" N GLN B 187 " --> pdb=" O THR B 183 " (cutoff:3.500A) Processing helix chain 'B' and resid 203 through 216 Processing helix chain 'B' and resid 233 through 253 Proline residue: B 240 - end of helix Processing helix chain 'B' and resid 265 through 277 Processing helix chain 'B' and resid 284 through 286 No H-bonds generated for 'chain 'B' and resid 284 through 286' Processing helix chain 'B' and resid 289 through 301 removed outlier: 4.061A pdb=" N PHE B 292 " --> pdb=" O GLY B 289 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N GLU B 300 " --> pdb=" O ARG B 297 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ARG B 301 " --> pdb=" O LEU B 298 " (cutoff:3.500A) Processing helix chain 'B' and resid 330 through 338 Processing helix chain 'B' and resid 347 through 351 Processing helix chain 'B' and resid 368 through 371 Processing helix chain 'B' and resid 374 through 379 Processing helix chain 'B' and resid 383 through 397 Processing helix chain 'B' and resid 405 through 421 removed outlier: 3.964A pdb=" N LEU B 421 " --> pdb=" O LEU B 417 " (cutoff:3.500A) Processing helix chain 'B' and resid 431 through 442 Processing helix chain 'B' and resid 453 through 468 removed outlier: 4.107A pdb=" N GLU B 460 " --> pdb=" O LYS B 456 " (cutoff:3.500A) Processing helix chain 'B' and resid 470 through 478 Processing helix chain 'B' and resid 484 through 502 Processing helix chain 'C' and resid 6 through 15 removed outlier: 3.941A pdb=" N SER C 10 " --> pdb=" O ALA C 6 " (cutoff:3.500A) removed outlier: 4.675A pdb=" N LYS C 11 " --> pdb=" O ASP C 7 " (cutoff:3.500A) removed outlier: 4.730A pdb=" N ARG C 14 " --> pdb=" O SER C 10 " (cutoff:3.500A) Processing helix chain 'C' and resid 102 through 104 No H-bonds generated for 'chain 'C' and resid 102 through 104' Processing helix chain 'C' and resid 152 through 157 Processing helix chain 'C' and resid 176 through 187 removed outlier: 3.654A pdb=" N GLN C 187 " --> pdb=" O THR C 183 " (cutoff:3.500A) Processing helix chain 'C' and resid 203 through 215 Processing helix chain 'C' and resid 219 through 221 No H-bonds generated for 'chain 'C' and resid 219 through 221' Processing helix chain 'C' and resid 233 through 252 Proline residue: C 240 - end of helix removed outlier: 3.882A pdb=" N PHE C 250 " --> pdb=" O LEU C 246 " (cutoff:3.500A) Processing helix chain 'C' and resid 264 through 277 Processing helix chain 'C' and resid 284 through 286 No H-bonds generated for 'chain 'C' and resid 284 through 286' Processing helix chain 'C' and resid 289 through 301 removed outlier: 4.369A pdb=" N PHE C 292 " --> pdb=" O GLY C 289 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N ARG C 297 " --> pdb=" O LEU C 294 " (cutoff:3.500A) removed outlier: 5.450A pdb=" N GLU C 300 " --> pdb=" O ARG C 297 " (cutoff:3.500A) Processing helix chain 'C' and resid 330 through 338 Processing helix chain 'C' and resid 347 through 352 Processing helix chain 'C' and resid 374 through 394 removed outlier: 5.187A pdb=" N LYS C 382 " --> pdb=" O LYS C 378 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N LEU C 383 " --> pdb=" O VAL C 379 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 412 Processing helix chain 'C' and resid 415 through 421 Processing helix chain 'C' and resid 431 through 443 removed outlier: 4.027A pdb=" N GLY C 441 " --> pdb=" O THR C 437 " (cutoff:3.500A) Processing helix chain 'C' and resid 454 through 467 Processing helix chain 'C' and resid 472 through 479 Processing helix chain 'C' and resid 484 through 502 Processing helix chain 'D' and resid 139 through 141 No H-bonds generated for 'chain 'D' and resid 139 through 141' Processing helix chain 'D' and resid 154 through 158 Processing helix chain 'D' and resid 178 through 189 Processing helix chain 'D' and resid 206 through 218 Processing helix chain 'D' and resid 243 through 262 removed outlier: 4.664A pdb=" N GLY D 250 " --> pdb=" O ARG D 246 " (cutoff:3.500A) removed outlier: 5.254A pdb=" N LEU D 251 " --> pdb=" O MET D 247 " (cutoff:3.500A) Processing helix chain 'D' and resid 275 through 286 Processing helix chain 'D' and resid 303 through 312 removed outlier: 4.859A pdb=" N ARG D 312 " --> pdb=" O SER D 308 " (cutoff:3.500A) Processing helix chain 'D' and resid 330 through 332 No H-bonds generated for 'chain 'D' and resid 330 through 332' Processing helix chain 'D' and resid 337 through 342 Processing helix chain 'D' and resid 355 through 358 No H-bonds generated for 'chain 'D' and resid 355 through 358' Processing helix chain 'D' and resid 377 through 380 No H-bonds generated for 'chain 'D' and resid 377 through 380' Processing helix chain 'D' and resid 382 through 405 removed outlier: 4.739A pdb=" N ASP D 403 " --> pdb=" O LYS D 399 " (cutoff:3.500A) removed outlier: 4.682A pdb=" N ILE D 404 " --> pdb=" O GLU D 400 " (cutoff:3.500A) Processing helix chain 'D' and resid 415 through 430 removed outlier: 4.001A pdb=" N ARG D 429 " --> pdb=" O ARG D 425 " (cutoff:3.500A) Processing helix chain 'D' and resid 439 through 442 No H-bonds generated for 'chain 'D' and resid 439 through 442' Processing helix chain 'D' and resid 451 through 463 Processing helix chain 'D' and resid 480 through 495 Processing helix chain 'E' and resid 139 through 141 No H-bonds generated for 'chain 'E' and resid 139 through 141' Processing helix chain 'E' and resid 154 through 158 Processing helix chain 'E' and resid 178 through 189 Processing helix chain 'E' and resid 206 through 219 removed outlier: 3.750A pdb=" N TYR E 213 " --> pdb=" O GLY E 209 " (cutoff:3.500A) Processing helix chain 'E' and resid 243 through 263 removed outlier: 5.136A pdb=" N GLY E 250 " --> pdb=" O ARG E 246 " (cutoff:3.500A) removed outlier: 5.121A pdb=" N LEU E 251 " --> pdb=" O MET E 247 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N PHE E 260 " --> pdb=" O MET E 256 " (cutoff:3.500A) Processing helix chain 'E' and resid 275 through 285 removed outlier: 3.715A pdb=" N GLY E 282 " --> pdb=" O PHE E 278 " (cutoff:3.500A) Processing helix chain 'E' and resid 303 through 313 removed outlier: 3.722A pdb=" N LEU E 309 " --> pdb=" O GLU E 305 " (cutoff:3.500A) removed outlier: 5.284A pdb=" N ARG E 312 " --> pdb=" O SER E 308 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ILE E 313 " --> pdb=" O LEU E 309 " (cutoff:3.500A) Processing helix chain 'E' and resid 330 through 332 No H-bonds generated for 'chain 'E' and resid 330 through 332' Processing helix chain 'E' and resid 337 through 345 removed outlier: 4.330A pdb=" N ALA E 344 " --> pdb=" O ALA E 340 " (cutoff:3.500A) removed outlier: 4.613A pdb=" N HIS E 345 " --> pdb=" O THR E 341 " (cutoff:3.500A) Processing helix chain 'E' and resid 355 through 358 No H-bonds generated for 'chain 'E' and resid 355 through 358' Processing helix chain 'E' and resid 377 through 407 removed outlier: 7.467A pdb=" N GLU E 382 " --> pdb=" O ARG E 378 " (cutoff:3.500A) removed outlier: 9.153A pdb=" N GLU E 383 " --> pdb=" O ILE E 379 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N HIS E 384 " --> pdb=" O VAL E 380 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N TYR E 385 " --> pdb=" O GLY E 381 " (cutoff:3.500A) removed outlier: 4.735A pdb=" N ASP E 403 " --> pdb=" O LYS E 399 " (cutoff:3.500A) removed outlier: 5.064A pdb=" N ILE E 404 " --> pdb=" O GLU E 400 " (cutoff:3.500A) Processing helix chain 'E' and resid 415 through 430 removed outlier: 3.803A pdb=" N THR E 420 " --> pdb=" O GLU E 416 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ARG E 429 " --> pdb=" O ARG E 425 " (cutoff:3.500A) Processing helix chain 'E' and resid 439 through 442 No H-bonds generated for 'chain 'E' and resid 439 through 442' Processing helix chain 'E' and resid 451 through 463 removed outlier: 3.866A pdb=" N ARG E 456 " --> pdb=" O ALA E 452 " (cutoff:3.500A) Processing helix chain 'E' and resid 480 through 489 Processing helix chain 'F' and resid 155 through 158 No H-bonds generated for 'chain 'F' and resid 155 through 158' Processing helix chain 'F' and resid 178 through 192 Processing helix chain 'F' and resid 206 through 218 Processing helix chain 'F' and resid 243 through 264 removed outlier: 3.796A pdb=" N MET F 247 " --> pdb=" O PRO F 243 " (cutoff:3.500A) removed outlier: 5.219A pdb=" N GLY F 250 " --> pdb=" O ARG F 246 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N LEU F 251 " --> pdb=" O MET F 247 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N PHE F 260 " --> pdb=" O MET F 256 " (cutoff:3.500A) Processing helix chain 'F' and resid 275 through 288 Processing helix chain 'F' and resid 302 through 310 removed outlier: 3.548A pdb=" N LEU F 309 " --> pdb=" O GLU F 305 " (cutoff:3.500A) Processing helix chain 'F' and resid 330 through 332 No H-bonds generated for 'chain 'F' and resid 330 through 332' Processing helix chain 'F' and resid 337 through 342 Processing helix chain 'F' and resid 355 through 359 Processing helix chain 'F' and resid 377 through 380 No H-bonds generated for 'chain 'F' and resid 377 through 380' Processing helix chain 'F' and resid 382 through 404 removed outlier: 3.629A pdb=" N GLU F 400 " --> pdb=" O GLN F 396 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N ASP F 403 " --> pdb=" O LYS F 399 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ILE F 404 " --> pdb=" O GLU F 400 " (cutoff:3.500A) Processing helix chain 'F' and resid 415 through 430 removed outlier: 4.016A pdb=" N THR F 420 " --> pdb=" O GLU F 416 " (cutoff:3.500A) Processing helix chain 'F' and resid 439 through 442 No H-bonds generated for 'chain 'F' and resid 439 through 442' Processing helix chain 'F' and resid 451 through 462 Processing helix chain 'F' and resid 471 through 474 removed outlier: 3.803A pdb=" N PHE F 474 " --> pdb=" O GLU F 471 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 471 through 474' Processing helix chain 'F' and resid 481 through 494 Processing helix chain 'd' and resid 76 through 89 Processing helix chain 'd' and resid 92 through 106 removed outlier: 4.206A pdb=" N SER d 97 " --> pdb=" O GLU d 93 " (cutoff:3.500A) Processing helix chain 'd' and resid 109 through 116 Processing helix chain 'd' and resid 122 through 136 Processing helix chain 'd' and resid 140 through 151 removed outlier: 4.999A pdb=" N PHE d 145 " --> pdb=" O HIS d 141 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N ILE d 146 " --> pdb=" O THR d 142 " (cutoff:3.500A) Processing helix chain 'd' and resid 155 through 173 removed outlier: 4.994A pdb=" N LYS d 159 " --> pdb=" O ASN d 156 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N PHE d 165 " --> pdb=" O LEU d 162 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N GLU d 166 " --> pdb=" O ASN d 163 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ILE d 172 " --> pdb=" O PHE d 169 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N THR d 173 " --> pdb=" O ASN d 170 " (cutoff:3.500A) Processing helix chain 'd' and resid 188 through 202 Processing helix chain 'd' and resid 238 through 248 removed outlier: 4.682A pdb=" N LEU d 248 " --> pdb=" O ILE d 244 " (cutoff:3.500A) Processing helix chain 'e' and resid 89 through 103 Processing helix chain 'e' and resid 109 through 114 removed outlier: 4.094A pdb=" N GLU e 114 " --> pdb=" O ARG e 110 " (cutoff:3.500A) Processing helix chain 'e' and resid 116 through 129 removed outlier: 3.882A pdb=" N ALA e 128 " --> pdb=" O THR e 124 " (cutoff:3.500A) Processing helix chain 'g' and resid 43 through 97 removed outlier: 3.612A pdb=" N VAL g 80 " --> pdb=" O GLN g 76 " (cutoff:3.500A) Proline residue: g 84 - end of helix removed outlier: 3.956A pdb=" N ASN g 97 " --> pdb=" O LEU g 93 " (cutoff:3.500A) Processing helix chain 'g' and resid 132 through 150 removed outlier: 4.393A pdb=" N LYS g 149 " --> pdb=" O ILE g 145 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N LYS g 150 " --> pdb=" O ALA g 146 " (cutoff:3.500A) Processing helix chain 'g' and resid 162 through 169 removed outlier: 4.397A pdb=" N TYR g 167 " --> pdb=" O LYS g 163 " (cutoff:3.500A) Processing helix chain 'g' and resid 189 through 203 Processing helix chain 'g' and resid 248 through 250 No H-bonds generated for 'chain 'g' and resid 248 through 250' Processing helix chain 'g' and resid 288 through 362 Proline residue: g 297 - end of helix Processing sheet with id= A, first strand: chain 'A' and resid 88 through 90 removed outlier: 3.601A pdb=" N VAL A 89 " --> pdb=" O GLY A 30 " (cutoff:3.500A) removed outlier: 6.973A pdb=" N VAL A 75 " --> pdb=" O ALA A 64 " (cutoff:3.500A) removed outlier: 5.824A pdb=" N ALA A 64 " --> pdb=" O VAL A 75 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 97 through 100 removed outlier: 4.059A pdb=" N GLU A 126 " --> pdb=" O VAL A 100 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 341 through 345 removed outlier: 3.573A pdb=" N VAL A 320 " --> pdb=" O ILE A 168 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N GLY A 170 " --> pdb=" O VAL A 320 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 223 through 227 removed outlier: 6.756A pdb=" N ILE A 260 " --> pdb=" O VAL A 197 " (cutoff:3.500A) removed outlier: 7.176A pdb=" N ILE A 199 " --> pdb=" O ILE A 260 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N ASP A 262 " --> pdb=" O ILE A 199 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 71 through 75 removed outlier: 6.246A pdb=" N HIS B 43 " --> pdb=" O VAL B 32 " (cutoff:3.500A) removed outlier: 5.218A pdb=" N VAL B 32 " --> pdb=" O HIS B 43 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 53 through 55 Processing sheet with id= G, first strand: chain 'B' and resid 97 through 99 Processing sheet with id= H, first strand: chain 'B' and resid 342 through 344 removed outlier: 6.397A pdb=" N LEU B 167 " --> pdb=" O ILE B 343 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 223 through 227 Processing sheet with id= J, first strand: chain 'C' and resid 32 through 36 removed outlier: 6.580A pdb=" N ARG C 41 " --> pdb=" O LEU C 33 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N VAL C 35 " --> pdb=" O ILE C 39 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N ILE C 39 " --> pdb=" O VAL C 35 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N VAL C 75 " --> pdb=" O ALA C 64 " (cutoff:3.500A) removed outlier: 5.347A pdb=" N ALA C 64 " --> pdb=" O VAL C 75 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'C' and resid 97 through 100 removed outlier: 3.718A pdb=" N GLU C 126 " --> pdb=" O VAL C 100 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'C' and resid 341 through 345 Processing sheet with id= M, first strand: chain 'C' and resid 313 through 316 Processing sheet with id= N, first strand: chain 'D' and resid 22 through 27 removed outlier: 6.180A pdb=" N ASP D 32 " --> pdb=" O ALA D 24 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N ILE D 26 " --> pdb=" O VAL D 30 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N VAL D 30 " --> pdb=" O ILE D 26 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N GLN D 67 " --> pdb=" O ARG D 75 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N VAL D 77 " --> pdb=" O VAL D 65 " (cutoff:3.500A) removed outlier: 5.616A pdb=" N VAL D 65 " --> pdb=" O VAL D 77 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N VAL D 61 " --> pdb=" O VAL D 49 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N VAL D 49 " --> pdb=" O VAL D 61 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'D' and resid 99 through 101 Processing sheet with id= P, first strand: chain 'D' and resid 323 through 328 removed outlier: 6.661A pdb=" N ALA D 348 " --> pdb=" O GLY D 169 " (cutoff:3.500A) removed outlier: 7.425A pdb=" N PHE D 171 " --> pdb=" O ALA D 348 " (cutoff:3.500A) removed outlier: 6.138A pdb=" N THR D 350 " --> pdb=" O PHE D 171 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'D' and resid 232 through 236 removed outlier: 7.091A pdb=" N SER D 197 " --> pdb=" O ALA D 233 " (cutoff:3.500A) removed outlier: 8.316A pdb=" N VAL D 235 " --> pdb=" O SER D 197 " (cutoff:3.500A) removed outlier: 6.054A pdb=" N PHE D 199 " --> pdb=" O VAL D 235 " (cutoff:3.500A) removed outlier: 5.918A pdb=" N LEU D 269 " --> pdb=" O VAL D 198 " (cutoff:3.500A) removed outlier: 7.322A pdb=" N GLY D 200 " --> pdb=" O LEU D 269 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N PHE D 271 " --> pdb=" O GLY D 200 " (cutoff:3.500A) No H-bonds generated for sheet with id= Q Processing sheet with id= R, first strand: chain 'E' and resid 20 through 22 removed outlier: 6.885A pdb=" N ARG E 75 " --> pdb=" O GLN E 66 " (cutoff:3.500A) removed outlier: 5.010A pdb=" N LEU E 68 " --> pdb=" O ARG E 73 " (cutoff:3.500A) removed outlier: 7.076A pdb=" N ARG E 73 " --> pdb=" O LEU E 68 " (cutoff:3.500A) removed outlier: 5.976A pdb=" N ALA E 34 " --> pdb=" O ILE E 23 " (cutoff:3.500A) removed outlier: 5.036A pdb=" N ILE E 23 " --> pdb=" O ALA E 34 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'E' and resid 99 through 101 Processing sheet with id= T, first strand: chain 'E' and resid 348 through 350 removed outlier: 3.540A pdb=" N PHE E 171 " --> pdb=" O THR E 350 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N GLY E 172 " --> pdb=" O VAL E 327 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ALA E 233 " --> pdb=" O SER E 197 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'F' and resid 23 through 27 removed outlier: 6.546A pdb=" N ASP F 32 " --> pdb=" O ALA F 24 " (cutoff:3.500A) removed outlier: 4.851A pdb=" N ILE F 26 " --> pdb=" O VAL F 30 " (cutoff:3.500A) removed outlier: 7.184A pdb=" N VAL F 30 " --> pdb=" O ILE F 26 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N GLN F 67 " --> pdb=" O ARG F 75 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N VAL F 77 " --> pdb=" O VAL F 65 " (cutoff:3.500A) removed outlier: 5.687A pdb=" N VAL F 65 " --> pdb=" O VAL F 77 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N GLU F 90 " --> pdb=" O LYS F 50 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'F' and resid 99 through 101 Processing sheet with id= W, first strand: chain 'F' and resid 348 through 350 removed outlier: 9.181A pdb=" N ILE F 168 " --> pdb=" O ILE F 321 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N SER F 323 " --> pdb=" O ILE F 168 " (cutoff:3.500A) removed outlier: 8.505A pdb=" N LEU F 170 " --> pdb=" O SER F 323 " (cutoff:3.500A) removed outlier: 7.484A pdb=" N GLN F 325 " --> pdb=" O LEU F 170 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ILE F 272 " --> pdb=" O ILE F 324 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N VAL F 196 " --> pdb=" O ASP F 267 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'd' and resid 175 through 182 removed outlier: 6.636A pdb=" N ASN d 206 " --> pdb=" O GLU d 176 " (cutoff:3.500A) removed outlier: 7.734A pdb=" N ALA d 178 " --> pdb=" O ASN d 206 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N ARG d 208 " --> pdb=" O ALA d 178 " (cutoff:3.500A) removed outlier: 8.341A pdb=" N VAL d 180 " --> pdb=" O ARG d 208 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N LYS d 210 " --> pdb=" O VAL d 180 " (cutoff:3.500A) removed outlier: 8.228A pdb=" N SER d 182 " --> pdb=" O LYS d 210 " (cutoff:3.500A) removed outlier: 6.014A pdb=" N VAL d 212 " --> pdb=" O SER d 182 " (cutoff:3.500A) No H-bonds generated for sheet with id= X Processing sheet with id= Y, first strand: chain 'd' and resid 222 through 225 Processing sheet with id= Z, first strand: chain 'e' and resid 4 through 8 Processing sheet with id= AA, first strand: chain 'e' and resid 49 through 52 removed outlier: 3.704A pdb=" N ILE e 22 " --> pdb=" O VAL e 33 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'e' and resid 60 through 62 Processing sheet with id= AC, first strand: chain 'g' and resid 118 through 122 removed outlier: 6.485A pdb=" N LYS g 209 " --> pdb=" O ALA g 119 " (cutoff:3.500A) removed outlier: 7.961A pdb=" N MET g 121 " --> pdb=" O LYS g 209 " (cutoff:3.500A) removed outlier: 7.102A pdb=" N GLU g 211 " --> pdb=" O MET g 121 " (cutoff:3.500A) 1077 hydrogen bonds defined for protein. 3123 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: 9.03 Time building geometry restraints manager: 11.85 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: 9163 1.34 - 1.46: 4451 1.46 - 1.58: 14062 1.58 - 1.70: 26 1.70 - 1.82: 195 Bond restraints: 27897 Sorted by residual: bond pdb=" C4 ATP C 601 " pdb=" C5 ATP C 601 " ideal model delta sigma weight residual 1.388 1.463 -0.075 1.00e-02 1.00e+04 5.59e+01 bond pdb=" C4 ATP A 600 " pdb=" C5 ATP A 600 " ideal model delta sigma weight residual 1.388 1.462 -0.074 1.00e-02 1.00e+04 5.49e+01 bond pdb=" C4 ATP B 601 " pdb=" C5 ATP B 601 " ideal model delta sigma weight residual 1.388 1.459 -0.071 1.00e-02 1.00e+04 5.11e+01 bond pdb=" C4 ATP E 601 " pdb=" C5 ATP E 601 " ideal model delta sigma weight residual 1.388 1.459 -0.071 1.00e-02 1.00e+04 4.99e+01 bond pdb=" C5 ATP A 600 " pdb=" C6 ATP A 600 " ideal model delta sigma weight residual 1.409 1.477 -0.068 1.00e-02 1.00e+04 4.64e+01 ... (remaining 27892 not shown) Histogram of bond angle deviations from ideal: 96.81 - 104.70: 499 104.70 - 112.59: 14689 112.59 - 120.48: 12503 120.48 - 128.37: 10031 128.37 - 136.26: 93 Bond angle restraints: 37815 Sorted by residual: angle pdb=" PB ATP C 601 " pdb=" O3B ATP C 601 " pdb=" PG ATP C 601 " ideal model delta sigma weight residual 139.87 115.98 23.89 1.00e+00 1.00e+00 5.71e+02 angle pdb=" PB ATP B 601 " pdb=" O3B ATP B 601 " pdb=" PG ATP B 601 " ideal model delta sigma weight residual 139.87 119.85 20.02 1.00e+00 1.00e+00 4.01e+02 angle pdb=" PB ATP A 600 " pdb=" O3B ATP A 600 " pdb=" PG ATP A 600 " ideal model delta sigma weight residual 139.87 120.56 19.31 1.00e+00 1.00e+00 3.73e+02 angle pdb=" PA ATP A 600 " pdb=" O3A ATP A 600 " pdb=" PB ATP A 600 " ideal model delta sigma weight residual 136.83 117.61 19.22 1.00e+00 1.00e+00 3.70e+02 angle pdb=" PA ATP B 601 " pdb=" O3A ATP B 601 " pdb=" PB ATP B 601 " ideal model delta sigma weight residual 136.83 117.69 19.14 1.00e+00 1.00e+00 3.66e+02 ... (remaining 37810 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.79: 16503 31.79 - 63.59: 610 63.59 - 95.38: 62 95.38 - 127.18: 2 127.18 - 158.97: 1 Dihedral angle restraints: 17178 sinusoidal: 6957 harmonic: 10221 Sorted by residual: dihedral pdb=" CA ALA E 295 " pdb=" C ALA E 295 " pdb=" N VAL E 296 " pdb=" CA VAL E 296 " ideal model delta harmonic sigma weight residual -180.00 -132.18 -47.82 0 5.00e+00 4.00e-02 9.15e+01 dihedral pdb=" CA ALA D 295 " pdb=" C ALA D 295 " pdb=" N VAL D 296 " pdb=" CA VAL D 296 " ideal model delta harmonic sigma weight residual -180.00 -135.24 -44.76 0 5.00e+00 4.00e-02 8.01e+01 dihedral pdb=" O1B ADP F 601 " pdb=" O3A ADP F 601 " pdb=" PB ADP F 601 " pdb=" PA ADP F 601 " ideal model delta sinusoidal sigma weight residual 300.00 141.03 158.97 1 2.00e+01 2.50e-03 4.64e+01 ... (remaining 17175 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.068: 3572 0.068 - 0.136: 803 0.136 - 0.203: 61 0.203 - 0.271: 8 0.271 - 0.339: 4 Chirality restraints: 4448 Sorted by residual: chirality pdb=" CB ILE g 227 " pdb=" CA ILE g 227 " pdb=" CG1 ILE g 227 " pdb=" CG2 ILE g 227 " both_signs ideal model delta sigma weight residual False 2.64 2.31 0.34 2.00e-01 2.50e+01 2.88e+00 chirality pdb=" C9 TTX C 602 " pdb=" C10 TTX C 602 " pdb=" C8 TTX C 602 " pdb=" N3 TTX C 602 " both_signs ideal model delta sigma weight residual False -2.28 -2.62 0.34 2.00e-01 2.50e+01 2.82e+00 chirality pdb=" CG LEU C 65 " pdb=" CB LEU C 65 " pdb=" CD1 LEU C 65 " pdb=" CD2 LEU C 65 " both_signs ideal model delta sigma weight residual False -2.59 -2.30 -0.29 2.00e-01 2.50e+01 2.07e+00 ... (remaining 4445 not shown) Planarity restraints: 4910 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C11 TTX C 602 " 0.416 2.00e-02 2.50e+03 3.60e-01 1.94e+03 pdb=" C12 TTX C 602 " 0.052 2.00e-02 2.50e+03 pdb=" C13 TTX C 602 " -0.474 2.00e-02 2.50e+03 pdb=" C9 TTX C 602 " -0.440 2.00e-02 2.50e+03 pdb=" N3 TTX C 602 " 0.021 2.00e-02 2.50e+03 pdb=" O3 TTX C 602 " 0.425 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C15 TTX C 602 " -0.219 2.00e-02 2.50e+03 2.00e-01 5.99e+02 pdb=" C5 TTX C 602 " 0.255 2.00e-02 2.50e+03 pdb=" C6 TTX C 602 " -0.042 2.00e-02 2.50e+03 pdb=" C7 TTX C 602 " 0.265 2.00e-02 2.50e+03 pdb=" N1 TTX C 602 " -0.028 2.00e-02 2.50e+03 pdb=" O1 TTX C 602 " -0.232 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5 TTX C 602 " -0.152 2.00e-02 2.50e+03 1.25e-01 1.95e+02 pdb=" C8 TTX C 602 " 0.058 2.00e-02 2.50e+03 pdb=" C9 TTX C 602 " -0.117 2.00e-02 2.50e+03 pdb=" N2 TTX C 602 " 0.194 2.00e-02 2.50e+03 pdb=" O2 TTX C 602 " 0.017 2.00e-02 2.50e+03 ... (remaining 4907 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 2981 2.74 - 3.28: 28414 3.28 - 3.82: 46975 3.82 - 4.36: 56632 4.36 - 4.90: 95523 Nonbonded interactions: 230525 Sorted by model distance: nonbonded pdb=" O GLN B 187 " pdb=" OH TYR B 221 " model vdw 2.198 2.440 nonbonded pdb=" O GLU A 474 " pdb=" OG SER A 478 " model vdw 2.211 2.440 nonbonded pdb=" O GLN B 84 " pdb=" OG SER B 87 " model vdw 2.221 2.440 nonbonded pdb=" O PRO F 337 " pdb=" OG1 THR F 341 " model vdw 2.223 2.440 nonbonded pdb=" O PHE d 169 " pdb=" OG1 THR d 173 " model vdw 2.224 2.440 ... (remaining 230520 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and resid 7 through 503) selection = (chain 'B' and resid 7 through 503) selection = (chain 'C' and resid 7 through 503) } ncs_group { reference = (chain 'D' and resid 18 through 494) selection = (chain 'E' and resid 18 through 494) selection = (chain 'F' and resid 18 through 494) } 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 group one per residue 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: 4.570 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: 0.020 Extract box with map and model: 16.120 Check model and map are aligned: 0.430 Set scattering table: 0.260 Process input model: 72.800 Find NCS groups from input model: 1.900 Set up NCS constraints: 0.130 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 99.610 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7067 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 : 0.007 0.077 27897 Z= 0.483 Angle : 1.017 23.891 37815 Z= 0.620 Chirality : 0.055 0.339 4448 Planarity : 0.009 0.360 4910 Dihedral : 16.325 158.970 10618 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 10.51 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.58 % Favored : 92.31 % Rotamer: Outliers : 0.51 % Allowed : 12.18 % Favored : 87.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.11 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -3.78 (0.11), residues: 3551 helix: -2.02 (0.11), residues: 1446 sheet: -2.83 (0.20), residues: 511 loop : -2.79 (0.13), residues: 1594 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP e 15 HIS 0.007 0.002 HIS C 43 PHE 0.029 0.003 PHE F 441 TYR 0.029 0.003 TYR g 214 ARG 0.007 0.001 ARG A 140 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7102 Ramachandran restraints generated. 3551 Oldfield, 0 Emsley, 3551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7102 Ramachandran restraints generated. 3551 Oldfield, 0 Emsley, 3551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 763 residues out of total 2939 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 748 time to evaluate : 2.844 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 166 GLU cc_start: 0.7459 (tp30) cc_final: 0.6868 (tp30) REVERT: A 385 LEU cc_start: 0.7696 (tt) cc_final: 0.7113 (tt) REVERT: A 389 GLN cc_start: 0.6813 (mt0) cc_final: 0.6264 (tm-30) REVERT: B 173 GLN cc_start: 0.7432 (tp-100) cc_final: 0.7218 (tp40) REVERT: B 227 GLU cc_start: 0.6760 (pm20) cc_final: 0.6491 (pm20) REVERT: B 297 ARG cc_start: 0.7855 (ttp80) cc_final: 0.7401 (ttp80) REVERT: B 314 MET cc_start: 0.7431 (ttt) cc_final: 0.6934 (tmm) REVERT: B 376 MET cc_start: 0.6702 (tpp) cc_final: 0.6376 (mmt) REVERT: B 382 LYS cc_start: 0.7118 (tmtt) cc_final: 0.6792 (tttp) REVERT: B 410 GLN cc_start: 0.7181 (tp40) cc_final: 0.6670 (tp40) REVERT: C 49 MET cc_start: 0.6471 (tpt) cc_final: 0.5927 (tpt) REVERT: C 241 TYR cc_start: 0.8030 (m-80) cc_final: 0.7457 (m-80) REVERT: C 433 GLU cc_start: 0.7156 (mp0) cc_final: 0.6826 (mp0) REVERT: C 455 ARG cc_start: 0.6306 (mtp180) cc_final: 0.6064 (mmm-85) REVERT: D 27 ILE cc_start: 0.8533 (mm) cc_final: 0.8320 (mp) REVERT: D 40 MET cc_start: 0.7452 (tpp) cc_final: 0.7044 (tpt) REVERT: D 66 GLN cc_start: 0.7668 (mm-40) cc_final: 0.7404 (mm-40) REVERT: D 208 GLU cc_start: 0.6652 (tt0) cc_final: 0.6336 (tt0) REVERT: D 247 MET cc_start: 0.6676 (ttp) cc_final: 0.6424 (ttp) REVERT: D 260 PHE cc_start: 0.8492 (m-80) cc_final: 0.8191 (m-80) REVERT: D 277 ARG cc_start: 0.6741 (mmt180) cc_final: 0.6367 (mmt180) REVERT: D 299 GLN cc_start: 0.8407 (pm20) cc_final: 0.8156 (pm20) REVERT: D 306 MET cc_start: 0.6613 (tpp) cc_final: 0.6302 (tpp) REVERT: D 310 GLN cc_start: 0.8052 (mm-40) cc_final: 0.7714 (tp40) REVERT: D 354 ARG cc_start: 0.7242 (tpp80) cc_final: 0.6981 (tpp-160) REVERT: D 359 LYS cc_start: 0.7987 (tptt) cc_final: 0.7636 (tppt) REVERT: D 392 LYS cc_start: 0.8401 (mttm) cc_final: 0.7889 (mtpt) REVERT: E 145 LYS cc_start: 0.6550 (tptp) cc_final: 0.5779 (ttpp) REVERT: E 167 LYS cc_start: 0.8275 (mtmm) cc_final: 0.7691 (mtmm) REVERT: E 272 ILE cc_start: 0.9163 (mp) cc_final: 0.8565 (tp) REVERT: E 292 MET cc_start: 0.5985 (mtp) cc_final: 0.5684 (ttp) REVERT: E 482 GLU cc_start: 0.7284 (mm-30) cc_final: 0.6789 (tp30) REVERT: F 112 ASN cc_start: 0.8135 (p0) cc_final: 0.7680 (p0) REVERT: F 116 GLU cc_start: 0.6577 (tm-30) cc_final: 0.6122 (tm-30) REVERT: F 184 GLU cc_start: 0.7029 (mm-30) cc_final: 0.6816 (tp30) REVERT: F 217 LYS cc_start: 0.8075 (mttt) cc_final: 0.7849 (mtpt) REVERT: F 280 GLN cc_start: 0.6639 (tm-30) cc_final: 0.6410 (tm-30) REVERT: F 298 TYR cc_start: 0.7539 (m-80) cc_final: 0.7206 (m-80) REVERT: F 306 MET cc_start: 0.7909 (tpp) cc_final: 0.7252 (tpt) REVERT: F 311 GLU cc_start: 0.7782 (mt-10) cc_final: 0.7553 (tm-30) REVERT: F 374 MET cc_start: 0.7683 (mmp) cc_final: 0.7350 (mmm) REVERT: F 383 GLU cc_start: 0.7150 (mp0) cc_final: 0.6818 (mp0) REVERT: F 454 THR cc_start: 0.7399 (p) cc_final: 0.7060 (p) REVERT: d 78 TYR cc_start: 0.7054 (m-80) cc_final: 0.6430 (m-80) REVERT: d 113 TYR cc_start: 0.7117 (t80) cc_final: 0.6734 (t80) REVERT: d 156 ASN cc_start: 0.5754 (p0) cc_final: 0.5546 (p0) REVERT: d 160 GLU cc_start: 0.6177 (tt0) cc_final: 0.5858 (tt0) REVERT: d 231 LYS cc_start: 0.6638 (mttt) cc_final: 0.6379 (mtpp) REVERT: e 121 ARG cc_start: 0.5691 (tpp80) cc_final: 0.5422 (tpp80) REVERT: g 163 LYS cc_start: 0.7838 (mmtm) cc_final: 0.7086 (tptp) REVERT: g 224 ASP cc_start: 0.7653 (m-30) cc_final: 0.7447 (m-30) REVERT: g 257 LEU cc_start: 0.7375 (pp) cc_final: 0.7005 (pt) REVERT: g 270 MET cc_start: 0.5783 (ppp) cc_final: 0.5115 (ppp) REVERT: g 300 LEU cc_start: 0.7609 (tt) cc_final: 0.6495 (mt) outliers start: 15 outliers final: 8 residues processed: 759 average time/residue: 0.4687 time to fit residues: 525.5276 Evaluate side-chains 565 residues out of total 2939 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 557 time to evaluate : 3.042 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 379 VAL Chi-restraints excluded: chain D residue 132 ILE Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain d residue 91 THR Chi-restraints excluded: chain e residue 44 VAL Chi-restraints excluded: chain g residue 258 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 353 random chunks: chunk 298 optimal weight: 2.9990 chunk 267 optimal weight: 0.5980 chunk 148 optimal weight: 3.9990 chunk 91 optimal weight: 0.0020 chunk 180 optimal weight: 0.0370 chunk 142 optimal weight: 0.5980 chunk 276 optimal weight: 0.6980 chunk 107 optimal weight: 1.9990 chunk 168 optimal weight: 0.7980 chunk 205 optimal weight: 4.9990 chunk 320 optimal weight: 2.9990 overall best weight: 0.3866 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 173 GLN A 214 GLN B 398 GLN C 208 GLN D 210 ASN ** D 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 472 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 45 ASN F 325 GLN ** d 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 199 GLN g 192 GLN g 290 GLN g 361 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7034 moved from start: 0.1668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 27897 Z= 0.180 Angle : 0.644 21.298 37815 Z= 0.322 Chirality : 0.044 0.251 4448 Planarity : 0.005 0.053 4910 Dihedral : 8.805 146.851 4058 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 14.21 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.44 % Favored : 94.51 % Rotamer: Outliers : 3.13 % Allowed : 16.67 % Favored : 80.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.11 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -2.49 (0.13), residues: 3551 helix: -0.64 (0.13), residues: 1454 sheet: -2.37 (0.21), residues: 485 loop : -2.34 (0.14), residues: 1612 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP e 57 HIS 0.004 0.001 HIS g 228 PHE 0.021 0.001 PHE D 149 TYR 0.023 0.001 TYR B 144 ARG 0.008 0.001 ARG d 77 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7102 Ramachandran restraints generated. 3551 Oldfield, 0 Emsley, 3551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7102 Ramachandran restraints generated. 3551 Oldfield, 0 Emsley, 3551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 697 residues out of total 2939 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 605 time to evaluate : 3.203 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 145 GLU cc_start: 0.6293 (mp0) cc_final: 0.5763 (pm20) REVERT: A 166 GLU cc_start: 0.7316 (tp30) cc_final: 0.7008 (tp30) REVERT: A 385 LEU cc_start: 0.7361 (tt) cc_final: 0.6976 (tt) REVERT: A 389 GLN cc_start: 0.6663 (mt0) cc_final: 0.6092 (tm-30) REVERT: B 114 LYS cc_start: 0.7831 (mtpt) cc_final: 0.7399 (mtpp) REVERT: B 314 MET cc_start: 0.7605 (ttt) cc_final: 0.7207 (tmm) REVERT: B 410 GLN cc_start: 0.6652 (tp40) cc_final: 0.6416 (tp40) REVERT: C 241 TYR cc_start: 0.7921 (m-80) cc_final: 0.7447 (m-80) REVERT: C 269 GLN cc_start: 0.7422 (mp-120) cc_final: 0.7134 (mp10) REVERT: C 292 PHE cc_start: 0.7504 (t80) cc_final: 0.7203 (t80) REVERT: C 433 GLU cc_start: 0.7223 (mp0) cc_final: 0.6990 (mp0) REVERT: C 468 ASN cc_start: 0.7034 (t0) cc_final: 0.6630 (t0) REVERT: D 27 ILE cc_start: 0.8381 (mm) cc_final: 0.8179 (mp) REVERT: D 66 GLN cc_start: 0.7702 (mm-40) cc_final: 0.7327 (mm110) REVERT: D 260 PHE cc_start: 0.8375 (m-80) cc_final: 0.8017 (m-80) REVERT: D 392 LYS cc_start: 0.8384 (mttm) cc_final: 0.7954 (mtpt) REVERT: D 488 MET cc_start: 0.7377 (ttp) cc_final: 0.7068 (ttp) REVERT: E 145 LYS cc_start: 0.6408 (tptp) cc_final: 0.5594 (ttpp) REVERT: E 167 LYS cc_start: 0.8250 (mtmm) cc_final: 0.7720 (mtmm) REVERT: E 277 ARG cc_start: 0.6793 (mmt-90) cc_final: 0.6412 (mmt-90) REVERT: E 292 MET cc_start: 0.5832 (mtp) cc_final: 0.5570 (mtp) REVERT: E 306 MET cc_start: 0.7609 (tpp) cc_final: 0.7264 (tpp) REVERT: E 482 GLU cc_start: 0.7176 (mm-30) cc_final: 0.6902 (tp30) REVERT: F 112 ASN cc_start: 0.8053 (p0) cc_final: 0.7616 (p0) REVERT: F 116 GLU cc_start: 0.6530 (tm-30) cc_final: 0.6140 (tm-30) REVERT: F 280 GLN cc_start: 0.6654 (tm-30) cc_final: 0.6369 (tm-30) REVERT: F 298 TYR cc_start: 0.7350 (m-80) cc_final: 0.7113 (m-80) REVERT: F 306 MET cc_start: 0.7852 (tpp) cc_final: 0.7230 (tpt) REVERT: F 311 GLU cc_start: 0.7781 (mt-10) cc_final: 0.7549 (tm-30) REVERT: F 398 TYR cc_start: 0.8287 (t80) cc_final: 0.7993 (t80) REVERT: F 425 ARG cc_start: 0.7379 (mmm-85) cc_final: 0.6324 (mmm160) REVERT: F 454 THR cc_start: 0.7274 (p) cc_final: 0.7057 (p) REVERT: F 488 MET cc_start: 0.6256 (tmm) cc_final: 0.5982 (tmm) REVERT: d 113 TYR cc_start: 0.6999 (t80) cc_final: 0.6774 (t80) REVERT: d 231 LYS cc_start: 0.6219 (mttt) cc_final: 0.5935 (mtpp) REVERT: e 35 PRO cc_start: 0.4284 (Cg_exo) cc_final: 0.4025 (Cg_endo) REVERT: g 270 MET cc_start: 0.5541 (ppp) cc_final: 0.5288 (ppp) REVERT: g 303 GLN cc_start: 0.6842 (mt0) cc_final: 0.6626 (mt0) outliers start: 92 outliers final: 58 residues processed: 656 average time/residue: 0.4345 time to fit residues: 435.5716 Evaluate side-chains 588 residues out of total 2939 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 530 time to evaluate : 3.422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 MET Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 379 VAL Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 437 THR Chi-restraints excluded: chain B residue 28 ASN Chi-restraints excluded: chain B residue 82 MET Chi-restraints excluded: chain B residue 197 VAL Chi-restraints excluded: chain B residue 252 TYR Chi-restraints excluded: chain B residue 339 THR Chi-restraints excluded: chain B residue 479 THR Chi-restraints excluded: chain C residue 98 ILE Chi-restraints excluded: chain C residue 130 ILE Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 171 ASP Chi-restraints excluded: chain C residue 197 VAL Chi-restraints excluded: chain C residue 199 ILE Chi-restraints excluded: chain C residue 230 ASP Chi-restraints excluded: chain C residue 294 LEU Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 383 LEU Chi-restraints excluded: chain C residue 431 VAL Chi-restraints excluded: chain C residue 436 MET Chi-restraints excluded: chain C residue 483 THR Chi-restraints excluded: chain D residue 72 ASN Chi-restraints excluded: chain D residue 85 LEU Chi-restraints excluded: chain D residue 106 THR Chi-restraints excluded: chain D residue 132 ILE Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain D residue 221 VAL Chi-restraints excluded: chain D residue 249 VAL Chi-restraints excluded: chain D residue 492 MET Chi-restraints excluded: chain E residue 61 VAL Chi-restraints excluded: chain E residue 63 CYS Chi-restraints excluded: chain E residue 93 ASP Chi-restraints excluded: chain E residue 144 THR Chi-restraints excluded: chain E residue 275 ILE Chi-restraints excluded: chain E residue 321 ILE Chi-restraints excluded: chain E residue 349 THR Chi-restraints excluded: chain E residue 462 LEU Chi-restraints excluded: chain F residue 68 LEU Chi-restraints excluded: chain F residue 124 VAL Chi-restraints excluded: chain F residue 349 THR Chi-restraints excluded: chain F residue 351 VAL Chi-restraints excluded: chain F residue 371 THR Chi-restraints excluded: chain F residue 373 THR Chi-restraints excluded: chain F residue 403 ASP Chi-restraints excluded: chain F residue 484 THR Chi-restraints excluded: chain d residue 129 LEU Chi-restraints excluded: chain d residue 207 VAL Chi-restraints excluded: chain d residue 223 ILE Chi-restraints excluded: chain e residue 44 VAL Chi-restraints excluded: chain e residue 96 LEU Chi-restraints excluded: chain e residue 129 SER Chi-restraints excluded: chain g residue 79 VAL Chi-restraints excluded: chain g residue 203 VAL Chi-restraints excluded: chain g residue 258 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 353 random chunks: chunk 178 optimal weight: 2.9990 chunk 99 optimal weight: 6.9990 chunk 266 optimal weight: 0.9980 chunk 218 optimal weight: 0.9990 chunk 88 optimal weight: 4.9990 chunk 321 optimal weight: 0.6980 chunk 346 optimal weight: 2.9990 chunk 286 optimal weight: 0.9990 chunk 318 optimal weight: 3.9990 chunk 109 optimal weight: 2.9990 chunk 257 optimal weight: 0.5980 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 173 GLN A 359 ASN B 398 GLN D 25 GLN D 310 GLN ** D 472 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** g 290 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7073 moved from start: 0.2009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 27897 Z= 0.253 Angle : 0.657 19.755 37815 Z= 0.327 Chirality : 0.045 0.224 4448 Planarity : 0.004 0.052 4910 Dihedral : 8.528 140.732 4055 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 15.63 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.73 % Favored : 93.19 % Rotamer: Outliers : 4.25 % Allowed : 19.60 % Favored : 76.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.11 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -2.06 (0.13), residues: 3551 helix: -0.20 (0.13), residues: 1445 sheet: -2.16 (0.21), residues: 493 loop : -2.18 (0.14), residues: 1613 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP e 57 HIS 0.003 0.001 HIS F 133 PHE 0.023 0.002 PHE D 149 TYR 0.021 0.002 TYR B 464 ARG 0.006 0.001 ARG F 52 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7102 Ramachandran restraints generated. 3551 Oldfield, 0 Emsley, 3551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7102 Ramachandran restraints generated. 3551 Oldfield, 0 Emsley, 3551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 685 residues out of total 2939 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 125 poor density : 560 time to evaluate : 3.434 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 145 GLU cc_start: 0.6355 (mp0) cc_final: 0.5984 (pm20) REVERT: A 166 GLU cc_start: 0.7406 (tp30) cc_final: 0.7008 (tp30) REVERT: A 385 LEU cc_start: 0.7288 (tt) cc_final: 0.6931 (tt) REVERT: A 389 GLN cc_start: 0.6711 (mt0) cc_final: 0.6128 (tm-30) REVERT: A 450 GLU cc_start: 0.5699 (tp30) cc_final: 0.4796 (tm-30) REVERT: B 498 MET cc_start: 0.7587 (tpp) cc_final: 0.7361 (tpp) REVERT: C 433 GLU cc_start: 0.7275 (mp0) cc_final: 0.6908 (mp0) REVERT: C 468 ASN cc_start: 0.7087 (t0) cc_final: 0.6665 (t0) REVERT: D 66 GLN cc_start: 0.7710 (mm-40) cc_final: 0.7351 (mm110) REVERT: D 208 GLU cc_start: 0.6606 (OUTLIER) cc_final: 0.6238 (tp30) REVERT: D 392 LYS cc_start: 0.8440 (mttm) cc_final: 0.7932 (mtpt) REVERT: E 145 LYS cc_start: 0.6405 (tptp) cc_final: 0.5626 (ttpp) REVERT: E 167 LYS cc_start: 0.8402 (mtmm) cc_final: 0.7780 (mtmm) REVERT: E 207 ARG cc_start: 0.6713 (tmm160) cc_final: 0.6428 (tmm-80) REVERT: E 273 ASP cc_start: 0.8165 (OUTLIER) cc_final: 0.7813 (t0) REVERT: E 277 ARG cc_start: 0.6989 (mmt-90) cc_final: 0.6491 (mmt-90) REVERT: E 306 MET cc_start: 0.7608 (tpp) cc_final: 0.7206 (tpp) REVERT: E 482 GLU cc_start: 0.7239 (mm-30) cc_final: 0.6920 (tp30) REVERT: F 112 ASN cc_start: 0.8051 (p0) cc_final: 0.7667 (p0) REVERT: F 270 LEU cc_start: 0.8558 (tp) cc_final: 0.8207 (mp) REVERT: F 280 GLN cc_start: 0.6702 (tm-30) cc_final: 0.6350 (tm-30) REVERT: F 306 MET cc_start: 0.7748 (tpp) cc_final: 0.7164 (tpt) REVERT: F 398 TYR cc_start: 0.8343 (t80) cc_final: 0.8002 (t80) REVERT: F 425 ARG cc_start: 0.7305 (mmm-85) cc_final: 0.6737 (mmm160) REVERT: F 465 GLU cc_start: 0.5866 (OUTLIER) cc_final: 0.5511 (tp30) REVERT: F 488 MET cc_start: 0.6194 (tmm) cc_final: 0.5681 (tmm) REVERT: d 78 TYR cc_start: 0.6913 (m-80) cc_final: 0.5940 (m-80) REVERT: d 82 LEU cc_start: 0.6174 (OUTLIER) cc_final: 0.5595 (mt) REVERT: d 113 TYR cc_start: 0.7023 (t80) cc_final: 0.6661 (t80) REVERT: d 231 LYS cc_start: 0.6154 (mttt) cc_final: 0.5885 (mtpp) REVERT: e 20 LYS cc_start: 0.4307 (mmmt) cc_final: 0.3995 (mmmt) REVERT: e 35 PRO cc_start: 0.4419 (Cg_exo) cc_final: 0.4133 (Cg_endo) REVERT: e 63 MET cc_start: 0.5807 (tmm) cc_final: 0.5409 (tmm) REVERT: g 179 TYR cc_start: 0.5604 (m-80) cc_final: 0.5372 (m-10) REVERT: g 236 LYS cc_start: 0.6151 (mmtm) cc_final: 0.5841 (mmtt) REVERT: g 270 MET cc_start: 0.5672 (ppp) cc_final: 0.5361 (ppp) REVERT: g 300 LEU cc_start: 0.7517 (tt) cc_final: 0.6235 (mt) REVERT: g 303 GLN cc_start: 0.6807 (mt0) cc_final: 0.6584 (mt0) outliers start: 125 outliers final: 85 residues processed: 635 average time/residue: 0.4237 time to fit residues: 411.1227 Evaluate side-chains 612 residues out of total 2939 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 523 time to evaluate : 3.010 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 ASP Chi-restraints excluded: chain A residue 49 MET Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 263 ASP Chi-restraints excluded: chain A residue 298 LEU Chi-restraints excluded: chain A residue 362 ILE Chi-restraints excluded: chain A residue 379 VAL Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain B residue 28 ASN Chi-restraints excluded: chain B residue 82 MET Chi-restraints excluded: chain B residue 92 THR Chi-restraints excluded: chain B residue 197 VAL Chi-restraints excluded: chain B residue 248 GLU Chi-restraints excluded: chain B residue 252 TYR Chi-restraints excluded: chain B residue 339 THR Chi-restraints excluded: chain B residue 449 LEU Chi-restraints excluded: chain B residue 479 THR Chi-restraints excluded: chain C residue 3 THR Chi-restraints excluded: chain C residue 77 MET Chi-restraints excluded: chain C residue 81 LEU Chi-restraints excluded: chain C residue 98 ILE Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 197 VAL Chi-restraints excluded: chain C residue 199 ILE Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 383 LEU Chi-restraints excluded: chain C residue 431 VAL Chi-restraints excluded: chain C residue 483 THR Chi-restraints excluded: chain D residue 72 ASN Chi-restraints excluded: chain D residue 85 LEU Chi-restraints excluded: chain D residue 90 GLU Chi-restraints excluded: chain D residue 100 VAL Chi-restraints excluded: chain D residue 106 THR Chi-restraints excluded: chain D residue 126 THR Chi-restraints excluded: chain D residue 132 ILE Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain D residue 208 GLU Chi-restraints excluded: chain D residue 221 VAL Chi-restraints excluded: chain D residue 249 VAL Chi-restraints excluded: chain E residue 61 VAL Chi-restraints excluded: chain E residue 63 CYS Chi-restraints excluded: chain E residue 64 GLU Chi-restraints excluded: chain E residue 91 VAL Chi-restraints excluded: chain E residue 93 ASP Chi-restraints excluded: chain E residue 144 THR Chi-restraints excluded: chain E residue 151 THR Chi-restraints excluded: chain E residue 273 ASP Chi-restraints excluded: chain E residue 275 ILE Chi-restraints excluded: chain E residue 321 ILE Chi-restraints excluded: chain E residue 323 SER Chi-restraints excluded: chain E residue 349 THR Chi-restraints excluded: chain E residue 420 THR Chi-restraints excluded: chain F residue 68 LEU Chi-restraints excluded: chain F residue 71 ASN Chi-restraints excluded: chain F residue 135 SER Chi-restraints excluded: chain F residue 196 VAL Chi-restraints excluded: chain F residue 202 VAL Chi-restraints excluded: chain F residue 303 SER Chi-restraints excluded: chain F residue 316 THR Chi-restraints excluded: chain F residue 335 THR Chi-restraints excluded: chain F residue 349 THR Chi-restraints excluded: chain F residue 351 VAL Chi-restraints excluded: chain F residue 371 THR Chi-restraints excluded: chain F residue 373 THR Chi-restraints excluded: chain F residue 403 ASP Chi-restraints excluded: chain F residue 415 GLU Chi-restraints excluded: chain F residue 465 GLU Chi-restraints excluded: chain F residue 477 VAL Chi-restraints excluded: chain F residue 479 ASN Chi-restraints excluded: chain F residue 484 THR Chi-restraints excluded: chain d residue 82 LEU Chi-restraints excluded: chain d residue 89 THR Chi-restraints excluded: chain d residue 91 THR Chi-restraints excluded: chain d residue 129 LEU Chi-restraints excluded: chain d residue 164 GLU Chi-restraints excluded: chain d residue 207 VAL Chi-restraints excluded: chain d residue 223 ILE Chi-restraints excluded: chain e residue 44 VAL Chi-restraints excluded: chain e residue 96 LEU Chi-restraints excluded: chain e residue 129 SER Chi-restraints excluded: chain g residue 79 VAL Chi-restraints excluded: chain g residue 105 VAL Chi-restraints excluded: chain g residue 203 VAL Chi-restraints excluded: chain g residue 231 LEU Chi-restraints excluded: chain g residue 258 THR Chi-restraints excluded: chain g residue 355 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 353 random chunks: chunk 317 optimal weight: 3.9990 chunk 241 optimal weight: 0.9990 chunk 166 optimal weight: 0.7980 chunk 35 optimal weight: 1.9990 chunk 153 optimal weight: 0.9980 chunk 215 optimal weight: 1.9990 chunk 322 optimal weight: 0.6980 chunk 341 optimal weight: 7.9990 chunk 168 optimal weight: 2.9990 chunk 305 optimal weight: 0.4980 chunk 91 optimal weight: 0.0050 overall best weight: 0.5994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 84 GLN ** A 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 173 GLN ** B 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 256 HIS D 299 GLN D 325 GLN D 472 GLN ** E 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 199 GLN g 290 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7052 moved from start: 0.2268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 27897 Z= 0.201 Angle : 0.623 19.863 37815 Z= 0.309 Chirality : 0.043 0.225 4448 Planarity : 0.004 0.052 4910 Dihedral : 8.239 134.003 4055 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 15.13 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.52 % Favored : 94.42 % Rotamer: Outliers : 4.66 % Allowed : 20.55 % Favored : 74.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.11 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.73 (0.13), residues: 3551 helix: 0.09 (0.13), residues: 1451 sheet: -1.97 (0.22), residues: 476 loop : -2.03 (0.14), residues: 1624 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP e 57 HIS 0.004 0.001 HIS B 43 PHE 0.023 0.001 PHE D 149 TYR 0.018 0.001 TYR F 475 ARG 0.012 0.000 ARG B 16 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7102 Ramachandran restraints generated. 3551 Oldfield, 0 Emsley, 3551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7102 Ramachandran restraints generated. 3551 Oldfield, 0 Emsley, 3551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 692 residues out of total 2939 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 137 poor density : 555 time to evaluate : 2.980 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 145 GLU cc_start: 0.6384 (mp0) cc_final: 0.6053 (pm20) REVERT: A 166 GLU cc_start: 0.7389 (tp30) cc_final: 0.7089 (tp30) REVERT: A 199 ILE cc_start: 0.7891 (OUTLIER) cc_final: 0.7635 (mt) REVERT: A 385 LEU cc_start: 0.7218 (tt) cc_final: 0.6852 (tt) REVERT: A 389 GLN cc_start: 0.6733 (mt0) cc_final: 0.6061 (tm-30) REVERT: A 450 GLU cc_start: 0.5749 (tp30) cc_final: 0.4816 (tm-30) REVERT: B 314 MET cc_start: 0.7515 (ttt) cc_final: 0.7052 (tmm) REVERT: B 376 MET cc_start: 0.6457 (mmt) cc_final: 0.6209 (mmt) REVERT: B 498 MET cc_start: 0.7716 (tpp) cc_final: 0.7439 (tpp) REVERT: C 292 PHE cc_start: 0.7432 (t80) cc_final: 0.7109 (t80) REVERT: D 66 GLN cc_start: 0.7747 (mm-40) cc_final: 0.7376 (mm110) REVERT: D 208 GLU cc_start: 0.6552 (OUTLIER) cc_final: 0.6203 (tp30) REVERT: D 392 LYS cc_start: 0.8414 (mttm) cc_final: 0.8123 (mtpt) REVERT: E 145 LYS cc_start: 0.6394 (tptp) cc_final: 0.5576 (ttpp) REVERT: E 167 LYS cc_start: 0.8396 (mtmm) cc_final: 0.7778 (mtmm) REVERT: E 273 ASP cc_start: 0.8111 (OUTLIER) cc_final: 0.7761 (t0) REVERT: E 277 ARG cc_start: 0.7043 (mmt-90) cc_final: 0.6605 (mmt-90) REVERT: E 306 MET cc_start: 0.7619 (tpp) cc_final: 0.7206 (tpp) REVERT: F 68 LEU cc_start: 0.7979 (OUTLIER) cc_final: 0.7647 (mt) REVERT: F 112 ASN cc_start: 0.8099 (p0) cc_final: 0.7676 (p0) REVERT: F 116 GLU cc_start: 0.6936 (tm-30) cc_final: 0.6198 (tm-30) REVERT: F 298 TYR cc_start: 0.7197 (m-80) cc_final: 0.6847 (m-80) REVERT: F 306 MET cc_start: 0.7699 (tpp) cc_final: 0.7209 (tpt) REVERT: F 398 TYR cc_start: 0.8307 (t80) cc_final: 0.7983 (t80) REVERT: F 425 ARG cc_start: 0.7332 (mmm-85) cc_final: 0.6798 (mmm160) REVERT: F 465 GLU cc_start: 0.5765 (OUTLIER) cc_final: 0.5443 (tp30) REVERT: F 488 MET cc_start: 0.6207 (tmm) cc_final: 0.5614 (tmm) REVERT: F 491 GLU cc_start: 0.6443 (mm-30) cc_final: 0.6124 (mm-30) REVERT: d 78 TYR cc_start: 0.6822 (m-80) cc_final: 0.5940 (m-80) REVERT: d 82 LEU cc_start: 0.6170 (OUTLIER) cc_final: 0.5567 (mt) REVERT: d 113 TYR cc_start: 0.6944 (t80) cc_final: 0.6669 (t80) REVERT: d 231 LYS cc_start: 0.5850 (mttt) cc_final: 0.5626 (mtpp) REVERT: e 35 PRO cc_start: 0.4292 (Cg_exo) cc_final: 0.3931 (Cg_endo) REVERT: g 270 MET cc_start: 0.5705 (ppp) cc_final: 0.5437 (ppp) REVERT: g 300 LEU cc_start: 0.7514 (tt) cc_final: 0.6237 (mt) REVERT: g 323 MET cc_start: 0.8465 (OUTLIER) cc_final: 0.8207 (mmp) outliers start: 137 outliers final: 100 residues processed: 640 average time/residue: 0.4325 time to fit residues: 432.8489 Evaluate side-chains 610 residues out of total 2939 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 107 poor density : 503 time to evaluate : 3.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 MET Chi-restraints excluded: chain A residue 70 ASN Chi-restraints excluded: chain A residue 84 GLN Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 199 ILE Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 263 ASP Chi-restraints excluded: chain A residue 298 LEU Chi-restraints excluded: chain A residue 362 ILE Chi-restraints excluded: chain A residue 379 VAL Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 454 VAL Chi-restraints excluded: chain B residue 28 ASN Chi-restraints excluded: chain B residue 82 MET Chi-restraints excluded: chain B residue 92 THR Chi-restraints excluded: chain B residue 192 VAL Chi-restraints excluded: chain B residue 197 VAL Chi-restraints excluded: chain B residue 210 VAL Chi-restraints excluded: chain B residue 248 GLU Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 339 THR Chi-restraints excluded: chain B residue 431 VAL Chi-restraints excluded: chain B residue 449 LEU Chi-restraints excluded: chain B residue 501 PHE Chi-restraints excluded: chain C residue 3 THR Chi-restraints excluded: chain C residue 77 MET Chi-restraints excluded: chain C residue 81 LEU Chi-restraints excluded: chain C residue 98 ILE Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 197 VAL Chi-restraints excluded: chain C residue 199 ILE Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 383 LEU Chi-restraints excluded: chain C residue 431 VAL Chi-restraints excluded: chain C residue 483 THR Chi-restraints excluded: chain D residue 72 ASN Chi-restraints excluded: chain D residue 85 LEU Chi-restraints excluded: chain D residue 90 GLU Chi-restraints excluded: chain D residue 106 THR Chi-restraints excluded: chain D residue 126 THR Chi-restraints excluded: chain D residue 132 ILE Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain D residue 180 VAL Chi-restraints excluded: chain D residue 185 LEU Chi-restraints excluded: chain D residue 208 GLU Chi-restraints excluded: chain D residue 221 VAL Chi-restraints excluded: chain D residue 249 VAL Chi-restraints excluded: chain D residue 299 GLN Chi-restraints excluded: chain D residue 313 ILE Chi-restraints excluded: chain D residue 356 LEU Chi-restraints excluded: chain D residue 472 GLN Chi-restraints excluded: chain E residue 61 VAL Chi-restraints excluded: chain E residue 63 CYS Chi-restraints excluded: chain E residue 64 GLU Chi-restraints excluded: chain E residue 91 VAL Chi-restraints excluded: chain E residue 93 ASP Chi-restraints excluded: chain E residue 144 THR Chi-restraints excluded: chain E residue 210 ASN Chi-restraints excluded: chain E residue 273 ASP Chi-restraints excluded: chain E residue 275 ILE Chi-restraints excluded: chain E residue 320 SER Chi-restraints excluded: chain E residue 321 ILE Chi-restraints excluded: chain E residue 349 THR Chi-restraints excluded: chain E residue 419 LEU Chi-restraints excluded: chain E residue 420 THR Chi-restraints excluded: chain F residue 68 LEU Chi-restraints excluded: chain F residue 71 ASN Chi-restraints excluded: chain F residue 102 VAL Chi-restraints excluded: chain F residue 124 VAL Chi-restraints excluded: chain F residue 135 SER Chi-restraints excluded: chain F residue 155 VAL Chi-restraints excluded: chain F residue 196 VAL Chi-restraints excluded: chain F residue 202 VAL Chi-restraints excluded: chain F residue 234 LEU Chi-restraints excluded: chain F residue 303 SER Chi-restraints excluded: chain F residue 335 THR Chi-restraints excluded: chain F residue 349 THR Chi-restraints excluded: chain F residue 351 VAL Chi-restraints excluded: chain F residue 371 THR Chi-restraints excluded: chain F residue 373 THR Chi-restraints excluded: chain F residue 403 ASP Chi-restraints excluded: chain F residue 415 GLU Chi-restraints excluded: chain F residue 465 GLU Chi-restraints excluded: chain F residue 477 VAL Chi-restraints excluded: chain F residue 479 ASN Chi-restraints excluded: chain F residue 484 THR Chi-restraints excluded: chain d residue 82 LEU Chi-restraints excluded: chain d residue 89 THR Chi-restraints excluded: chain d residue 91 THR Chi-restraints excluded: chain d residue 164 GLU Chi-restraints excluded: chain d residue 180 VAL Chi-restraints excluded: chain d residue 207 VAL Chi-restraints excluded: chain d residue 214 ASP Chi-restraints excluded: chain d residue 223 ILE Chi-restraints excluded: chain e residue 44 VAL Chi-restraints excluded: chain e residue 87 ILE Chi-restraints excluded: chain e residue 96 LEU Chi-restraints excluded: chain e residue 103 LEU Chi-restraints excluded: chain e residue 129 SER Chi-restraints excluded: chain g residue 79 VAL Chi-restraints excluded: chain g residue 105 VAL Chi-restraints excluded: chain g residue 203 VAL Chi-restraints excluded: chain g residue 231 LEU Chi-restraints excluded: chain g residue 258 THR Chi-restraints excluded: chain g residue 323 MET Chi-restraints excluded: chain g residue 355 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 353 random chunks: chunk 284 optimal weight: 0.6980 chunk 193 optimal weight: 0.0870 chunk 4 optimal weight: 0.9980 chunk 254 optimal weight: 0.0170 chunk 140 optimal weight: 0.9990 chunk 291 optimal weight: 4.9990 chunk 235 optimal weight: 0.8980 chunk 0 optimal weight: 7.9990 chunk 174 optimal weight: 1.9990 chunk 306 optimal weight: 0.0470 chunk 86 optimal weight: 1.9990 overall best weight: 0.3494 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 173 GLN ** B 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 473 GLN C 372 GLN D 66 GLN D 299 GLN ** E 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 139 GLN d 141 HIS e 102 ASN g 290 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7027 moved from start: 0.2509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 27897 Z= 0.164 Angle : 0.609 19.738 37815 Z= 0.299 Chirality : 0.043 0.203 4448 Planarity : 0.004 0.052 4910 Dihedral : 7.963 128.156 4055 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 14.84 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.72 % Favored : 94.23 % Rotamer: Outliers : 4.08 % Allowed : 22.32 % Favored : 73.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.11 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.46 (0.14), residues: 3551 helix: 0.32 (0.14), residues: 1446 sheet: -1.84 (0.22), residues: 480 loop : -1.87 (0.14), residues: 1625 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP e 57 HIS 0.004 0.001 HIS B 43 PHE 0.022 0.001 PHE D 149 TYR 0.020 0.001 TYR F 475 ARG 0.011 0.000 ARG B 16 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7102 Ramachandran restraints generated. 3551 Oldfield, 0 Emsley, 3551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7102 Ramachandran restraints generated. 3551 Oldfield, 0 Emsley, 3551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 663 residues out of total 2939 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 120 poor density : 543 time to evaluate : 3.120 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 145 GLU cc_start: 0.6370 (mp0) cc_final: 0.6047 (pm20) REVERT: A 171 ASP cc_start: 0.7898 (t0) cc_final: 0.7537 (t0) REVERT: A 199 ILE cc_start: 0.7836 (OUTLIER) cc_final: 0.7547 (mt) REVERT: A 385 LEU cc_start: 0.7172 (tt) cc_final: 0.6790 (tt) REVERT: A 389 GLN cc_start: 0.6664 (mt0) cc_final: 0.6069 (tm-30) REVERT: A 450 GLU cc_start: 0.5694 (tp30) cc_final: 0.4820 (tm-30) REVERT: B 16 ARG cc_start: 0.6091 (ttt-90) cc_final: 0.5865 (ttp-170) REVERT: B 314 MET cc_start: 0.7549 (ttt) cc_final: 0.7106 (tmm) REVERT: B 420 LEU cc_start: 0.8323 (tt) cc_final: 0.8083 (tp) REVERT: B 498 MET cc_start: 0.7770 (tpp) cc_final: 0.7529 (tpp) REVERT: C 52 GLU cc_start: 0.7467 (mm-30) cc_final: 0.7160 (tp30) REVERT: C 405 LYS cc_start: 0.7174 (pptt) cc_final: 0.6922 (pptt) REVERT: D 66 GLN cc_start: 0.7683 (mm110) cc_final: 0.7300 (mm110) REVERT: D 208 GLU cc_start: 0.6497 (OUTLIER) cc_final: 0.6139 (tp30) REVERT: D 224 GLU cc_start: 0.5292 (pm20) cc_final: 0.5009 (pp20) REVERT: D 374 MET cc_start: 0.6307 (mmt) cc_final: 0.5618 (mmt) REVERT: D 392 LYS cc_start: 0.8448 (mttm) cc_final: 0.8218 (mttt) REVERT: E 40 MET cc_start: 0.6150 (tpp) cc_final: 0.5945 (mmt) REVERT: E 145 LYS cc_start: 0.6282 (tptp) cc_final: 0.5529 (ttpp) REVERT: E 167 LYS cc_start: 0.8389 (mtmm) cc_final: 0.7756 (mtmm) REVERT: E 204 GLU cc_start: 0.6680 (mm-30) cc_final: 0.6289 (mm-30) REVERT: E 273 ASP cc_start: 0.8079 (OUTLIER) cc_final: 0.7656 (t0) REVERT: E 277 ARG cc_start: 0.7051 (mmt-90) cc_final: 0.6564 (mmt-90) REVERT: E 306 MET cc_start: 0.7640 (tpp) cc_final: 0.7207 (tpp) REVERT: F 112 ASN cc_start: 0.8092 (p0) cc_final: 0.7681 (p0) REVERT: F 116 GLU cc_start: 0.6938 (tm-30) cc_final: 0.6241 (tm-30) REVERT: F 298 TYR cc_start: 0.7186 (m-80) cc_final: 0.6784 (m-80) REVERT: F 306 MET cc_start: 0.7721 (tpp) cc_final: 0.7222 (tpt) REVERT: F 398 TYR cc_start: 0.8311 (t80) cc_final: 0.8058 (t80) REVERT: F 425 ARG cc_start: 0.7195 (mmm-85) cc_final: 0.6698 (mmm160) REVERT: F 465 GLU cc_start: 0.5613 (OUTLIER) cc_final: 0.5344 (mp0) REVERT: F 488 MET cc_start: 0.6151 (tmm) cc_final: 0.5577 (tmm) REVERT: d 78 TYR cc_start: 0.6524 (m-80) cc_final: 0.5982 (m-80) REVERT: d 113 TYR cc_start: 0.6883 (t80) cc_final: 0.6612 (t80) REVERT: d 231 LYS cc_start: 0.5843 (mttt) cc_final: 0.5627 (mtpp) REVERT: e 35 PRO cc_start: 0.4273 (Cg_exo) cc_final: 0.3838 (Cg_endo) REVERT: g 270 MET cc_start: 0.5729 (ppp) cc_final: 0.5505 (ppp) REVERT: g 300 LEU cc_start: 0.7469 (tt) cc_final: 0.6267 (mt) REVERT: g 303 GLN cc_start: 0.6513 (mt0) cc_final: 0.6165 (mt0) REVERT: g 323 MET cc_start: 0.8473 (OUTLIER) cc_final: 0.8187 (mmp) outliers start: 120 outliers final: 98 residues processed: 617 average time/residue: 0.4113 time to fit residues: 395.5177 Evaluate side-chains 608 residues out of total 2939 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 505 time to evaluate : 3.160 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 ASP Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 70 ASN Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 199 ILE Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 263 ASP Chi-restraints excluded: chain A residue 298 LEU Chi-restraints excluded: chain A residue 362 ILE Chi-restraints excluded: chain A residue 379 VAL Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain B residue 28 ASN Chi-restraints excluded: chain B residue 82 MET Chi-restraints excluded: chain B residue 92 THR Chi-restraints excluded: chain B residue 192 VAL Chi-restraints excluded: chain B residue 197 VAL Chi-restraints excluded: chain B residue 210 VAL Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 339 THR Chi-restraints excluded: chain B residue 431 VAL Chi-restraints excluded: chain B residue 449 LEU Chi-restraints excluded: chain B residue 479 THR Chi-restraints excluded: chain B residue 501 PHE Chi-restraints excluded: chain C residue 3 THR Chi-restraints excluded: chain C residue 60 THR Chi-restraints excluded: chain C residue 70 ASN Chi-restraints excluded: chain C residue 77 MET Chi-restraints excluded: chain C residue 81 LEU Chi-restraints excluded: chain C residue 98 ILE Chi-restraints excluded: chain C residue 197 VAL Chi-restraints excluded: chain C residue 199 ILE Chi-restraints excluded: chain C residue 337 SER Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 383 LEU Chi-restraints excluded: chain C residue 431 VAL Chi-restraints excluded: chain C residue 483 THR Chi-restraints excluded: chain D residue 72 ASN Chi-restraints excluded: chain D residue 85 LEU Chi-restraints excluded: chain D residue 90 GLU Chi-restraints excluded: chain D residue 100 VAL Chi-restraints excluded: chain D residue 106 THR Chi-restraints excluded: chain D residue 126 THR Chi-restraints excluded: chain D residue 132 ILE Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain D residue 185 LEU Chi-restraints excluded: chain D residue 208 GLU Chi-restraints excluded: chain D residue 221 VAL Chi-restraints excluded: chain D residue 249 VAL Chi-restraints excluded: chain D residue 313 ILE Chi-restraints excluded: chain D residue 356 LEU Chi-restraints excluded: chain D residue 472 GLN Chi-restraints excluded: chain E residue 61 VAL Chi-restraints excluded: chain E residue 63 CYS Chi-restraints excluded: chain E residue 64 GLU Chi-restraints excluded: chain E residue 91 VAL Chi-restraints excluded: chain E residue 142 LEU Chi-restraints excluded: chain E residue 151 THR Chi-restraints excluded: chain E residue 206 THR Chi-restraints excluded: chain E residue 210 ASN Chi-restraints excluded: chain E residue 273 ASP Chi-restraints excluded: chain E residue 275 ILE Chi-restraints excluded: chain E residue 321 ILE Chi-restraints excluded: chain E residue 420 THR Chi-restraints excluded: chain F residue 102 VAL Chi-restraints excluded: chain F residue 155 VAL Chi-restraints excluded: chain F residue 196 VAL Chi-restraints excluded: chain F residue 202 VAL Chi-restraints excluded: chain F residue 234 LEU Chi-restraints excluded: chain F residue 316 THR Chi-restraints excluded: chain F residue 335 THR Chi-restraints excluded: chain F residue 349 THR Chi-restraints excluded: chain F residue 351 VAL Chi-restraints excluded: chain F residue 371 THR Chi-restraints excluded: chain F residue 373 THR Chi-restraints excluded: chain F residue 403 ASP Chi-restraints excluded: chain F residue 415 GLU Chi-restraints excluded: chain F residue 465 GLU Chi-restraints excluded: chain F residue 477 VAL Chi-restraints excluded: chain F residue 479 ASN Chi-restraints excluded: chain F residue 484 THR Chi-restraints excluded: chain d residue 82 LEU Chi-restraints excluded: chain d residue 89 THR Chi-restraints excluded: chain d residue 91 THR Chi-restraints excluded: chain d residue 129 LEU Chi-restraints excluded: chain d residue 161 ILE Chi-restraints excluded: chain d residue 164 GLU Chi-restraints excluded: chain d residue 207 VAL Chi-restraints excluded: chain d residue 223 ILE Chi-restraints excluded: chain e residue 44 VAL Chi-restraints excluded: chain e residue 75 THR Chi-restraints excluded: chain e residue 87 ILE Chi-restraints excluded: chain e residue 96 LEU Chi-restraints excluded: chain e residue 129 SER Chi-restraints excluded: chain g residue 64 MET Chi-restraints excluded: chain g residue 105 VAL Chi-restraints excluded: chain g residue 203 VAL Chi-restraints excluded: chain g residue 231 LEU Chi-restraints excluded: chain g residue 257 LEU Chi-restraints excluded: chain g residue 258 THR Chi-restraints excluded: chain g residue 323 MET Chi-restraints excluded: chain g residue 355 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 353 random chunks: chunk 114 optimal weight: 0.5980 chunk 307 optimal weight: 6.9990 chunk 67 optimal weight: 0.0020 chunk 200 optimal weight: 2.9990 chunk 84 optimal weight: 0.0770 chunk 341 optimal weight: 3.9990 chunk 283 optimal weight: 0.0270 chunk 158 optimal weight: 2.9990 chunk 28 optimal weight: 0.9980 chunk 112 optimal weight: 0.0270 chunk 179 optimal weight: 0.8980 overall best weight: 0.1462 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 84 GLN ** A 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 173 GLN ** B 473 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 497 GLN ** C 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 299 GLN D 472 GLN ** E 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 489 ASN ** g 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 286 GLN g 290 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6989 moved from start: 0.2795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 27897 Z= 0.142 Angle : 0.589 19.608 37815 Z= 0.288 Chirality : 0.042 0.178 4448 Planarity : 0.004 0.051 4910 Dihedral : 7.647 120.098 4055 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 13.63 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.65 % Favored : 95.30 % Rotamer: Outliers : 4.15 % Allowed : 22.52 % Favored : 73.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.11 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.17 (0.14), residues: 3551 helix: 0.55 (0.14), residues: 1450 sheet: -1.61 (0.23), residues: 468 loop : -1.73 (0.15), residues: 1633 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP e 57 HIS 0.005 0.001 HIS B 43 PHE 0.024 0.001 PHE B 390 TYR 0.019 0.001 TYR B 237 ARG 0.009 0.000 ARG g 170 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7102 Ramachandran restraints generated. 3551 Oldfield, 0 Emsley, 3551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7102 Ramachandran restraints generated. 3551 Oldfield, 0 Emsley, 3551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 685 residues out of total 2939 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 122 poor density : 563 time to evaluate : 2.963 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 171 ASP cc_start: 0.7798 (t0) cc_final: 0.7460 (t0) REVERT: A 199 ILE cc_start: 0.7794 (OUTLIER) cc_final: 0.7548 (mt) REVERT: A 385 LEU cc_start: 0.7194 (tt) cc_final: 0.6841 (tt) REVERT: A 389 GLN cc_start: 0.6828 (mt0) cc_final: 0.6025 (tm-30) REVERT: A 450 GLU cc_start: 0.5738 (tp30) cc_final: 0.4940 (tm-30) REVERT: B 16 ARG cc_start: 0.6010 (ttt-90) cc_final: 0.5806 (ttt-90) REVERT: B 115 PRO cc_start: 0.8457 (Cg_endo) cc_final: 0.8215 (Cg_exo) REVERT: B 122 ILE cc_start: 0.8144 (mm) cc_final: 0.7785 (mm) REVERT: B 314 MET cc_start: 0.7592 (ttt) cc_final: 0.7203 (tmm) REVERT: B 498 MET cc_start: 0.7624 (tpp) cc_final: 0.7378 (tpp) REVERT: C 52 GLU cc_start: 0.7322 (mm-30) cc_final: 0.7100 (tp30) REVERT: C 405 LYS cc_start: 0.7154 (pptt) cc_final: 0.6898 (pptt) REVERT: D 66 GLN cc_start: 0.7497 (mm110) cc_final: 0.7220 (mm110) REVERT: D 208 GLU cc_start: 0.6450 (OUTLIER) cc_final: 0.6075 (tp30) REVERT: D 224 GLU cc_start: 0.5283 (pm20) cc_final: 0.5023 (pp20) REVERT: D 374 MET cc_start: 0.6315 (mmt) cc_final: 0.5740 (mmt) REVERT: E 145 LYS cc_start: 0.6456 (tptp) cc_final: 0.5768 (ttpp) REVERT: E 167 LYS cc_start: 0.8359 (mtmm) cc_final: 0.7741 (mtmm) REVERT: E 214 MET cc_start: 0.6715 (mmt) cc_final: 0.6509 (mmt) REVERT: E 267 ASP cc_start: 0.6728 (t0) cc_final: 0.6306 (t70) REVERT: E 277 ARG cc_start: 0.6837 (mmt-90) cc_final: 0.6374 (mmt-90) REVERT: E 306 MET cc_start: 0.7651 (tpp) cc_final: 0.7229 (tpp) REVERT: F 298 TYR cc_start: 0.7081 (m-80) cc_final: 0.6747 (m-80) REVERT: F 306 MET cc_start: 0.7726 (tpp) cc_final: 0.7266 (tpt) REVERT: F 425 ARG cc_start: 0.7112 (mmm-85) cc_final: 0.6685 (mmm160) REVERT: F 465 GLU cc_start: 0.5522 (OUTLIER) cc_final: 0.5307 (mp0) REVERT: F 488 MET cc_start: 0.6130 (tmm) cc_final: 0.5791 (tmm) REVERT: d 78 TYR cc_start: 0.6403 (m-80) cc_final: 0.6035 (m-80) REVERT: d 231 LYS cc_start: 0.5763 (mttt) cc_final: 0.5517 (mtpp) REVERT: e 35 PRO cc_start: 0.4230 (Cg_exo) cc_final: 0.3806 (Cg_endo) REVERT: g 73 ARG cc_start: 0.6930 (tpm170) cc_final: 0.6099 (tpm170) REVERT: g 76 GLN cc_start: 0.7105 (tm-30) cc_final: 0.6882 (tm-30) REVERT: g 300 LEU cc_start: 0.7565 (tt) cc_final: 0.6381 (mt) REVERT: g 303 GLN cc_start: 0.6539 (mt0) cc_final: 0.6256 (mt0) REVERT: g 323 MET cc_start: 0.8413 (OUTLIER) cc_final: 0.8089 (mmp) REVERT: g 350 THR cc_start: 0.7559 (m) cc_final: 0.7022 (p) outliers start: 122 outliers final: 81 residues processed: 639 average time/residue: 0.4157 time to fit residues: 411.6079 Evaluate side-chains 602 residues out of total 2939 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 517 time to evaluate : 3.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 MET Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 97 GLN Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 199 ILE Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 263 ASP Chi-restraints excluded: chain A residue 362 ILE Chi-restraints excluded: chain A residue 379 VAL Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 449 LEU Chi-restraints excluded: chain B residue 28 ASN Chi-restraints excluded: chain B residue 92 THR Chi-restraints excluded: chain B residue 197 VAL Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 339 THR Chi-restraints excluded: chain B residue 431 VAL Chi-restraints excluded: chain B residue 449 LEU Chi-restraints excluded: chain B residue 479 THR Chi-restraints excluded: chain C residue 3 THR Chi-restraints excluded: chain C residue 70 ASN Chi-restraints excluded: chain C residue 197 VAL Chi-restraints excluded: chain C residue 199 ILE Chi-restraints excluded: chain C residue 337 SER Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 383 LEU Chi-restraints excluded: chain C residue 453 GLN Chi-restraints excluded: chain C residue 483 THR Chi-restraints excluded: chain D residue 40 MET Chi-restraints excluded: chain D residue 72 ASN Chi-restraints excluded: chain D residue 85 LEU Chi-restraints excluded: chain D residue 90 GLU Chi-restraints excluded: chain D residue 100 VAL Chi-restraints excluded: chain D residue 106 THR Chi-restraints excluded: chain D residue 126 THR Chi-restraints excluded: chain D residue 132 ILE Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain D residue 185 LEU Chi-restraints excluded: chain D residue 208 GLU Chi-restraints excluded: chain D residue 221 VAL Chi-restraints excluded: chain D residue 249 VAL Chi-restraints excluded: chain D residue 313 ILE Chi-restraints excluded: chain E residue 31 LEU Chi-restraints excluded: chain E residue 61 VAL Chi-restraints excluded: chain E residue 64 GLU Chi-restraints excluded: chain E residue 91 VAL Chi-restraints excluded: chain E residue 93 ASP Chi-restraints excluded: chain E residue 206 THR Chi-restraints excluded: chain E residue 210 ASN Chi-restraints excluded: chain E residue 275 ILE Chi-restraints excluded: chain E residue 321 ILE Chi-restraints excluded: chain E residue 349 THR Chi-restraints excluded: chain E residue 419 LEU Chi-restraints excluded: chain F residue 102 VAL Chi-restraints excluded: chain F residue 118 VAL Chi-restraints excluded: chain F residue 124 VAL Chi-restraints excluded: chain F residue 196 VAL Chi-restraints excluded: chain F residue 202 VAL Chi-restraints excluded: chain F residue 335 THR Chi-restraints excluded: chain F residue 349 THR Chi-restraints excluded: chain F residue 371 THR Chi-restraints excluded: chain F residue 373 THR Chi-restraints excluded: chain F residue 403 ASP Chi-restraints excluded: chain F residue 415 GLU Chi-restraints excluded: chain F residue 461 ILE Chi-restraints excluded: chain F residue 465 GLU Chi-restraints excluded: chain d residue 82 LEU Chi-restraints excluded: chain d residue 89 THR Chi-restraints excluded: chain d residue 91 THR Chi-restraints excluded: chain d residue 129 LEU Chi-restraints excluded: chain d residue 138 LEU Chi-restraints excluded: chain d residue 161 ILE Chi-restraints excluded: chain d residue 180 VAL Chi-restraints excluded: chain d residue 207 VAL Chi-restraints excluded: chain d residue 214 ASP Chi-restraints excluded: chain d residue 223 ILE Chi-restraints excluded: chain e residue 44 VAL Chi-restraints excluded: chain e residue 75 THR Chi-restraints excluded: chain e residue 96 LEU Chi-restraints excluded: chain g residue 165 ASN Chi-restraints excluded: chain g residue 203 VAL Chi-restraints excluded: chain g residue 231 LEU Chi-restraints excluded: chain g residue 258 THR Chi-restraints excluded: chain g residue 323 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 353 random chunks: chunk 329 optimal weight: 4.9990 chunk 38 optimal weight: 0.0020 chunk 194 optimal weight: 3.9990 chunk 249 optimal weight: 1.9990 chunk 193 optimal weight: 1.9990 chunk 287 optimal weight: 0.9990 chunk 190 optimal weight: 0.5980 chunk 340 optimal weight: 2.9990 chunk 212 optimal weight: 0.9990 chunk 207 optimal weight: 0.0270 chunk 157 optimal weight: 1.9990 overall best weight: 0.5250 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 173 GLN ** B 473 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 497 GLN C 173 GLN D 67 GLN ** D 472 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 472 GLN ** F 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 290 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7019 moved from start: 0.2884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 27897 Z= 0.188 Angle : 0.621 19.624 37815 Z= 0.303 Chirality : 0.043 0.289 4448 Planarity : 0.004 0.051 4910 Dihedral : 7.647 117.697 4055 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 14.91 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.74 % Favored : 94.20 % Rotamer: Outliers : 4.12 % Allowed : 23.41 % Favored : 72.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.11 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.12 (0.14), residues: 3551 helix: 0.59 (0.14), residues: 1450 sheet: -1.68 (0.22), residues: 479 loop : -1.66 (0.15), residues: 1622 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP e 57 HIS 0.002 0.001 HIS E 133 PHE 0.023 0.001 PHE D 149 TYR 0.026 0.001 TYR F 398 ARG 0.008 0.000 ARG g 170 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7102 Ramachandran restraints generated. 3551 Oldfield, 0 Emsley, 3551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7102 Ramachandran restraints generated. 3551 Oldfield, 0 Emsley, 3551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 651 residues out of total 2939 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 121 poor density : 530 time to evaluate : 3.359 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 14 ARG cc_start: 0.5839 (tmm160) cc_final: 0.5594 (tmm160) REVERT: A 171 ASP cc_start: 0.7835 (t0) cc_final: 0.7459 (t0) REVERT: A 199 ILE cc_start: 0.7837 (OUTLIER) cc_final: 0.7557 (mt) REVERT: A 385 LEU cc_start: 0.7165 (tt) cc_final: 0.6802 (mt) REVERT: A 389 GLN cc_start: 0.6840 (mt0) cc_final: 0.5881 (tm-30) REVERT: A 450 GLU cc_start: 0.5828 (tp30) cc_final: 0.4956 (tm-30) REVERT: B 314 MET cc_start: 0.7607 (ttt) cc_final: 0.7174 (tmm) REVERT: B 378 LYS cc_start: 0.7821 (ptpt) cc_final: 0.7280 (mtmt) REVERT: B 498 MET cc_start: 0.7639 (tpp) cc_final: 0.7420 (tpp) REVERT: C 49 MET cc_start: 0.6233 (tpt) cc_final: 0.5878 (tpt) REVERT: C 405 LYS cc_start: 0.7190 (pptt) cc_final: 0.6957 (pptt) REVERT: D 66 GLN cc_start: 0.7553 (mm110) cc_final: 0.7231 (mm110) REVERT: D 89 MET cc_start: 0.8157 (mtm) cc_final: 0.7880 (mtt) REVERT: D 208 GLU cc_start: 0.6427 (OUTLIER) cc_final: 0.6133 (tp30) REVERT: D 224 GLU cc_start: 0.5445 (pm20) cc_final: 0.5217 (pp20) REVERT: D 374 MET cc_start: 0.6319 (mmt) cc_final: 0.5747 (mmt) REVERT: D 392 LYS cc_start: 0.9030 (mmmm) cc_final: 0.8621 (mmtp) REVERT: E 145 LYS cc_start: 0.6445 (tptp) cc_final: 0.5834 (ttpp) REVERT: E 167 LYS cc_start: 0.8382 (mtmm) cc_final: 0.7710 (mtmm) REVERT: E 214 MET cc_start: 0.6805 (mmt) cc_final: 0.6550 (mmt) REVERT: E 267 ASP cc_start: 0.6814 (t0) cc_final: 0.6472 (t70) REVERT: E 273 ASP cc_start: 0.8126 (OUTLIER) cc_final: 0.7776 (t0) REVERT: E 277 ARG cc_start: 0.6990 (mmt-90) cc_final: 0.6577 (mmt-90) REVERT: E 306 MET cc_start: 0.7660 (tpp) cc_final: 0.7226 (tpp) REVERT: F 298 TYR cc_start: 0.7161 (m-80) cc_final: 0.6815 (m-80) REVERT: F 306 MET cc_start: 0.7752 (tpp) cc_final: 0.7541 (tpt) REVERT: F 425 ARG cc_start: 0.7191 (mmm-85) cc_final: 0.6637 (mmm160) REVERT: F 456 ARG cc_start: 0.6881 (ttp80) cc_final: 0.6647 (ttp80) REVERT: F 465 GLU cc_start: 0.5507 (OUTLIER) cc_final: 0.5301 (tp30) REVERT: d 78 TYR cc_start: 0.6471 (m-80) cc_final: 0.6122 (m-80) REVERT: d 231 LYS cc_start: 0.5736 (mttt) cc_final: 0.5503 (mtpp) REVERT: g 73 ARG cc_start: 0.7009 (tpm170) cc_final: 0.6801 (tpm170) REVERT: g 300 LEU cc_start: 0.7581 (tt) cc_final: 0.6342 (mt) REVERT: g 303 GLN cc_start: 0.6736 (mt0) cc_final: 0.6501 (mt0) REVERT: g 323 MET cc_start: 0.8499 (OUTLIER) cc_final: 0.8214 (mmp) outliers start: 121 outliers final: 97 residues processed: 608 average time/residue: 0.4146 time to fit residues: 391.0697 Evaluate side-chains 616 residues out of total 2939 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 514 time to evaluate : 2.838 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 MET Chi-restraints excluded: chain A residue 55 GLU Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 199 ILE Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 263 ASP Chi-restraints excluded: chain A residue 298 LEU Chi-restraints excluded: chain A residue 362 ILE Chi-restraints excluded: chain A residue 379 VAL Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 454 VAL Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain B residue 21 ASN Chi-restraints excluded: chain B residue 28 ASN Chi-restraints excluded: chain B residue 82 MET Chi-restraints excluded: chain B residue 92 THR Chi-restraints excluded: chain B residue 197 VAL Chi-restraints excluded: chain B residue 210 VAL Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 339 THR Chi-restraints excluded: chain B residue 449 LEU Chi-restraints excluded: chain B residue 479 THR Chi-restraints excluded: chain B residue 501 PHE Chi-restraints excluded: chain C residue 3 THR Chi-restraints excluded: chain C residue 60 THR Chi-restraints excluded: chain C residue 70 ASN Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain C residue 98 ILE Chi-restraints excluded: chain C residue 197 VAL Chi-restraints excluded: chain C residue 199 ILE Chi-restraints excluded: chain C residue 337 SER Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 383 LEU Chi-restraints excluded: chain C residue 431 VAL Chi-restraints excluded: chain C residue 483 THR Chi-restraints excluded: chain D residue 72 ASN Chi-restraints excluded: chain D residue 85 LEU Chi-restraints excluded: chain D residue 90 GLU Chi-restraints excluded: chain D residue 100 VAL Chi-restraints excluded: chain D residue 106 THR Chi-restraints excluded: chain D residue 126 THR Chi-restraints excluded: chain D residue 132 ILE Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain D residue 208 GLU Chi-restraints excluded: chain D residue 221 VAL Chi-restraints excluded: chain D residue 249 VAL Chi-restraints excluded: chain D residue 313 ILE Chi-restraints excluded: chain D residue 472 GLN Chi-restraints excluded: chain E residue 31 LEU Chi-restraints excluded: chain E residue 61 VAL Chi-restraints excluded: chain E residue 64 GLU Chi-restraints excluded: chain E residue 91 VAL Chi-restraints excluded: chain E residue 93 ASP Chi-restraints excluded: chain E residue 142 LEU Chi-restraints excluded: chain E residue 144 THR Chi-restraints excluded: chain E residue 210 ASN Chi-restraints excluded: chain E residue 273 ASP Chi-restraints excluded: chain E residue 275 ILE Chi-restraints excluded: chain E residue 321 ILE Chi-restraints excluded: chain E residue 349 THR Chi-restraints excluded: chain E residue 419 LEU Chi-restraints excluded: chain F residue 102 VAL Chi-restraints excluded: chain F residue 116 GLU Chi-restraints excluded: chain F residue 118 VAL Chi-restraints excluded: chain F residue 124 VAL Chi-restraints excluded: chain F residue 155 VAL Chi-restraints excluded: chain F residue 196 VAL Chi-restraints excluded: chain F residue 202 VAL Chi-restraints excluded: chain F residue 218 GLU Chi-restraints excluded: chain F residue 335 THR Chi-restraints excluded: chain F residue 349 THR Chi-restraints excluded: chain F residue 371 THR Chi-restraints excluded: chain F residue 373 THR Chi-restraints excluded: chain F residue 403 ASP Chi-restraints excluded: chain F residue 415 GLU Chi-restraints excluded: chain F residue 461 ILE Chi-restraints excluded: chain F residue 465 GLU Chi-restraints excluded: chain d residue 82 LEU Chi-restraints excluded: chain d residue 89 THR Chi-restraints excluded: chain d residue 91 THR Chi-restraints excluded: chain d residue 129 LEU Chi-restraints excluded: chain d residue 161 ILE Chi-restraints excluded: chain d residue 164 GLU Chi-restraints excluded: chain d residue 180 VAL Chi-restraints excluded: chain d residue 207 VAL Chi-restraints excluded: chain d residue 214 ASP Chi-restraints excluded: chain d residue 223 ILE Chi-restraints excluded: chain e residue 1 MET Chi-restraints excluded: chain e residue 44 VAL Chi-restraints excluded: chain e residue 75 THR Chi-restraints excluded: chain e residue 87 ILE Chi-restraints excluded: chain e residue 96 LEU Chi-restraints excluded: chain e residue 129 SER Chi-restraints excluded: chain g residue 105 VAL Chi-restraints excluded: chain g residue 165 ASN Chi-restraints excluded: chain g residue 203 VAL Chi-restraints excluded: chain g residue 231 LEU Chi-restraints excluded: chain g residue 258 THR Chi-restraints excluded: chain g residue 323 MET Chi-restraints excluded: chain g residue 355 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 353 random chunks: chunk 210 optimal weight: 2.9990 chunk 135 optimal weight: 3.9990 chunk 203 optimal weight: 4.9990 chunk 102 optimal weight: 2.9990 chunk 66 optimal weight: 2.9990 chunk 65 optimal weight: 2.9990 chunk 216 optimal weight: 1.9990 chunk 231 optimal weight: 0.0370 chunk 168 optimal weight: 0.7980 chunk 31 optimal weight: 2.9990 chunk 267 optimal weight: 0.9990 overall best weight: 1.3664 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 84 GLN A 173 GLN ** B 473 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 389 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 410 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 42 ASN D 67 GLN D 210 ASN ** E 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 280 GLN ** F 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 165 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7106 moved from start: 0.2784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 27897 Z= 0.353 Angle : 0.738 19.657 37815 Z= 0.367 Chirality : 0.047 0.281 4448 Planarity : 0.005 0.054 4910 Dihedral : 8.270 126.547 4055 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 18.36 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.49 % Favored : 92.45 % Rotamer: Outliers : 5.00 % Allowed : 23.44 % Favored : 71.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.11 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.47 (0.14), residues: 3551 helix: 0.24 (0.13), residues: 1443 sheet: -1.82 (0.21), residues: 504 loop : -1.79 (0.15), residues: 1604 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP e 15 HIS 0.005 0.001 HIS A 43 PHE 0.025 0.002 PHE D 149 TYR 0.024 0.002 TYR A 271 ARG 0.009 0.001 ARG E 291 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7102 Ramachandran restraints generated. 3551 Oldfield, 0 Emsley, 3551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7102 Ramachandran restraints generated. 3551 Oldfield, 0 Emsley, 3551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 676 residues out of total 2939 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 147 poor density : 529 time to evaluate : 3.357 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 14 ARG cc_start: 0.5795 (tmm160) cc_final: 0.5534 (tmm160) REVERT: A 82 MET cc_start: 0.7139 (mmm) cc_final: 0.6908 (mmm) REVERT: A 95 ILE cc_start: 0.6830 (mp) cc_final: 0.6528 (mm) REVERT: A 171 ASP cc_start: 0.7871 (t0) cc_final: 0.7507 (t0) REVERT: A 385 LEU cc_start: 0.7196 (tt) cc_final: 0.6864 (tt) REVERT: A 389 GLN cc_start: 0.6185 (mt0) cc_final: 0.5853 (tm-30) REVERT: B 314 MET cc_start: 0.7588 (ttt) cc_final: 0.7162 (tmm) REVERT: B 498 MET cc_start: 0.7645 (tpp) cc_final: 0.7376 (tpp) REVERT: C 49 MET cc_start: 0.6302 (tpt) cc_final: 0.6007 (tpt) REVERT: C 77 MET cc_start: 0.7564 (mmp) cc_final: 0.7319 (mmp) REVERT: C 266 LYS cc_start: 0.7235 (mmmt) cc_final: 0.6890 (tptp) REVERT: C 451 LEU cc_start: 0.7680 (mp) cc_final: 0.7423 (mp) REVERT: D 66 GLN cc_start: 0.7679 (mm110) cc_final: 0.7251 (mm110) REVERT: D 208 GLU cc_start: 0.6572 (OUTLIER) cc_final: 0.6261 (tp30) REVERT: D 374 MET cc_start: 0.6502 (mmt) cc_final: 0.5931 (mmt) REVERT: D 392 LYS cc_start: 0.9058 (mmmm) cc_final: 0.8597 (mmtp) REVERT: E 145 LYS cc_start: 0.6515 (tptp) cc_final: 0.5847 (ttpp) REVERT: E 167 LYS cc_start: 0.8448 (mtmm) cc_final: 0.7659 (mtmm) REVERT: E 277 ARG cc_start: 0.7292 (mmt-90) cc_final: 0.6857 (mmt-90) REVERT: E 309 LEU cc_start: 0.8100 (mt) cc_final: 0.7781 (mt) REVERT: F 270 LEU cc_start: 0.8601 (tp) cc_final: 0.8220 (mp) REVERT: F 306 MET cc_start: 0.7880 (tpp) cc_final: 0.7306 (tpt) REVERT: d 82 LEU cc_start: 0.6248 (OUTLIER) cc_final: 0.5558 (mt) REVERT: d 113 TYR cc_start: 0.6800 (t80) cc_final: 0.6592 (t80) REVERT: d 130 ASP cc_start: 0.6323 (m-30) cc_final: 0.6089 (m-30) REVERT: d 231 LYS cc_start: 0.5855 (mttt) cc_final: 0.5624 (mtpp) REVERT: e 30 GLN cc_start: 0.2861 (OUTLIER) cc_final: 0.2307 (pm20) REVERT: g 300 LEU cc_start: 0.7658 (tt) cc_final: 0.6434 (mt) REVERT: g 303 GLN cc_start: 0.7012 (mt0) cc_final: 0.6796 (mt0) REVERT: g 323 MET cc_start: 0.8588 (OUTLIER) cc_final: 0.8307 (mmp) REVERT: g 354 LEU cc_start: 0.8719 (mt) cc_final: 0.8450 (mm) outliers start: 147 outliers final: 115 residues processed: 626 average time/residue: 0.4140 time to fit residues: 402.5471 Evaluate side-chains 627 residues out of total 2939 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 119 poor density : 508 time to evaluate : 3.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 ASP Chi-restraints excluded: chain A residue 55 GLU Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 70 ASN Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 97 GLN Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 263 ASP Chi-restraints excluded: chain A residue 291 VAL Chi-restraints excluded: chain A residue 298 LEU Chi-restraints excluded: chain A residue 362 ILE Chi-restraints excluded: chain A residue 379 VAL Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 454 VAL Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain B residue 21 ASN Chi-restraints excluded: chain B residue 28 ASN Chi-restraints excluded: chain B residue 82 MET Chi-restraints excluded: chain B residue 92 THR Chi-restraints excluded: chain B residue 192 VAL Chi-restraints excluded: chain B residue 197 VAL Chi-restraints excluded: chain B residue 210 VAL Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 339 THR Chi-restraints excluded: chain B residue 431 VAL Chi-restraints excluded: chain B residue 449 LEU Chi-restraints excluded: chain B residue 479 THR Chi-restraints excluded: chain B residue 496 GLU Chi-restraints excluded: chain B residue 501 PHE Chi-restraints excluded: chain C residue 3 THR Chi-restraints excluded: chain C residue 32 VAL Chi-restraints excluded: chain C residue 60 THR Chi-restraints excluded: chain C residue 70 ASN Chi-restraints excluded: chain C residue 81 LEU Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain C residue 98 ILE Chi-restraints excluded: chain C residue 184 ILE Chi-restraints excluded: chain C residue 197 VAL Chi-restraints excluded: chain C residue 199 ILE Chi-restraints excluded: chain C residue 298 LEU Chi-restraints excluded: chain C residue 337 SER Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 373 ILE Chi-restraints excluded: chain C residue 383 LEU Chi-restraints excluded: chain C residue 431 VAL Chi-restraints excluded: chain C residue 483 THR Chi-restraints excluded: chain D residue 72 ASN Chi-restraints excluded: chain D residue 85 LEU Chi-restraints excluded: chain D residue 100 VAL Chi-restraints excluded: chain D residue 126 THR Chi-restraints excluded: chain D residue 132 ILE Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain D residue 208 GLU Chi-restraints excluded: chain D residue 221 VAL Chi-restraints excluded: chain D residue 249 VAL Chi-restraints excluded: chain D residue 347 ASP Chi-restraints excluded: chain D residue 472 GLN Chi-restraints excluded: chain E residue 31 LEU Chi-restraints excluded: chain E residue 63 CYS Chi-restraints excluded: chain E residue 64 GLU Chi-restraints excluded: chain E residue 91 VAL Chi-restraints excluded: chain E residue 93 ASP Chi-restraints excluded: chain E residue 144 THR Chi-restraints excluded: chain E residue 151 THR Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain E residue 210 ASN Chi-restraints excluded: chain E residue 262 ASP Chi-restraints excluded: chain E residue 275 ILE Chi-restraints excluded: chain E residue 320 SER Chi-restraints excluded: chain E residue 321 ILE Chi-restraints excluded: chain E residue 349 THR Chi-restraints excluded: chain E residue 419 LEU Chi-restraints excluded: chain E residue 420 THR Chi-restraints excluded: chain F residue 102 VAL Chi-restraints excluded: chain F residue 124 VAL Chi-restraints excluded: chain F residue 155 VAL Chi-restraints excluded: chain F residue 196 VAL Chi-restraints excluded: chain F residue 202 VAL Chi-restraints excluded: chain F residue 218 GLU Chi-restraints excluded: chain F residue 291 ARG Chi-restraints excluded: chain F residue 303 SER Chi-restraints excluded: chain F residue 316 THR Chi-restraints excluded: chain F residue 335 THR Chi-restraints excluded: chain F residue 349 THR Chi-restraints excluded: chain F residue 371 THR Chi-restraints excluded: chain F residue 373 THR Chi-restraints excluded: chain F residue 403 ASP Chi-restraints excluded: chain F residue 415 GLU Chi-restraints excluded: chain F residue 477 VAL Chi-restraints excluded: chain F residue 479 ASN Chi-restraints excluded: chain F residue 484 THR Chi-restraints excluded: chain d residue 82 LEU Chi-restraints excluded: chain d residue 89 THR Chi-restraints excluded: chain d residue 91 THR Chi-restraints excluded: chain d residue 129 LEU Chi-restraints excluded: chain d residue 161 ILE Chi-restraints excluded: chain d residue 164 GLU Chi-restraints excluded: chain d residue 180 VAL Chi-restraints excluded: chain d residue 207 VAL Chi-restraints excluded: chain d residue 214 ASP Chi-restraints excluded: chain d residue 223 ILE Chi-restraints excluded: chain e residue 1 MET Chi-restraints excluded: chain e residue 30 GLN Chi-restraints excluded: chain e residue 44 VAL Chi-restraints excluded: chain e residue 75 THR Chi-restraints excluded: chain e residue 87 ILE Chi-restraints excluded: chain e residue 96 LEU Chi-restraints excluded: chain e residue 103 LEU Chi-restraints excluded: chain e residue 129 SER Chi-restraints excluded: chain g residue 79 VAL Chi-restraints excluded: chain g residue 105 VAL Chi-restraints excluded: chain g residue 203 VAL Chi-restraints excluded: chain g residue 231 LEU Chi-restraints excluded: chain g residue 233 LEU Chi-restraints excluded: chain g residue 258 THR Chi-restraints excluded: chain g residue 296 LEU Chi-restraints excluded: chain g residue 323 MET Chi-restraints excluded: chain g residue 355 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 353 random chunks: chunk 309 optimal weight: 0.6980 chunk 325 optimal weight: 0.7980 chunk 297 optimal weight: 4.9990 chunk 317 optimal weight: 0.8980 chunk 190 optimal weight: 0.5980 chunk 138 optimal weight: 0.7980 chunk 248 optimal weight: 3.9990 chunk 97 optimal weight: 0.7980 chunk 286 optimal weight: 0.6980 chunk 299 optimal weight: 3.9990 chunk 315 optimal weight: 0.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 173 GLN B 187 GLN ** B 473 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 295 HIS ** C 389 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 410 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 67 GLN D 210 ASN ** E 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 72 ASN ** F 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 345 HIS d 199 GLN g 290 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7065 moved from start: 0.2902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.078 27897 Z= 0.234 Angle : 0.674 19.567 37815 Z= 0.332 Chirality : 0.045 0.233 4448 Planarity : 0.004 0.052 4910 Dihedral : 8.043 124.047 4055 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 17.24 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.00 % Favored : 93.95 % Rotamer: Outliers : 4.22 % Allowed : 24.57 % Favored : 71.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.11 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.29 (0.14), residues: 3551 helix: 0.40 (0.14), residues: 1446 sheet: -1.81 (0.22), residues: 481 loop : -1.70 (0.15), residues: 1624 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP e 57 HIS 0.003 0.001 HIS C 295 PHE 0.022 0.002 PHE D 149 TYR 0.027 0.002 TYR E 162 ARG 0.009 0.001 ARG F 246 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7102 Ramachandran restraints generated. 3551 Oldfield, 0 Emsley, 3551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7102 Ramachandran restraints generated. 3551 Oldfield, 0 Emsley, 3551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 632 residues out of total 2939 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 124 poor density : 508 time to evaluate : 3.583 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 14 ARG cc_start: 0.5780 (tmm160) cc_final: 0.5560 (tmm160) REVERT: A 171 ASP cc_start: 0.7852 (t0) cc_final: 0.7463 (t0) REVERT: A 385 LEU cc_start: 0.7139 (tt) cc_final: 0.6714 (tt) REVERT: A 389 GLN cc_start: 0.6147 (mt0) cc_final: 0.5828 (tm-30) REVERT: B 314 MET cc_start: 0.7560 (ttt) cc_final: 0.7183 (tmm) REVERT: B 378 LYS cc_start: 0.7781 (ptpt) cc_final: 0.7141 (mtmt) REVERT: B 498 MET cc_start: 0.7681 (tpp) cc_final: 0.7427 (tpp) REVERT: C 49 MET cc_start: 0.6314 (tpt) cc_final: 0.5861 (tpt) REVERT: C 266 LYS cc_start: 0.7251 (mmmt) cc_final: 0.6913 (tptp) REVERT: D 66 GLN cc_start: 0.7649 (mm110) cc_final: 0.7190 (mm110) REVERT: D 392 LYS cc_start: 0.9024 (mmmm) cc_final: 0.8581 (mmtp) REVERT: E 145 LYS cc_start: 0.6498 (tptp) cc_final: 0.5847 (ttpp) REVERT: E 167 LYS cc_start: 0.8466 (mtmm) cc_final: 0.7700 (mtmm) REVERT: E 277 ARG cc_start: 0.7207 (mmt-90) cc_final: 0.6813 (mmt-90) REVERT: E 309 LEU cc_start: 0.8106 (mt) cc_final: 0.7763 (mt) REVERT: F 270 LEU cc_start: 0.8601 (tp) cc_final: 0.8253 (mp) REVERT: F 298 TYR cc_start: 0.7211 (m-80) cc_final: 0.6885 (m-80) REVERT: F 425 ARG cc_start: 0.7276 (mmm-85) cc_final: 0.6508 (mmm160) REVERT: d 82 LEU cc_start: 0.6157 (OUTLIER) cc_final: 0.5464 (mt) REVERT: d 113 TYR cc_start: 0.6845 (t80) cc_final: 0.6608 (t80) REVERT: g 123 VAL cc_start: 0.6574 (t) cc_final: 0.6205 (t) REVERT: g 300 LEU cc_start: 0.7666 (tt) cc_final: 0.6414 (mt) REVERT: g 312 LEU cc_start: 0.7603 (OUTLIER) cc_final: 0.7373 (tp) REVERT: g 323 MET cc_start: 0.8582 (OUTLIER) cc_final: 0.8263 (mmp) REVERT: g 354 LEU cc_start: 0.8725 (mt) cc_final: 0.8469 (mm) outliers start: 124 outliers final: 108 residues processed: 590 average time/residue: 0.4107 time to fit residues: 376.3053 Evaluate side-chains 611 residues out of total 2939 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 111 poor density : 500 time to evaluate : 3.272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 ASP Chi-restraints excluded: chain A residue 55 GLU Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 97 GLN Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 168 ILE Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 263 ASP Chi-restraints excluded: chain A residue 291 VAL Chi-restraints excluded: chain A residue 298 LEU Chi-restraints excluded: chain A residue 362 ILE Chi-restraints excluded: chain A residue 379 VAL Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 454 VAL Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain B residue 21 ASN Chi-restraints excluded: chain B residue 28 ASN Chi-restraints excluded: chain B residue 82 MET Chi-restraints excluded: chain B residue 92 THR Chi-restraints excluded: chain B residue 192 VAL Chi-restraints excluded: chain B residue 197 VAL Chi-restraints excluded: chain B residue 210 VAL Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 339 THR Chi-restraints excluded: chain B residue 431 VAL Chi-restraints excluded: chain B residue 449 LEU Chi-restraints excluded: chain B residue 479 THR Chi-restraints excluded: chain B residue 501 PHE Chi-restraints excluded: chain C residue 3 THR Chi-restraints excluded: chain C residue 32 VAL Chi-restraints excluded: chain C residue 60 THR Chi-restraints excluded: chain C residue 70 ASN Chi-restraints excluded: chain C residue 81 LEU Chi-restraints excluded: chain C residue 83 ILE Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain C residue 98 ILE Chi-restraints excluded: chain C residue 197 VAL Chi-restraints excluded: chain C residue 199 ILE Chi-restraints excluded: chain C residue 298 LEU Chi-restraints excluded: chain C residue 337 SER Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 383 LEU Chi-restraints excluded: chain C residue 431 VAL Chi-restraints excluded: chain C residue 483 THR Chi-restraints excluded: chain D residue 72 ASN Chi-restraints excluded: chain D residue 85 LEU Chi-restraints excluded: chain D residue 100 VAL Chi-restraints excluded: chain D residue 126 THR Chi-restraints excluded: chain D residue 132 ILE Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain D residue 221 VAL Chi-restraints excluded: chain D residue 249 VAL Chi-restraints excluded: chain D residue 305 GLU Chi-restraints excluded: chain D residue 356 LEU Chi-restraints excluded: chain E residue 31 LEU Chi-restraints excluded: chain E residue 61 VAL Chi-restraints excluded: chain E residue 63 CYS Chi-restraints excluded: chain E residue 64 GLU Chi-restraints excluded: chain E residue 91 VAL Chi-restraints excluded: chain E residue 93 ASP Chi-restraints excluded: chain E residue 142 LEU Chi-restraints excluded: chain E residue 144 THR Chi-restraints excluded: chain E residue 151 THR Chi-restraints excluded: chain E residue 210 ASN Chi-restraints excluded: chain E residue 275 ILE Chi-restraints excluded: chain E residue 320 SER Chi-restraints excluded: chain E residue 321 ILE Chi-restraints excluded: chain E residue 349 THR Chi-restraints excluded: chain E residue 408 LEU Chi-restraints excluded: chain E residue 419 LEU Chi-restraints excluded: chain E residue 420 THR Chi-restraints excluded: chain F residue 102 VAL Chi-restraints excluded: chain F residue 124 VAL Chi-restraints excluded: chain F residue 155 VAL Chi-restraints excluded: chain F residue 196 VAL Chi-restraints excluded: chain F residue 202 VAL Chi-restraints excluded: chain F residue 218 GLU Chi-restraints excluded: chain F residue 291 ARG Chi-restraints excluded: chain F residue 303 SER Chi-restraints excluded: chain F residue 316 THR Chi-restraints excluded: chain F residue 335 THR Chi-restraints excluded: chain F residue 349 THR Chi-restraints excluded: chain F residue 371 THR Chi-restraints excluded: chain F residue 373 THR Chi-restraints excluded: chain F residue 403 ASP Chi-restraints excluded: chain F residue 415 GLU Chi-restraints excluded: chain F residue 477 VAL Chi-restraints excluded: chain F residue 479 ASN Chi-restraints excluded: chain d residue 82 LEU Chi-restraints excluded: chain d residue 89 THR Chi-restraints excluded: chain d residue 91 THR Chi-restraints excluded: chain d residue 129 LEU Chi-restraints excluded: chain d residue 161 ILE Chi-restraints excluded: chain d residue 164 GLU Chi-restraints excluded: chain d residue 180 VAL Chi-restraints excluded: chain d residue 214 ASP Chi-restraints excluded: chain d residue 223 ILE Chi-restraints excluded: chain e residue 1 MET Chi-restraints excluded: chain e residue 44 VAL Chi-restraints excluded: chain e residue 75 THR Chi-restraints excluded: chain e residue 87 ILE Chi-restraints excluded: chain e residue 103 LEU Chi-restraints excluded: chain e residue 129 SER Chi-restraints excluded: chain g residue 105 VAL Chi-restraints excluded: chain g residue 203 VAL Chi-restraints excluded: chain g residue 231 LEU Chi-restraints excluded: chain g residue 258 THR Chi-restraints excluded: chain g residue 312 LEU Chi-restraints excluded: chain g residue 323 MET Chi-restraints excluded: chain g residue 355 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 353 random chunks: chunk 208 optimal weight: 4.9990 chunk 335 optimal weight: 0.0980 chunk 204 optimal weight: 2.9990 chunk 159 optimal weight: 0.7980 chunk 233 optimal weight: 0.9980 chunk 351 optimal weight: 0.9980 chunk 323 optimal weight: 1.9990 chunk 280 optimal weight: 0.0980 chunk 29 optimal weight: 0.9980 chunk 216 optimal weight: 0.9990 chunk 171 optimal weight: 0.9980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 173 GLN ** B 473 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 389 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 410 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 67 GLN ** E 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 72 ASN ** F 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7048 moved from start: 0.3046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 27897 Z= 0.213 Angle : 0.667 19.583 37815 Z= 0.328 Chirality : 0.045 0.333 4448 Planarity : 0.004 0.051 4910 Dihedral : 7.898 120.659 4055 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 16.86 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.25 % Favored : 93.69 % Rotamer: Outliers : 4.08 % Allowed : 25.01 % Favored : 70.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.11 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.16 (0.14), residues: 3551 helix: 0.49 (0.14), residues: 1444 sheet: -1.71 (0.23), residues: 468 loop : -1.61 (0.15), residues: 1639 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP e 57 HIS 0.004 0.001 HIS E 133 PHE 0.022 0.001 PHE B 390 TYR 0.030 0.002 TYR E 162 ARG 0.010 0.000 ARG E 291 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7102 Ramachandran restraints generated. 3551 Oldfield, 0 Emsley, 3551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7102 Ramachandran restraints generated. 3551 Oldfield, 0 Emsley, 3551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 632 residues out of total 2939 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 120 poor density : 512 time to evaluate : 2.977 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 14 ARG cc_start: 0.5800 (tmm160) cc_final: 0.5558 (tmm160) REVERT: A 171 ASP cc_start: 0.7856 (t0) cc_final: 0.7458 (t0) REVERT: A 199 ILE cc_start: 0.7968 (OUTLIER) cc_final: 0.7675 (mt) REVERT: A 385 LEU cc_start: 0.7094 (tt) cc_final: 0.6686 (tt) REVERT: A 389 GLN cc_start: 0.6108 (mt0) cc_final: 0.5787 (tm-30) REVERT: A 450 GLU cc_start: 0.5836 (tp30) cc_final: 0.5148 (tm-30) REVERT: B 314 MET cc_start: 0.7615 (ttt) cc_final: 0.7250 (tmm) REVERT: B 378 LYS cc_start: 0.7814 (ptpt) cc_final: 0.7162 (mtmt) REVERT: B 498 MET cc_start: 0.7666 (tpp) cc_final: 0.7430 (tpp) REVERT: C 34 GLN cc_start: 0.7052 (mt0) cc_final: 0.6842 (mt0) REVERT: C 49 MET cc_start: 0.6159 (tpt) cc_final: 0.5733 (tpt) REVERT: C 266 LYS cc_start: 0.7184 (mmmt) cc_final: 0.6771 (tptp) REVERT: D 66 GLN cc_start: 0.7688 (mm110) cc_final: 0.7189 (mm110) REVERT: D 248 ARG cc_start: 0.6857 (mmt180) cc_final: 0.6568 (mmt180) REVERT: D 392 LYS cc_start: 0.8984 (mmmm) cc_final: 0.8554 (mmtp) REVERT: E 145 LYS cc_start: 0.6562 (tptp) cc_final: 0.5870 (ttpp) REVERT: E 167 LYS cc_start: 0.8456 (mtmm) cc_final: 0.7672 (mtmm) REVERT: E 309 LEU cc_start: 0.8073 (mt) cc_final: 0.7758 (mt) REVERT: F 298 TYR cc_start: 0.7207 (m-80) cc_final: 0.6923 (m-80) REVERT: F 306 MET cc_start: 0.8049 (mmm) cc_final: 0.7580 (tpt) REVERT: F 359 LYS cc_start: 0.4835 (mtmt) cc_final: 0.4226 (tptp) REVERT: d 82 LEU cc_start: 0.6202 (OUTLIER) cc_final: 0.5590 (mt) REVERT: d 164 GLU cc_start: 0.5083 (OUTLIER) cc_final: 0.4801 (mm-30) REVERT: g 123 VAL cc_start: 0.6354 (t) cc_final: 0.6020 (t) REVERT: g 158 ILE cc_start: 0.4574 (OUTLIER) cc_final: 0.4171 (tp) REVERT: g 300 LEU cc_start: 0.7621 (tt) cc_final: 0.6465 (mt) REVERT: g 323 MET cc_start: 0.8583 (OUTLIER) cc_final: 0.8262 (mmp) REVERT: g 354 LEU cc_start: 0.8666 (mt) cc_final: 0.8391 (mm) outliers start: 120 outliers final: 105 residues processed: 593 average time/residue: 0.4095 time to fit residues: 376.6229 Evaluate side-chains 607 residues out of total 2939 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 110 poor density : 497 time to evaluate : 3.055 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 ASP Chi-restraints excluded: chain A residue 55 GLU Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 97 GLN Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 168 ILE Chi-restraints excluded: chain A residue 199 ILE Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 263 ASP Chi-restraints excluded: chain A residue 298 LEU Chi-restraints excluded: chain A residue 362 ILE Chi-restraints excluded: chain A residue 379 VAL Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 454 VAL Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain B residue 21 ASN Chi-restraints excluded: chain B residue 28 ASN Chi-restraints excluded: chain B residue 82 MET Chi-restraints excluded: chain B residue 92 THR Chi-restraints excluded: chain B residue 197 VAL Chi-restraints excluded: chain B residue 210 VAL Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 339 THR Chi-restraints excluded: chain B residue 449 LEU Chi-restraints excluded: chain B residue 479 THR Chi-restraints excluded: chain B residue 496 GLU Chi-restraints excluded: chain B residue 501 PHE Chi-restraints excluded: chain C residue 3 THR Chi-restraints excluded: chain C residue 32 VAL Chi-restraints excluded: chain C residue 60 THR Chi-restraints excluded: chain C residue 70 ASN Chi-restraints excluded: chain C residue 83 ILE Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain C residue 98 ILE Chi-restraints excluded: chain C residue 197 VAL Chi-restraints excluded: chain C residue 199 ILE Chi-restraints excluded: chain C residue 337 SER Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 383 LEU Chi-restraints excluded: chain C residue 431 VAL Chi-restraints excluded: chain C residue 483 THR Chi-restraints excluded: chain D residue 72 ASN Chi-restraints excluded: chain D residue 85 LEU Chi-restraints excluded: chain D residue 100 VAL Chi-restraints excluded: chain D residue 126 THR Chi-restraints excluded: chain D residue 132 ILE Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain D residue 221 VAL Chi-restraints excluded: chain D residue 249 VAL Chi-restraints excluded: chain D residue 305 GLU Chi-restraints excluded: chain D residue 313 ILE Chi-restraints excluded: chain D residue 356 LEU Chi-restraints excluded: chain E residue 31 LEU Chi-restraints excluded: chain E residue 49 VAL Chi-restraints excluded: chain E residue 61 VAL Chi-restraints excluded: chain E residue 63 CYS Chi-restraints excluded: chain E residue 64 GLU Chi-restraints excluded: chain E residue 91 VAL Chi-restraints excluded: chain E residue 93 ASP Chi-restraints excluded: chain E residue 144 THR Chi-restraints excluded: chain E residue 151 THR Chi-restraints excluded: chain E residue 210 ASN Chi-restraints excluded: chain E residue 262 ASP Chi-restraints excluded: chain E residue 275 ILE Chi-restraints excluded: chain E residue 320 SER Chi-restraints excluded: chain E residue 321 ILE Chi-restraints excluded: chain E residue 349 THR Chi-restraints excluded: chain E residue 408 LEU Chi-restraints excluded: chain E residue 419 LEU Chi-restraints excluded: chain E residue 420 THR Chi-restraints excluded: chain F residue 102 VAL Chi-restraints excluded: chain F residue 116 GLU Chi-restraints excluded: chain F residue 124 VAL Chi-restraints excluded: chain F residue 155 VAL Chi-restraints excluded: chain F residue 196 VAL Chi-restraints excluded: chain F residue 202 VAL Chi-restraints excluded: chain F residue 291 ARG Chi-restraints excluded: chain F residue 303 SER Chi-restraints excluded: chain F residue 316 THR Chi-restraints excluded: chain F residue 335 THR Chi-restraints excluded: chain F residue 349 THR Chi-restraints excluded: chain F residue 371 THR Chi-restraints excluded: chain F residue 373 THR Chi-restraints excluded: chain F residue 403 ASP Chi-restraints excluded: chain F residue 415 GLU Chi-restraints excluded: chain F residue 477 VAL Chi-restraints excluded: chain F residue 479 ASN Chi-restraints excluded: chain F residue 484 THR Chi-restraints excluded: chain d residue 82 LEU Chi-restraints excluded: chain d residue 89 THR Chi-restraints excluded: chain d residue 91 THR Chi-restraints excluded: chain d residue 129 LEU Chi-restraints excluded: chain d residue 161 ILE Chi-restraints excluded: chain d residue 164 GLU Chi-restraints excluded: chain d residue 180 VAL Chi-restraints excluded: chain d residue 214 ASP Chi-restraints excluded: chain d residue 223 ILE Chi-restraints excluded: chain e residue 1 MET Chi-restraints excluded: chain e residue 44 VAL Chi-restraints excluded: chain e residue 75 THR Chi-restraints excluded: chain e residue 129 SER Chi-restraints excluded: chain g residue 105 VAL Chi-restraints excluded: chain g residue 158 ILE Chi-restraints excluded: chain g residue 203 VAL Chi-restraints excluded: chain g residue 231 LEU Chi-restraints excluded: chain g residue 258 THR Chi-restraints excluded: chain g residue 296 LEU Chi-restraints excluded: chain g residue 323 MET Chi-restraints excluded: chain g residue 355 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 353 random chunks: chunk 222 optimal weight: 0.6980 chunk 298 optimal weight: 0.9990 chunk 85 optimal weight: 3.9990 chunk 258 optimal weight: 0.7980 chunk 41 optimal weight: 0.9990 chunk 77 optimal weight: 1.9990 chunk 280 optimal weight: 0.7980 chunk 117 optimal weight: 2.9990 chunk 288 optimal weight: 0.6980 chunk 35 optimal weight: 2.9990 chunk 51 optimal weight: 3.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 173 GLN B 97 GLN ** B 473 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 389 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 410 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 67 GLN ** E 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 290 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.150354 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.133285 restraints weight = 45641.318| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.135377 restraints weight = 27934.050| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.136719 restraints weight = 19016.182| |-----------------------------------------------------------------------------| r_work (final): 0.3609 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7063 moved from start: 0.3073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 27897 Z= 0.248 Angle : 0.681 19.635 37815 Z= 0.336 Chirality : 0.045 0.372 4448 Planarity : 0.004 0.051 4910 Dihedral : 7.935 120.312 4055 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 17.55 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.79 % Favored : 93.16 % Rotamer: Outliers : 4.08 % Allowed : 25.01 % Favored : 70.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.11 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.19 (0.14), residues: 3551 helix: 0.43 (0.14), residues: 1445 sheet: -1.67 (0.23), residues: 477 loop : -1.61 (0.15), residues: 1629 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP e 57 HIS 0.004 0.001 HIS E 133 PHE 0.024 0.002 PHE D 149 TYR 0.040 0.002 TYR E 162 ARG 0.009 0.001 ARG E 291 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7251.73 seconds wall clock time: 131 minutes 14.14 seconds (7874.14 seconds total)