Starting phenix.real_space_refine on Tue Feb 20 02:49:20 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ly8_30014/02_2024/6ly8_30014_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ly8_30014/02_2024/6ly8_30014.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ly8_30014/02_2024/6ly8_30014.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ly8_30014/02_2024/6ly8_30014.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ly8_30014/02_2024/6ly8_30014_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ly8_30014/02_2024/6ly8_30014_updated.pdb" } resolution = 3.5 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= 0.001 sd= 0.011 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 2 5.49 5 S 101 5.16 5 C 16918 2.51 5 N 4595 2.21 5 O 5015 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 284": "NH1" <-> "NH2" Residue "B TYR 184": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 284": "NH1" <-> "NH2" Residue "B GLU 332": "OE1" <-> "OE2" Residue "B TYR 428": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 284": "NH1" <-> "NH2" Residue "C GLU 300": "OE1" <-> "OE2" Residue "C GLU 569": "OE1" <-> "OE2" Residue "D GLU 87": "OE1" <-> "OE2" Residue "D GLU 109": "OE1" <-> "OE2" Residue "D GLU 406": "OE1" <-> "OE2" Residue "E TYR 288": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 386": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 406": "OE1" <-> "OE2" Residue "G ARG 14": "NH1" <-> "NH2" Residue "G ARG 15": "NH1" <-> "NH2" Residue "G ARG 32": "NH1" <-> "NH2" Residue "G GLU 87": "OE1" <-> "OE2" Residue "G ARG 128": "NH1" <-> "NH2" Residue "G ARG 132": "NH1" <-> "NH2" Residue "G GLU 135": "OE1" <-> "OE2" Residue "G ARG 146": "NH1" <-> "NH2" Residue "G ARG 173": "NH1" <-> "NH2" Residue "G ARG 188": "NH1" <-> "NH2" Residue "G ARG 193": "NH1" <-> "NH2" Residue "G ARG 196": "NH1" <-> "NH2" Residue "G ARG 204": "NH1" <-> "NH2" Residue "H GLU 38": "OE1" <-> "OE2" Residue "H ARG 61": "NH1" <-> "NH2" Residue "H ARG 91": "NH1" <-> "NH2" Residue "H PHE 100": "CD1" <-> "CD2" "CE1" <-> "CE2" 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: 26631 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 4472 Number of conformers: 1 Conformer: "" Number of residues, atoms: 577, 4472 Classifications: {'peptide': 577} Link IDs: {'PCIS': 1, 'PTRANS': 34, 'TRANS': 541} Chain: "B" Number of atoms: 4472 Number of conformers: 1 Conformer: "" Number of residues, atoms: 577, 4472 Classifications: {'peptide': 577} Link IDs: {'PCIS': 1, 'PTRANS': 34, 'TRANS': 541} Chain: "C" Number of atoms: 4472 Number of conformers: 1 Conformer: "" Number of residues, atoms: 577, 4472 Classifications: {'peptide': 577} Link IDs: {'PTRANS': 35, 'TRANS': 541} Chain: "D" Number of atoms: 3596 Number of conformers: 1 Conformer: "" Number of residues, atoms: 459, 3596 Classifications: {'peptide': 459} Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 432} Chain: "E" Number of atoms: 3596 Number of conformers: 1 Conformer: "" Number of residues, atoms: 459, 3596 Classifications: {'peptide': 459} Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 432} Chain: "F" Number of atoms: 3596 Number of conformers: 1 Conformer: "" Number of residues, atoms: 459, 3596 Classifications: {'peptide': 459} Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 432} Chain: "G" Number of atoms: 1642 Number of conformers: 1 Conformer: "" Number of residues, atoms: 210, 1642 Classifications: {'peptide': 210} Link IDs: {'PTRANS': 9, 'TRANS': 200} Chain: "H" Number of atoms: 758 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 758 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 5, 'TRANS': 94} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "A" 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: 13.34, per 1000 atoms: 0.50 Number of scatterers: 26631 At special positions: 0 Unit cell: (139.7, 129.8, 162.8, 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 101 16.00 P 2 15.00 O 5015 8.00 N 4595 7.00 C 16918 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 9.71 Conformation dependent library (CDL) restraints added in 4.8 seconds 6804 Ramachandran restraints generated. 3402 Oldfield, 0 Emsley, 3402 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6214 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 99 helices and 38 sheets defined 35.8% alpha, 8.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.36 Creating SS restraints... Processing helix chain 'A' and resid 91 through 98 Processing helix chain 'A' and resid 210 through 214 Processing helix chain 'A' and resid 236 through 243 Processing helix chain 'A' and resid 259 through 266 removed outlier: 4.608A pdb=" N VAL A 265 " --> pdb=" O GLU A 261 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N LEU A 266 " --> pdb=" O MET A 262 " (cutoff:3.500A) Processing helix chain 'A' and resid 281 through 283 No H-bonds generated for 'chain 'A' and resid 281 through 283' Processing helix chain 'A' and resid 298 through 316 Processing helix chain 'A' and resid 327 through 341 Processing helix chain 'A' and resid 347 through 349 No H-bonds generated for 'chain 'A' and resid 347 through 349' Processing helix chain 'A' and resid 354 through 362 Processing helix chain 'A' and resid 394 through 398 Processing helix chain 'A' and resid 412 through 415 No H-bonds generated for 'chain 'A' and resid 412 through 415' Processing helix chain 'A' and resid 436 through 442 Processing helix chain 'A' and resid 447 through 470 removed outlier: 5.098A pdb=" N GLY A 463 " --> pdb=" O GLN A 459 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LEU A 464 " --> pdb=" O ARG A 460 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ILE A 467 " --> pdb=" O GLY A 463 " (cutoff:3.500A) Processing helix chain 'A' and resid 478 through 493 Processing helix chain 'A' and resid 509 through 532 Processing helix chain 'A' and resid 536 through 541 Processing helix chain 'A' and resid 544 through 552 removed outlier: 5.146A pdb=" N ARG A 552 " --> pdb=" O ILE A 548 " (cutoff:3.500A) Processing helix chain 'A' and resid 559 through 576 removed outlier: 3.898A pdb=" N GLU A 564 " --> pdb=" O PRO A 560 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N LYS A 575 " --> pdb=" O GLN A 571 " (cutoff:3.500A) Processing helix chain 'B' and resid 91 through 98 removed outlier: 3.908A pdb=" N LYS B 97 " --> pdb=" O ARG B 93 " (cutoff:3.500A) Processing helix chain 'B' and resid 210 through 215 Processing helix chain 'B' and resid 234 through 244 Processing helix chain 'B' and resid 261 through 268 Processing helix chain 'B' and resid 281 through 284 Processing helix chain 'B' and resid 296 through 315 Processing helix chain 'B' and resid 327 through 340 Processing helix chain 'B' and resid 354 through 361 removed outlier: 3.754A pdb=" N LEU B 358 " --> pdb=" O LEU B 354 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ALA B 359 " --> pdb=" O ALA B 355 " (cutoff:3.500A) Processing helix chain 'B' and resid 394 through 402 removed outlier: 4.952A pdb=" N ARG B 401 " --> pdb=" O GLN B 397 " (cutoff:3.500A) Processing helix chain 'B' and resid 412 through 415 No H-bonds generated for 'chain 'B' and resid 412 through 415' Processing helix chain 'B' and resid 433 through 442 Proline residue: B 437 - end of helix Processing helix chain 'B' and resid 447 through 471 removed outlier: 5.073A pdb=" N ILE B 467 " --> pdb=" O GLY B 463 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N VAL B 468 " --> pdb=" O LEU B 464 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N GLN B 469 " --> pdb=" O GLN B 465 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N LEU B 470 " --> pdb=" O GLU B 466 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N VAL B 471 " --> pdb=" O ILE B 467 " (cutoff:3.500A) Processing helix chain 'B' and resid 478 through 493 Processing helix chain 'B' and resid 509 through 532 removed outlier: 3.709A pdb=" N ARG B 532 " --> pdb=" O ALA B 528 " (cutoff:3.500A) Processing helix chain 'B' and resid 538 through 541 No H-bonds generated for 'chain 'B' and resid 538 through 541' Processing helix chain 'B' and resid 544 through 549 Processing helix chain 'B' and resid 559 through 573 Processing helix chain 'C' and resid 91 through 98 Processing helix chain 'C' and resid 210 through 214 Processing helix chain 'C' and resid 234 through 244 Processing helix chain 'C' and resid 259 through 271 Proline residue: C 270 - end of helix Processing helix chain 'C' and resid 281 through 284 Processing helix chain 'C' and resid 298 through 316 Processing helix chain 'C' and resid 327 through 341 Processing helix chain 'C' and resid 347 through 349 No H-bonds generated for 'chain 'C' and resid 347 through 349' Processing helix chain 'C' and resid 354 through 364 Processing helix chain 'C' and resid 394 through 397 No H-bonds generated for 'chain 'C' and resid 394 through 397' Processing helix chain 'C' and resid 411 through 415 Processing helix chain 'C' and resid 436 through 442 Processing helix chain 'C' and resid 447 through 471 removed outlier: 3.914A pdb=" N ASP C 452 " --> pdb=" O PRO C 448 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ALA C 453 " --> pdb=" O GLU C 449 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ILE C 454 " --> pdb=" O LEU C 450 " (cutoff:3.500A) removed outlier: 4.569A pdb=" N GLY C 463 " --> pdb=" O GLN C 459 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N LEU C 464 " --> pdb=" O ARG C 460 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ILE C 467 " --> pdb=" O GLY C 463 " (cutoff:3.500A) Processing helix chain 'C' and resid 478 through 493 Processing helix chain 'C' and resid 509 through 532 Processing helix chain 'C' and resid 536 through 540 Processing helix chain 'C' and resid 543 through 549 Processing helix chain 'C' and resid 559 through 573 Processing helix chain 'D' and resid 137 through 140 No H-bonds generated for 'chain 'D' and resid 137 through 140' Processing helix chain 'D' and resid 161 through 170 Processing helix chain 'D' and resid 182 through 184 No H-bonds generated for 'chain 'D' and resid 182 through 184' Processing helix chain 'D' and resid 198 through 211 removed outlier: 3.553A pdb=" N SER D 202 " --> pdb=" O GLN D 198 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N THR D 211 " --> pdb=" O GLU D 207 " (cutoff:3.500A) Processing helix chain 'D' and resid 228 through 249 Proline residue: D 235 - end of helix Processing helix chain 'D' and resid 260 through 274 Processing helix chain 'D' and resid 285 through 294 removed outlier: 4.480A pdb=" N TYR D 288 " --> pdb=" O GLY D 285 " (cutoff:3.500A) Processing helix chain 'D' and resid 324 through 332 Processing helix chain 'D' and resid 341 through 346 Processing helix chain 'D' and resid 375 through 399 removed outlier: 4.267A pdb=" N LYS D 394 " --> pdb=" O VAL D 390 " (cutoff:3.500A) Processing helix chain 'D' and resid 406 through 421 Processing helix chain 'D' and resid 432 through 445 removed outlier: 4.012A pdb=" N MET D 445 " --> pdb=" O ALA D 441 " (cutoff:3.500A) Processing helix chain 'D' and resid 456 through 461 removed outlier: 4.227A pdb=" N LYS D 461 " --> pdb=" O ASP D 457 " (cutoff:3.500A) Processing helix chain 'E' and resid 136 through 141 Processing helix chain 'E' and resid 161 through 170 Processing helix chain 'E' and resid 198 through 210 Processing helix chain 'E' and resid 213 through 216 Processing helix chain 'E' and resid 228 through 249 Proline residue: E 235 - end of helix Processing helix chain 'E' and resid 260 through 274 removed outlier: 3.869A pdb=" N ALA E 273 " --> pdb=" O GLU E 269 " (cutoff:3.500A) removed outlier: 4.905A pdb=" N ARG E 274 " --> pdb=" O ILE E 270 " (cutoff:3.500A) Processing helix chain 'E' and resid 285 through 295 removed outlier: 4.444A pdb=" N TYR E 288 " --> pdb=" O GLY E 285 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ALA E 292 " --> pdb=" O THR E 289 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N TYR E 295 " --> pdb=" O ALA E 292 " (cutoff:3.500A) Processing helix chain 'E' and resid 324 through 332 Processing helix chain 'E' and resid 342 through 345 No H-bonds generated for 'chain 'E' and resid 342 through 345' Processing helix chain 'E' and resid 375 through 398 Processing helix chain 'E' and resid 401 through 403 No H-bonds generated for 'chain 'E' and resid 401 through 403' Processing helix chain 'E' and resid 406 through 421 removed outlier: 3.554A pdb=" N TYR E 411 " --> pdb=" O ASN E 407 " (cutoff:3.500A) Processing helix chain 'E' and resid 432 through 445 removed outlier: 4.486A pdb=" N MET E 445 " --> pdb=" O ALA E 441 " (cutoff:3.500A) Processing helix chain 'E' and resid 457 through 461 Processing helix chain 'F' and resid 161 through 170 Processing helix chain 'F' and resid 175 through 177 No H-bonds generated for 'chain 'F' and resid 175 through 177' Processing helix chain 'F' and resid 198 through 210 Processing helix chain 'F' and resid 229 through 247 Proline residue: F 235 - end of helix Processing helix chain 'F' and resid 260 through 274 Processing helix chain 'F' and resid 285 through 295 removed outlier: 4.244A pdb=" N TYR F 288 " --> pdb=" O GLY F 285 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LEU F 291 " --> pdb=" O TYR F 288 " (cutoff:3.500A) Processing helix chain 'F' and resid 324 through 332 Processing helix chain 'F' and resid 341 through 345 Processing helix chain 'F' and resid 375 through 399 removed outlier: 3.649A pdb=" N LYS F 394 " --> pdb=" O VAL F 390 " (cutoff:3.500A) Processing helix chain 'F' and resid 408 through 421 Processing helix chain 'F' and resid 432 through 443 Processing helix chain 'F' and resid 456 through 461 Processing helix chain 'G' and resid 10 through 69 removed outlier: 4.027A pdb=" N LYS G 30 " --> pdb=" O ASP G 26 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ALA G 34 " --> pdb=" O LYS G 30 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N GLY G 41 " --> pdb=" O ALA G 37 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N MET G 47 " --> pdb=" O VAL G 43 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N GLU G 48 " --> pdb=" O ARG G 44 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N LEU G 66 " --> pdb=" O ALA G 62 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N ALA G 67 " --> pdb=" O ALA G 63 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ALA G 69 " --> pdb=" O LEU G 65 " (cutoff:3.500A) Processing helix chain 'G' and resid 73 through 81 Processing helix chain 'G' and resid 122 through 207 removed outlier: 4.202A pdb=" N THR G 145 " --> pdb=" O ALA G 141 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N ARG G 146 " --> pdb=" O ASN G 142 " (cutoff:3.500A) removed outlier: 5.446A pdb=" N ILE G 169 " --> pdb=" O GLU G 165 " (cutoff:3.500A) Proline residue: G 170 - end of helix removed outlier: 3.862A pdb=" N GLU G 187 " --> pdb=" O LEU G 183 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N ARG G 188 " --> pdb=" O GLU G 184 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N GLU G 189 " --> pdb=" O GLN G 185 " (cutoff:3.500A) removed outlier: 4.710A pdb=" N ASP G 190 " --> pdb=" O ARG G 186 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N GLU G 207 " --> pdb=" O ALA G 203 " (cutoff:3.500A) Processing helix chain 'H' and resid 7 through 16 removed outlier: 4.234A pdb=" N ALA H 16 " --> pdb=" O GLY H 12 " (cutoff:3.500A) Processing helix chain 'H' and resid 30 through 39 Processing helix chain 'H' and resid 57 through 63 Processing helix chain 'H' and resid 84 through 94 Processing sheet with id= A, first strand: chain 'A' and resid 3 through 5 Processing sheet with id= B, first strand: chain 'A' and resid 72 through 76 removed outlier: 3.536A pdb=" N TRP A 187 " --> pdb=" O VAL A 73 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 138 through 140 Processing sheet with id= D, first strand: chain 'A' and resid 225 through 227 removed outlier: 7.604A pdb=" N GLY A 382 " --> pdb=" O ILE A 226 " (cutoff:3.500A) No H-bonds generated for sheet with id= D Processing sheet with id= E, first strand: chain 'A' and resid 322 through 325 removed outlier: 6.857A pdb=" N VAL A 251 " --> pdb=" O MET A 323 " (cutoff:3.500A) removed outlier: 7.731A pdb=" N ASP A 325 " --> pdb=" O VAL A 251 " (cutoff:3.500A) removed outlier: 7.429A pdb=" N VAL A 253 " --> pdb=" O ASP A 325 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N ILE A 288 " --> pdb=" O GLY A 254 " (cutoff:3.500A) removed outlier: 7.449A pdb=" N GLY A 256 " --> pdb=" O ILE A 288 " (cutoff:3.500A) removed outlier: 8.100A pdb=" N ASN A 290 " --> pdb=" O GLY A 256 " (cutoff:3.500A) No H-bonds generated for sheet with id= E Processing sheet with id= F, first strand: chain 'A' and resid 319 through 321 removed outlier: 5.793A pdb=" N ALA A 377 " --> pdb=" O VAL A 320 " (cutoff:3.500A) No H-bonds generated for sheet with id= F Processing sheet with id= G, first strand: chain 'A' and resid 157 through 160 removed outlier: 7.118A pdb=" N VAL A 174 " --> pdb=" O LYS A 158 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 5 through 10 removed outlier: 6.760A pdb=" N ILE B 15 " --> pdb=" O GLN B 7 " (cutoff:3.500A) removed outlier: 4.708A pdb=" N ILE B 9 " --> pdb=" O ALA B 13 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N ALA B 13 " --> pdb=" O ILE B 9 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ALA B 47 " --> pdb=" O ALA B 16 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N ARG B 41 " --> pdb=" O PHE B 48 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N GLN B 50 " --> pdb=" O ILE B 39 " (cutoff:3.500A) removed outlier: 5.989A pdb=" N ILE B 39 " --> pdb=" O GLN B 50 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 28 through 30 removed outlier: 3.668A pdb=" N VAL B 65 " --> pdb=" O LYS B 29 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'B' and resid 72 through 75 Processing sheet with id= K, first strand: chain 'B' and resid 117 through 119 Processing sheet with id= L, first strand: chain 'B' and resid 223 through 227 removed outlier: 8.669A pdb=" N ALA B 224 " --> pdb=" O VAL B 378 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N ILE B 380 " --> pdb=" O ALA B 224 " (cutoff:3.500A) removed outlier: 7.753A pdb=" N ILE B 226 " --> pdb=" O ILE B 380 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N GLY B 382 " --> pdb=" O ILE B 226 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N THR B 379 " --> pdb=" O VAL B 320 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ALA B 324 " --> pdb=" O VAL B 381 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N VAL B 249 " --> pdb=" O ALA B 321 " (cutoff:3.500A) removed outlier: 8.285A pdb=" N MET B 323 " --> pdb=" O VAL B 249 " (cutoff:3.500A) removed outlier: 7.254A pdb=" N VAL B 251 " --> pdb=" O MET B 323 " (cutoff:3.500A) removed outlier: 7.857A pdb=" N ASP B 325 " --> pdb=" O VAL B 251 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N VAL B 253 " --> pdb=" O ASP B 325 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'B' and resid 134 through 140 removed outlier: 7.084A pdb=" N ILE B 147 " --> pdb=" O LEU B 135 " (cutoff:3.500A) removed outlier: 4.886A pdb=" N THR B 137 " --> pdb=" O HIS B 145 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N HIS B 145 " --> pdb=" O THR B 137 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N PHE B 143 " --> pdb=" O PRO B 139 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'B' and resid 157 through 160 removed outlier: 6.774A pdb=" N VAL B 174 " --> pdb=" O LYS B 158 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'C' and resid 28 through 30 removed outlier: 6.725A pdb=" N ILE C 15 " --> pdb=" O GLN C 7 " (cutoff:3.500A) removed outlier: 4.909A pdb=" N ILE C 9 " --> pdb=" O ALA C 13 " (cutoff:3.500A) removed outlier: 7.232A pdb=" N ALA C 13 " --> pdb=" O ILE C 9 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'C' and resid 72 through 76 Processing sheet with id= Q, first strand: chain 'C' and resid 117 through 119 removed outlier: 3.738A pdb=" N GLY C 164 " --> pdb=" O TRP C 119 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'C' and resid 137 through 140 removed outlier: 3.741A pdb=" N GLU C 140 " --> pdb=" O PHE C 143 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'C' and resid 250 through 252 removed outlier: 8.396A pdb=" N VAL C 251 " --> pdb=" O SER C 319 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N ALA C 321 " --> pdb=" O VAL C 251 " (cutoff:3.500A) removed outlier: 6.012A pdb=" N ALA C 377 " --> pdb=" O VAL C 320 " (cutoff:3.500A) removed outlier: 7.120A pdb=" N LEU C 322 " --> pdb=" O ALA C 377 " (cutoff:3.500A) removed outlier: 5.932A pdb=" N THR C 379 " --> pdb=" O LEU C 322 " (cutoff:3.500A) No H-bonds generated for sheet with id= S Processing sheet with id= T, first strand: chain 'C' and resid 253 through 255 removed outlier: 6.701A pdb=" N ILE C 288 " --> pdb=" O GLY C 254 " (cutoff:3.500A) No H-bonds generated for sheet with id= T Processing sheet with id= U, first strand: chain 'D' and resid 55 through 58 removed outlier: 3.868A pdb=" N VAL D 21 " --> pdb=" O ALA D 55 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N TYR D 13 " --> pdb=" O PHE D 20 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'D' and resid 81 through 84 removed outlier: 3.536A pdb=" N VAL D 84 " --> pdb=" O LYS D 110 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N LYS D 110 " --> pdb=" O VAL D 84 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'D' and resid 152 through 154 Processing sheet with id= X, first strand: chain 'D' and resid 192 through 194 removed outlier: 6.359A pdb=" N PHE D 220 " --> pdb=" O ALA D 193 " (cutoff:3.500A) No H-bonds generated for sheet with id= X Processing sheet with id= Y, first strand: chain 'D' and resid 252 through 255 removed outlier: 6.288A pdb=" N SER D 307 " --> pdb=" O VAL D 253 " (cutoff:3.500A) removed outlier: 7.702A pdb=" N VAL D 255 " --> pdb=" O SER D 307 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N THR D 309 " --> pdb=" O VAL D 255 " (cutoff:3.500A) No H-bonds generated for sheet with id= Y Processing sheet with id= Z, first strand: chain 'D' and resid 32 through 36 removed outlier: 5.655A pdb=" N ASP D 34 " --> pdb=" O LEU D 75 " (cutoff:3.500A) removed outlier: 5.784A pdb=" N LEU D 75 " --> pdb=" O ASP D 34 " (cutoff:3.500A) removed outlier: 7.181A pdb=" N LYS D 36 " --> pdb=" O VAL D 73 " (cutoff:3.500A) removed outlier: 5.769A pdb=" N VAL D 73 " --> pdb=" O LYS D 36 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'E' and resid 45 through 47 removed outlier: 3.684A pdb=" N SER E 15 " --> pdb=" O LEU E 18 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N TYR E 13 " --> pdb=" O PHE E 20 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'E' and resid 81 through 84 removed outlier: 3.747A pdb=" N LYS E 110 " --> pdb=" O VAL E 84 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'E' and resid 336 through 338 Processing sheet with id= AD, first strand: chain 'E' and resid 255 through 257 removed outlier: 3.929A pdb=" N LEU E 257 " --> pdb=" O ILE E 311 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'E' and resid 32 through 37 removed outlier: 3.906A pdb=" N ILE E 32 " --> pdb=" O GLU E 77 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N GLU E 77 " --> pdb=" O ILE E 32 " (cutoff:3.500A) removed outlier: 6.120A pdb=" N ASP E 34 " --> pdb=" O LEU E 75 " (cutoff:3.500A) removed outlier: 6.190A pdb=" N LEU E 75 " --> pdb=" O ASP E 34 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N LYS E 36 " --> pdb=" O VAL E 73 " (cutoff:3.500A) removed outlier: 5.332A pdb=" N VAL E 73 " --> pdb=" O LYS E 36 " (cutoff:3.500A) No H-bonds generated for sheet with id= AE Processing sheet with id= AF, first strand: chain 'F' and resid 55 through 58 removed outlier: 3.660A pdb=" N LEU F 19 " --> pdb=" O ILE F 57 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N LEU F 18 " --> pdb=" O SER F 15 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N SER F 15 " --> pdb=" O LEU F 18 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N TYR F 13 " --> pdb=" O PHE F 20 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'F' and resid 42 through 44 removed outlier: 3.842A pdb=" N GLU F 77 " --> pdb=" O ILE F 32 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N ASP F 34 " --> pdb=" O LEU F 75 " (cutoff:3.500A) removed outlier: 6.119A pdb=" N LEU F 75 " --> pdb=" O ASP F 34 " (cutoff:3.500A) Processing sheet with id= AH, first strand: chain 'F' and resid 81 through 84 removed outlier: 3.509A pdb=" N LEU F 112 " --> pdb=" O LEU F 82 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N LYS F 110 " --> pdb=" O VAL F 84 " (cutoff:3.500A) Processing sheet with id= AI, first strand: chain 'F' and resid 336 through 338 Processing sheet with id= AJ, first strand: chain 'F' and resid 192 through 194 removed outlier: 6.223A pdb=" N PHE F 220 " --> pdb=" O ALA F 193 " (cutoff:3.500A) No H-bonds generated for sheet with id= AJ Processing sheet with id= AK, first strand: chain 'F' and resid 252 through 255 removed outlier: 6.472A pdb=" N SER F 307 " --> pdb=" O VAL F 253 " (cutoff:3.500A) removed outlier: 7.687A pdb=" N VAL F 255 " --> pdb=" O SER F 307 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N THR F 309 " --> pdb=" O VAL F 255 " (cutoff:3.500A) No H-bonds generated for sheet with id= AK Processing sheet with id= AL, first strand: chain 'H' and resid 44 through 47 removed outlier: 6.245A pdb=" N VAL H 70 " --> pdb=" O VAL H 45 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N VAL H 47 " --> pdb=" O VAL H 70 " (cutoff:3.500A) removed outlier: 6.202A pdb=" N LEU H 72 " --> pdb=" O VAL H 47 " (cutoff:3.500A) No H-bonds generated for sheet with id= AL 858 hydrogen bonds defined for protein. 2457 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 8.62 Time building geometry restraints manager: 10.56 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: 8889 1.34 - 1.45: 3067 1.45 - 1.57: 15004 1.57 - 1.69: 3 1.69 - 1.80: 190 Bond restraints: 27153 Sorted by residual: bond pdb=" N ILE E 459 " pdb=" CA ILE E 459 " ideal model delta sigma weight residual 1.461 1.435 0.026 1.19e-02 7.06e+03 4.62e+00 bond pdb=" N ILE D 459 " pdb=" CA ILE D 459 " ideal model delta sigma weight residual 1.461 1.441 0.020 1.19e-02 7.06e+03 2.79e+00 bond pdb=" C HIS D 458 " pdb=" N ILE D 459 " ideal model delta sigma weight residual 1.335 1.316 0.019 1.26e-02 6.30e+03 2.20e+00 bond pdb=" C ILE F 459 " pdb=" O ILE F 459 " ideal model delta sigma weight residual 1.237 1.220 0.017 1.17e-02 7.31e+03 2.05e+00 bond pdb=" N GLY F 299 " pdb=" CA GLY F 299 " ideal model delta sigma weight residual 1.453 1.441 0.012 8.60e-03 1.35e+04 1.90e+00 ... (remaining 27148 not shown) Histogram of bond angle deviations from ideal: 98.77 - 106.08: 814 106.08 - 113.40: 14779 113.40 - 120.71: 12143 120.71 - 128.02: 8891 128.02 - 135.34: 166 Bond angle restraints: 36793 Sorted by residual: angle pdb=" N ILE E 459 " pdb=" CA ILE E 459 " pdb=" C ILE E 459 " ideal model delta sigma weight residual 110.62 105.55 5.07 1.02e+00 9.61e-01 2.47e+01 angle pdb=" N THR G 119 " pdb=" CA THR G 119 " pdb=" C THR G 119 " ideal model delta sigma weight residual 109.81 117.08 -7.27 2.21e+00 2.05e-01 1.08e+01 angle pdb=" N GLU E 276 " pdb=" CA GLU E 276 " pdb=" C GLU E 276 " ideal model delta sigma weight residual 110.44 114.37 -3.93 1.20e+00 6.94e-01 1.07e+01 angle pdb=" C ASN B 442 " pdb=" N VAL B 443 " pdb=" CA VAL B 443 " ideal model delta sigma weight residual 122.97 120.00 2.97 9.80e-01 1.04e+00 9.19e+00 angle pdb=" C GLY E 179 " pdb=" N GLU E 180 " pdb=" CA GLU E 180 " ideal model delta sigma weight residual 121.54 127.08 -5.54 1.91e+00 2.74e-01 8.41e+00 ... (remaining 36788 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.67: 15692 27.67 - 55.34: 712 55.34 - 83.01: 74 83.01 - 110.68: 15 110.68 - 138.35: 1 Dihedral angle restraints: 16494 sinusoidal: 6744 harmonic: 9750 Sorted by residual: dihedral pdb=" CA PHE C 419 " pdb=" C PHE C 419 " pdb=" N PRO C 420 " pdb=" CA PRO C 420 " ideal model delta harmonic sigma weight residual 180.00 -103.55 -76.45 0 5.00e+00 4.00e-02 2.34e+02 dihedral pdb=" C5' ADP A 600 " pdb=" O5' ADP A 600 " pdb=" PA ADP A 600 " pdb=" O2A ADP A 600 " ideal model delta sinusoidal sigma weight residual 300.00 161.66 138.35 1 2.00e+01 2.50e-03 4.19e+01 dihedral pdb=" CA THR B 273 " pdb=" C THR B 273 " pdb=" N ASP B 274 " pdb=" CA ASP B 274 " ideal model delta harmonic sigma weight residual 180.00 151.58 28.42 0 5.00e+00 4.00e-02 3.23e+01 ... (remaining 16491 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 2352 0.034 - 0.068: 1207 0.068 - 0.103: 374 0.103 - 0.137: 164 0.137 - 0.171: 12 Chirality restraints: 4109 Sorted by residual: chirality pdb=" CA PHE C 419 " pdb=" N PHE C 419 " pdb=" C PHE C 419 " pdb=" CB PHE C 419 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.33e-01 chirality pdb=" CA ILE E 459 " pdb=" N ILE E 459 " pdb=" C ILE E 459 " pdb=" CB ILE E 459 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.45e-01 chirality pdb=" CA THR G 119 " pdb=" N THR G 119 " pdb=" C THR G 119 " pdb=" CB THR G 119 " both_signs ideal model delta sigma weight residual False 2.53 2.38 0.15 2.00e-01 2.50e+01 5.29e-01 ... (remaining 4106 not shown) Planarity restraints: 4818 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE C 419 " 0.064 5.00e-02 4.00e+02 9.70e-02 1.51e+01 pdb=" N PRO C 420 " -0.168 5.00e-02 4.00e+02 pdb=" CA PRO C 420 " 0.051 5.00e-02 4.00e+02 pdb=" CD PRO C 420 " 0.053 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE B 269 " -0.040 5.00e-02 4.00e+02 6.00e-02 5.76e+00 pdb=" N PRO B 270 " 0.104 5.00e-02 4.00e+02 pdb=" CA PRO B 270 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO B 270 " -0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU F 185 " -0.039 5.00e-02 4.00e+02 5.93e-02 5.62e+00 pdb=" N PRO F 186 " 0.102 5.00e-02 4.00e+02 pdb=" CA PRO F 186 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO F 186 " -0.032 5.00e-02 4.00e+02 ... (remaining 4815 not shown) Histogram of nonbonded interaction distances: 1.80 - 2.42: 87 2.42 - 3.04: 16956 3.04 - 3.66: 36231 3.66 - 4.28: 53331 4.28 - 4.90: 94246 Nonbonded interactions: 200851 Sorted by model distance: nonbonded pdb=" O ALA C 576 " pdb=" CD2 LEU C 577 " model vdw 1.805 3.460 nonbonded pdb=" O ARG C 547 " pdb=" OH TYR C 562 " model vdw 2.045 2.440 nonbonded pdb=" NH2 ARG C 401 " pdb=" OE2 GLU F 265 " model vdw 2.146 2.520 nonbonded pdb=" NH2 ARG E 91 " pdb=" O PRO E 104 " model vdw 2.148 2.520 nonbonded pdb=" OG SER D 455 " pdb=" OD1 ASP D 457 " model vdw 2.157 2.440 ... (remaining 200846 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 1 through 577) selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' } 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: 2.170 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: 9.390 Check model and map are aligned: 0.390 Set scattering table: 0.230 Process input model: 66.170 Find NCS groups from input model: 1.710 Set up NCS constraints: 0.170 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 83.650 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8299 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 : 0.006 0.052 27153 Z= 0.405 Angle : 0.684 9.940 36793 Z= 0.383 Chirality : 0.047 0.171 4109 Planarity : 0.005 0.097 4818 Dihedral : 15.322 138.345 10280 Min Nonbonded Distance : 1.805 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.03 % Allowed : 11.08 % Favored : 88.89 % Rotamer: Outliers : 11.59 % Allowed : 11.84 % Favored : 76.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.54 % Cis-general : 0.00 % Twisted Proline : 0.51 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.29 (0.12), residues: 3402 helix: -1.22 (0.13), residues: 1309 sheet: -3.57 (0.21), residues: 469 loop : -4.13 (0.12), residues: 1624 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 117 HIS 0.004 0.001 HIS F 323 PHE 0.019 0.002 PHE C 419 TYR 0.020 0.002 TYR D 13 ARG 0.005 0.001 ARG C 314 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6804 Ramachandran restraints generated. 3402 Oldfield, 0 Emsley, 3402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6804 Ramachandran restraints generated. 3402 Oldfield, 0 Emsley, 3402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 732 residues out of total 2804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 325 poor density : 407 time to evaluate : 2.857 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "PHE H 100 " (corrupted residue). Skipping it. REVERT: A 24 MET cc_start: 0.8934 (OUTLIER) cc_final: 0.6946 (tmm) REVERT: A 124 LYS cc_start: 0.8442 (tppp) cc_final: 0.7832 (mtpp) REVERT: A 165 GLU cc_start: 0.7540 (OUTLIER) cc_final: 0.7001 (mt-10) REVERT: A 191 ARG cc_start: 0.8003 (OUTLIER) cc_final: 0.7727 (mtm110) REVERT: A 323 MET cc_start: 0.7585 (ttm) cc_final: 0.7349 (mtp) REVERT: A 410 ASP cc_start: 0.7995 (t0) cc_final: 0.7702 (m-30) REVERT: A 458 LEU cc_start: 0.8353 (OUTLIER) cc_final: 0.8134 (mm) REVERT: A 464 LEU cc_start: 0.8312 (OUTLIER) cc_final: 0.8015 (mm) REVERT: A 541 GLN cc_start: 0.7660 (OUTLIER) cc_final: 0.7451 (mp10) REVERT: A 574 PHE cc_start: 0.7460 (OUTLIER) cc_final: 0.7061 (m-80) REVERT: B 157 VAL cc_start: 0.9076 (t) cc_final: 0.8841 (p) REVERT: B 294 MET cc_start: 0.8395 (mtt) cc_final: 0.8159 (mtp) REVERT: B 332 GLU cc_start: 0.8165 (OUTLIER) cc_final: 0.7963 (tm-30) REVERT: B 369 ILE cc_start: 0.8865 (OUTLIER) cc_final: 0.8558 (mt) REVERT: B 423 ASN cc_start: 0.8504 (t0) cc_final: 0.8193 (t0) REVERT: B 509 MET cc_start: 0.7330 (tpt) cc_final: 0.6954 (mmm) REVERT: B 550 ARG cc_start: 0.7784 (mmm160) cc_final: 0.7548 (tpt170) REVERT: B 558 GLU cc_start: 0.7353 (tp30) cc_final: 0.6674 (tp30) REVERT: C 8 LYS cc_start: 0.8928 (tttt) cc_final: 0.8682 (tttm) REVERT: C 130 ARG cc_start: 0.7992 (ptm160) cc_final: 0.7668 (ptt90) REVERT: C 159 GLU cc_start: 0.7492 (tt0) cc_final: 0.7291 (pt0) REVERT: C 266 LEU cc_start: 0.8736 (OUTLIER) cc_final: 0.8467 (mt) REVERT: C 304 TYR cc_start: 0.8757 (m-80) cc_final: 0.8473 (m-80) REVERT: C 393 GLU cc_start: 0.7646 (tt0) cc_final: 0.7427 (tt0) REVERT: C 538 GLU cc_start: 0.7443 (OUTLIER) cc_final: 0.5751 (tm-30) REVERT: C 571 GLN cc_start: 0.8073 (OUTLIER) cc_final: 0.7505 (mp10) REVERT: D 7 GLU cc_start: 0.7024 (OUTLIER) cc_final: 0.6216 (pt0) REVERT: D 215 SER cc_start: 0.8757 (m) cc_final: 0.8513 (p) REVERT: D 216 ARG cc_start: 0.9393 (OUTLIER) cc_final: 0.6400 (ppt-90) REVERT: D 268 ARG cc_start: 0.8361 (OUTLIER) cc_final: 0.6952 (ttt180) REVERT: D 381 GLN cc_start: 0.8850 (OUTLIER) cc_final: 0.7389 (tm130) REVERT: D 392 ILE cc_start: 0.8115 (pt) cc_final: 0.7879 (mt) REVERT: D 442 LEU cc_start: 0.9230 (OUTLIER) cc_final: 0.8994 (mp) REVERT: D 457 ASP cc_start: 0.6986 (OUTLIER) cc_final: 0.6781 (p0) REVERT: E 67 ASP cc_start: 0.8122 (t0) cc_final: 0.7768 (t0) REVERT: E 82 LEU cc_start: 0.9053 (OUTLIER) cc_final: 0.8707 (pt) REVERT: E 130 PHE cc_start: 0.9067 (OUTLIER) cc_final: 0.8724 (p90) REVERT: E 269 GLU cc_start: 0.7636 (tt0) cc_final: 0.7424 (tt0) REVERT: E 327 ASP cc_start: 0.8336 (OUTLIER) cc_final: 0.8085 (m-30) REVERT: E 334 GLU cc_start: 0.8302 (pt0) cc_final: 0.8030 (pt0) REVERT: E 368 LYS cc_start: 0.7593 (tptt) cc_final: 0.6659 (tptt) REVERT: E 372 ARG cc_start: 0.8297 (OUTLIER) cc_final: 0.7418 (mtm110) REVERT: E 373 GLU cc_start: 0.8078 (mp0) cc_final: 0.7647 (mt-10) REVERT: E 394 LYS cc_start: 0.7951 (ttpt) cc_final: 0.7612 (tppt) REVERT: E 401 GLU cc_start: 0.7691 (tm-30) cc_final: 0.7406 (tm-30) REVERT: E 437 GLN cc_start: 0.7873 (OUTLIER) cc_final: 0.7575 (tm-30) REVERT: E 453 ARG cc_start: 0.7123 (OUTLIER) cc_final: 0.6782 (tpp-160) REVERT: F 111 ARG cc_start: 0.8744 (OUTLIER) cc_final: 0.7629 (mtm-85) REVERT: F 172 THR cc_start: 0.9275 (OUTLIER) cc_final: 0.8687 (p) REVERT: F 327 ASP cc_start: 0.7821 (t70) cc_final: 0.7536 (t0) REVERT: F 331 TYR cc_start: 0.8075 (m-80) cc_final: 0.7627 (m-80) REVERT: F 362 MET cc_start: 0.8877 (ttt) cc_final: 0.8514 (ttt) REVERT: F 410 ARG cc_start: 0.7409 (mtt-85) cc_final: 0.6788 (mtp180) REVERT: F 412 LEU cc_start: 0.7822 (OUTLIER) cc_final: 0.7484 (mt) REVERT: G 26 ASP cc_start: 0.7817 (m-30) cc_final: 0.7556 (m-30) REVERT: G 44 ARG cc_start: 0.7266 (ttm-80) cc_final: 0.6904 (tpt90) REVERT: G 59 GLU cc_start: 0.6882 (tp30) cc_final: 0.6223 (tm-30) REVERT: G 64 LEU cc_start: 0.6496 (OUTLIER) cc_final: 0.6258 (tp) REVERT: G 135 GLU cc_start: 0.7034 (mp0) cc_final: 0.6613 (mp0) REVERT: G 166 GLN cc_start: 0.7980 (mt0) cc_final: 0.7573 (mt0) REVERT: G 193 ARG cc_start: 0.8177 (mtt180) cc_final: 0.7951 (mtm110) REVERT: G 200 LYS cc_start: 0.7251 (ttmm) cc_final: 0.6926 (mptt) REVERT: H 3 VAL cc_start: 0.5769 (p) cc_final: 0.5461 (t) REVERT: H 77 LEU cc_start: 0.2414 (OUTLIER) cc_final: 0.2106 (tp) REVERT: H 87 GLU cc_start: 0.7515 (tt0) cc_final: 0.7261 (tm-30) REVERT: H 92 GLU cc_start: 0.7699 (pt0) cc_final: 0.7472 (pt0) REVERT: H 96 LYS cc_start: 0.7093 (OUTLIER) cc_final: 0.5565 (pttm) outliers start: 325 outliers final: 190 residues processed: 678 average time/residue: 0.4060 time to fit residues: 420.0475 Evaluate side-chains 545 residues out of total 2804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 220 poor density : 325 time to evaluate : 3.024 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 VAL Chi-restraints excluded: chain A residue 9 ILE Chi-restraints excluded: chain A residue 14 VAL Chi-restraints excluded: chain A residue 24 MET Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 83 ILE Chi-restraints excluded: chain A residue 88 GLN Chi-restraints excluded: chain A residue 122 MET Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 165 GLU Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 191 ARG Chi-restraints excluded: chain A residue 207 THR Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 273 THR Chi-restraints excluded: chain A residue 274 ASP Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 293 ASN Chi-restraints excluded: chain A residue 316 GLN Chi-restraints excluded: chain A residue 329 ARG Chi-restraints excluded: chain A residue 353 TYR Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain A residue 370 THR Chi-restraints excluded: chain A residue 425 ASN Chi-restraints excluded: chain A residue 458 LEU Chi-restraints excluded: chain A residue 464 LEU Chi-restraints excluded: chain A residue 466 GLU Chi-restraints excluded: chain A residue 530 ILE Chi-restraints excluded: chain A residue 536 ILE Chi-restraints excluded: chain A residue 541 GLN Chi-restraints excluded: chain A residue 574 PHE Chi-restraints excluded: chain A residue 577 LEU Chi-restraints excluded: chain B residue 27 ILE Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 88 GLN Chi-restraints excluded: chain B residue 96 GLU Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 152 ASP Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain B residue 200 ASP Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 230 PHE Chi-restraints excluded: chain B residue 255 CYS Chi-restraints excluded: chain B residue 260 ASN Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 284 ARG Chi-restraints excluded: chain B residue 285 THR Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 299 ARG Chi-restraints excluded: chain B residue 303 ILE Chi-restraints excluded: chain B residue 315 ASP Chi-restraints excluded: chain B residue 319 SER Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain B residue 332 GLU Chi-restraints excluded: chain B residue 354 LEU Chi-restraints excluded: chain B residue 368 VAL Chi-restraints excluded: chain B residue 369 ILE Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 443 VAL Chi-restraints excluded: chain B residue 450 LEU Chi-restraints excluded: chain B residue 469 GLN Chi-restraints excluded: chain B residue 476 LEU Chi-restraints excluded: chain B residue 520 LEU Chi-restraints excluded: chain B residue 524 LYS Chi-restraints excluded: chain B residue 536 ILE Chi-restraints excluded: chain B residue 548 ILE Chi-restraints excluded: chain B residue 554 VAL Chi-restraints excluded: chain B residue 565 GLU Chi-restraints excluded: chain B residue 577 LEU Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 83 ILE Chi-restraints excluded: chain C residue 96 GLU Chi-restraints excluded: chain C residue 103 THR Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 141 PHE Chi-restraints excluded: chain C residue 145 HIS Chi-restraints excluded: chain C residue 152 ASP Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 186 THR Chi-restraints excluded: chain C residue 200 ASP Chi-restraints excluded: chain C residue 207 THR Chi-restraints excluded: chain C residue 211 ILE Chi-restraints excluded: chain C residue 249 VAL Chi-restraints excluded: chain C residue 266 LEU Chi-restraints excluded: chain C residue 284 ARG Chi-restraints excluded: chain C residue 287 LEU Chi-restraints excluded: chain C residue 315 ASP Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 337 ILE Chi-restraints excluded: chain C residue 354 LEU Chi-restraints excluded: chain C residue 363 GLU Chi-restraints excluded: chain C residue 396 THR Chi-restraints excluded: chain C residue 461 GLU Chi-restraints excluded: chain C residue 520 LEU Chi-restraints excluded: chain C residue 531 LYS Chi-restraints excluded: chain C residue 538 GLU Chi-restraints excluded: chain C residue 570 ILE Chi-restraints excluded: chain C residue 571 GLN Chi-restraints excluded: chain C residue 574 PHE Chi-restraints excluded: chain D residue 7 GLU Chi-restraints excluded: chain D residue 37 ASP Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 59 VAL Chi-restraints excluded: chain D residue 119 LEU Chi-restraints excluded: chain D residue 130 PHE Chi-restraints excluded: chain D residue 131 ILE Chi-restraints excluded: chain D residue 183 LYS Chi-restraints excluded: chain D residue 197 THR Chi-restraints excluded: chain D residue 214 LEU Chi-restraints excluded: chain D residue 216 ARG Chi-restraints excluded: chain D residue 250 ASP Chi-restraints excluded: chain D residue 258 THR Chi-restraints excluded: chain D residue 268 ARG Chi-restraints excluded: chain D residue 270 ILE Chi-restraints excluded: chain D residue 294 ILE Chi-restraints excluded: chain D residue 309 THR Chi-restraints excluded: chain D residue 315 SER Chi-restraints excluded: chain D residue 318 ASP Chi-restraints excluded: chain D residue 322 THR Chi-restraints excluded: chain D residue 334 GLU Chi-restraints excluded: chain D residue 370 LYS Chi-restraints excluded: chain D residue 379 SER Chi-restraints excluded: chain D residue 381 GLN Chi-restraints excluded: chain D residue 390 VAL Chi-restraints excluded: chain D residue 399 ILE Chi-restraints excluded: chain D residue 401 GLU Chi-restraints excluded: chain D residue 442 LEU Chi-restraints excluded: chain D residue 457 ASP Chi-restraints excluded: chain E residue 7 GLU Chi-restraints excluded: chain E residue 26 ASP Chi-restraints excluded: chain E residue 73 VAL Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain E residue 94 ASN Chi-restraints excluded: chain E residue 111 ARG Chi-restraints excluded: chain E residue 130 PHE Chi-restraints excluded: chain E residue 131 ILE Chi-restraints excluded: chain E residue 133 THR Chi-restraints excluded: chain E residue 137 THR Chi-restraints excluded: chain E residue 143 THR Chi-restraints excluded: chain E residue 180 GLU Chi-restraints excluded: chain E residue 194 MET Chi-restraints excluded: chain E residue 206 GLN Chi-restraints excluded: chain E residue 257 LEU Chi-restraints excluded: chain E residue 258 THR Chi-restraints excluded: chain E residue 270 ILE Chi-restraints excluded: chain E residue 290 ASP Chi-restraints excluded: chain E residue 294 ILE Chi-restraints excluded: chain E residue 327 ASP Chi-restraints excluded: chain E residue 336 GLN Chi-restraints excluded: chain E residue 372 ARG Chi-restraints excluded: chain E residue 379 SER Chi-restraints excluded: chain E residue 384 SER Chi-restraints excluded: chain E residue 405 THR Chi-restraints excluded: chain E residue 413 GLN Chi-restraints excluded: chain E residue 427 GLN Chi-restraints excluded: chain E residue 437 GLN Chi-restraints excluded: chain E residue 452 LYS Chi-restraints excluded: chain E residue 453 ARG Chi-restraints excluded: chain E residue 459 ILE Chi-restraints excluded: chain F residue 9 THR Chi-restraints excluded: chain F residue 11 ILE Chi-restraints excluded: chain F residue 53 GLU Chi-restraints excluded: chain F residue 54 TYR Chi-restraints excluded: chain F residue 68 LEU Chi-restraints excluded: chain F residue 73 VAL Chi-restraints excluded: chain F residue 74 SER Chi-restraints excluded: chain F residue 78 ASP Chi-restraints excluded: chain F residue 79 VAL Chi-restraints excluded: chain F residue 96 ILE Chi-restraints excluded: chain F residue 111 ARG Chi-restraints excluded: chain F residue 112 LEU Chi-restraints excluded: chain F residue 128 GLU Chi-restraints excluded: chain F residue 131 ILE Chi-restraints excluded: chain F residue 133 THR Chi-restraints excluded: chain F residue 137 THR Chi-restraints excluded: chain F residue 148 GLN Chi-restraints excluded: chain F residue 172 THR Chi-restraints excluded: chain F residue 180 GLU Chi-restraints excluded: chain F residue 183 LYS Chi-restraints excluded: chain F residue 197 THR Chi-restraints excluded: chain F residue 206 GLN Chi-restraints excluded: chain F residue 225 ASP Chi-restraints excluded: chain F residue 232 ILE Chi-restraints excluded: chain F residue 254 LEU Chi-restraints excluded: chain F residue 255 VAL Chi-restraints excluded: chain F residue 270 ILE Chi-restraints excluded: chain F residue 294 ILE Chi-restraints excluded: chain F residue 309 THR Chi-restraints excluded: chain F residue 315 SER Chi-restraints excluded: chain F residue 318 ASP Chi-restraints excluded: chain F residue 343 LEU Chi-restraints excluded: chain F residue 376 LYS Chi-restraints excluded: chain F residue 393 ARG Chi-restraints excluded: chain F residue 412 LEU Chi-restraints excluded: chain F residue 451 LEU Chi-restraints excluded: chain F residue 459 ILE Chi-restraints excluded: chain G residue 54 ASP Chi-restraints excluded: chain G residue 64 LEU Chi-restraints excluded: chain G residue 86 LEU Chi-restraints excluded: chain G residue 105 LYS Chi-restraints excluded: chain G residue 172 ILE Chi-restraints excluded: chain G residue 182 VAL Chi-restraints excluded: chain G residue 201 ILE Chi-restraints excluded: chain H residue 6 ASP Chi-restraints excluded: chain H residue 35 THR Chi-restraints excluded: chain H residue 71 LEU Chi-restraints excluded: chain H residue 77 LEU Chi-restraints excluded: chain H residue 93 LEU Chi-restraints excluded: chain H residue 96 LYS Chi-restraints excluded: chain H residue 98 ILE Chi-restraints excluded: chain H residue 100 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 337 random chunks: chunk 284 optimal weight: 0.7980 chunk 255 optimal weight: 5.9990 chunk 141 optimal weight: 0.9980 chunk 87 optimal weight: 0.5980 chunk 172 optimal weight: 0.9990 chunk 136 optimal weight: 4.9990 chunk 264 optimal weight: 1.9990 chunk 102 optimal weight: 2.9990 chunk 160 optimal weight: 3.9990 chunk 196 optimal weight: 2.9990 chunk 306 optimal weight: 4.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 50 GLN A 88 GLN A 196 GLN A 496 GLN A 571 GLN B 3 GLN B 7 GLN B 50 GLN B 81 ASN B 88 GLN B 185 HIS B 202 ASN ** B 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 316 GLN B 418 HIS B 496 GLN B 498 ASN C 238 GLN ** C 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 316 GLN C 469 GLN C 496 GLN C 497 GLN D 142 ASN D 148 GLN D 249 HIS D 252 HIS ** D 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 310 GLN D 407 ASN D 425 GLN E 23 ASN E 142 ASN E 148 GLN E 252 HIS ** E 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 336 GLN ** E 407 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 427 GLN E 437 GLN E 448 GLN F 46 GLN F 129 GLN F 142 ASN F 148 GLN F 166 GLN F 252 HIS F 310 GLN F 323 HIS F 363 ASN F 413 GLN F 448 GLN G 10 ASN G 17 GLN G 95 ASN G 180 GLN H 11 GLN Total number of N/Q/H flips: 52 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8266 moved from start: 0.1201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 27153 Z= 0.228 Angle : 0.576 7.841 36793 Z= 0.293 Chirality : 0.044 0.215 4109 Planarity : 0.005 0.084 4818 Dihedral : 11.399 117.076 4236 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.03 % Allowed : 9.02 % Favored : 90.95 % Rotamer: Outliers : 8.63 % Allowed : 17.05 % Favored : 74.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.54 % Cis-general : 0.00 % Twisted Proline : 0.51 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.99 (0.14), residues: 3402 helix: 0.11 (0.15), residues: 1297 sheet: -3.04 (0.21), residues: 492 loop : -3.54 (0.13), residues: 1613 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP G 97 HIS 0.004 0.001 HIS F 323 PHE 0.017 0.001 PHE C 419 TYR 0.016 0.001 TYR A 562 ARG 0.003 0.000 ARG E 321 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6804 Ramachandran restraints generated. 3402 Oldfield, 0 Emsley, 3402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6804 Ramachandran restraints generated. 3402 Oldfield, 0 Emsley, 3402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 597 residues out of total 2804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 242 poor density : 355 time to evaluate : 2.932 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "PHE H 100 " (corrupted residue). Skipping it. REVERT: A 8 LYS cc_start: 0.8522 (tttp) cc_final: 0.8316 (tptm) REVERT: A 124 LYS cc_start: 0.8263 (tppp) cc_final: 0.7733 (mtpp) REVERT: A 125 PRO cc_start: 0.8754 (Cg_endo) cc_final: 0.8554 (Cg_exo) REVERT: A 165 GLU cc_start: 0.7450 (OUTLIER) cc_final: 0.6981 (mt-10) REVERT: A 175 LEU cc_start: 0.8609 (tp) cc_final: 0.8359 (mt) REVERT: A 323 MET cc_start: 0.7445 (ttm) cc_final: 0.7206 (mtp) REVERT: A 410 ASP cc_start: 0.8003 (t0) cc_final: 0.7671 (m-30) REVERT: A 464 LEU cc_start: 0.8266 (OUTLIER) cc_final: 0.7927 (mm) REVERT: A 496 GLN cc_start: 0.8910 (OUTLIER) cc_final: 0.8687 (tt0) REVERT: A 540 LEU cc_start: 0.8968 (mm) cc_final: 0.8749 (mm) REVERT: B 9 ILE cc_start: 0.9198 (mt) cc_final: 0.8993 (mt) REVERT: B 88 GLN cc_start: 0.9328 (OUTLIER) cc_final: 0.8865 (tt0) REVERT: B 213 ASP cc_start: 0.7932 (t0) cc_final: 0.7631 (t0) REVERT: B 282 MET cc_start: 0.9230 (mmt) cc_final: 0.9026 (tpt) REVERT: B 423 ASN cc_start: 0.8456 (t0) cc_final: 0.8149 (t0) REVERT: B 488 ARG cc_start: 0.7702 (ttt-90) cc_final: 0.7478 (tmt170) REVERT: B 523 TYR cc_start: 0.8025 (t80) cc_final: 0.7825 (t80) REVERT: B 550 ARG cc_start: 0.7768 (mmm160) cc_final: 0.7505 (tpt170) REVERT: B 558 GLU cc_start: 0.7135 (tp30) cc_final: 0.6684 (tp30) REVERT: C 220 MET cc_start: 0.8098 (tmm) cc_final: 0.7260 (tmm) REVERT: C 266 LEU cc_start: 0.8697 (OUTLIER) cc_final: 0.8427 (mt) REVERT: C 304 TYR cc_start: 0.8687 (m-80) cc_final: 0.8368 (m-80) REVERT: C 393 GLU cc_start: 0.7585 (tt0) cc_final: 0.7383 (tt0) REVERT: C 538 GLU cc_start: 0.7494 (OUTLIER) cc_final: 0.5863 (tm-30) REVERT: D 381 GLN cc_start: 0.8773 (OUTLIER) cc_final: 0.7183 (tm130) REVERT: D 442 LEU cc_start: 0.9207 (OUTLIER) cc_final: 0.8950 (mp) REVERT: D 457 ASP cc_start: 0.6863 (OUTLIER) cc_final: 0.6644 (p0) REVERT: E 111 ARG cc_start: 0.8515 (OUTLIER) cc_final: 0.8163 (mtp85) REVERT: E 130 PHE cc_start: 0.9033 (OUTLIER) cc_final: 0.8731 (p90) REVERT: E 321 ARG cc_start: 0.8307 (tpp80) cc_final: 0.7829 (ttt180) REVERT: E 327 ASP cc_start: 0.8192 (OUTLIER) cc_final: 0.7970 (m-30) REVERT: E 372 ARG cc_start: 0.8293 (OUTLIER) cc_final: 0.7354 (mtm110) REVERT: E 381 GLN cc_start: 0.8170 (mm-40) cc_final: 0.7602 (tp40) REVERT: E 394 LYS cc_start: 0.7428 (ttpt) cc_final: 0.7149 (tppt) REVERT: E 401 GLU cc_start: 0.7507 (tm-30) cc_final: 0.7304 (tm-30) REVERT: E 427 GLN cc_start: 0.8797 (OUTLIER) cc_final: 0.8258 (mp10) REVERT: F 111 ARG cc_start: 0.8728 (OUTLIER) cc_final: 0.7595 (mtm-85) REVERT: F 131 ILE cc_start: 0.8809 (OUTLIER) cc_final: 0.8537 (pt) REVERT: F 185 GLU cc_start: 0.7166 (OUTLIER) cc_final: 0.6275 (mm-30) REVERT: F 362 MET cc_start: 0.8840 (ttt) cc_final: 0.8445 (ttt) REVERT: F 410 ARG cc_start: 0.7253 (mtt-85) cc_final: 0.6631 (mtm-85) REVERT: F 412 LEU cc_start: 0.7587 (OUTLIER) cc_final: 0.7384 (mt) REVERT: G 26 ASP cc_start: 0.7684 (m-30) cc_final: 0.7438 (m-30) REVERT: G 44 ARG cc_start: 0.7292 (ttm-80) cc_final: 0.6917 (tpt90) REVERT: G 55 GLN cc_start: 0.7136 (tm-30) cc_final: 0.6935 (tm-30) REVERT: G 58 LYS cc_start: 0.7381 (mtpt) cc_final: 0.6478 (tptt) REVERT: G 59 GLU cc_start: 0.7095 (tp30) cc_final: 0.6789 (mm-30) REVERT: G 64 LEU cc_start: 0.6466 (OUTLIER) cc_final: 0.6261 (tp) REVERT: G 185 GLN cc_start: 0.9039 (OUTLIER) cc_final: 0.7916 (tp40) REVERT: G 193 ARG cc_start: 0.8168 (mtt180) cc_final: 0.7949 (mtm110) REVERT: G 200 LYS cc_start: 0.7276 (ttmm) cc_final: 0.6867 (mptt) REVERT: H 1 MET cc_start: 0.7357 (mpt) cc_final: 0.7113 (mpt) REVERT: H 77 LEU cc_start: 0.2529 (OUTLIER) cc_final: 0.2209 (tp) REVERT: H 96 LYS cc_start: 0.6980 (OUTLIER) cc_final: 0.5457 (pttm) outliers start: 242 outliers final: 167 residues processed: 552 average time/residue: 0.4064 time to fit residues: 353.9777 Evaluate side-chains 502 residues out of total 2804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 189 poor density : 313 time to evaluate : 2.982 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 ILE Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 83 ILE Chi-restraints excluded: chain A residue 122 MET Chi-restraints excluded: chain A residue 147 ILE Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 165 GLU Chi-restraints excluded: chain A residue 207 THR Chi-restraints excluded: chain A residue 220 MET Chi-restraints excluded: chain A residue 223 THR Chi-restraints excluded: chain A residue 261 GLU Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 293 ASN Chi-restraints excluded: chain A residue 316 GLN Chi-restraints excluded: chain A residue 329 ARG Chi-restraints excluded: chain A residue 353 TYR Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain A residue 370 THR Chi-restraints excluded: chain A residue 393 GLU Chi-restraints excluded: chain A residue 425 ASN Chi-restraints excluded: chain A residue 457 LEU Chi-restraints excluded: chain A residue 458 LEU Chi-restraints excluded: chain A residue 464 LEU Chi-restraints excluded: chain A residue 496 GLN Chi-restraints excluded: chain A residue 530 ILE Chi-restraints excluded: chain A residue 541 GLN Chi-restraints excluded: chain A residue 545 LEU Chi-restraints excluded: chain A residue 574 PHE Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 88 GLN Chi-restraints excluded: chain B residue 96 GLU Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain B residue 200 ASP Chi-restraints excluded: chain B residue 226 ILE Chi-restraints excluded: chain B residue 230 PHE Chi-restraints excluded: chain B residue 260 ASN Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 264 ASP Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 285 THR Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 315 ASP Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain B residue 339 SER Chi-restraints excluded: chain B residue 354 LEU Chi-restraints excluded: chain B residue 368 VAL Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 443 VAL Chi-restraints excluded: chain B residue 446 ASP Chi-restraints excluded: chain B residue 450 LEU Chi-restraints excluded: chain B residue 455 SER Chi-restraints excluded: chain B residue 469 GLN Chi-restraints excluded: chain B residue 476 LEU Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 520 LEU Chi-restraints excluded: chain B residue 524 LYS Chi-restraints excluded: chain B residue 536 ILE Chi-restraints excluded: chain B residue 548 ILE Chi-restraints excluded: chain B residue 554 VAL Chi-restraints excluded: chain B residue 565 GLU Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 83 ILE Chi-restraints excluded: chain C residue 96 GLU Chi-restraints excluded: chain C residue 103 THR Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 141 PHE Chi-restraints excluded: chain C residue 145 HIS Chi-restraints excluded: chain C residue 152 ASP Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 186 THR Chi-restraints excluded: chain C residue 200 ASP Chi-restraints excluded: chain C residue 207 THR Chi-restraints excluded: chain C residue 211 ILE Chi-restraints excluded: chain C residue 249 VAL Chi-restraints excluded: chain C residue 266 LEU Chi-restraints excluded: chain C residue 284 ARG Chi-restraints excluded: chain C residue 287 LEU Chi-restraints excluded: chain C residue 315 ASP Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 337 ILE Chi-restraints excluded: chain C residue 354 LEU Chi-restraints excluded: chain C residue 363 GLU Chi-restraints excluded: chain C residue 398 SER Chi-restraints excluded: chain C residue 461 GLU Chi-restraints excluded: chain C residue 520 LEU Chi-restraints excluded: chain C residue 531 LYS Chi-restraints excluded: chain C residue 538 GLU Chi-restraints excluded: chain C residue 570 ILE Chi-restraints excluded: chain C residue 574 PHE Chi-restraints excluded: chain D residue 37 ASP Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 59 VAL Chi-restraints excluded: chain D residue 119 LEU Chi-restraints excluded: chain D residue 130 PHE Chi-restraints excluded: chain D residue 131 ILE Chi-restraints excluded: chain D residue 183 LYS Chi-restraints excluded: chain D residue 197 THR Chi-restraints excluded: chain D residue 258 THR Chi-restraints excluded: chain D residue 270 ILE Chi-restraints excluded: chain D residue 294 ILE Chi-restraints excluded: chain D residue 309 THR Chi-restraints excluded: chain D residue 315 SER Chi-restraints excluded: chain D residue 318 ASP Chi-restraints excluded: chain D residue 370 LYS Chi-restraints excluded: chain D residue 371 THR Chi-restraints excluded: chain D residue 379 SER Chi-restraints excluded: chain D residue 381 GLN Chi-restraints excluded: chain D residue 390 VAL Chi-restraints excluded: chain D residue 399 ILE Chi-restraints excluded: chain D residue 401 GLU Chi-restraints excluded: chain D residue 442 LEU Chi-restraints excluded: chain D residue 457 ASP Chi-restraints excluded: chain E residue 7 GLU Chi-restraints excluded: chain E residue 26 ASP Chi-restraints excluded: chain E residue 43 ARG Chi-restraints excluded: chain E residue 73 VAL Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain E residue 94 ASN Chi-restraints excluded: chain E residue 111 ARG Chi-restraints excluded: chain E residue 130 PHE Chi-restraints excluded: chain E residue 131 ILE Chi-restraints excluded: chain E residue 137 THR Chi-restraints excluded: chain E residue 143 THR Chi-restraints excluded: chain E residue 180 GLU Chi-restraints excluded: chain E residue 206 GLN Chi-restraints excluded: chain E residue 258 THR Chi-restraints excluded: chain E residue 270 ILE Chi-restraints excluded: chain E residue 290 ASP Chi-restraints excluded: chain E residue 304 LYS Chi-restraints excluded: chain E residue 327 ASP Chi-restraints excluded: chain E residue 372 ARG Chi-restraints excluded: chain E residue 392 ILE Chi-restraints excluded: chain E residue 405 THR Chi-restraints excluded: chain E residue 413 GLN Chi-restraints excluded: chain E residue 427 GLN Chi-restraints excluded: chain E residue 452 LYS Chi-restraints excluded: chain E residue 459 ILE Chi-restraints excluded: chain F residue 11 ILE Chi-restraints excluded: chain F residue 53 GLU Chi-restraints excluded: chain F residue 54 TYR Chi-restraints excluded: chain F residue 68 LEU Chi-restraints excluded: chain F residue 73 VAL Chi-restraints excluded: chain F residue 78 ASP Chi-restraints excluded: chain F residue 79 VAL Chi-restraints excluded: chain F residue 96 ILE Chi-restraints excluded: chain F residue 111 ARG Chi-restraints excluded: chain F residue 112 LEU Chi-restraints excluded: chain F residue 128 GLU Chi-restraints excluded: chain F residue 131 ILE Chi-restraints excluded: chain F residue 133 THR Chi-restraints excluded: chain F residue 137 THR Chi-restraints excluded: chain F residue 180 GLU Chi-restraints excluded: chain F residue 185 GLU Chi-restraints excluded: chain F residue 197 THR Chi-restraints excluded: chain F residue 206 GLN Chi-restraints excluded: chain F residue 225 ASP Chi-restraints excluded: chain F residue 232 ILE Chi-restraints excluded: chain F residue 270 ILE Chi-restraints excluded: chain F residue 309 THR Chi-restraints excluded: chain F residue 315 SER Chi-restraints excluded: chain F residue 318 ASP Chi-restraints excluded: chain F residue 343 LEU Chi-restraints excluded: chain F residue 366 VAL Chi-restraints excluded: chain F residue 376 LYS Chi-restraints excluded: chain F residue 393 ARG Chi-restraints excluded: chain F residue 412 LEU Chi-restraints excluded: chain F residue 451 LEU Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain G residue 54 ASP Chi-restraints excluded: chain G residue 64 LEU Chi-restraints excluded: chain G residue 86 LEU Chi-restraints excluded: chain G residue 117 VAL Chi-restraints excluded: chain G residue 185 GLN Chi-restraints excluded: chain G residue 201 ILE Chi-restraints excluded: chain H residue 51 LEU Chi-restraints excluded: chain H residue 77 LEU Chi-restraints excluded: chain H residue 93 LEU Chi-restraints excluded: chain H residue 96 LYS Chi-restraints excluded: chain H residue 98 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 337 random chunks: chunk 170 optimal weight: 3.9990 chunk 94 optimal weight: 0.3980 chunk 254 optimal weight: 5.9990 chunk 208 optimal weight: 2.9990 chunk 84 optimal weight: 4.9990 chunk 306 optimal weight: 2.9990 chunk 331 optimal weight: 9.9990 chunk 273 optimal weight: 4.9990 chunk 304 optimal weight: 3.9990 chunk 104 optimal weight: 1.9990 chunk 245 optimal weight: 1.9990 overall best weight: 2.0788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 425 ASN ** A 496 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 571 GLN B 290 ASN C 283 HIS D 262 ASN ** E 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 407 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 58 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8309 moved from start: 0.1360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 27153 Z= 0.378 Angle : 0.628 7.766 36793 Z= 0.321 Chirality : 0.047 0.270 4109 Planarity : 0.005 0.088 4818 Dihedral : 10.718 105.985 4114 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.03 % Allowed : 10.61 % Favored : 89.36 % Rotamer: Outliers : 9.45 % Allowed : 17.94 % Favored : 72.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.54 % Cis-general : 0.00 % Twisted Proline : 0.51 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.70 (0.14), residues: 3402 helix: 0.32 (0.15), residues: 1305 sheet: -2.88 (0.21), residues: 529 loop : -3.35 (0.14), residues: 1568 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 117 HIS 0.004 0.001 HIS B 145 PHE 0.017 0.002 PHE A 563 TYR 0.020 0.002 TYR D 13 ARG 0.004 0.000 ARG C 416 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6804 Ramachandran restraints generated. 3402 Oldfield, 0 Emsley, 3402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6804 Ramachandran restraints generated. 3402 Oldfield, 0 Emsley, 3402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 593 residues out of total 2804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 265 poor density : 328 time to evaluate : 3.183 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "PHE H 100 " (corrupted residue). Skipping it. REVERT: A 8 LYS cc_start: 0.8651 (tttp) cc_final: 0.8295 (tptp) REVERT: A 24 MET cc_start: 0.8898 (OUTLIER) cc_final: 0.7111 (tmm) REVERT: A 124 LYS cc_start: 0.8205 (tppp) cc_final: 0.7637 (mtpp) REVERT: A 125 PRO cc_start: 0.8743 (Cg_endo) cc_final: 0.8536 (Cg_exo) REVERT: A 165 GLU cc_start: 0.7490 (OUTLIER) cc_final: 0.7003 (mt-10) REVERT: A 175 LEU cc_start: 0.8491 (OUTLIER) cc_final: 0.8280 (mt) REVERT: A 323 MET cc_start: 0.7638 (ttm) cc_final: 0.7308 (mtp) REVERT: A 410 ASP cc_start: 0.8039 (t0) cc_final: 0.7703 (m-30) REVERT: A 464 LEU cc_start: 0.8360 (OUTLIER) cc_final: 0.8043 (mm) REVERT: A 574 PHE cc_start: 0.7364 (OUTLIER) cc_final: 0.7023 (m-80) REVERT: B 9 ILE cc_start: 0.9236 (mt) cc_final: 0.9034 (mt) REVERT: B 423 ASN cc_start: 0.8500 (t0) cc_final: 0.8155 (t0) REVERT: B 488 ARG cc_start: 0.7641 (ttt-90) cc_final: 0.7435 (tmt170) REVERT: B 558 GLU cc_start: 0.7271 (tp30) cc_final: 0.6832 (tp30) REVERT: C 116 LYS cc_start: 0.8737 (OUTLIER) cc_final: 0.7979 (ptpp) REVERT: C 220 MET cc_start: 0.8306 (tmm) cc_final: 0.7309 (tmm) REVERT: C 266 LEU cc_start: 0.8744 (OUTLIER) cc_final: 0.8483 (mt) REVERT: C 304 TYR cc_start: 0.8803 (m-80) cc_final: 0.8476 (m-80) REVERT: C 538 GLU cc_start: 0.7514 (OUTLIER) cc_final: 0.5928 (tm-30) REVERT: D 215 SER cc_start: 0.8777 (m) cc_final: 0.8466 (p) REVERT: D 216 ARG cc_start: 0.9388 (OUTLIER) cc_final: 0.6453 (ppt-90) REVERT: D 381 GLN cc_start: 0.8879 (OUTLIER) cc_final: 0.7314 (tm130) REVERT: D 442 LEU cc_start: 0.9255 (OUTLIER) cc_final: 0.9021 (mp) REVERT: D 457 ASP cc_start: 0.6960 (OUTLIER) cc_final: 0.6757 (p0) REVERT: E 67 ASP cc_start: 0.7969 (t0) cc_final: 0.7676 (t0) REVERT: E 111 ARG cc_start: 0.8515 (OUTLIER) cc_final: 0.8165 (mtp85) REVERT: E 130 PHE cc_start: 0.9066 (OUTLIER) cc_final: 0.8761 (p90) REVERT: E 321 ARG cc_start: 0.8309 (tpp80) cc_final: 0.7873 (ttt180) REVERT: E 327 ASP cc_start: 0.8224 (OUTLIER) cc_final: 0.7983 (m-30) REVERT: E 372 ARG cc_start: 0.8339 (OUTLIER) cc_final: 0.7450 (mtm110) REVERT: E 381 GLN cc_start: 0.8372 (mm-40) cc_final: 0.7995 (tm-30) REVERT: E 394 LYS cc_start: 0.7473 (ttpt) cc_final: 0.7064 (tppt) REVERT: E 398 ILE cc_start: 0.7163 (tp) cc_final: 0.6687 (pt) REVERT: E 401 GLU cc_start: 0.7581 (tm-30) cc_final: 0.7307 (tm-30) REVERT: E 427 GLN cc_start: 0.8870 (OUTLIER) cc_final: 0.8297 (mp10) REVERT: F 111 ARG cc_start: 0.8753 (OUTLIER) cc_final: 0.7743 (mtm-85) REVERT: F 172 THR cc_start: 0.9218 (OUTLIER) cc_final: 0.8694 (p) REVERT: F 185 GLU cc_start: 0.7214 (OUTLIER) cc_final: 0.6486 (mm-30) REVERT: F 362 MET cc_start: 0.8898 (ttt) cc_final: 0.8491 (ttt) REVERT: F 406 GLU cc_start: 0.6903 (tm-30) cc_final: 0.6555 (tm-30) REVERT: F 410 ARG cc_start: 0.7365 (mtt-85) cc_final: 0.6648 (mtm-85) REVERT: F 412 LEU cc_start: 0.7731 (OUTLIER) cc_final: 0.7459 (mt) REVERT: G 26 ASP cc_start: 0.7706 (m-30) cc_final: 0.7438 (m-30) REVERT: G 44 ARG cc_start: 0.7307 (ttm-80) cc_final: 0.6917 (tpt90) REVERT: G 55 GLN cc_start: 0.7222 (tm-30) cc_final: 0.7022 (tm-30) REVERT: G 58 LYS cc_start: 0.7381 (mtpt) cc_final: 0.6499 (tptt) REVERT: G 59 GLU cc_start: 0.7080 (tp30) cc_final: 0.6821 (mm-30) REVERT: G 185 GLN cc_start: 0.9036 (OUTLIER) cc_final: 0.7904 (tp40) REVERT: G 200 LYS cc_start: 0.7290 (ttmm) cc_final: 0.6944 (mptt) REVERT: H 1 MET cc_start: 0.7430 (mpt) cc_final: 0.7090 (mpt) REVERT: H 96 LYS cc_start: 0.6897 (OUTLIER) cc_final: 0.5443 (pttp) outliers start: 265 outliers final: 195 residues processed: 547 average time/residue: 0.3838 time to fit residues: 330.4975 Evaluate side-chains 525 residues out of total 2804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 218 poor density : 307 time to evaluate : 2.867 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 VAL Chi-restraints excluded: chain A residue 9 ILE Chi-restraints excluded: chain A residue 14 VAL Chi-restraints excluded: chain A residue 24 MET Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 83 ILE Chi-restraints excluded: chain A residue 122 MET Chi-restraints excluded: chain A residue 147 ILE Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 165 GLU Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 207 THR Chi-restraints excluded: chain A residue 220 MET Chi-restraints excluded: chain A residue 223 THR Chi-restraints excluded: chain A residue 261 GLU Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 273 THR Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain A residue 293 ASN Chi-restraints excluded: chain A residue 316 GLN Chi-restraints excluded: chain A residue 329 ARG Chi-restraints excluded: chain A residue 353 TYR Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain A residue 370 THR Chi-restraints excluded: chain A residue 393 GLU Chi-restraints excluded: chain A residue 427 SER Chi-restraints excluded: chain A residue 457 LEU Chi-restraints excluded: chain A residue 458 LEU Chi-restraints excluded: chain A residue 464 LEU Chi-restraints excluded: chain A residue 468 VAL Chi-restraints excluded: chain A residue 530 ILE Chi-restraints excluded: chain A residue 541 GLN Chi-restraints excluded: chain A residue 545 LEU Chi-restraints excluded: chain A residue 574 PHE Chi-restraints excluded: chain B residue 27 ILE Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 96 GLU Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 152 ASP Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain B residue 200 ASP Chi-restraints excluded: chain B residue 211 ILE Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 226 ILE Chi-restraints excluded: chain B residue 260 ASN Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 285 THR Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 303 ILE Chi-restraints excluded: chain B residue 315 ASP Chi-restraints excluded: chain B residue 339 SER Chi-restraints excluded: chain B residue 354 LEU Chi-restraints excluded: chain B residue 368 VAL Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 443 VAL Chi-restraints excluded: chain B residue 446 ASP Chi-restraints excluded: chain B residue 450 LEU Chi-restraints excluded: chain B residue 455 SER Chi-restraints excluded: chain B residue 469 GLN Chi-restraints excluded: chain B residue 476 LEU Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 520 LEU Chi-restraints excluded: chain B residue 524 LYS Chi-restraints excluded: chain B residue 536 ILE Chi-restraints excluded: chain B residue 548 ILE Chi-restraints excluded: chain B residue 554 VAL Chi-restraints excluded: chain B residue 565 GLU Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 73 VAL Chi-restraints excluded: chain C residue 83 ILE Chi-restraints excluded: chain C residue 96 GLU Chi-restraints excluded: chain C residue 103 THR Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 116 LYS Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 141 PHE Chi-restraints excluded: chain C residue 145 HIS Chi-restraints excluded: chain C residue 152 ASP Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 186 THR Chi-restraints excluded: chain C residue 200 ASP Chi-restraints excluded: chain C residue 207 THR Chi-restraints excluded: chain C residue 211 ILE Chi-restraints excluded: chain C residue 249 VAL Chi-restraints excluded: chain C residue 266 LEU Chi-restraints excluded: chain C residue 284 ARG Chi-restraints excluded: chain C residue 287 LEU Chi-restraints excluded: chain C residue 315 ASP Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 337 ILE Chi-restraints excluded: chain C residue 354 LEU Chi-restraints excluded: chain C residue 363 GLU Chi-restraints excluded: chain C residue 398 SER Chi-restraints excluded: chain C residue 461 GLU Chi-restraints excluded: chain C residue 520 LEU Chi-restraints excluded: chain C residue 531 LYS Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 538 GLU Chi-restraints excluded: chain C residue 570 ILE Chi-restraints excluded: chain C residue 574 PHE Chi-restraints excluded: chain D residue 37 ASP Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 59 VAL Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain D residue 119 LEU Chi-restraints excluded: chain D residue 130 PHE Chi-restraints excluded: chain D residue 131 ILE Chi-restraints excluded: chain D residue 183 LYS Chi-restraints excluded: chain D residue 197 THR Chi-restraints excluded: chain D residue 216 ARG Chi-restraints excluded: chain D residue 218 VAL Chi-restraints excluded: chain D residue 250 ASP Chi-restraints excluded: chain D residue 258 THR Chi-restraints excluded: chain D residue 270 ILE Chi-restraints excluded: chain D residue 290 ASP Chi-restraints excluded: chain D residue 294 ILE Chi-restraints excluded: chain D residue 309 THR Chi-restraints excluded: chain D residue 315 SER Chi-restraints excluded: chain D residue 318 ASP Chi-restraints excluded: chain D residue 331 TYR Chi-restraints excluded: chain D residue 334 GLU Chi-restraints excluded: chain D residue 370 LYS Chi-restraints excluded: chain D residue 371 THR Chi-restraints excluded: chain D residue 379 SER Chi-restraints excluded: chain D residue 381 GLN Chi-restraints excluded: chain D residue 390 VAL Chi-restraints excluded: chain D residue 401 GLU Chi-restraints excluded: chain D residue 442 LEU Chi-restraints excluded: chain D residue 457 ASP Chi-restraints excluded: chain E residue 7 GLU Chi-restraints excluded: chain E residue 26 ASP Chi-restraints excluded: chain E residue 43 ARG Chi-restraints excluded: chain E residue 73 VAL Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain E residue 94 ASN Chi-restraints excluded: chain E residue 111 ARG Chi-restraints excluded: chain E residue 130 PHE Chi-restraints excluded: chain E residue 131 ILE Chi-restraints excluded: chain E residue 133 THR Chi-restraints excluded: chain E residue 137 THR Chi-restraints excluded: chain E residue 143 THR Chi-restraints excluded: chain E residue 180 GLU Chi-restraints excluded: chain E residue 206 GLN Chi-restraints excluded: chain E residue 257 LEU Chi-restraints excluded: chain E residue 270 ILE Chi-restraints excluded: chain E residue 304 LYS Chi-restraints excluded: chain E residue 327 ASP Chi-restraints excluded: chain E residue 372 ARG Chi-restraints excluded: chain E residue 379 SER Chi-restraints excluded: chain E residue 384 SER Chi-restraints excluded: chain E residue 392 ILE Chi-restraints excluded: chain E residue 405 THR Chi-restraints excluded: chain E residue 413 GLN Chi-restraints excluded: chain E residue 427 GLN Chi-restraints excluded: chain E residue 452 LYS Chi-restraints excluded: chain E residue 459 ILE Chi-restraints excluded: chain F residue 11 ILE Chi-restraints excluded: chain F residue 37 ASP Chi-restraints excluded: chain F residue 53 GLU Chi-restraints excluded: chain F residue 54 TYR Chi-restraints excluded: chain F residue 68 LEU Chi-restraints excluded: chain F residue 73 VAL Chi-restraints excluded: chain F residue 78 ASP Chi-restraints excluded: chain F residue 79 VAL Chi-restraints excluded: chain F residue 96 ILE Chi-restraints excluded: chain F residue 111 ARG Chi-restraints excluded: chain F residue 112 LEU Chi-restraints excluded: chain F residue 128 GLU Chi-restraints excluded: chain F residue 131 ILE Chi-restraints excluded: chain F residue 133 THR Chi-restraints excluded: chain F residue 137 THR Chi-restraints excluded: chain F residue 172 THR Chi-restraints excluded: chain F residue 180 GLU Chi-restraints excluded: chain F residue 185 GLU Chi-restraints excluded: chain F residue 197 THR Chi-restraints excluded: chain F residue 206 GLN Chi-restraints excluded: chain F residue 225 ASP Chi-restraints excluded: chain F residue 232 ILE Chi-restraints excluded: chain F residue 270 ILE Chi-restraints excluded: chain F residue 309 THR Chi-restraints excluded: chain F residue 315 SER Chi-restraints excluded: chain F residue 318 ASP Chi-restraints excluded: chain F residue 343 LEU Chi-restraints excluded: chain F residue 366 VAL Chi-restraints excluded: chain F residue 376 LYS Chi-restraints excluded: chain F residue 393 ARG Chi-restraints excluded: chain F residue 396 VAL Chi-restraints excluded: chain F residue 401 GLU Chi-restraints excluded: chain F residue 412 LEU Chi-restraints excluded: chain F residue 451 LEU Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain G residue 54 ASP Chi-restraints excluded: chain G residue 86 LEU Chi-restraints excluded: chain G residue 117 VAL Chi-restraints excluded: chain G residue 172 ILE Chi-restraints excluded: chain G residue 182 VAL Chi-restraints excluded: chain G residue 185 GLN Chi-restraints excluded: chain G residue 201 ILE Chi-restraints excluded: chain H residue 35 THR Chi-restraints excluded: chain H residue 51 LEU Chi-restraints excluded: chain H residue 77 LEU Chi-restraints excluded: chain H residue 86 VAL Chi-restraints excluded: chain H residue 90 MET Chi-restraints excluded: chain H residue 93 LEU Chi-restraints excluded: chain H residue 96 LYS Chi-restraints excluded: chain H residue 98 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 337 random chunks: chunk 302 optimal weight: 2.9990 chunk 230 optimal weight: 2.9990 chunk 159 optimal weight: 0.8980 chunk 33 optimal weight: 1.9990 chunk 146 optimal weight: 1.9990 chunk 205 optimal weight: 0.6980 chunk 307 optimal weight: 2.9990 chunk 325 optimal weight: 3.9990 chunk 160 optimal weight: 2.9990 chunk 291 optimal weight: 0.5980 chunk 87 optimal weight: 0.7980 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 496 GLN A 571 GLN ** E 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 375 HIS E 407 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8262 moved from start: 0.1657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 27153 Z= 0.208 Angle : 0.546 8.508 36793 Z= 0.278 Chirality : 0.044 0.251 4109 Planarity : 0.005 0.080 4818 Dihedral : 10.199 96.268 4098 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.52 % Favored : 92.45 % Rotamer: Outliers : 8.52 % Allowed : 19.51 % Favored : 71.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.54 % Cis-general : 0.00 % Twisted Proline : 0.51 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.22 (0.14), residues: 3402 helix: 0.70 (0.15), residues: 1291 sheet: -2.47 (0.23), residues: 487 loop : -3.10 (0.14), residues: 1624 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP G 97 HIS 0.002 0.001 HIS A 185 PHE 0.015 0.001 PHE C 419 TYR 0.011 0.001 TYR A 562 ARG 0.005 0.000 ARG C 416 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6804 Ramachandran restraints generated. 3402 Oldfield, 0 Emsley, 3402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6804 Ramachandran restraints generated. 3402 Oldfield, 0 Emsley, 3402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 572 residues out of total 2804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 239 poor density : 333 time to evaluate : 2.997 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 LYS cc_start: 0.8361 (tttp) cc_final: 0.8143 (tptp) REVERT: A 124 LYS cc_start: 0.8250 (tppp) cc_final: 0.7699 (mtpp) REVERT: A 323 MET cc_start: 0.7485 (ttm) cc_final: 0.7190 (mtp) REVERT: A 353 TYR cc_start: 0.9140 (OUTLIER) cc_final: 0.7548 (p90) REVERT: A 410 ASP cc_start: 0.8074 (t0) cc_final: 0.7738 (m-30) REVERT: A 464 LEU cc_start: 0.8148 (OUTLIER) cc_final: 0.7821 (mm) REVERT: A 542 LEU cc_start: 0.7257 (OUTLIER) cc_final: 0.6953 (mt) REVERT: B 9 ILE cc_start: 0.9186 (mt) cc_final: 0.8973 (mt) REVERT: B 423 ASN cc_start: 0.8436 (t0) cc_final: 0.8156 (t0) REVERT: B 558 GLU cc_start: 0.7179 (tp30) cc_final: 0.6768 (tp30) REVERT: C 116 LYS cc_start: 0.8727 (OUTLIER) cc_final: 0.7948 (ptpp) REVERT: C 220 MET cc_start: 0.8371 (tmm) cc_final: 0.7475 (tmm) REVERT: C 266 LEU cc_start: 0.8664 (OUTLIER) cc_final: 0.8392 (mt) REVERT: C 304 TYR cc_start: 0.8746 (m-80) cc_final: 0.8428 (m-80) REVERT: C 393 GLU cc_start: 0.7593 (tt0) cc_final: 0.7357 (tt0) REVERT: C 433 SER cc_start: 0.9228 (t) cc_final: 0.8999 (t) REVERT: C 538 GLU cc_start: 0.7522 (OUTLIER) cc_final: 0.6038 (tm-30) REVERT: D 215 SER cc_start: 0.8755 (m) cc_final: 0.8453 (p) REVERT: D 216 ARG cc_start: 0.9370 (OUTLIER) cc_final: 0.6410 (ppt-90) REVERT: D 268 ARG cc_start: 0.8294 (OUTLIER) cc_final: 0.6794 (ttt180) REVERT: D 345 ARG cc_start: 0.8417 (OUTLIER) cc_final: 0.8098 (mtt90) REVERT: D 381 GLN cc_start: 0.8778 (OUTLIER) cc_final: 0.7225 (tm130) REVERT: D 442 LEU cc_start: 0.9228 (OUTLIER) cc_final: 0.8975 (mp) REVERT: E 111 ARG cc_start: 0.8485 (OUTLIER) cc_final: 0.8104 (mtp85) REVERT: E 274 ARG cc_start: 0.7337 (mtm180) cc_final: 0.7120 (mtm-85) REVERT: E 327 ASP cc_start: 0.8232 (OUTLIER) cc_final: 0.8011 (m-30) REVERT: E 358 LEU cc_start: 0.8453 (OUTLIER) cc_final: 0.8093 (pt) REVERT: E 372 ARG cc_start: 0.8268 (OUTLIER) cc_final: 0.7160 (mtm110) REVERT: E 381 GLN cc_start: 0.8289 (mm-40) cc_final: 0.7787 (tp40) REVERT: E 394 LYS cc_start: 0.7455 (ttpt) cc_final: 0.7044 (tppt) REVERT: E 398 ILE cc_start: 0.7148 (tp) cc_final: 0.6697 (pt) REVERT: E 427 GLN cc_start: 0.8837 (OUTLIER) cc_final: 0.8258 (mp10) REVERT: F 111 ARG cc_start: 0.8696 (OUTLIER) cc_final: 0.7613 (mtm-85) REVERT: F 131 ILE cc_start: 0.8776 (OUTLIER) cc_final: 0.8519 (pt) REVERT: F 172 THR cc_start: 0.9201 (OUTLIER) cc_final: 0.8642 (p) REVERT: F 185 GLU cc_start: 0.7162 (OUTLIER) cc_final: 0.6472 (mm-30) REVERT: F 331 TYR cc_start: 0.8024 (m-80) cc_final: 0.7684 (m-80) REVERT: F 362 MET cc_start: 0.8819 (ttt) cc_final: 0.8496 (ttt) REVERT: F 410 ARG cc_start: 0.7299 (mtt-85) cc_final: 0.6659 (mtm-85) REVERT: G 26 ASP cc_start: 0.7631 (m-30) cc_final: 0.7376 (m-30) REVERT: G 44 ARG cc_start: 0.7362 (ttm-80) cc_final: 0.6999 (tpt90) REVERT: G 55 GLN cc_start: 0.7220 (tm-30) cc_final: 0.6987 (tm-30) REVERT: G 58 LYS cc_start: 0.7205 (mtpt) cc_final: 0.6396 (tptt) REVERT: G 59 GLU cc_start: 0.7040 (tp30) cc_final: 0.6792 (mm-30) REVERT: G 154 ILE cc_start: 0.7586 (OUTLIER) cc_final: 0.7309 (tt) REVERT: G 185 GLN cc_start: 0.8994 (OUTLIER) cc_final: 0.7836 (tp40) REVERT: G 200 LYS cc_start: 0.7311 (ttmm) cc_final: 0.7017 (mptt) REVERT: H 1 MET cc_start: 0.7505 (mpt) cc_final: 0.7018 (mpt) REVERT: H 56 GLU cc_start: 0.5749 (pt0) cc_final: 0.5491 (pt0) REVERT: H 60 GLU cc_start: 0.5947 (tt0) cc_final: 0.5183 (pp20) REVERT: H 96 LYS cc_start: 0.6876 (OUTLIER) cc_final: 0.5446 (pttp) outliers start: 239 outliers final: 170 residues processed: 536 average time/residue: 0.3856 time to fit residues: 323.6935 Evaluate side-chains 494 residues out of total 2804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 193 poor density : 301 time to evaluate : 3.155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 ILE Chi-restraints excluded: chain A residue 14 VAL Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 83 ILE Chi-restraints excluded: chain A residue 122 MET Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 147 ILE Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 207 THR Chi-restraints excluded: chain A residue 211 ILE Chi-restraints excluded: chain A residue 220 MET Chi-restraints excluded: chain A residue 223 THR Chi-restraints excluded: chain A residue 261 GLU Chi-restraints excluded: chain A residue 268 GLU Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain A residue 293 ASN Chi-restraints excluded: chain A residue 311 GLU Chi-restraints excluded: chain A residue 316 GLN Chi-restraints excluded: chain A residue 329 ARG Chi-restraints excluded: chain A residue 353 TYR Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain A residue 363 GLU Chi-restraints excluded: chain A residue 370 THR Chi-restraints excluded: chain A residue 393 GLU Chi-restraints excluded: chain A residue 427 SER Chi-restraints excluded: chain A residue 457 LEU Chi-restraints excluded: chain A residue 464 LEU Chi-restraints excluded: chain A residue 530 ILE Chi-restraints excluded: chain A residue 540 LEU Chi-restraints excluded: chain A residue 541 GLN Chi-restraints excluded: chain A residue 542 LEU Chi-restraints excluded: chain A residue 545 LEU Chi-restraints excluded: chain A residue 546 GLU Chi-restraints excluded: chain A residue 574 PHE Chi-restraints excluded: chain B residue 27 ILE Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 96 GLU Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 152 ASP Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain B residue 200 ASP Chi-restraints excluded: chain B residue 226 ILE Chi-restraints excluded: chain B residue 230 PHE Chi-restraints excluded: chain B residue 260 ASN Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 303 ILE Chi-restraints excluded: chain B residue 315 ASP Chi-restraints excluded: chain B residue 339 SER Chi-restraints excluded: chain B residue 354 LEU Chi-restraints excluded: chain B residue 368 VAL Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 443 VAL Chi-restraints excluded: chain B residue 450 LEU Chi-restraints excluded: chain B residue 455 SER Chi-restraints excluded: chain B residue 469 GLN Chi-restraints excluded: chain B residue 476 LEU Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 524 LYS Chi-restraints excluded: chain B residue 536 ILE Chi-restraints excluded: chain B residue 548 ILE Chi-restraints excluded: chain B residue 565 GLU Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 73 VAL Chi-restraints excluded: chain C residue 83 ILE Chi-restraints excluded: chain C residue 96 GLU Chi-restraints excluded: chain C residue 103 THR Chi-restraints excluded: chain C residue 116 LYS Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 141 PHE Chi-restraints excluded: chain C residue 145 HIS Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 200 ASP Chi-restraints excluded: chain C residue 207 THR Chi-restraints excluded: chain C residue 211 ILE Chi-restraints excluded: chain C residue 249 VAL Chi-restraints excluded: chain C residue 266 LEU Chi-restraints excluded: chain C residue 284 ARG Chi-restraints excluded: chain C residue 287 LEU Chi-restraints excluded: chain C residue 294 MET Chi-restraints excluded: chain C residue 315 ASP Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 337 ILE Chi-restraints excluded: chain C residue 354 LEU Chi-restraints excluded: chain C residue 363 GLU Chi-restraints excluded: chain C residue 419 PHE Chi-restraints excluded: chain C residue 520 LEU Chi-restraints excluded: chain C residue 531 LYS Chi-restraints excluded: chain C residue 538 GLU Chi-restraints excluded: chain C residue 574 PHE Chi-restraints excluded: chain D residue 37 ASP Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain D residue 119 LEU Chi-restraints excluded: chain D residue 130 PHE Chi-restraints excluded: chain D residue 131 ILE Chi-restraints excluded: chain D residue 183 LYS Chi-restraints excluded: chain D residue 197 THR Chi-restraints excluded: chain D residue 216 ARG Chi-restraints excluded: chain D residue 218 VAL Chi-restraints excluded: chain D residue 268 ARG Chi-restraints excluded: chain D residue 270 ILE Chi-restraints excluded: chain D residue 290 ASP Chi-restraints excluded: chain D residue 294 ILE Chi-restraints excluded: chain D residue 309 THR Chi-restraints excluded: chain D residue 315 SER Chi-restraints excluded: chain D residue 318 ASP Chi-restraints excluded: chain D residue 331 TYR Chi-restraints excluded: chain D residue 334 GLU Chi-restraints excluded: chain D residue 345 ARG Chi-restraints excluded: chain D residue 364 ASN Chi-restraints excluded: chain D residue 370 LYS Chi-restraints excluded: chain D residue 379 SER Chi-restraints excluded: chain D residue 381 GLN Chi-restraints excluded: chain D residue 390 VAL Chi-restraints excluded: chain D residue 401 GLU Chi-restraints excluded: chain D residue 442 LEU Chi-restraints excluded: chain E residue 7 GLU Chi-restraints excluded: chain E residue 9 THR Chi-restraints excluded: chain E residue 26 ASP Chi-restraints excluded: chain E residue 43 ARG Chi-restraints excluded: chain E residue 73 VAL Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain E residue 94 ASN Chi-restraints excluded: chain E residue 111 ARG Chi-restraints excluded: chain E residue 131 ILE Chi-restraints excluded: chain E residue 133 THR Chi-restraints excluded: chain E residue 137 THR Chi-restraints excluded: chain E residue 143 THR Chi-restraints excluded: chain E residue 257 LEU Chi-restraints excluded: chain E residue 270 ILE Chi-restraints excluded: chain E residue 327 ASP Chi-restraints excluded: chain E residue 358 LEU Chi-restraints excluded: chain E residue 372 ARG Chi-restraints excluded: chain E residue 379 SER Chi-restraints excluded: chain E residue 384 SER Chi-restraints excluded: chain E residue 392 ILE Chi-restraints excluded: chain E residue 405 THR Chi-restraints excluded: chain E residue 413 GLN Chi-restraints excluded: chain E residue 427 GLN Chi-restraints excluded: chain E residue 452 LYS Chi-restraints excluded: chain E residue 459 ILE Chi-restraints excluded: chain F residue 11 ILE Chi-restraints excluded: chain F residue 53 GLU Chi-restraints excluded: chain F residue 54 TYR Chi-restraints excluded: chain F residue 68 LEU Chi-restraints excluded: chain F residue 73 VAL Chi-restraints excluded: chain F residue 78 ASP Chi-restraints excluded: chain F residue 96 ILE Chi-restraints excluded: chain F residue 111 ARG Chi-restraints excluded: chain F residue 112 LEU Chi-restraints excluded: chain F residue 131 ILE Chi-restraints excluded: chain F residue 133 THR Chi-restraints excluded: chain F residue 137 THR Chi-restraints excluded: chain F residue 172 THR Chi-restraints excluded: chain F residue 180 GLU Chi-restraints excluded: chain F residue 185 GLU Chi-restraints excluded: chain F residue 197 THR Chi-restraints excluded: chain F residue 206 GLN Chi-restraints excluded: chain F residue 225 ASP Chi-restraints excluded: chain F residue 232 ILE Chi-restraints excluded: chain F residue 270 ILE Chi-restraints excluded: chain F residue 309 THR Chi-restraints excluded: chain F residue 315 SER Chi-restraints excluded: chain F residue 343 LEU Chi-restraints excluded: chain F residue 366 VAL Chi-restraints excluded: chain F residue 376 LYS Chi-restraints excluded: chain F residue 393 ARG Chi-restraints excluded: chain F residue 396 VAL Chi-restraints excluded: chain F residue 401 GLU Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain G residue 54 ASP Chi-restraints excluded: chain G residue 86 LEU Chi-restraints excluded: chain G residue 117 VAL Chi-restraints excluded: chain G residue 154 ILE Chi-restraints excluded: chain G residue 185 GLN Chi-restraints excluded: chain G residue 201 ILE Chi-restraints excluded: chain H residue 35 THR Chi-restraints excluded: chain H residue 51 LEU Chi-restraints excluded: chain H residue 77 LEU Chi-restraints excluded: chain H residue 86 VAL Chi-restraints excluded: chain H residue 93 LEU Chi-restraints excluded: chain H residue 96 LYS Chi-restraints excluded: chain H residue 98 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 337 random chunks: chunk 271 optimal weight: 3.9990 chunk 184 optimal weight: 0.8980 chunk 4 optimal weight: 3.9990 chunk 242 optimal weight: 0.0980 chunk 134 optimal weight: 0.8980 chunk 277 optimal weight: 1.9990 chunk 225 optimal weight: 6.9990 chunk 0 optimal weight: 4.9990 chunk 166 optimal weight: 4.9990 chunk 292 optimal weight: 1.9990 chunk 82 optimal weight: 3.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 166 GLN E 170 GLN ** E 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8266 moved from start: 0.1780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 27153 Z= 0.238 Angle : 0.555 8.051 36793 Z= 0.282 Chirality : 0.044 0.212 4109 Planarity : 0.005 0.081 4818 Dihedral : 9.690 89.428 4054 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.03 % Allowed : 8.88 % Favored : 91.09 % Rotamer: Outliers : 8.63 % Allowed : 19.51 % Favored : 71.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.54 % Cis-general : 0.00 % Twisted Proline : 0.51 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.05 (0.14), residues: 3402 helix: 0.81 (0.15), residues: 1295 sheet: -2.29 (0.23), residues: 489 loop : -3.00 (0.14), residues: 1618 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 119 HIS 0.003 0.001 HIS B 283 PHE 0.014 0.001 PHE C 419 TYR 0.018 0.001 TYR A 513 ARG 0.004 0.000 ARG E 321 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6804 Ramachandran restraints generated. 3402 Oldfield, 0 Emsley, 3402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6804 Ramachandran restraints generated. 3402 Oldfield, 0 Emsley, 3402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 556 residues out of total 2804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 242 poor density : 314 time to evaluate : 2.875 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 LYS cc_start: 0.8423 (tttp) cc_final: 0.8221 (tptm) REVERT: A 124 LYS cc_start: 0.8228 (tppp) cc_final: 0.7694 (mtpp) REVERT: A 165 GLU cc_start: 0.7446 (OUTLIER) cc_final: 0.6956 (mt-10) REVERT: A 191 ARG cc_start: 0.8014 (OUTLIER) cc_final: 0.7732 (mtm110) REVERT: A 323 MET cc_start: 0.7575 (ttm) cc_final: 0.7227 (mtp) REVERT: A 353 TYR cc_start: 0.9140 (OUTLIER) cc_final: 0.7461 (p90) REVERT: A 410 ASP cc_start: 0.8076 (t0) cc_final: 0.7736 (m-30) REVERT: A 464 LEU cc_start: 0.8124 (OUTLIER) cc_final: 0.7787 (mm) REVERT: A 542 LEU cc_start: 0.7231 (OUTLIER) cc_final: 0.7019 (mt) REVERT: B 9 ILE cc_start: 0.9204 (mt) cc_final: 0.8983 (mt) REVERT: B 88 GLN cc_start: 0.9315 (OUTLIER) cc_final: 0.8857 (tt0) REVERT: B 299 ARG cc_start: 0.6439 (OUTLIER) cc_final: 0.4849 (mtp180) REVERT: B 364 ARG cc_start: 0.9219 (OUTLIER) cc_final: 0.8373 (mtt180) REVERT: B 423 ASN cc_start: 0.8414 (t0) cc_final: 0.8098 (t0) REVERT: B 558 GLU cc_start: 0.7210 (tp30) cc_final: 0.6823 (tp30) REVERT: C 116 LYS cc_start: 0.8728 (OUTLIER) cc_final: 0.7946 (ptpp) REVERT: C 220 MET cc_start: 0.8481 (tmm) cc_final: 0.7601 (tmm) REVERT: C 266 LEU cc_start: 0.8672 (OUTLIER) cc_final: 0.8405 (mt) REVERT: C 304 TYR cc_start: 0.8768 (m-80) cc_final: 0.8424 (m-80) REVERT: C 433 SER cc_start: 0.9229 (t) cc_final: 0.9014 (t) REVERT: C 538 GLU cc_start: 0.7461 (OUTLIER) cc_final: 0.5959 (tm-30) REVERT: D 215 SER cc_start: 0.8765 (m) cc_final: 0.8469 (p) REVERT: D 216 ARG cc_start: 0.9362 (OUTLIER) cc_final: 0.6505 (ppt-90) REVERT: D 268 ARG cc_start: 0.8304 (OUTLIER) cc_final: 0.6810 (ttt180) REVERT: D 345 ARG cc_start: 0.8435 (OUTLIER) cc_final: 0.7993 (mtt90) REVERT: D 381 GLN cc_start: 0.8785 (OUTLIER) cc_final: 0.7259 (tm130) REVERT: D 442 LEU cc_start: 0.9224 (OUTLIER) cc_final: 0.8976 (mp) REVERT: E 111 ARG cc_start: 0.8493 (OUTLIER) cc_final: 0.8123 (mtp85) REVERT: E 274 ARG cc_start: 0.7408 (mtm180) cc_final: 0.7150 (mtm-85) REVERT: E 358 LEU cc_start: 0.8499 (OUTLIER) cc_final: 0.8116 (pt) REVERT: E 372 ARG cc_start: 0.8292 (OUTLIER) cc_final: 0.7178 (mtm110) REVERT: E 381 GLN cc_start: 0.8236 (mm-40) cc_final: 0.7705 (tp40) REVERT: E 394 LYS cc_start: 0.7343 (ttpt) cc_final: 0.6948 (tppt) REVERT: E 398 ILE cc_start: 0.7206 (tp) cc_final: 0.6734 (pt) REVERT: E 427 GLN cc_start: 0.8830 (OUTLIER) cc_final: 0.8251 (mp10) REVERT: F 111 ARG cc_start: 0.8720 (OUTLIER) cc_final: 0.7536 (mtm-85) REVERT: F 172 THR cc_start: 0.9145 (OUTLIER) cc_final: 0.8618 (p) REVERT: F 185 GLU cc_start: 0.7159 (OUTLIER) cc_final: 0.6499 (mm-30) REVERT: F 331 TYR cc_start: 0.8186 (m-80) cc_final: 0.7812 (m-80) REVERT: F 362 MET cc_start: 0.8810 (ttt) cc_final: 0.8554 (ttt) REVERT: F 406 GLU cc_start: 0.6903 (tm-30) cc_final: 0.6553 (tm-30) REVERT: F 410 ARG cc_start: 0.7350 (mtt-85) cc_final: 0.6609 (mtm-85) REVERT: G 44 ARG cc_start: 0.7296 (ttm-80) cc_final: 0.6927 (tpt90) REVERT: G 55 GLN cc_start: 0.7187 (tm-30) cc_final: 0.6950 (tm-30) REVERT: G 58 LYS cc_start: 0.7183 (mtpt) cc_final: 0.6395 (tptt) REVERT: G 59 GLU cc_start: 0.7002 (tp30) cc_final: 0.6762 (mm-30) REVERT: G 154 ILE cc_start: 0.7586 (OUTLIER) cc_final: 0.7338 (tt) REVERT: G 162 ASN cc_start: 0.8092 (m110) cc_final: 0.7841 (m110) REVERT: G 185 GLN cc_start: 0.8996 (OUTLIER) cc_final: 0.7826 (tp40) REVERT: G 200 LYS cc_start: 0.7294 (ttmm) cc_final: 0.6929 (mptt) REVERT: H 1 MET cc_start: 0.7495 (mpt) cc_final: 0.7055 (mpt) REVERT: H 60 GLU cc_start: 0.6031 (tt0) cc_final: 0.5287 (pp20) REVERT: H 96 LYS cc_start: 0.6631 (OUTLIER) cc_final: 0.5448 (pttp) outliers start: 242 outliers final: 181 residues processed: 515 average time/residue: 0.3974 time to fit residues: 321.0006 Evaluate side-chains 508 residues out of total 2804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 207 poor density : 301 time to evaluate : 4.482 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 ILE Chi-restraints excluded: chain A residue 14 VAL Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 83 ILE Chi-restraints excluded: chain A residue 122 MET Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 147 ILE Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 165 GLU Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 191 ARG Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 207 THR Chi-restraints excluded: chain A residue 209 MET Chi-restraints excluded: chain A residue 211 ILE Chi-restraints excluded: chain A residue 220 MET Chi-restraints excluded: chain A residue 223 THR Chi-restraints excluded: chain A residue 261 GLU Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 268 GLU Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 293 ASN Chi-restraints excluded: chain A residue 311 GLU Chi-restraints excluded: chain A residue 316 GLN Chi-restraints excluded: chain A residue 329 ARG Chi-restraints excluded: chain A residue 353 TYR Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain A residue 370 THR Chi-restraints excluded: chain A residue 393 GLU Chi-restraints excluded: chain A residue 427 SER Chi-restraints excluded: chain A residue 457 LEU Chi-restraints excluded: chain A residue 464 LEU Chi-restraints excluded: chain A residue 540 LEU Chi-restraints excluded: chain A residue 541 GLN Chi-restraints excluded: chain A residue 542 LEU Chi-restraints excluded: chain A residue 545 LEU Chi-restraints excluded: chain A residue 546 GLU Chi-restraints excluded: chain A residue 555 SER Chi-restraints excluded: chain A residue 574 PHE Chi-restraints excluded: chain B residue 27 ILE Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 88 GLN Chi-restraints excluded: chain B residue 96 GLU Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 152 ASP Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain B residue 200 ASP Chi-restraints excluded: chain B residue 226 ILE Chi-restraints excluded: chain B residue 230 PHE Chi-restraints excluded: chain B residue 255 CYS Chi-restraints excluded: chain B residue 260 ASN Chi-restraints excluded: chain B residue 285 THR Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 299 ARG Chi-restraints excluded: chain B residue 303 ILE Chi-restraints excluded: chain B residue 339 SER Chi-restraints excluded: chain B residue 354 LEU Chi-restraints excluded: chain B residue 364 ARG Chi-restraints excluded: chain B residue 368 VAL Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 443 VAL Chi-restraints excluded: chain B residue 450 LEU Chi-restraints excluded: chain B residue 455 SER Chi-restraints excluded: chain B residue 469 GLN Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 524 LYS Chi-restraints excluded: chain B residue 536 ILE Chi-restraints excluded: chain B residue 548 ILE Chi-restraints excluded: chain B residue 554 VAL Chi-restraints excluded: chain B residue 565 GLU Chi-restraints excluded: chain C residue 73 VAL Chi-restraints excluded: chain C residue 83 ILE Chi-restraints excluded: chain C residue 96 GLU Chi-restraints excluded: chain C residue 103 THR Chi-restraints excluded: chain C residue 116 LYS Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 141 PHE Chi-restraints excluded: chain C residue 145 HIS Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 186 THR Chi-restraints excluded: chain C residue 207 THR Chi-restraints excluded: chain C residue 249 VAL Chi-restraints excluded: chain C residue 266 LEU Chi-restraints excluded: chain C residue 284 ARG Chi-restraints excluded: chain C residue 287 LEU Chi-restraints excluded: chain C residue 294 MET Chi-restraints excluded: chain C residue 315 ASP Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 337 ILE Chi-restraints excluded: chain C residue 354 LEU Chi-restraints excluded: chain C residue 363 GLU Chi-restraints excluded: chain C residue 398 SER Chi-restraints excluded: chain C residue 461 GLU Chi-restraints excluded: chain C residue 468 VAL Chi-restraints excluded: chain C residue 520 LEU Chi-restraints excluded: chain C residue 531 LYS Chi-restraints excluded: chain C residue 538 GLU Chi-restraints excluded: chain C residue 542 LEU Chi-restraints excluded: chain C residue 570 ILE Chi-restraints excluded: chain C residue 574 PHE Chi-restraints excluded: chain D residue 37 ASP Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain D residue 130 PHE Chi-restraints excluded: chain D residue 131 ILE Chi-restraints excluded: chain D residue 183 LYS Chi-restraints excluded: chain D residue 197 THR Chi-restraints excluded: chain D residue 216 ARG Chi-restraints excluded: chain D residue 218 VAL Chi-restraints excluded: chain D residue 268 ARG Chi-restraints excluded: chain D residue 270 ILE Chi-restraints excluded: chain D residue 290 ASP Chi-restraints excluded: chain D residue 294 ILE Chi-restraints excluded: chain D residue 309 THR Chi-restraints excluded: chain D residue 315 SER Chi-restraints excluded: chain D residue 318 ASP Chi-restraints excluded: chain D residue 331 TYR Chi-restraints excluded: chain D residue 334 GLU Chi-restraints excluded: chain D residue 345 ARG Chi-restraints excluded: chain D residue 364 ASN Chi-restraints excluded: chain D residue 371 THR Chi-restraints excluded: chain D residue 379 SER Chi-restraints excluded: chain D residue 381 GLN Chi-restraints excluded: chain D residue 390 VAL Chi-restraints excluded: chain D residue 401 GLU Chi-restraints excluded: chain D residue 442 LEU Chi-restraints excluded: chain E residue 7 GLU Chi-restraints excluded: chain E residue 9 THR Chi-restraints excluded: chain E residue 26 ASP Chi-restraints excluded: chain E residue 43 ARG Chi-restraints excluded: chain E residue 73 VAL Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain E residue 94 ASN Chi-restraints excluded: chain E residue 111 ARG Chi-restraints excluded: chain E residue 130 PHE Chi-restraints excluded: chain E residue 131 ILE Chi-restraints excluded: chain E residue 133 THR Chi-restraints excluded: chain E residue 137 THR Chi-restraints excluded: chain E residue 143 THR Chi-restraints excluded: chain E residue 206 GLN Chi-restraints excluded: chain E residue 257 LEU Chi-restraints excluded: chain E residue 258 THR Chi-restraints excluded: chain E residue 270 ILE Chi-restraints excluded: chain E residue 304 LYS Chi-restraints excluded: chain E residue 358 LEU Chi-restraints excluded: chain E residue 372 ARG Chi-restraints excluded: chain E residue 379 SER Chi-restraints excluded: chain E residue 384 SER Chi-restraints excluded: chain E residue 392 ILE Chi-restraints excluded: chain E residue 413 GLN Chi-restraints excluded: chain E residue 427 GLN Chi-restraints excluded: chain E residue 452 LYS Chi-restraints excluded: chain E residue 459 ILE Chi-restraints excluded: chain F residue 11 ILE Chi-restraints excluded: chain F residue 53 GLU Chi-restraints excluded: chain F residue 54 TYR Chi-restraints excluded: chain F residue 68 LEU Chi-restraints excluded: chain F residue 73 VAL Chi-restraints excluded: chain F residue 78 ASP Chi-restraints excluded: chain F residue 96 ILE Chi-restraints excluded: chain F residue 111 ARG Chi-restraints excluded: chain F residue 112 LEU Chi-restraints excluded: chain F residue 131 ILE Chi-restraints excluded: chain F residue 137 THR Chi-restraints excluded: chain F residue 172 THR Chi-restraints excluded: chain F residue 180 GLU Chi-restraints excluded: chain F residue 185 GLU Chi-restraints excluded: chain F residue 197 THR Chi-restraints excluded: chain F residue 206 GLN Chi-restraints excluded: chain F residue 225 ASP Chi-restraints excluded: chain F residue 232 ILE Chi-restraints excluded: chain F residue 255 VAL Chi-restraints excluded: chain F residue 270 ILE Chi-restraints excluded: chain F residue 309 THR Chi-restraints excluded: chain F residue 315 SER Chi-restraints excluded: chain F residue 318 ASP Chi-restraints excluded: chain F residue 342 GLU Chi-restraints excluded: chain F residue 343 LEU Chi-restraints excluded: chain F residue 366 VAL Chi-restraints excluded: chain F residue 376 LYS Chi-restraints excluded: chain F residue 393 ARG Chi-restraints excluded: chain F residue 396 VAL Chi-restraints excluded: chain F residue 401 GLU Chi-restraints excluded: chain F residue 451 LEU Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain G residue 54 ASP Chi-restraints excluded: chain G residue 86 LEU Chi-restraints excluded: chain G residue 117 VAL Chi-restraints excluded: chain G residue 154 ILE Chi-restraints excluded: chain G residue 185 GLN Chi-restraints excluded: chain G residue 201 ILE Chi-restraints excluded: chain H residue 35 THR Chi-restraints excluded: chain H residue 51 LEU Chi-restraints excluded: chain H residue 77 LEU Chi-restraints excluded: chain H residue 86 VAL Chi-restraints excluded: chain H residue 90 MET Chi-restraints excluded: chain H residue 93 LEU Chi-restraints excluded: chain H residue 96 LYS Chi-restraints excluded: chain H residue 98 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 337 random chunks: chunk 109 optimal weight: 5.9990 chunk 293 optimal weight: 0.8980 chunk 64 optimal weight: 0.5980 chunk 191 optimal weight: 2.9990 chunk 80 optimal weight: 5.9990 chunk 326 optimal weight: 0.0770 chunk 270 optimal weight: 3.9990 chunk 150 optimal weight: 0.9980 chunk 27 optimal weight: 0.0970 chunk 107 optimal weight: 0.3980 chunk 171 optimal weight: 0.0170 overall best weight: 0.2374 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 501 HIS D 375 HIS E 166 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8200 moved from start: 0.2157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 27153 Z= 0.138 Angle : 0.509 8.586 36793 Z= 0.257 Chirality : 0.042 0.194 4109 Planarity : 0.004 0.073 4818 Dihedral : 8.940 80.935 4031 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.50 % Favored : 93.47 % Rotamer: Outliers : 6.67 % Allowed : 21.58 % Favored : 71.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.54 % Cis-general : 0.00 % Twisted Proline : 0.51 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.68 (0.15), residues: 3402 helix: 1.17 (0.15), residues: 1271 sheet: -2.01 (0.24), residues: 479 loop : -2.81 (0.14), residues: 1652 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.000 TRP G 97 HIS 0.003 0.000 HIS E 323 PHE 0.012 0.001 PHE C 419 TYR 0.011 0.001 TYR A 513 ARG 0.004 0.000 ARG G 103 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6804 Ramachandran restraints generated. 3402 Oldfield, 0 Emsley, 3402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6804 Ramachandran restraints generated. 3402 Oldfield, 0 Emsley, 3402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 535 residues out of total 2804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 187 poor density : 348 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 124 LYS cc_start: 0.8143 (tppp) cc_final: 0.7586 (mtpp) REVERT: A 191 ARG cc_start: 0.8042 (OUTLIER) cc_final: 0.7774 (mtm110) REVERT: A 323 MET cc_start: 0.7439 (ttm) cc_final: 0.7149 (mtp) REVERT: A 410 ASP cc_start: 0.8063 (t0) cc_final: 0.7695 (m-30) REVERT: A 542 LEU cc_start: 0.7228 (OUTLIER) cc_final: 0.7010 (mt) REVERT: B 9 ILE cc_start: 0.9113 (mt) cc_final: 0.8896 (mt) REVERT: B 423 ASN cc_start: 0.8327 (t0) cc_final: 0.8051 (t0) REVERT: B 558 GLU cc_start: 0.7049 (tp30) cc_final: 0.6744 (tp30) REVERT: C 116 LYS cc_start: 0.8687 (OUTLIER) cc_final: 0.7898 (ptpp) REVERT: C 145 HIS cc_start: 0.8677 (OUTLIER) cc_final: 0.8199 (t-90) REVERT: C 220 MET cc_start: 0.8497 (OUTLIER) cc_final: 0.7946 (tmm) REVERT: C 304 TYR cc_start: 0.8739 (m-80) cc_final: 0.8399 (m-80) REVERT: D 215 SER cc_start: 0.8736 (m) cc_final: 0.8439 (p) REVERT: D 268 ARG cc_start: 0.8245 (OUTLIER) cc_final: 0.6571 (ttt180) REVERT: D 345 ARG cc_start: 0.8289 (OUTLIER) cc_final: 0.7792 (mtt90) REVERT: D 381 GLN cc_start: 0.8655 (OUTLIER) cc_final: 0.7123 (tm130) REVERT: D 401 GLU cc_start: 0.7113 (OUTLIER) cc_final: 0.6522 (mt-10) REVERT: D 442 LEU cc_start: 0.9182 (OUTLIER) cc_final: 0.8920 (mp) REVERT: E 111 ARG cc_start: 0.8521 (OUTLIER) cc_final: 0.8291 (mtp85) REVERT: E 381 GLN cc_start: 0.8082 (mm-40) cc_final: 0.7643 (tp40) REVERT: E 394 LYS cc_start: 0.7302 (ttpt) cc_final: 0.6967 (tppt) REVERT: E 398 ILE cc_start: 0.7143 (tp) cc_final: 0.6747 (pt) REVERT: E 427 GLN cc_start: 0.8679 (OUTLIER) cc_final: 0.8166 (mp10) REVERT: F 91 ARG cc_start: 0.8437 (mmm160) cc_final: 0.7962 (mmm-85) REVERT: F 172 THR cc_start: 0.9094 (OUTLIER) cc_final: 0.8565 (p) REVERT: F 180 GLU cc_start: 0.7411 (OUTLIER) cc_final: 0.6762 (mp0) REVERT: F 327 ASP cc_start: 0.7520 (t0) cc_final: 0.7287 (t0) REVERT: F 331 TYR cc_start: 0.8190 (m-80) cc_final: 0.7791 (m-80) REVERT: F 362 MET cc_start: 0.8710 (ttt) cc_final: 0.8431 (ttt) REVERT: F 376 LYS cc_start: 0.6284 (OUTLIER) cc_final: 0.5992 (ptmt) REVERT: F 406 GLU cc_start: 0.6754 (tm-30) cc_final: 0.6413 (tm-30) REVERT: F 410 ARG cc_start: 0.7234 (mtt-85) cc_final: 0.6448 (mtm-85) REVERT: G 44 ARG cc_start: 0.7300 (ttm-80) cc_final: 0.7046 (tpt90) REVERT: G 55 GLN cc_start: 0.7193 (tm-30) cc_final: 0.6955 (tm-30) REVERT: G 58 LYS cc_start: 0.7114 (mtpt) cc_final: 0.6373 (tptt) REVERT: G 59 GLU cc_start: 0.6913 (tp30) cc_final: 0.6696 (mm-30) REVERT: G 154 ILE cc_start: 0.7543 (OUTLIER) cc_final: 0.7323 (tt) REVERT: G 185 GLN cc_start: 0.8849 (OUTLIER) cc_final: 0.7605 (tp40) REVERT: G 200 LYS cc_start: 0.7163 (ttmm) cc_final: 0.6832 (mptt) REVERT: H 1 MET cc_start: 0.7352 (mpt) cc_final: 0.7089 (mpt) REVERT: H 56 GLU cc_start: 0.5914 (pt0) cc_final: 0.5635 (pt0) REVERT: H 60 GLU cc_start: 0.5921 (tt0) cc_final: 0.5245 (pp20) REVERT: H 77 LEU cc_start: 0.2591 (OUTLIER) cc_final: 0.2304 (tp) REVERT: H 96 LYS cc_start: 0.6480 (OUTLIER) cc_final: 0.5378 (pttp) outliers start: 187 outliers final: 122 residues processed: 499 average time/residue: 0.3911 time to fit residues: 305.1970 Evaluate side-chains 451 residues out of total 2804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 141 poor density : 310 time to evaluate : 3.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 9 ILE Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 83 ILE Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 147 ILE Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 191 ARG Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 207 THR Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 316 GLN Chi-restraints excluded: chain A residue 329 ARG Chi-restraints excluded: chain A residue 393 GLU Chi-restraints excluded: chain A residue 484 ILE Chi-restraints excluded: chain A residue 541 GLN Chi-restraints excluded: chain A residue 542 LEU Chi-restraints excluded: chain A residue 545 LEU Chi-restraints excluded: chain A residue 546 GLU Chi-restraints excluded: chain A residue 555 SER Chi-restraints excluded: chain A residue 574 PHE Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 87 ILE Chi-restraints excluded: chain B residue 96 GLU Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 200 ASP Chi-restraints excluded: chain B residue 226 ILE Chi-restraints excluded: chain B residue 230 PHE Chi-restraints excluded: chain B residue 260 ASN Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 315 ASP Chi-restraints excluded: chain B residue 354 LEU Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 468 VAL Chi-restraints excluded: chain B residue 476 LEU Chi-restraints excluded: chain B residue 524 LYS Chi-restraints excluded: chain B residue 548 ILE Chi-restraints excluded: chain B residue 565 GLU Chi-restraints excluded: chain C residue 83 ILE Chi-restraints excluded: chain C residue 96 GLU Chi-restraints excluded: chain C residue 103 THR Chi-restraints excluded: chain C residue 116 LYS Chi-restraints excluded: chain C residue 141 PHE Chi-restraints excluded: chain C residue 145 HIS Chi-restraints excluded: chain C residue 200 ASP Chi-restraints excluded: chain C residue 220 MET Chi-restraints excluded: chain C residue 261 GLU Chi-restraints excluded: chain C residue 284 ARG Chi-restraints excluded: chain C residue 287 LEU Chi-restraints excluded: chain C residue 315 ASP Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 354 LEU Chi-restraints excluded: chain C residue 363 GLU Chi-restraints excluded: chain C residue 398 SER Chi-restraints excluded: chain C residue 419 PHE Chi-restraints excluded: chain C residue 461 GLU Chi-restraints excluded: chain C residue 468 VAL Chi-restraints excluded: chain C residue 520 LEU Chi-restraints excluded: chain C residue 531 LYS Chi-restraints excluded: chain C residue 542 LEU Chi-restraints excluded: chain C residue 570 ILE Chi-restraints excluded: chain C residue 574 PHE Chi-restraints excluded: chain D residue 37 ASP Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain D residue 130 PHE Chi-restraints excluded: chain D residue 131 ILE Chi-restraints excluded: chain D residue 183 LYS Chi-restraints excluded: chain D residue 194 MET Chi-restraints excluded: chain D residue 197 THR Chi-restraints excluded: chain D residue 218 VAL Chi-restraints excluded: chain D residue 268 ARG Chi-restraints excluded: chain D residue 290 ASP Chi-restraints excluded: chain D residue 294 ILE Chi-restraints excluded: chain D residue 309 THR Chi-restraints excluded: chain D residue 315 SER Chi-restraints excluded: chain D residue 318 ASP Chi-restraints excluded: chain D residue 331 TYR Chi-restraints excluded: chain D residue 334 GLU Chi-restraints excluded: chain D residue 345 ARG Chi-restraints excluded: chain D residue 364 ASN Chi-restraints excluded: chain D residue 379 SER Chi-restraints excluded: chain D residue 381 GLN Chi-restraints excluded: chain D residue 401 GLU Chi-restraints excluded: chain D residue 442 LEU Chi-restraints excluded: chain E residue 7 GLU Chi-restraints excluded: chain E residue 26 ASP Chi-restraints excluded: chain E residue 43 ARG Chi-restraints excluded: chain E residue 73 VAL Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain E residue 111 ARG Chi-restraints excluded: chain E residue 130 PHE Chi-restraints excluded: chain E residue 133 THR Chi-restraints excluded: chain E residue 137 THR Chi-restraints excluded: chain E residue 143 THR Chi-restraints excluded: chain E residue 270 ILE Chi-restraints excluded: chain E residue 372 ARG Chi-restraints excluded: chain E residue 379 SER Chi-restraints excluded: chain E residue 392 ILE Chi-restraints excluded: chain E residue 427 GLN Chi-restraints excluded: chain E residue 452 LYS Chi-restraints excluded: chain E residue 459 ILE Chi-restraints excluded: chain F residue 9 THR Chi-restraints excluded: chain F residue 11 ILE Chi-restraints excluded: chain F residue 53 GLU Chi-restraints excluded: chain F residue 54 TYR Chi-restraints excluded: chain F residue 68 LEU Chi-restraints excluded: chain F residue 73 VAL Chi-restraints excluded: chain F residue 78 ASP Chi-restraints excluded: chain F residue 96 ILE Chi-restraints excluded: chain F residue 112 LEU Chi-restraints excluded: chain F residue 137 THR Chi-restraints excluded: chain F residue 172 THR Chi-restraints excluded: chain F residue 180 GLU Chi-restraints excluded: chain F residue 197 THR Chi-restraints excluded: chain F residue 206 GLN Chi-restraints excluded: chain F residue 225 ASP Chi-restraints excluded: chain F residue 270 ILE Chi-restraints excluded: chain F residue 309 THR Chi-restraints excluded: chain F residue 315 SER Chi-restraints excluded: chain F residue 318 ASP Chi-restraints excluded: chain F residue 376 LYS Chi-restraints excluded: chain F residue 393 ARG Chi-restraints excluded: chain F residue 396 VAL Chi-restraints excluded: chain G residue 8 ARG Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain G residue 54 ASP Chi-restraints excluded: chain G residue 86 LEU Chi-restraints excluded: chain G residue 114 LEU Chi-restraints excluded: chain G residue 117 VAL Chi-restraints excluded: chain G residue 154 ILE Chi-restraints excluded: chain G residue 185 GLN Chi-restraints excluded: chain G residue 201 ILE Chi-restraints excluded: chain H residue 51 LEU Chi-restraints excluded: chain H residue 77 LEU Chi-restraints excluded: chain H residue 93 LEU Chi-restraints excluded: chain H residue 96 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 337 random chunks: chunk 314 optimal weight: 9.9990 chunk 36 optimal weight: 3.9990 chunk 185 optimal weight: 2.9990 chunk 238 optimal weight: 0.6980 chunk 184 optimal weight: 2.9990 chunk 274 optimal weight: 0.0020 chunk 182 optimal weight: 1.9990 chunk 324 optimal weight: 3.9990 chunk 203 optimal weight: 0.5980 chunk 198 optimal weight: 1.9990 chunk 149 optimal weight: 2.9990 overall best weight: 1.0592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8242 moved from start: 0.2158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 27153 Z= 0.221 Angle : 0.546 8.344 36793 Z= 0.275 Chirality : 0.044 0.191 4109 Planarity : 0.004 0.077 4818 Dihedral : 8.353 74.606 3973 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.03 % Allowed : 8.32 % Favored : 91.65 % Rotamer: Outliers : 6.49 % Allowed : 21.33 % Favored : 72.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.54 % Cis-general : 0.00 % Twisted Proline : 0.51 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.60 (0.15), residues: 3402 helix: 1.15 (0.15), residues: 1279 sheet: -1.93 (0.23), residues: 500 loop : -2.72 (0.14), residues: 1623 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 119 HIS 0.004 0.001 HIS B 283 PHE 0.012 0.001 PHE B 559 TYR 0.015 0.001 TYR A 513 ARG 0.005 0.000 ARG G 103 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6804 Ramachandran restraints generated. 3402 Oldfield, 0 Emsley, 3402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6804 Ramachandran restraints generated. 3402 Oldfield, 0 Emsley, 3402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 505 residues out of total 2804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 182 poor density : 323 time to evaluate : 2.859 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 124 LYS cc_start: 0.8169 (tppp) cc_final: 0.7624 (mtpp) REVERT: A 165 GLU cc_start: 0.7427 (OUTLIER) cc_final: 0.6939 (mt-10) REVERT: A 191 ARG cc_start: 0.8078 (OUTLIER) cc_final: 0.7790 (mtm110) REVERT: A 316 GLN cc_start: 0.8034 (OUTLIER) cc_final: 0.7784 (tt0) REVERT: A 410 ASP cc_start: 0.8086 (t0) cc_final: 0.7724 (m-30) REVERT: A 542 LEU cc_start: 0.7278 (OUTLIER) cc_final: 0.7064 (mt) REVERT: B 9 ILE cc_start: 0.9209 (mt) cc_final: 0.8985 (mt) REVERT: B 88 GLN cc_start: 0.9283 (OUTLIER) cc_final: 0.8822 (tt0) REVERT: B 423 ASN cc_start: 0.8392 (t0) cc_final: 0.7929 (t0) REVERT: B 558 GLU cc_start: 0.7144 (tp30) cc_final: 0.6814 (tp30) REVERT: C 116 LYS cc_start: 0.8735 (OUTLIER) cc_final: 0.7961 (ptpp) REVERT: C 220 MET cc_start: 0.8544 (tmm) cc_final: 0.8096 (tmm) REVERT: C 304 TYR cc_start: 0.8795 (m-80) cc_final: 0.8424 (m-80) REVERT: D 215 SER cc_start: 0.8764 (m) cc_final: 0.8442 (p) REVERT: D 216 ARG cc_start: 0.9326 (OUTLIER) cc_final: 0.6499 (ppt-90) REVERT: D 268 ARG cc_start: 0.8296 (OUTLIER) cc_final: 0.6732 (ttt180) REVERT: D 345 ARG cc_start: 0.8355 (OUTLIER) cc_final: 0.7912 (mtt90) REVERT: D 370 LYS cc_start: 0.8146 (OUTLIER) cc_final: 0.7923 (mttp) REVERT: D 381 GLN cc_start: 0.8735 (OUTLIER) cc_final: 0.7215 (tm130) REVERT: D 401 GLU cc_start: 0.7083 (OUTLIER) cc_final: 0.6452 (mt-10) REVERT: D 442 LEU cc_start: 0.9208 (OUTLIER) cc_final: 0.8992 (mp) REVERT: E 111 ARG cc_start: 0.8498 (OUTLIER) cc_final: 0.8275 (mtp85) REVERT: E 358 LEU cc_start: 0.8541 (OUTLIER) cc_final: 0.8154 (pt) REVERT: E 381 GLN cc_start: 0.8164 (mm-40) cc_final: 0.7697 (tp40) REVERT: E 394 LYS cc_start: 0.7276 (ttpt) cc_final: 0.6947 (tppt) REVERT: E 398 ILE cc_start: 0.7186 (tp) cc_final: 0.6808 (pt) REVERT: E 427 GLN cc_start: 0.8788 (OUTLIER) cc_final: 0.8223 (mp10) REVERT: F 91 ARG cc_start: 0.8527 (mmm160) cc_final: 0.8056 (mmm-85) REVERT: F 172 THR cc_start: 0.9012 (OUTLIER) cc_final: 0.8511 (p) REVERT: F 327 ASP cc_start: 0.7652 (t0) cc_final: 0.7447 (t0) REVERT: F 331 TYR cc_start: 0.8283 (m-80) cc_final: 0.7848 (m-80) REVERT: F 362 MET cc_start: 0.8794 (ttt) cc_final: 0.8550 (ttt) REVERT: F 410 ARG cc_start: 0.7395 (mtt-85) cc_final: 0.6831 (mtp180) REVERT: G 44 ARG cc_start: 0.7266 (ttm-80) cc_final: 0.7044 (tpt90) REVERT: G 55 GLN cc_start: 0.7207 (tm-30) cc_final: 0.6978 (tm-30) REVERT: G 58 LYS cc_start: 0.7133 (mtpt) cc_final: 0.6387 (tptt) REVERT: G 59 GLU cc_start: 0.6931 (tp30) cc_final: 0.6718 (mm-30) REVERT: G 181 GLN cc_start: 0.7781 (mm-40) cc_final: 0.7572 (mm-40) REVERT: G 185 GLN cc_start: 0.8957 (OUTLIER) cc_final: 0.7773 (tp40) REVERT: G 200 LYS cc_start: 0.7247 (ttmm) cc_final: 0.6901 (mptt) REVERT: H 1 MET cc_start: 0.7409 (mpt) cc_final: 0.7112 (mpt) REVERT: H 60 GLU cc_start: 0.5999 (tt0) cc_final: 0.5354 (pp20) REVERT: H 77 LEU cc_start: 0.2690 (OUTLIER) cc_final: 0.2390 (tp) REVERT: H 87 GLU cc_start: 0.7998 (tm-30) cc_final: 0.6747 (mt-10) REVERT: H 96 LYS cc_start: 0.6494 (OUTLIER) cc_final: 0.5388 (pttp) outliers start: 182 outliers final: 145 residues processed: 473 average time/residue: 0.3814 time to fit residues: 282.9834 Evaluate side-chains 477 residues out of total 2804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 165 poor density : 312 time to evaluate : 2.655 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 ILE Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 83 ILE Chi-restraints excluded: chain A residue 122 MET Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 147 ILE Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 165 GLU Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 191 ARG Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 207 THR Chi-restraints excluded: chain A residue 209 MET Chi-restraints excluded: chain A residue 261 GLU Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 293 ASN Chi-restraints excluded: chain A residue 316 GLN Chi-restraints excluded: chain A residue 329 ARG Chi-restraints excluded: chain A residue 363 GLU Chi-restraints excluded: chain A residue 393 GLU Chi-restraints excluded: chain A residue 425 ASN Chi-restraints excluded: chain A residue 540 LEU Chi-restraints excluded: chain A residue 541 GLN Chi-restraints excluded: chain A residue 542 LEU Chi-restraints excluded: chain A residue 545 LEU Chi-restraints excluded: chain A residue 546 GLU Chi-restraints excluded: chain A residue 555 SER Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 88 GLN Chi-restraints excluded: chain B residue 96 GLU Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain B residue 152 ASP Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 200 ASP Chi-restraints excluded: chain B residue 226 ILE Chi-restraints excluded: chain B residue 230 PHE Chi-restraints excluded: chain B residue 260 ASN Chi-restraints excluded: chain B residue 285 THR Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 303 ILE Chi-restraints excluded: chain B residue 315 ASP Chi-restraints excluded: chain B residue 339 SER Chi-restraints excluded: chain B residue 354 LEU Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 476 LEU Chi-restraints excluded: chain B residue 548 ILE Chi-restraints excluded: chain B residue 554 VAL Chi-restraints excluded: chain B residue 565 GLU Chi-restraints excluded: chain C residue 83 ILE Chi-restraints excluded: chain C residue 96 GLU Chi-restraints excluded: chain C residue 103 THR Chi-restraints excluded: chain C residue 116 LYS Chi-restraints excluded: chain C residue 141 PHE Chi-restraints excluded: chain C residue 145 HIS Chi-restraints excluded: chain C residue 186 THR Chi-restraints excluded: chain C residue 200 ASP Chi-restraints excluded: chain C residue 211 ILE Chi-restraints excluded: chain C residue 284 ARG Chi-restraints excluded: chain C residue 287 LEU Chi-restraints excluded: chain C residue 315 ASP Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 354 LEU Chi-restraints excluded: chain C residue 363 GLU Chi-restraints excluded: chain C residue 396 THR Chi-restraints excluded: chain C residue 398 SER Chi-restraints excluded: chain C residue 419 PHE Chi-restraints excluded: chain C residue 468 VAL Chi-restraints excluded: chain C residue 520 LEU Chi-restraints excluded: chain C residue 531 LYS Chi-restraints excluded: chain C residue 542 LEU Chi-restraints excluded: chain C residue 570 ILE Chi-restraints excluded: chain C residue 574 PHE Chi-restraints excluded: chain D residue 37 ASP Chi-restraints excluded: chain D residue 130 PHE Chi-restraints excluded: chain D residue 131 ILE Chi-restraints excluded: chain D residue 183 LYS Chi-restraints excluded: chain D residue 197 THR Chi-restraints excluded: chain D residue 216 ARG Chi-restraints excluded: chain D residue 218 VAL Chi-restraints excluded: chain D residue 268 ARG Chi-restraints excluded: chain D residue 290 ASP Chi-restraints excluded: chain D residue 294 ILE Chi-restraints excluded: chain D residue 309 THR Chi-restraints excluded: chain D residue 315 SER Chi-restraints excluded: chain D residue 318 ASP Chi-restraints excluded: chain D residue 331 TYR Chi-restraints excluded: chain D residue 334 GLU Chi-restraints excluded: chain D residue 345 ARG Chi-restraints excluded: chain D residue 364 ASN Chi-restraints excluded: chain D residue 370 LYS Chi-restraints excluded: chain D residue 379 SER Chi-restraints excluded: chain D residue 381 GLN Chi-restraints excluded: chain D residue 401 GLU Chi-restraints excluded: chain D residue 442 LEU Chi-restraints excluded: chain E residue 7 GLU Chi-restraints excluded: chain E residue 73 VAL Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain E residue 94 ASN Chi-restraints excluded: chain E residue 111 ARG Chi-restraints excluded: chain E residue 130 PHE Chi-restraints excluded: chain E residue 133 THR Chi-restraints excluded: chain E residue 137 THR Chi-restraints excluded: chain E residue 143 THR Chi-restraints excluded: chain E residue 206 GLN Chi-restraints excluded: chain E residue 257 LEU Chi-restraints excluded: chain E residue 258 THR Chi-restraints excluded: chain E residue 270 ILE Chi-restraints excluded: chain E residue 358 LEU Chi-restraints excluded: chain E residue 372 ARG Chi-restraints excluded: chain E residue 379 SER Chi-restraints excluded: chain E residue 384 SER Chi-restraints excluded: chain E residue 392 ILE Chi-restraints excluded: chain E residue 405 THR Chi-restraints excluded: chain E residue 427 GLN Chi-restraints excluded: chain E residue 452 LYS Chi-restraints excluded: chain E residue 459 ILE Chi-restraints excluded: chain F residue 11 ILE Chi-restraints excluded: chain F residue 53 GLU Chi-restraints excluded: chain F residue 54 TYR Chi-restraints excluded: chain F residue 68 LEU Chi-restraints excluded: chain F residue 73 VAL Chi-restraints excluded: chain F residue 78 ASP Chi-restraints excluded: chain F residue 96 ILE Chi-restraints excluded: chain F residue 112 LEU Chi-restraints excluded: chain F residue 128 GLU Chi-restraints excluded: chain F residue 133 THR Chi-restraints excluded: chain F residue 137 THR Chi-restraints excluded: chain F residue 172 THR Chi-restraints excluded: chain F residue 180 GLU Chi-restraints excluded: chain F residue 197 THR Chi-restraints excluded: chain F residue 206 GLN Chi-restraints excluded: chain F residue 225 ASP Chi-restraints excluded: chain F residue 232 ILE Chi-restraints excluded: chain F residue 255 VAL Chi-restraints excluded: chain F residue 270 ILE Chi-restraints excluded: chain F residue 309 THR Chi-restraints excluded: chain F residue 315 SER Chi-restraints excluded: chain F residue 318 ASP Chi-restraints excluded: chain F residue 342 GLU Chi-restraints excluded: chain F residue 366 VAL Chi-restraints excluded: chain F residue 376 LYS Chi-restraints excluded: chain F residue 393 ARG Chi-restraints excluded: chain F residue 396 VAL Chi-restraints excluded: chain F residue 401 GLU Chi-restraints excluded: chain G residue 8 ARG Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain G residue 54 ASP Chi-restraints excluded: chain G residue 86 LEU Chi-restraints excluded: chain G residue 117 VAL Chi-restraints excluded: chain G residue 182 VAL Chi-restraints excluded: chain G residue 185 GLN Chi-restraints excluded: chain G residue 201 ILE Chi-restraints excluded: chain H residue 35 THR Chi-restraints excluded: chain H residue 51 LEU Chi-restraints excluded: chain H residue 77 LEU Chi-restraints excluded: chain H residue 93 LEU Chi-restraints excluded: chain H residue 96 LYS Chi-restraints excluded: chain H residue 98 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 337 random chunks: chunk 200 optimal weight: 2.9990 chunk 129 optimal weight: 0.0030 chunk 193 optimal weight: 0.8980 chunk 97 optimal weight: 3.9990 chunk 63 optimal weight: 0.0370 chunk 62 optimal weight: 2.9990 chunk 206 optimal weight: 1.9990 chunk 221 optimal weight: 0.9990 chunk 160 optimal weight: 2.9990 chunk 30 optimal weight: 0.8980 chunk 255 optimal weight: 2.9990 overall best weight: 0.5670 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 413 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8207 moved from start: 0.2354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 27153 Z= 0.159 Angle : 0.521 7.784 36793 Z= 0.262 Chirality : 0.043 0.192 4109 Planarity : 0.004 0.074 4818 Dihedral : 8.038 75.744 3965 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.38 % Favored : 93.59 % Rotamer: Outliers : 6.10 % Allowed : 21.93 % Favored : 71.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.54 % Cis-general : 0.00 % Twisted Proline : 0.51 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.41 (0.15), residues: 3402 helix: 1.29 (0.15), residues: 1276 sheet: -1.74 (0.24), residues: 494 loop : -2.61 (0.14), residues: 1632 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.000 TRP G 97 HIS 0.002 0.001 HIS F 375 PHE 0.012 0.001 PHE C 419 TYR 0.012 0.001 TYR A 513 ARG 0.004 0.000 ARG A 401 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6804 Ramachandran restraints generated. 3402 Oldfield, 0 Emsley, 3402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6804 Ramachandran restraints generated. 3402 Oldfield, 0 Emsley, 3402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 503 residues out of total 2804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 171 poor density : 332 time to evaluate : 3.047 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 124 LYS cc_start: 0.8037 (tppp) cc_final: 0.7489 (mtpp) REVERT: A 323 MET cc_start: 0.7449 (ttm) cc_final: 0.7117 (mtp) REVERT: A 410 ASP cc_start: 0.8089 (t0) cc_final: 0.7707 (m-30) REVERT: B 9 ILE cc_start: 0.9155 (mt) cc_final: 0.8938 (mt) REVERT: B 423 ASN cc_start: 0.8346 (t0) cc_final: 0.8074 (t0) REVERT: B 558 GLU cc_start: 0.7062 (tp30) cc_final: 0.6599 (tp30) REVERT: C 116 LYS cc_start: 0.8705 (OUTLIER) cc_final: 0.7925 (ptpp) REVERT: C 220 MET cc_start: 0.8594 (OUTLIER) cc_final: 0.8201 (tmm) REVERT: C 304 TYR cc_start: 0.8765 (m-80) cc_final: 0.8406 (m-80) REVERT: C 527 GLU cc_start: 0.8170 (tp30) cc_final: 0.7873 (tp30) REVERT: D 215 SER cc_start: 0.8752 (m) cc_final: 0.8431 (p) REVERT: D 216 ARG cc_start: 0.9327 (OUTLIER) cc_final: 0.6395 (ppt-90) REVERT: D 268 ARG cc_start: 0.8293 (OUTLIER) cc_final: 0.6636 (ttt180) REVERT: D 370 LYS cc_start: 0.8140 (OUTLIER) cc_final: 0.7908 (mttp) REVERT: D 381 GLN cc_start: 0.8668 (OUTLIER) cc_final: 0.7153 (tm130) REVERT: D 401 GLU cc_start: 0.7048 (OUTLIER) cc_final: 0.6382 (mt-10) REVERT: D 442 LEU cc_start: 0.9185 (OUTLIER) cc_final: 0.8947 (mp) REVERT: E 111 ARG cc_start: 0.8503 (OUTLIER) cc_final: 0.8283 (mtp85) REVERT: E 394 LYS cc_start: 0.7263 (ttpt) cc_final: 0.6938 (tppt) REVERT: E 398 ILE cc_start: 0.7070 (tp) cc_final: 0.6730 (pt) REVERT: E 427 GLN cc_start: 0.8790 (OUTLIER) cc_final: 0.8219 (mp10) REVERT: F 91 ARG cc_start: 0.8476 (mmm160) cc_final: 0.8011 (mmm-85) REVERT: F 172 THR cc_start: 0.9084 (OUTLIER) cc_final: 0.8576 (p) REVERT: F 180 GLU cc_start: 0.7412 (OUTLIER) cc_final: 0.6758 (mp0) REVERT: F 327 ASP cc_start: 0.7491 (t0) cc_final: 0.7267 (t0) REVERT: F 331 TYR cc_start: 0.8273 (m-80) cc_final: 0.7834 (m-80) REVERT: F 362 MET cc_start: 0.8754 (ttt) cc_final: 0.8472 (ttt) REVERT: F 376 LYS cc_start: 0.6338 (OUTLIER) cc_final: 0.6112 (ptmt) REVERT: F 388 ASN cc_start: 0.8246 (m-40) cc_final: 0.7833 (m110) REVERT: F 410 ARG cc_start: 0.7191 (mtt-85) cc_final: 0.6359 (mtm-85) REVERT: F 413 GLN cc_start: 0.8265 (OUTLIER) cc_final: 0.7691 (mp-120) REVERT: G 44 ARG cc_start: 0.7299 (ttm-80) cc_final: 0.7044 (tpt90) REVERT: G 55 GLN cc_start: 0.7209 (tm-30) cc_final: 0.6968 (tm-30) REVERT: G 58 LYS cc_start: 0.6986 (mtpt) cc_final: 0.6257 (tptt) REVERT: G 185 GLN cc_start: 0.8806 (OUTLIER) cc_final: 0.7563 (tp40) REVERT: G 200 LYS cc_start: 0.7211 (ttmm) cc_final: 0.6862 (mptt) REVERT: H 1 MET cc_start: 0.7359 (mpt) cc_final: 0.7044 (mpt) REVERT: H 60 GLU cc_start: 0.5886 (tt0) cc_final: 0.5269 (pp20) outliers start: 171 outliers final: 138 residues processed: 465 average time/residue: 0.3796 time to fit residues: 275.9105 Evaluate side-chains 464 residues out of total 2804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 153 poor density : 311 time to evaluate : 3.165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 ILE Chi-restraints excluded: chain A residue 83 ILE Chi-restraints excluded: chain A residue 122 MET Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 147 ILE Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 207 THR Chi-restraints excluded: chain A residue 261 GLU Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 293 ASN Chi-restraints excluded: chain A residue 329 ARG Chi-restraints excluded: chain A residue 393 GLU Chi-restraints excluded: chain A residue 425 ASN Chi-restraints excluded: chain A residue 427 SER Chi-restraints excluded: chain A residue 484 ILE Chi-restraints excluded: chain A residue 520 LEU Chi-restraints excluded: chain A residue 540 LEU Chi-restraints excluded: chain A residue 541 GLN Chi-restraints excluded: chain A residue 545 LEU Chi-restraints excluded: chain A residue 546 GLU Chi-restraints excluded: chain A residue 555 SER Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 87 ILE Chi-restraints excluded: chain B residue 96 GLU Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 200 ASP Chi-restraints excluded: chain B residue 226 ILE Chi-restraints excluded: chain B residue 230 PHE Chi-restraints excluded: chain B residue 260 ASN Chi-restraints excluded: chain B residue 285 THR Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 315 ASP Chi-restraints excluded: chain B residue 354 LEU Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 468 VAL Chi-restraints excluded: chain B residue 476 LEU Chi-restraints excluded: chain B residue 548 ILE Chi-restraints excluded: chain B residue 554 VAL Chi-restraints excluded: chain B residue 565 GLU Chi-restraints excluded: chain C residue 79 MET Chi-restraints excluded: chain C residue 96 GLU Chi-restraints excluded: chain C residue 103 THR Chi-restraints excluded: chain C residue 116 LYS Chi-restraints excluded: chain C residue 141 PHE Chi-restraints excluded: chain C residue 145 HIS Chi-restraints excluded: chain C residue 186 THR Chi-restraints excluded: chain C residue 200 ASP Chi-restraints excluded: chain C residue 220 MET Chi-restraints excluded: chain C residue 284 ARG Chi-restraints excluded: chain C residue 287 LEU Chi-restraints excluded: chain C residue 315 ASP Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 354 LEU Chi-restraints excluded: chain C residue 363 GLU Chi-restraints excluded: chain C residue 398 SER Chi-restraints excluded: chain C residue 419 PHE Chi-restraints excluded: chain C residue 468 VAL Chi-restraints excluded: chain C residue 520 LEU Chi-restraints excluded: chain C residue 531 LYS Chi-restraints excluded: chain C residue 542 LEU Chi-restraints excluded: chain C residue 570 ILE Chi-restraints excluded: chain C residue 574 PHE Chi-restraints excluded: chain D residue 37 ASP Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain D residue 130 PHE Chi-restraints excluded: chain D residue 131 ILE Chi-restraints excluded: chain D residue 183 LYS Chi-restraints excluded: chain D residue 197 THR Chi-restraints excluded: chain D residue 216 ARG Chi-restraints excluded: chain D residue 218 VAL Chi-restraints excluded: chain D residue 268 ARG Chi-restraints excluded: chain D residue 290 ASP Chi-restraints excluded: chain D residue 294 ILE Chi-restraints excluded: chain D residue 309 THR Chi-restraints excluded: chain D residue 315 SER Chi-restraints excluded: chain D residue 318 ASP Chi-restraints excluded: chain D residue 331 TYR Chi-restraints excluded: chain D residue 334 GLU Chi-restraints excluded: chain D residue 364 ASN Chi-restraints excluded: chain D residue 370 LYS Chi-restraints excluded: chain D residue 379 SER Chi-restraints excluded: chain D residue 381 GLN Chi-restraints excluded: chain D residue 401 GLU Chi-restraints excluded: chain D residue 442 LEU Chi-restraints excluded: chain E residue 7 GLU Chi-restraints excluded: chain E residue 9 THR Chi-restraints excluded: chain E residue 26 ASP Chi-restraints excluded: chain E residue 43 ARG Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain E residue 111 ARG Chi-restraints excluded: chain E residue 130 PHE Chi-restraints excluded: chain E residue 133 THR Chi-restraints excluded: chain E residue 143 THR Chi-restraints excluded: chain E residue 253 VAL Chi-restraints excluded: chain E residue 257 LEU Chi-restraints excluded: chain E residue 258 THR Chi-restraints excluded: chain E residue 270 ILE Chi-restraints excluded: chain E residue 320 ASP Chi-restraints excluded: chain E residue 372 ARG Chi-restraints excluded: chain E residue 379 SER Chi-restraints excluded: chain E residue 384 SER Chi-restraints excluded: chain E residue 392 ILE Chi-restraints excluded: chain E residue 405 THR Chi-restraints excluded: chain E residue 427 GLN Chi-restraints excluded: chain E residue 452 LYS Chi-restraints excluded: chain E residue 459 ILE Chi-restraints excluded: chain F residue 9 THR Chi-restraints excluded: chain F residue 11 ILE Chi-restraints excluded: chain F residue 53 GLU Chi-restraints excluded: chain F residue 54 TYR Chi-restraints excluded: chain F residue 68 LEU Chi-restraints excluded: chain F residue 73 VAL Chi-restraints excluded: chain F residue 78 ASP Chi-restraints excluded: chain F residue 96 ILE Chi-restraints excluded: chain F residue 112 LEU Chi-restraints excluded: chain F residue 133 THR Chi-restraints excluded: chain F residue 137 THR Chi-restraints excluded: chain F residue 172 THR Chi-restraints excluded: chain F residue 180 GLU Chi-restraints excluded: chain F residue 197 THR Chi-restraints excluded: chain F residue 206 GLN Chi-restraints excluded: chain F residue 225 ASP Chi-restraints excluded: chain F residue 232 ILE Chi-restraints excluded: chain F residue 270 ILE Chi-restraints excluded: chain F residue 309 THR Chi-restraints excluded: chain F residue 318 ASP Chi-restraints excluded: chain F residue 366 VAL Chi-restraints excluded: chain F residue 376 LYS Chi-restraints excluded: chain F residue 393 ARG Chi-restraints excluded: chain F residue 396 VAL Chi-restraints excluded: chain F residue 413 GLN Chi-restraints excluded: chain G residue 8 ARG Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain G residue 54 ASP Chi-restraints excluded: chain G residue 86 LEU Chi-restraints excluded: chain G residue 114 LEU Chi-restraints excluded: chain G residue 117 VAL Chi-restraints excluded: chain G residue 172 ILE Chi-restraints excluded: chain G residue 185 GLN Chi-restraints excluded: chain H residue 35 THR Chi-restraints excluded: chain H residue 51 LEU Chi-restraints excluded: chain H residue 77 LEU Chi-restraints excluded: chain H residue 90 MET Chi-restraints excluded: chain H residue 93 LEU Chi-restraints excluded: chain H residue 96 LYS Chi-restraints excluded: chain H residue 98 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 337 random chunks: chunk 295 optimal weight: 1.9990 chunk 311 optimal weight: 4.9990 chunk 283 optimal weight: 2.9990 chunk 302 optimal weight: 0.8980 chunk 182 optimal weight: 0.8980 chunk 131 optimal weight: 4.9990 chunk 237 optimal weight: 1.9990 chunk 92 optimal weight: 2.9990 chunk 273 optimal weight: 4.9990 chunk 286 optimal weight: 3.9990 chunk 301 optimal weight: 0.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 145 HIS A 316 GLN ** E 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8249 moved from start: 0.2247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 27153 Z= 0.264 Angle : 0.566 9.624 36793 Z= 0.287 Chirality : 0.044 0.188 4109 Planarity : 0.005 0.078 4818 Dihedral : 8.036 73.911 3954 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.03 % Allowed : 8.47 % Favored : 91.50 % Rotamer: Outliers : 6.38 % Allowed : 21.61 % Favored : 72.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.54 % Cis-general : 0.00 % Twisted Proline : 0.51 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.45 (0.15), residues: 3402 helix: 1.18 (0.15), residues: 1292 sheet: -1.84 (0.23), residues: 509 loop : -2.59 (0.15), residues: 1601 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP G 97 HIS 0.004 0.001 HIS A 145 PHE 0.018 0.001 PHE A 574 TYR 0.015 0.001 TYR A 513 ARG 0.004 0.000 ARG A 401 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6804 Ramachandran restraints generated. 3402 Oldfield, 0 Emsley, 3402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6804 Ramachandran restraints generated. 3402 Oldfield, 0 Emsley, 3402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 487 residues out of total 2804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 179 poor density : 308 time to evaluate : 3.012 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 124 LYS cc_start: 0.8180 (tppp) cc_final: 0.7638 (mtpp) REVERT: A 165 GLU cc_start: 0.7439 (OUTLIER) cc_final: 0.6960 (mt-10) REVERT: A 191 ARG cc_start: 0.8113 (OUTLIER) cc_final: 0.7834 (mtm110) REVERT: A 410 ASP cc_start: 0.8110 (t0) cc_final: 0.7735 (m-30) REVERT: B 9 ILE cc_start: 0.9229 (mt) cc_final: 0.9013 (mt) REVERT: B 88 GLN cc_start: 0.9301 (OUTLIER) cc_final: 0.8843 (tt0) REVERT: B 423 ASN cc_start: 0.8359 (t0) cc_final: 0.8072 (t0) REVERT: B 558 GLU cc_start: 0.7143 (tp30) cc_final: 0.6859 (tp30) REVERT: C 116 LYS cc_start: 0.8741 (OUTLIER) cc_final: 0.7963 (ptpp) REVERT: C 220 MET cc_start: 0.8633 (tmm) cc_final: 0.8209 (tmm) REVERT: C 304 TYR cc_start: 0.8807 (m-80) cc_final: 0.8416 (m-80) REVERT: D 215 SER cc_start: 0.8728 (m) cc_final: 0.8417 (p) REVERT: D 216 ARG cc_start: 0.9330 (OUTLIER) cc_final: 0.6500 (ppt-90) REVERT: D 268 ARG cc_start: 0.8338 (OUTLIER) cc_final: 0.6765 (ttt180) REVERT: D 370 LYS cc_start: 0.8286 (OUTLIER) cc_final: 0.8035 (mttt) REVERT: D 381 GLN cc_start: 0.8770 (OUTLIER) cc_final: 0.7240 (tm130) REVERT: D 401 GLU cc_start: 0.7035 (OUTLIER) cc_final: 0.6281 (mt-10) REVERT: D 442 LEU cc_start: 0.9215 (OUTLIER) cc_final: 0.8992 (mp) REVERT: E 111 ARG cc_start: 0.8538 (OUTLIER) cc_final: 0.8273 (mtp85) REVERT: E 358 LEU cc_start: 0.8529 (OUTLIER) cc_final: 0.8146 (pt) REVERT: E 394 LYS cc_start: 0.7278 (ttpt) cc_final: 0.6953 (tppt) REVERT: E 398 ILE cc_start: 0.7153 (tp) cc_final: 0.6793 (pt) REVERT: E 427 GLN cc_start: 0.8825 (OUTLIER) cc_final: 0.8157 (mp10) REVERT: F 91 ARG cc_start: 0.8528 (mmm160) cc_final: 0.8060 (mmm-85) REVERT: F 172 THR cc_start: 0.9023 (OUTLIER) cc_final: 0.8541 (p) REVERT: F 327 ASP cc_start: 0.7675 (t0) cc_final: 0.7471 (t0) REVERT: F 331 TYR cc_start: 0.8269 (m-80) cc_final: 0.7787 (m-80) REVERT: F 362 MET cc_start: 0.8792 (ttt) cc_final: 0.8465 (ttt) REVERT: F 410 ARG cc_start: 0.7277 (mtt-85) cc_final: 0.6761 (mtp180) REVERT: G 44 ARG cc_start: 0.7312 (ttm-80) cc_final: 0.7056 (tpt90) REVERT: G 55 GLN cc_start: 0.7210 (tm-30) cc_final: 0.6992 (tm-30) REVERT: G 58 LYS cc_start: 0.6984 (mtpt) cc_final: 0.6303 (tptt) REVERT: G 185 GLN cc_start: 0.8908 (OUTLIER) cc_final: 0.7731 (tp40) REVERT: G 200 LYS cc_start: 0.7255 (ttmm) cc_final: 0.6903 (mptt) REVERT: H 1 MET cc_start: 0.7383 (mpt) cc_final: 0.7057 (mpt) REVERT: H 60 GLU cc_start: 0.5912 (tt0) cc_final: 0.5305 (pp20) outliers start: 179 outliers final: 152 residues processed: 451 average time/residue: 0.3751 time to fit residues: 264.3051 Evaluate side-chains 474 residues out of total 2804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 167 poor density : 307 time to evaluate : 2.979 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 ILE Chi-restraints excluded: chain A residue 14 VAL Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 83 ILE Chi-restraints excluded: chain A residue 122 MET Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 145 HIS Chi-restraints excluded: chain A residue 147 ILE Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 165 GLU Chi-restraints excluded: chain A residue 191 ARG Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 207 THR Chi-restraints excluded: chain A residue 209 MET Chi-restraints excluded: chain A residue 261 GLU Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 293 ASN Chi-restraints excluded: chain A residue 311 GLU Chi-restraints excluded: chain A residue 316 GLN Chi-restraints excluded: chain A residue 329 ARG Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 393 GLU Chi-restraints excluded: chain A residue 425 ASN Chi-restraints excluded: chain A residue 427 SER Chi-restraints excluded: chain A residue 520 LEU Chi-restraints excluded: chain A residue 540 LEU Chi-restraints excluded: chain A residue 545 LEU Chi-restraints excluded: chain A residue 546 GLU Chi-restraints excluded: chain A residue 555 SER Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 88 GLN Chi-restraints excluded: chain B residue 96 GLU Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain B residue 152 ASP Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 200 ASP Chi-restraints excluded: chain B residue 226 ILE Chi-restraints excluded: chain B residue 230 PHE Chi-restraints excluded: chain B residue 255 CYS Chi-restraints excluded: chain B residue 260 ASN Chi-restraints excluded: chain B residue 285 THR Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 315 ASP Chi-restraints excluded: chain B residue 339 SER Chi-restraints excluded: chain B residue 354 LEU Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 468 VAL Chi-restraints excluded: chain B residue 476 LEU Chi-restraints excluded: chain B residue 548 ILE Chi-restraints excluded: chain B residue 554 VAL Chi-restraints excluded: chain B residue 565 GLU Chi-restraints excluded: chain C residue 79 MET Chi-restraints excluded: chain C residue 96 GLU Chi-restraints excluded: chain C residue 103 THR Chi-restraints excluded: chain C residue 116 LYS Chi-restraints excluded: chain C residue 141 PHE Chi-restraints excluded: chain C residue 145 HIS Chi-restraints excluded: chain C residue 186 THR Chi-restraints excluded: chain C residue 200 ASP Chi-restraints excluded: chain C residue 211 ILE Chi-restraints excluded: chain C residue 284 ARG Chi-restraints excluded: chain C residue 315 ASP Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 354 LEU Chi-restraints excluded: chain C residue 363 GLU Chi-restraints excluded: chain C residue 396 THR Chi-restraints excluded: chain C residue 398 SER Chi-restraints excluded: chain C residue 419 PHE Chi-restraints excluded: chain C residue 461 GLU Chi-restraints excluded: chain C residue 468 VAL Chi-restraints excluded: chain C residue 520 LEU Chi-restraints excluded: chain C residue 531 LYS Chi-restraints excluded: chain C residue 542 LEU Chi-restraints excluded: chain C residue 570 ILE Chi-restraints excluded: chain C residue 574 PHE Chi-restraints excluded: chain D residue 37 ASP Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain D residue 130 PHE Chi-restraints excluded: chain D residue 131 ILE Chi-restraints excluded: chain D residue 183 LYS Chi-restraints excluded: chain D residue 197 THR Chi-restraints excluded: chain D residue 216 ARG Chi-restraints excluded: chain D residue 218 VAL Chi-restraints excluded: chain D residue 268 ARG Chi-restraints excluded: chain D residue 290 ASP Chi-restraints excluded: chain D residue 294 ILE Chi-restraints excluded: chain D residue 309 THR Chi-restraints excluded: chain D residue 315 SER Chi-restraints excluded: chain D residue 318 ASP Chi-restraints excluded: chain D residue 331 TYR Chi-restraints excluded: chain D residue 334 GLU Chi-restraints excluded: chain D residue 364 ASN Chi-restraints excluded: chain D residue 370 LYS Chi-restraints excluded: chain D residue 379 SER Chi-restraints excluded: chain D residue 381 GLN Chi-restraints excluded: chain D residue 401 GLU Chi-restraints excluded: chain D residue 442 LEU Chi-restraints excluded: chain E residue 7 GLU Chi-restraints excluded: chain E residue 9 THR Chi-restraints excluded: chain E residue 26 ASP Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain E residue 89 LEU Chi-restraints excluded: chain E residue 94 ASN Chi-restraints excluded: chain E residue 111 ARG Chi-restraints excluded: chain E residue 133 THR Chi-restraints excluded: chain E residue 143 THR Chi-restraints excluded: chain E residue 257 LEU Chi-restraints excluded: chain E residue 258 THR Chi-restraints excluded: chain E residue 270 ILE Chi-restraints excluded: chain E residue 320 ASP Chi-restraints excluded: chain E residue 358 LEU Chi-restraints excluded: chain E residue 361 LEU Chi-restraints excluded: chain E residue 372 ARG Chi-restraints excluded: chain E residue 379 SER Chi-restraints excluded: chain E residue 384 SER Chi-restraints excluded: chain E residue 392 ILE Chi-restraints excluded: chain E residue 405 THR Chi-restraints excluded: chain E residue 427 GLN Chi-restraints excluded: chain E residue 452 LYS Chi-restraints excluded: chain E residue 459 ILE Chi-restraints excluded: chain F residue 9 THR Chi-restraints excluded: chain F residue 11 ILE Chi-restraints excluded: chain F residue 53 GLU Chi-restraints excluded: chain F residue 54 TYR Chi-restraints excluded: chain F residue 68 LEU Chi-restraints excluded: chain F residue 73 VAL Chi-restraints excluded: chain F residue 78 ASP Chi-restraints excluded: chain F residue 96 ILE Chi-restraints excluded: chain F residue 112 LEU Chi-restraints excluded: chain F residue 128 GLU Chi-restraints excluded: chain F residue 133 THR Chi-restraints excluded: chain F residue 137 THR Chi-restraints excluded: chain F residue 172 THR Chi-restraints excluded: chain F residue 180 GLU Chi-restraints excluded: chain F residue 197 THR Chi-restraints excluded: chain F residue 206 GLN Chi-restraints excluded: chain F residue 225 ASP Chi-restraints excluded: chain F residue 232 ILE Chi-restraints excluded: chain F residue 270 ILE Chi-restraints excluded: chain F residue 309 THR Chi-restraints excluded: chain F residue 318 ASP Chi-restraints excluded: chain F residue 366 VAL Chi-restraints excluded: chain F residue 376 LYS Chi-restraints excluded: chain F residue 393 ARG Chi-restraints excluded: chain F residue 396 VAL Chi-restraints excluded: chain F residue 451 LEU Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain G residue 54 ASP Chi-restraints excluded: chain G residue 86 LEU Chi-restraints excluded: chain G residue 114 LEU Chi-restraints excluded: chain G residue 117 VAL Chi-restraints excluded: chain G residue 172 ILE Chi-restraints excluded: chain G residue 185 GLN Chi-restraints excluded: chain H residue 35 THR Chi-restraints excluded: chain H residue 51 LEU Chi-restraints excluded: chain H residue 77 LEU Chi-restraints excluded: chain H residue 90 MET Chi-restraints excluded: chain H residue 93 LEU Chi-restraints excluded: chain H residue 96 LYS Chi-restraints excluded: chain H residue 98 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 337 random chunks: chunk 198 optimal weight: 0.8980 chunk 320 optimal weight: 0.9980 chunk 195 optimal weight: 2.9990 chunk 151 optimal weight: 4.9990 chunk 222 optimal weight: 1.9990 chunk 335 optimal weight: 6.9990 chunk 309 optimal weight: 1.9990 chunk 267 optimal weight: 3.9990 chunk 27 optimal weight: 0.0470 chunk 206 optimal weight: 0.9990 chunk 163 optimal weight: 3.9990 overall best weight: 0.9882 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 413 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8237 moved from start: 0.2315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 27153 Z= 0.213 Angle : 0.554 9.039 36793 Z= 0.281 Chirality : 0.044 0.189 4109 Planarity : 0.004 0.077 4818 Dihedral : 7.911 74.333 3949 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.52 % Favored : 92.45 % Rotamer: Outliers : 6.03 % Allowed : 21.90 % Favored : 72.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.54 % Cis-general : 0.00 % Twisted Proline : 0.51 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.42 (0.15), residues: 3402 helix: 1.20 (0.15), residues: 1283 sheet: -1.77 (0.24), residues: 504 loop : -2.54 (0.15), residues: 1615 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP G 97 HIS 0.021 0.001 HIS A 145 PHE 0.016 0.001 PHE A 574 TYR 0.014 0.001 TYR A 513 ARG 0.007 0.000 ARG G 103 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6804 Ramachandran restraints generated. 3402 Oldfield, 0 Emsley, 3402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6804 Ramachandran restraints generated. 3402 Oldfield, 0 Emsley, 3402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 482 residues out of total 2804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 169 poor density : 313 time to evaluate : 3.185 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 124 LYS cc_start: 0.8078 (tppp) cc_final: 0.7526 (mtpp) REVERT: A 165 GLU cc_start: 0.7431 (OUTLIER) cc_final: 0.6955 (mt-10) REVERT: A 410 ASP cc_start: 0.8115 (t0) cc_final: 0.7727 (m-30) REVERT: B 9 ILE cc_start: 0.9214 (mt) cc_final: 0.8994 (mt) REVERT: B 423 ASN cc_start: 0.8371 (t0) cc_final: 0.7924 (t0) REVERT: B 558 GLU cc_start: 0.7123 (tp30) cc_final: 0.6856 (tp30) REVERT: C 116 LYS cc_start: 0.8737 (OUTLIER) cc_final: 0.7955 (ptpp) REVERT: C 220 MET cc_start: 0.8662 (tmm) cc_final: 0.7833 (tmm) REVERT: C 304 TYR cc_start: 0.8786 (m-80) cc_final: 0.8400 (m-80) REVERT: D 215 SER cc_start: 0.8726 (m) cc_final: 0.8413 (p) REVERT: D 216 ARG cc_start: 0.9338 (OUTLIER) cc_final: 0.6413 (ppt-90) REVERT: D 268 ARG cc_start: 0.8316 (OUTLIER) cc_final: 0.6753 (ttt180) REVERT: D 370 LYS cc_start: 0.8238 (OUTLIER) cc_final: 0.7908 (mttp) REVERT: D 381 GLN cc_start: 0.8755 (OUTLIER) cc_final: 0.7217 (tm130) REVERT: D 442 LEU cc_start: 0.9206 (OUTLIER) cc_final: 0.8980 (mp) REVERT: E 111 ARG cc_start: 0.8530 (OUTLIER) cc_final: 0.8257 (mtp85) REVERT: E 358 LEU cc_start: 0.8463 (OUTLIER) cc_final: 0.8086 (pt) REVERT: E 394 LYS cc_start: 0.7269 (ttpt) cc_final: 0.6944 (tppt) REVERT: E 398 ILE cc_start: 0.7155 (tp) cc_final: 0.6790 (pt) REVERT: E 427 GLN cc_start: 0.8824 (OUTLIER) cc_final: 0.8153 (mp10) REVERT: F 91 ARG cc_start: 0.8514 (mmm160) cc_final: 0.8047 (mmm-85) REVERT: F 172 THR cc_start: 0.9008 (OUTLIER) cc_final: 0.8529 (p) REVERT: F 180 GLU cc_start: 0.7454 (OUTLIER) cc_final: 0.6764 (mp0) REVERT: F 331 TYR cc_start: 0.8280 (m-80) cc_final: 0.7858 (m-80) REVERT: F 362 MET cc_start: 0.8791 (ttt) cc_final: 0.8497 (ttt) REVERT: F 388 ASN cc_start: 0.8281 (m-40) cc_final: 0.7845 (m110) REVERT: F 410 ARG cc_start: 0.7268 (mtt-85) cc_final: 0.6553 (mtm-85) REVERT: G 44 ARG cc_start: 0.7300 (ttm-80) cc_final: 0.7039 (tpt90) REVERT: G 55 GLN cc_start: 0.7196 (tm-30) cc_final: 0.6977 (tm-30) REVERT: G 58 LYS cc_start: 0.6972 (mtpt) cc_final: 0.6294 (tptt) REVERT: G 185 GLN cc_start: 0.8899 (OUTLIER) cc_final: 0.7731 (tp40) REVERT: G 200 LYS cc_start: 0.7244 (ttmm) cc_final: 0.6892 (mptt) REVERT: H 1 MET cc_start: 0.7369 (mpt) cc_final: 0.7022 (mpt) REVERT: H 60 GLU cc_start: 0.5898 (tt0) cc_final: 0.5305 (pp20) REVERT: H 87 GLU cc_start: 0.8073 (tm-30) cc_final: 0.6731 (mt-10) outliers start: 169 outliers final: 144 residues processed: 451 average time/residue: 0.3943 time to fit residues: 280.0543 Evaluate side-chains 461 residues out of total 2804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 157 poor density : 304 time to evaluate : 3.080 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 ILE Chi-restraints excluded: chain A residue 14 VAL Chi-restraints excluded: chain A residue 83 ILE Chi-restraints excluded: chain A residue 122 MET Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 141 PHE Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 165 GLU Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 207 THR Chi-restraints excluded: chain A residue 209 MET Chi-restraints excluded: chain A residue 261 GLU Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 293 ASN Chi-restraints excluded: chain A residue 311 GLU Chi-restraints excluded: chain A residue 329 ARG Chi-restraints excluded: chain A residue 393 GLU Chi-restraints excluded: chain A residue 425 ASN Chi-restraints excluded: chain A residue 427 SER Chi-restraints excluded: chain A residue 484 ILE Chi-restraints excluded: chain A residue 520 LEU Chi-restraints excluded: chain A residue 540 LEU Chi-restraints excluded: chain A residue 545 LEU Chi-restraints excluded: chain A residue 546 GLU Chi-restraints excluded: chain A residue 555 SER Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 96 GLU Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 200 ASP Chi-restraints excluded: chain B residue 226 ILE Chi-restraints excluded: chain B residue 230 PHE Chi-restraints excluded: chain B residue 260 ASN Chi-restraints excluded: chain B residue 285 THR Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 315 ASP Chi-restraints excluded: chain B residue 354 LEU Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 468 VAL Chi-restraints excluded: chain B residue 476 LEU Chi-restraints excluded: chain B residue 548 ILE Chi-restraints excluded: chain B residue 554 VAL Chi-restraints excluded: chain B residue 565 GLU Chi-restraints excluded: chain C residue 79 MET Chi-restraints excluded: chain C residue 96 GLU Chi-restraints excluded: chain C residue 103 THR Chi-restraints excluded: chain C residue 116 LYS Chi-restraints excluded: chain C residue 141 PHE Chi-restraints excluded: chain C residue 145 HIS Chi-restraints excluded: chain C residue 186 THR Chi-restraints excluded: chain C residue 200 ASP Chi-restraints excluded: chain C residue 211 ILE Chi-restraints excluded: chain C residue 284 ARG Chi-restraints excluded: chain C residue 315 ASP Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 354 LEU Chi-restraints excluded: chain C residue 363 GLU Chi-restraints excluded: chain C residue 398 SER Chi-restraints excluded: chain C residue 419 PHE Chi-restraints excluded: chain C residue 461 GLU Chi-restraints excluded: chain C residue 468 VAL Chi-restraints excluded: chain C residue 520 LEU Chi-restraints excluded: chain C residue 531 LYS Chi-restraints excluded: chain C residue 542 LEU Chi-restraints excluded: chain C residue 570 ILE Chi-restraints excluded: chain C residue 574 PHE Chi-restraints excluded: chain D residue 37 ASP Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain D residue 130 PHE Chi-restraints excluded: chain D residue 131 ILE Chi-restraints excluded: chain D residue 183 LYS Chi-restraints excluded: chain D residue 197 THR Chi-restraints excluded: chain D residue 216 ARG Chi-restraints excluded: chain D residue 218 VAL Chi-restraints excluded: chain D residue 268 ARG Chi-restraints excluded: chain D residue 290 ASP Chi-restraints excluded: chain D residue 294 ILE Chi-restraints excluded: chain D residue 309 THR Chi-restraints excluded: chain D residue 318 ASP Chi-restraints excluded: chain D residue 331 TYR Chi-restraints excluded: chain D residue 334 GLU Chi-restraints excluded: chain D residue 364 ASN Chi-restraints excluded: chain D residue 370 LYS Chi-restraints excluded: chain D residue 379 SER Chi-restraints excluded: chain D residue 381 GLN Chi-restraints excluded: chain D residue 442 LEU Chi-restraints excluded: chain E residue 7 GLU Chi-restraints excluded: chain E residue 9 THR Chi-restraints excluded: chain E residue 26 ASP Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain E residue 89 LEU Chi-restraints excluded: chain E residue 94 ASN Chi-restraints excluded: chain E residue 111 ARG Chi-restraints excluded: chain E residue 133 THR Chi-restraints excluded: chain E residue 143 THR Chi-restraints excluded: chain E residue 257 LEU Chi-restraints excluded: chain E residue 258 THR Chi-restraints excluded: chain E residue 270 ILE Chi-restraints excluded: chain E residue 320 ASP Chi-restraints excluded: chain E residue 358 LEU Chi-restraints excluded: chain E residue 361 LEU Chi-restraints excluded: chain E residue 372 ARG Chi-restraints excluded: chain E residue 379 SER Chi-restraints excluded: chain E residue 384 SER Chi-restraints excluded: chain E residue 392 ILE Chi-restraints excluded: chain E residue 405 THR Chi-restraints excluded: chain E residue 427 GLN Chi-restraints excluded: chain E residue 444 SER Chi-restraints excluded: chain E residue 452 LYS Chi-restraints excluded: chain E residue 459 ILE Chi-restraints excluded: chain F residue 9 THR Chi-restraints excluded: chain F residue 11 ILE Chi-restraints excluded: chain F residue 53 GLU Chi-restraints excluded: chain F residue 54 TYR Chi-restraints excluded: chain F residue 73 VAL Chi-restraints excluded: chain F residue 78 ASP Chi-restraints excluded: chain F residue 96 ILE Chi-restraints excluded: chain F residue 112 LEU Chi-restraints excluded: chain F residue 128 GLU Chi-restraints excluded: chain F residue 133 THR Chi-restraints excluded: chain F residue 137 THR Chi-restraints excluded: chain F residue 172 THR Chi-restraints excluded: chain F residue 180 GLU Chi-restraints excluded: chain F residue 197 THR Chi-restraints excluded: chain F residue 206 GLN Chi-restraints excluded: chain F residue 225 ASP Chi-restraints excluded: chain F residue 232 ILE Chi-restraints excluded: chain F residue 270 ILE Chi-restraints excluded: chain F residue 309 THR Chi-restraints excluded: chain F residue 318 ASP Chi-restraints excluded: chain F residue 366 VAL Chi-restraints excluded: chain F residue 376 LYS Chi-restraints excluded: chain F residue 393 ARG Chi-restraints excluded: chain F residue 396 VAL Chi-restraints excluded: chain F residue 451 LEU Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain G residue 54 ASP Chi-restraints excluded: chain G residue 86 LEU Chi-restraints excluded: chain G residue 114 LEU Chi-restraints excluded: chain G residue 117 VAL Chi-restraints excluded: chain G residue 172 ILE Chi-restraints excluded: chain G residue 185 GLN Chi-restraints excluded: chain H residue 35 THR Chi-restraints excluded: chain H residue 51 LEU Chi-restraints excluded: chain H residue 77 LEU Chi-restraints excluded: chain H residue 90 MET Chi-restraints excluded: chain H residue 93 LEU Chi-restraints excluded: chain H residue 96 LYS Chi-restraints excluded: chain H residue 98 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 337 random chunks: chunk 212 optimal weight: 3.9990 chunk 284 optimal weight: 2.9990 chunk 81 optimal weight: 5.9990 chunk 246 optimal weight: 0.1980 chunk 39 optimal weight: 0.9990 chunk 74 optimal weight: 0.4980 chunk 267 optimal weight: 2.9990 chunk 112 optimal weight: 4.9990 chunk 274 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 chunk 49 optimal weight: 1.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 145 HIS A 316 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.124033 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.100764 restraints weight = 41006.028| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.104226 restraints weight = 26022.357| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.105451 restraints weight = 15899.213| |-----------------------------------------------------------------------------| r_work (final): 0.3147 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8273 moved from start: 0.2313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 27153 Z= 0.234 Angle : 0.558 7.915 36793 Z= 0.283 Chirality : 0.044 0.184 4109 Planarity : 0.005 0.078 4818 Dihedral : 7.782 74.287 3943 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.03 % Allowed : 8.11 % Favored : 91.86 % Rotamer: Outliers : 6.42 % Allowed : 21.72 % Favored : 71.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.54 % Cis-general : 0.00 % Twisted Proline : 0.51 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.42 (0.15), residues: 3402 helix: 1.17 (0.15), residues: 1286 sheet: -1.77 (0.24), residues: 509 loop : -2.53 (0.15), residues: 1607 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP G 97 HIS 0.003 0.001 HIS A 145 PHE 0.015 0.001 PHE A 574 TYR 0.014 0.001 TYR A 513 ARG 0.004 0.000 ARG F 410 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5927.42 seconds wall clock time: 107 minutes 45.66 seconds (6465.66 seconds total)